Ircinia_paper.bib

@article{Adams2006,
  ids = {adams2006a},
  title = {Nursery Function of Tropical Back-Reef Systems},
  author = {Adams, Aj and Dahlgren, Cp and Kellison, Gt and Kendall, Ms and Layman, Ca and Ley, Ja and Nagelkerken, I and Serafy, Je},
  year = {2006},
  month = aug,
  journal = {Marine Ecology Progress Series},
  volume = {318},
  pages = {287--301},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps318287},
  abstract = {Similar to nearshore systems in temperate latitudes, the nursery paradigm for tropical back-reef systems is that they provide a habitat for juveniles of species that subsequently make ontogenetic shifts to adult populations on coral reefs (we refer to this as the nursery function of back-reef systems). Nevertheless, we lack a full understanding of the importance of the nursery function of back-reef systems to the maintenance of coral reef fishes and invertebrate populations; the few studies that have examined the nursery function of multiple habitats indicate that the relationship between juvenile production in back-reef habitats and their subsequent contribution to adult populations on reefs remain poorly understood. In this synopsis we (1) synthesize current knowledge of life history, ecological and habitat influences on juvenile distribution patterns and nursery function within back-reef systems; (2) outline a research strategy for assessing the nursery function of various habitat types in back-reef systems; and (3) discuss management recommendations, particularly in regard to how improved knowledge of the nursery function of back-reef systems can be used in fisheries and ecosystem management, including habitat conservation and restoration decisions. The research strategy builds on research recommendations for assessing the nursery function of temperate habitats and includes 4 levels of research: (1) building conceptual models to guide research and management; (2) identifying juvenile habitat use patterns; (3) measuring connectivity of juvenile and adult populations between habitats; and (4) examining ecological processes that may influence patterns assessed in Level 2 and Level 3 research. Research and modeling output from Levels 1 to 4 will provide an improved ecological understanding of the degree and importance of interconnections between coral reef and adjacent back-reef systems, and will provide information to managers that will facilitate wise decisions pertaining to habitat conservation, habitat restoration, and ecosystembased management, and the maintenance of sustainable fisheries.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\JELHHMIA\\Adams et al. - 2006 - Nursery function of tropical back-reef systems.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\SXYLQUS3\\Adamsetal2006.pdf}
}

@article{allgeier2010,
  title = {Synergistic Nutrient Colimitation across a Gradient of Ecosystem Fragmentation in Subtropical Mangrove-Dominated Wetlands},
  author = {Allgeier, J. E. and Rosemond, A. D. and Mehring, A. S. and Layman, C. A.},
  year = {2010},
  month = nov,
  journal = {Limnology and Oceanography},
  volume = {55},
  number = {6},
  pages = {2660--2668},
  issn = {0024-3590},
  doi = {10.4319/lo.2010.55.6.2660},
  abstract = {We examined benthic algal response to nutrient enrichment by nitrogen (N), phosphorus (P), and N + P in mangrove wetlands of The Bahamas, to test the hypothesis that human impacts (fragmentation) on these ecosystems altered nutrient limitation, thereby changing the frequency and/or magnitude at which ecological synergies occurred. Fragmentation occurred due to road construction, resulting in reduced hydrological connectivity between the wetlands and marine environment. Strong, persistent, and synergistic nutrient colimitation occurred in both pristine and fragmented estuaries. Ecosystem fragmentation did not alter the biomass response to dual nutrient enrichment, but did alter the relative magnitude of the nonadditive response. That is, synergistic responses were less extreme in fragmented systems. This was supported by the strong, negative relationship between ambient algal biomass (a surrogate for background productivity) and the strength of synergistic responses (R-2 = 0.69 and 0.79, year 1 and year 2, respectively). Bahamian coastal ecosystems exhibited the greatest synergistic responses reported for a marine ecosystem, suggesting that the benthic algal communities associated with Bahamian wetlands are among the most nutrient-limited marine ecosystems. Our findings provide a case study illustrating how altered nutrient dynamics associated with land-use change may decrease the frequency and/or magnitude of synergistic responses to nutrients in aquatic ecosystems.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\FCWUWGLI\\Allgeier et al 2010_LO (1).pdf}
}

@article{allgeier2013,
  title = {Consumers Regulate Nutrient Limitation Regimes and Primary Production in Seagrass Ecosystems},
  author = {Allgeier, Jacob Edward and Yeager, Lauren A. and Layman, Craig A.},
  year = {2013},
  journal = {Ecology},
  volume = {94},
  number = {2},
  pages = {521--529},
  issn = {0012-9658},
  doi = {10.1890/12-1122.1},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\96PRC28B\\allgeieretal2013.pdf}
}

@article{allgeier2018,
  title = {Anthropogenic versus Fish-Derived Nutrient Effects on Seagrass Community Structure and Function},
  author = {Allgeier, Jacob E. and Layman, Craig A. and Monta{\~n}a, Carmen G. and Hensel, Enie and Appaldo, Richard and Rosemond, Amy D.},
  year = {2018},
  month = aug,
  journal = {Ecology},
  volume = {99},
  number = {8},
  pages = {1792--1801},
  issn = {00129658},
  doi = {10.1002/ecy.2388},
  abstract = {Humans are altering nutrient dynamics through myriad pathways globally. Concurrent with the addition of nutrients via municipal, industrial, and agricultural sources, widespread consumer exploitation is changing consumer-mediated nutrient dynamics drastically. Thus, altered nutrient dynamics can occur through changes in the supply of multiple nutrients, as well as through changes in the sources of these nutrients. Seagrass ecosystems are heavily impacted by human activities, with highly altered nutrient dynamics from multiple causes. We simulate scenarios of altered nutrient supply and ratios, nitrogen: phosphorus (N:P), from two nutrient sources in seagrass ecosystems: anthropogenic fertilizer and fish excretion. In doing so we tested expectations rooted in ecological theory that suggest the importance of resource dynamics for predicting primary producer dynamics. Ecosystem functions were strongly altered by artificial fertilizer (e.g., seagrass growth increased by as much as 140\%), whereas plant/algae community structure was most affected by fish-mediated nutrients or the interaction of both treatments (e.g., evenness increased by \textasciitilde 140\% under conditions of low fish nutrients and high anthropogenic nutrients). Interactions between the nutrient sources were found for only two of six response variables, and the ratio of nutrient supply was the best predictor for only one response. These findings show that seagrass structure and function are well predicted by supply of a single nutrient (either N or P). Importantly, no single nutrient best explained the majority of responses\textemdash measures of community structure were best explained by the primary limiting nutrient to this system (P), whereas measures of growth and density of the dominant producer in the system were best explained by N. Thus, while our findings support aspects of theoretical expectations, the complexity of producer community responses belies broad generalities, underscoring the need to manage for multiple simultaneous nutrients in these imperiled coastal ecosystems.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\6HFNPWC2\\Allgeier et al. - 2018 - Anthropogenic versus fish-derived nutrient effects.pdf}
}

@article{altieri2007,
  title = {Hierarchical Organization via a Facilitation Cascade in Intertidal Cordgrass Bed Communities},
  author = {Altieri, Andrew H and Silliman, Brian R and Bertness, Mark D},
  year = {2007},
  journal = {The American Naturalist},
  volume = {169},
  number = {2},
  pages = {195--206},
  doi = {10.1086/510603},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\ITE2AZ35\\altierietal2007.pdf}
}

@article{altieri2010,
  title = {Facilitation Cascade Drives Positive Relationship between Native Biodiversity and Invasion Success},
  author = {Altieri, A. H. and {van Wesenbeeck}, B. K. and Bertness, M. D. and Silliman, B. R.},
  year = {2010},
  month = may,
  journal = {Ecology},
  volume = {91},
  number = {5},
  pages = {1269--1275},
  issn = {0012-9658},
  doi = {10.1890/09-1301.1},
  abstract = {The pervasive impact of invasive species has motivated considerable research to understand how characteristics of invaded communities, such as native species diversity, affect the establishment of invasive species. Efforts to identify general mechanisms that limit invasion success, however, have been frustrated by disagreement between landscape-scale observations that generally find a positive relationship between native diversity and invasibility and smaller-scale experiments that consistently reveal competitive interactions that generate the opposite relationship. Here we experimentally elucidate the mechanism explaining the large-scale positive associations between invasion success and native intertidal diversity revealed in our landscape-scale surveys of New England shorelines. Experimental manipulations revealed this large-scale pattern is driven by a facilitation cascade where ecosystem-engineering species interact nonlinearly to enhance native diversity and invasion success by alleviating thermal stress and substrate instability. Our findings reveal that large-scale diversity-invasion relationships can be explained by small-scale positive interactions that commonly occur across multiple trophic levels and functional groups. We argue that facilitation has played an important but unrecognized role in the invasion of other well studied systems, and will be of increasing importance with anticipated climate change.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\D5ZG8LEP\\Altieri.pdf}
}

@incollection{altieri2014,
  title = {Foundation {{Species}} in {{Marine Ecosystems}}},
  booktitle = {Marine {{Community Ecology}} and {{Conservation}}},
  author = {Altieri, A. H. and {van de Koppel}, J.},
  editor = {Bertness, M. D. and Bruno, J. F. and Silliman, B. R. and Stachowicz, J. J.},
  year = {2014},
  pages = {37--56},
  publisher = {{Sinauer Associates, Inc.}},
  address = {{Sunderland, MA}},
  isbn = {978-1-60535-228-2}
}

@article{angelini2016,
  ids = {angelini2016a},
  title = {A Keystone Mutualism Underpins Resilience of a Coastal Ecosystem to Drought},
  author = {Angelini, Christine and Griffin, John N. and {van de Koppel}, Johan and Lamers, Leon P. M. and Smolders, Alfons J. P. and {Derksen-Hooijberg}, Marlous and {van der Heide}, Tjisse and Silliman, Brian R.},
  year = {2016},
  month = nov,
  journal = {Nature Communications},
  volume = {7},
  number = {1},
  pages = {12473},
  issn = {2041-1723},
  doi = {10.1038/ncomms12473},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\82XSDWCV\\Angelini et al. - 2016 - A keystone mutualism underpins resilience of a coa.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\AIHM7CWV\\Angelini et al. - 2016 - A keystone mutualism underpins resilience of a coa.pdf}
}

@article{archer2015,
  title = {A Complex Interaction between a Sponge ({{{\emph{Halichondria}}}}{\emph{ Melanadocia}}) and a Seagrass ({{{\emph{Thalassia}}}}{\emph{ Testudinum}}) in a Subtropical Coastal Ecosystem},
  author = {Archer, Stephanie K. and Stoner, Elizabeth W. and Layman, Craig A.},
  year = {2015},
  journal = {Journal of Experimental Marine Biology and Ecology},
  volume = {465},
  number = {0},
  pages = {33--40},
  issn = {0022-0981},
  doi = {10.1016/j.jembe.2015.01.003},
  abstract = {Foundation species, such as oysters, corals, and seagrasses, form the basis for entire ecosystems and are characterized by positive interactions with community members. However, many species interactions are context dependent, where the outcome or strength of the interaction depends on the biotic or abiotic conditions. Therefore, a mechanistic knowledge of species interactions, especially those involving foundation species, may allow for a more complete understanding of how anthropogenic changes influence nearshore ecosystems. This study describes the interaction between the seagrass Thalassia testudinum and the sponge Halichondria melanadocia, a species that grows around the base of seagrass shoots. A combination of surveys and experimental manipulations on Abaco Island, The Bahamas, revealed that the interaction between T. testudinum and H. melanadocia is a commensal relationship with the sponge benefiting from the presence of T. testudinum up to medium shoot densities (589\textendash 615 shoots per m2). The net neutral effect of H. melanadocia on T. testudinum is likely a balance of the negative effect of the sponge shading the seagrass with the positive effect of nitrogen and phosphorus supplied by the sponge. The mechanisms underlying the interaction between H. melanadocia and T. testudinum suggest that the interaction is likely context dependent. As such, environmental change, namely eutrophication, has the potential to shift the nature of this interaction from commensal to parasitic. A simple simulation showed that if this relationship becomes parasitic, above ground production in seagrass beds could be reduced. This study highlights the importance of a mechanistic understanding of species interactions involving foundation species when predicting human impact on the environment.},
  keywords = {Context dependence,Foundation species,Halichondria melanadocia,Nutrient flux,Species interactions,Thalassia testudinum},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\EEH7B8PF\\ARcheretal2015.pdf}
}

@article{archer2017,
  ids = {archer2017a},
  title = {Abiotic Conditions Drive Significant Variability in Nutrient Processing by a Common {{Caribbean}} Sponge, {{{\emph{Ircinia}}}}{\emph{ Felix}}},
  author = {Archer, Stephanie K. and Stevens, Julia L. and Rossi, Ryann E. and Matterson, Kenan O. and Layman, Craig A.},
  year = {2017},
  month = jul,
  journal = {Limnology and Oceanography},
  volume = {62},
  number = {4},
  pages = {1783--1793},
  issn = {0024-3590, 1939-5590},
  doi = {10.1002/lno.10533},
  abstract = {Coral reefs typically occur in oligotrophic waters, where tight recycling of energy and nutrients is essential in order to support their high productivity. Sponges are efficient filter feeders that host diverse and abundant microbial communities that often contain members capable of carrying out complex nutrient transformations. Consequently, sponges often act as significant sources of bioavailable forms of nitrogen and phosphorus while acting as sinks for dissolved organic carbon (DOC). However, little attention has focused on variability of nutrient release by sponges and no studies have reported how abiotic conditions may impact sponge-driven changes in nutrient concentrations. Here, we show that a common Caribbean sponge, Ircinia felix, is capable of being both a source and a sink for DOC, ammonium, nitrate/nitrite (NO2x ), and phosphate (PO432). Additionally, we show that abiotic conditions, particularly ambient nutrient availability, seem to explain a significant amount of the variability (R2 range from 0.40 to 0.65). Interestingly, as ambient nutrient concentrations increased, I. felix transitioned from acting as a source to serving as a sink for all nutrient forms measured. We also found I. felix-associated bacteria exhibit a significantly higher abundance of predicted nitrogen metabolism, carbon fixation, and photosynthetic genes relative to ambient water and sediment. These results suggest that sponges play an important and dynamic role in biogeochemical cycling on reefs, particularly as human activities alter natural nutrient dynamics in coastal systems.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\5K9272UX\\Archer et al. - 2017 - Abiotic conditions drive significant variability i.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\969WYLXQ\\Archeretal_2017.pdf}
}

@article{archer2018c,
  title = {Ambient Nutrient Availability Drives the Outcome of an Interaction between a Sponge ({{{\emph{Halichondria}}}}{\emph{ Melanadocia}}) and Seagrass ({{{\emph{Thalassia}}}}{\emph{ Testudinum}})},
  author = {Archer, Stephanie K. and Hensel, Enie and Layman, Craig A.},
  year = {2018},
  journal = {Journal of Experimental Marine Biology and Ecology},
  volume = {503},
  pages = {86--91},
  issn = {0022-0981},
  doi = {10.1016/j.jembe.2018.02.005},
  abstract = {Nutrient loading is a common human impact in coastal habitats which is driving significant losses of seagrass habitat worldwide. This is concerning, as seagrass beds provide numerous ecosystem services. Although nutrient loading can result in eutrophication and mass mortality of seagrasses, it more often results in subtle alterations of abiotic conditions which, by themselves, are insufficient to drive widespread seagrass mortality. Here we used a month-long field-based experiment to test the influence of anthropogenic nutrient loading on the outcome of an interaction between an epizootic sponge (Halichondria melanadocia) and a seagrass (Thalassia testudinum). Using a factorial design we manipulated ambient nutrient concentrations by adding fertilizer to plots with and without a sponge in a relatively pristine seagrass bed on Abaco Island, The Bahamas. We measured seagrass growth, below- and above-ground biomass, and the change in shoot density. We found that low levels of nutrient loading (i.e., insufficient to cause increased algal growth and decreased oxygen levels associated with eutrophication) resulted in a non-significant increase in seagrass growth, biomass, and shoot density when a sponge was absent. When a sponge was present, the same level of fertilization resulted in a significant reduction in the response variables. Our results show that anthropogenic nutrient loading can shift the sponge-seagrass interaction away from commensalism toward an interaction that has negative consequences for the seagrass. Additionally, a shift in the outcome of this context-dependent interaction can alter the impact of nutrient loading on seagrass productivity. Our study provides an example of how simple classifications of interspecific interactions (e.g., commensalism) often mask underlying variability. Characterizing the mechanisms driving the variability will allow us to understand when and how the outcome of an interaction will change. Ultimately, this will allow us to better predict how human activities will indirectly impact various ecosystem functions.},
  keywords = {Context-dependent,Ecosystem function,Interspecific interactions,Nutrient loading,Porifera,Productivity,Seagrass},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\D5WPDHNN\\Archeretal2018_JEMBE.pdf}
}

@article{archer2020a,
  title = {Foundation {{Species Abundance Influences Food Web Topology}} on {{Glass Sponge Reefs}}},
  author = {Archer, Stephanie K. and Kahn, Amanda S. and Thiess, Mary and Law, Lauren and Leys, Sally P. and Johannessen, Sophia C. and Layman, Craig A. and Burke, Lily and Dunham, Anya},
  year = {2020},
  month = sep,
  journal = {Frontiers in Marine Science},
  volume = {7},
  pages = {549478},
  issn = {2296-7745},
  doi = {10.3389/fmars.2020.549478},
  abstract = {Foundation species support communities across a wide range of ecosystems. Nontrophic interactions are considered the primary way foundation species influence communities, with their trophic interactions having little impact on community structure. Here we assess the relative trophic importance of a foundation species and assess how its abundance can influence food web topology. Using empirical data and published trophic interactions we built food web models for 20 glass sponge reefs to examine how average live reef-building sponge abundance (proxied by percent cover) at the reef level is correlated with community structure and food web network topology. Then, using a generalized food web model and stable isotope data we examined the relative importance of sponges. Sponges were consumed by all species examined and contributed significantly to their diets. Additionally, sponges were the second most important node in our generalized reef food web. Several metrics of food web topology (connectance, clustering, and median degree) and community structure exhibited a threshold response to reef-building sponge cover, with the change point occurring between 8 and 13\% live sponge cover. Below this threshold, as average sponge cover increases, the consumers observed on a reef rely on fewer sources and are consumed by fewer predators, resulting in food webs that are more clustered and less connected. Above the threshold, as average sponge cover increases, the reefs' food webs are less clustered and more connected, with consumers utilizing more sources and having more predators. This corresponds with the finding that several generalist predators (e.g., rockfishes) are associated with high sponge cover reefs. Our results are not consistent with previous reports that increasing foundation species abundance decreases connectance in food webs. We propose that the influence of foundation species on food web topology may be dependent on palatability, and therefore relative trophic importance, of the foundation species. Finally, our findings have important implications for sponge reef conservation and management, as they suggest that reefs below the 10\% sponge cover threshold support different communities than high live sponge cover reefs.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\QKDMAHYA\\Archer et al. - 2020 - Foundation Species Abundance Influences Food Web T.pdf}
}

@article{armitage2005,
  title = {Experimental Nutrient Enrichment Causes Complex Changes in Seagrass, Microalgae, and Macroalgae Community Structure in {{Florida Bay}}},
  author = {Armitage, A. R. and Frankovich, T. A. and Heck, K. L. and Fourqurean, J. W.},
  year = {2005},
  month = jun,
  journal = {Estuaries},
  volume = {28},
  number = {3},
  pages = {422--434},
  issn = {0160-8347},
  doi = {10.1007/bf02693924},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\P9MLB8SH\\Armitageetal2005.pdf}
}

@article{attrill2000,
  title = {Are Macroinvertebrate Communities Influenced by Seagrass Structural Complexity?},
  author = {Attrill, M. J. and Strong, J. A. and Rowden, A. A.},
  year = {2000},
  month = feb,
  journal = {Ecography},
  volume = {23},
  number = {1},
  pages = {114--121},
  issn = {0906-7590},
  doi = {10.1034/j.1600-0587.2000.230112.x},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\P7PQBPMI\\atrilletal.pdf}
}

@article{bates2015,
  title = {Fitting Linear Mixed-Effects Models Using {{lme4}}},
  author = {Bates, Douglas and M{\"a}chler, Martin and Bolker, Ben and Walker, Steve},
  year = {2015},
  journal = {Journal of Statistical Software},
  volume = {67},
  number = {1},
  pages = {1--48},
  doi = {10.18637/jss.v067.i01}
}

@article{bishop2012,
  title = {Density-Dependent Facilitation Cascades Determine Epifaunal Community Structure in Temperate {{Australian}} Mangroves},
  author = {Bishop, Melanie J and Byers, James E and Marcek, Benjamin J and Gribben, Paul E},
  year = {2012},
  journal = {Ecology},
  volume = {93},
  number = {6},
  pages = {1388--1401},
  issn = {0012-9658},
  doi = {10.1890/10-2296.1},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\EABE37Q2\\Bishop et al. 2012.pdf}
}

@article{bologna2000,
  title = {Impacts of {{Seagrass Habitat Architecture}} on {{Bivalve Settlement}}},
  author = {Bologna, Paul A. X. and Heck, Kenneth L.},
  year = {2000},
  month = aug,
  journal = {Estuaries},
  volume = {23},
  number = {4},
  pages = {449},
  issn = {01608347},
  doi = {10.2307/1353138},
  abstract = {We investigated the effects of differing spatial scales of seagrass habitat architecture on the composition and abundance of settling bivalves in a sub-tropical seagrass community. The density of newly settled bivalves was generally greater at Thalassia testudinum grass bed edge (Ͻ 1 m) compared to interior portions of the bed (Ͼ 10 m). Deviation from this generalized pattern occurred when high densities of newly settled tulip mussels (Modiolus americanus) were recorded from the interior of the meadow, associated with aggregations of adult mussels. Bivalve settling densities appear to reflect settlement shadows of passively delivered larvae, bedload transport of newly settled individuals from unvegetated regions, as well as gregarious settlement among adult conspecifics. We also investigated the impact of seagrass patch shape and size on settlement by using artificial seagrass units (ASU) in separate short-term and long-term experiments. We found a positive relationship between ASU perimeter and bivalve abundance, suggesting that larval encounter rates with seagrass habitat may determine initial settlement patterns. Using ASUs we also investigated the relative role seagrass epiphytes play in determining the density of settling bivalves. Results showed greater settling densities where epiphytic secondary structure was elevated compared to controls, and bivalve density was significantly greater when ASUs were fouled with a natural community of epiphytes, suggesting that both microstructure and biofilms positively influenced bivalve settlement. We conclude that structural components of seagrass habitats increase bivalve settlement at multiple spatial scales, including epiphytic micro-structure, small-scale patch shape and size, and large-scale within habitat differences.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\2LDM7DDC\\Bologna and Heck - 2000 - Impacts of Seagrass Habitat Architecture on Bivalv.pdf}
}

@article{borst2018,
  title = {Foundation Species Enhance Food Web Complexity through Non-Trophic Facilitation},
  author = {Borst, Annieke C. W. and Verberk, Wilco C. E. P. and Angelini, Christine and Schotanus, Jildou and Wolters, Jan-Willem and Christianen, Marjolijn J. A. and Van Der Zee, Els M. and {Derksen-Hooijberg}, Marlous and Van Der Heide, Tjisse},
  year = {2018},
  journal = {PLOS ONE},
  volume = {13},
  number = {8},
  pages = {e0199152},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0199152},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\LMMLRW3T\\Borst-2018-Foundation-species-enhance-food-web.pdf}
}

@article{bos2007,
  title = {Ecosystem Engineering by Annual Intertidal Seagrass Beds: Sediment Accretion and Modification},
  author = {Bos, Arthur R and Bouma, Tjeerd J and {de Kort}, Geertje LJ and {van Katwijk}, Marieke M},
  year = {2007},
  journal = {Estuarine, Coastal and Shelf Science},
  volume = {74},
  number = {1},
  pages = {344--348},
  issn = {0272-7714},
  doi = {10.1016/j.ecss.2007.04.006},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\QWWU8TXS\\Bos 2007 ECSS74 - Sediment accretion in eelgrass.pdf}
}

@article{bozec2013,
  title = {Reciprocal Facilitation and Non-linearity Maintain Habitat Engineering on Coral Reefs},
  author = {Bozec, Yves-Marie and Yakob, Laith and Bejarano, Sonia and Mumby, Peter J},
  year = {2013},
  journal = {Oikos},
  volume = {122},
  number = {3},
  pages = {428--440},
  issn = {1600-0706},
  doi = {10.1111/j.1600-0706.2012.20576.x}
}

@article{bronstein2009,
  title = {The Evolution of Facilitation and Mutualism},
  author = {Bronstein, J. L.},
  year = {2009},
  month = nov,
  journal = {Journal of Ecology},
  volume = {97},
  number = {6},
  pages = {1160--1170},
  issn = {0022-0477},
  doi = {10.1111/j.1365-2745.2009.01566.x},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\M74X5BYJ\\Bronstein.pdf}
}

@article{Brooks2017a,
  ids = {Brooks2017},
  title = {{{glmmTMB}} Balances Speed and Flexibility among Packages for Zero-Inflated Generalized Linear Mixed Modeling},
  author = {Brooks, Mollie E. and Kristensen, Kasper and {van Benthem}, Koen J. and Magnusson, Arni and Berg, Casper W. and Nielsen, Anders and Skaug, Hans J. and Maechler, Martin and Bolker, Benjamin M.},
  year = {2017},
  journal = {The R Journal},
  volume = {9},
  number = {2},
  pages = {378--400},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\PKEBHH7J\\Brooks et al. - 2017 - glmmTMB Balances Speed and Flexibility Among Packa.pdf}
}

@incollection{bruno2001,
  title = {Habitat Modification and Facilitation in Benthic Marine Communities},
  booktitle = {Marine {{Community Ecology}}},
  author = {Bruno, J. F. and Bertness, M. D.},
  editor = {Bertness, M.D.},
  year = {2001},
  pages = {201--218},
  publisher = {{Sinauer}}
}

@article{bruno2003,
  title = {Inclusion of Facilitation into Ecological Theory},
  author = {Bruno, John F and Stachowicz, John J and Bertness, Mark D},
  year = {2003},
  journal = {Trends in Ecology \& Evolution},
  volume = {18},
  number = {3},
  pages = {119--125},
  issn = {0169-5347},
  doi = {10.1016/S0169-5347(02)00045-9},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\Y86DVKLP\\brunoetal2003.pdf}
}

@article{bulleri2009,
  title = {Facilitation Research in Marine Systems: State of the Art, Emerging Patterns and Insights for Future Developments},
  author = {Bulleri, Fabio},
  year = {2009},
  journal = {Journal of Ecology},
  volume = {97},
  number = {6},
  pages = {1121--1130},
  issn = {1365-2745},
  doi = {10.1111/j.1365-2745.2009.01567.x},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\3PLR7AZ4\\Bulleri2009.pdf}
}

@article{bulleri2014,
  title = {Intensity and Temporal Variability as Components of Stress Gradients: Implications for the Balance between Competition and Facilitation},
  author = {Bulleri, F. and Xiao, S. and Maggi, E. and {Benedetti-Cecchi}, L.},
  year = {2014},
  month = jan,
  journal = {Oikos},
  volume = {123},
  number = {1},
  pages = {47--55},
  issn = {0030-1299},
  doi = {10.1111/j.1600-0706.2013.00604.x},
  abstract = {The mechanisms regulating switches in species interactions along gradients of stress are yet to be fully elucidated. In particular, the role of temporal variability in environmental severity or consumer pressure has been not explored either empirically or theoretically. Here, through a spatially explicit model (i.e. a two-dimensional lattice), we show that variations in the temporal variance of environmental stress can be as important as those in the mean intensity in regulating the spatial distribution and coexistence range of species differing in their relative competitive ability and tolerance to stress, as well as the direction and magnitude of their interactions. In addition, our simulations suggest that enhanced temporal fluctuations in environmental stressors can enhance absolute levels of stress perceived by interacting species. This study shows that tests including both the mean and temporal variance of environmental stress will be key to forecast changes in species interactions under different scenarios of climate change.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\2U9BR7RM\\Bulleri2014.pdf}
}

@article{bulleri2015,
  title = {Facilitation and the Niche: Implications for Coexistence, Range Shifts and Ecosystem Functioning},
  author = {Bulleri, Fabio and Bruno, John F. and Silliman, Brian R. and Stachowicz, John J.},
  year = {2015},
  journal = {Functional Ecology},
  pages = {n/a-n/a},
  issn = {1365-2435},
  doi = {10.1111/1365-2435.12528},
  keywords = {biodiversity and ecosystem functioning,climate change,competitive exclusion,environmental stress,foundation species,micro-habitat,niche overlapping,niche segregation,positive species interactions,spatial and temporal heterogeneity},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\MFRX8XXS\\Bulleri_et_al-2015-Functional_Ecology.pdf}
}

@article{callaway1997a,
  title = {Competition and Facilitation: {{A}} Synthetic Approach to Interactions in Plant Communities},
  author = {Callaway, R. M. and Walker, L. R.},
  year = {1997},
  month = oct,
  journal = {Ecology},
  volume = {78},
  number = {7},
  pages = {1958--1965},
  issn = {0012-9658},
  doi = {10.1890/0012-9658(1997)078[1958:cafasa]2.0.co;2},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\V8UTEIEN\\callaway.pdf}
}

@article{cardinale2002,
  title = {Species Diversity Enhances Ecosystem Functioning through Interspecific Facilitation},
  author = {Cardinale, B. J. and Palmer, M. A. and Collins, S. L.},
  year = {2002},
  month = jan,
  journal = {Nature},
  volume = {415},
  number = {6870},
  pages = {426--429},
  issn = {0028-0836},
  doi = {10.1038/415426a},
  abstract = {Facilitation between species is thought to be a key mechanism by which biodiversity affects the rates of resource use that govern the efficiency and productivity of ecosystems(1-4); however, there is no direct empirical evidence to support this hypothesis. Here we show that increasing the species diversity of a functional group of aquatic organisms induces facilitative interactions, leading to non-additive changes in resource consumption. We increased the richness and evenness of suspension-feeding caddisfly larvae (Insecta, Trichoptera) in stream mesocosms and found that the increased topographical complexity of the benthic habitat alters patterns of near-bed flow such that the feeding success of individuals is enhanced. Species diversity reduces 'current shading' (that is, the deceleration of flow from upstream to downstream neighbours), allowing diverse assemblages to capture a greater fraction of suspended resources than is caught by any species monoculture. The fundamental nature of this form of hydrodynamic facilitation suggests that it is broadly applicable to freshwater and marine habitats; in addition, it has several analogues in terrestrial ecosystems where fluxes of energy and matter can be influenced by biophysical complexity(3,5,6). Thus, changes in species diversity may alter the probability of positive species interactions, resulting in disproportionately large changes in the functioning of ecosystems.},
  langid = {english},
  keywords = {changing biodiversity,consequences,flow,particle capture,plant diversity,productivity,sediments},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\BFBZR8WY\\cardinaleetal.pdf}
}

@article{cardini2019,
  title = {Chemosymbiotic Bivalves Contribute to the Nitrogen Budget of Seagrass Ecosystems},
  author = {Cardini, Ulisse and Bartoli, Marco and L{\"u}cker, Sebastian and Mooshammer, Maria and Polzin, Julia and Lee, Raymond W. and Mici{\'c}, Vesna and Hofmann, Thilo and Weber, Miriam and Petersen, Jillian M.},
  year = {2019},
  month = dec,
  journal = {The ISME Journal},
  volume = {13},
  number = {12},
  pages = {3131--3134},
  issn = {1751-7362, 1751-7370},
  doi = {10.1038/s41396-019-0486-9},
  abstract = {In many seagrass sediments, lucinid bivalves and their sulfur-oxidizing symbionts are thought to underpin key ecosystem functions, but little is known about their role in nutrient cycles, particularly nitrogen. We used natural stable isotopes, elemental analyses, and stable isotope probing to study the ecological stoichiometry of a lucinid symbiosis in spring and fall. Chemoautotrophy appeared to dominate in fall, when chemoautotrophic carbon fixation rates were up to one order of magnitude higher as compared with the spring, suggesting a flexible nutritional mutualism. In fall, an isotope pool dilution experiment revealed carbon limitation of the symbiosis and ammonium excretion rates up to tenfold higher compared with fluxes reported for nonsymbiotic marine bivalves. These results provide evidence that lucinid bivalves can contribute substantial amounts of ammonium to the ecosystem. Given the preference of seagrasses for this nitrogen source, lucinid bivalves' contribution may boost productivity of these important blue carbon ecosystems.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\EVF8C4R7\\Cardini et al. - 2019 - Chemosymbiotic bivalves contribute to the nitrogen.pdf}
}

@article{cavieres2016,
  title = {Facilitation among Plants as an Insurance Policy for Diversity in {{Alpine}} Communities},
  author = {Cavieres, Lohengrin A and Hern{\'a}ndez-Fuentes, Carolina and Sierra-Almeida, Angela and Kikvidze, Zaal},
  year = {2016},
  journal = {Functional Ecology},
  volume = {30},
  number = {1},
  pages = {52--59},
  issn = {1365-2435},
  doi = {10.1111/1365-2435.12545},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\Q5K383T9\\Cavieres.pdf}
}

@article{degoeij2013,
  title = {Surviving in a Marine Desert: {{The}} Sponge Loop Retains Resources within Coral Reefs},
  author = {{de Goeij}, Jasper M. and {van Oevelen}, Dick and Vermeij, Mark J. A. and Osinga, Ronald and Middelburg, Jack J. and {de Goeij}, Anton F. P. M. and Admiraal, Wim},
  year = {2013},
  month = oct,
  journal = {Science},
  volume = {342},
  number = {6154},
  pages = {108--110},
  doi = {10.1126/science.1241981},
  abstract = {Ever since Darwin's early descriptions of coral reefs, scientists have debated how one of the world's most productive and diverse ecosystems can thrive in the marine equivalent of a desert. It is an enigma how the flux of dissolved organic matter (DOM), the largest resource produced on reefs, is transferred to higher trophic levels. Here we show that sponges make DOM available to fauna by rapidly expelling filter cells as detritus that is subsequently consumed by reef fauna. This ``sponge loop'' was confirmed in aquarium and in situ food web experiments, using 13C- and 15N-enriched DOM. The DOM-sponge-fauna pathway explains why biological hot spots such as coral reefs persist in oligotrophic seas\textemdash the reef's paradox\textemdash and has implications for reef ecosystem functioning and conservation strategies.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\327XNM9K\\Science-2013-de Goeij-108-10.pdf}
}

@article{Diaz2005,
  title = {Common Sponges from Shallow Marine Habitats from {{Bocas}} Del {{Toro}} Region, {{Panama}}},
  author = {Diaz, M. C.},
  year = {2005},
  journal = {Caribbean Journal of Science},
  volume = {41},
  number = {3},
  pages = {465--475},
  issn = {0008-6452},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\4Q4E6XUQ\\Diaz2005.pdf}
}

@article{duarte1990,
  title = {Seagrass Nutrient Content},
  author = {Duarte, Carlos M},
  year = {1990},
  journal = {Marine ecology progress series. Oldendorf},
  volume = {6},
  number = {2},
  pages = {201--207},
  issn = {0171-8630},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\QJBDE4JF\\Duarte1990.pdf}
}

@incollection{duarte2006,
  title = {Dynamics of Seagrass Stability and Change},
  booktitle = {Seagrasses: Biology Ecology and Conservation},
  author = {Duarte, Carlos M and Fourqurean, James W and {Krause-Jensen}, Dorte and Olesen, Birgit},
  year = {2006},
  pages = {271--294},
  publisher = {{Springer}},
  isbn = {1-4020-2942-X}
}

@article{Duffy2006,
  ids = {duffy2006a},
  title = {Biodiversity and the Functioning of Seagrass Ecosystems},
  author = {Duffy, Je},
  year = {2006},
  month = apr,
  journal = {Marine Ecology Progress Series},
  volume = {311},
  pages = {233--250},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps311233},
  abstract = {Biodiversity at multiple levels \textemdash{} genotypes within species, species within functional groups, habitats within a landscape \textemdash{} enhances productivity, resource use, and stability of seagrass ecosystems. Several themes emerge from a review of the mostly indirect evidence and the few experiments that explicitly manipulated diversity in seagrass systems. First, because many seagrass communities are dominated by 1 or a few plant species, genetic and phenotypic diversity within such foundation species has important influences on ecosystem productivity and stability. Second, in seagrass beds and many other aquatic systems, consumer control is strong, extinction is biased toward large body size and high trophic levels, and thus human impacts are often mediated by interactions of changing `vertical diversity' (food chain length) with changing `horizontal diversity' (heterogeneity within trophic levels). Third, the openness of marine systems means that ecosystem structure and processes often depend on interactions among habitats within a landscape (landscape diversity). There is clear evidence from seagrass systems that advection of resources and active movement of consumers among adjacent habitats influence nutrient fluxes, trophic transfer, fishery production, and species diversity. Future investigations of biodiversity effects on processes within seagrass and other aquatic ecosystems would benefit from broadening the concept of biodiversity to encompass the hierarchy of genetic through landscape diversity, focusing on links between diversity and trophic interactions, and on links between regional diversity, local diversity, and ecosystem processes. Maintaining biodiversity and biocomplexity of seagrass and other coastal ecosystems has important conservation and management implications.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\R4S8WGKE\\Duffy - 2006 - Biodiversity and the functioning of seagrass ecosy.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\TVYVFCWI\\Duffy2006.pdf}
}

@article{easson2014,
  title = {Complex Ecological Associations: Competition and Facilitation in a Sponge-Algal Interaction},
  author = {Easson, C. G. and Slattery, M. and Baker, D. M. and Gochfeld, D. J.},
  year = {2014},
  month = jul,
  journal = {Marine Ecology Progress Series},
  volume = {507},
  pages = {153--167},
  issn = {0171-8630},
  doi = {10.3354/meps10852},
  abstract = {Over the past few decades, Caribbean coral reefs have undergone a phase shift from coral-dominated to algal-dominated communities due to several factors, including increased input of anthropogenic nutrients. With the decline in coral cover, sponges have also become more dominant members of Caribbean coral reef communities. Increased algal and sponge dominance on Caribbean reefs has led to an increase in the frequency of interaction between these 2 groups. This study used a factorial design to assess the independent and interactive effects of contact and elevated nutrient levels on 2 common members of these communities, the sponge Aplysina cauliformis, and the macroalga Microdictyon marinum. Algal contact had a significant negative physiological effect on A. cauliformis, affecting both the host sponge and its cyanobacterial symbionts. While elevated nutrient levels had some positive effects on the sponge photosymbionts, this only occurred in the absence of algal contact or a shading/abrasion control, and elevated nutrient levels had a negative effect on the sponge holobiont. In contrast, M. marinum responded positively to experimentally enhanced nutrient levels and to sponge contact under ambient nutrient regimes, but was not affected by sponge contact under elevated nutrient concentrations. Stable isotope enrichment experiments showed that the alga's positive response to sponge contact was associated with nitrogen transfer from the sponge over the course of the experiment. Thus, while A. cauliformis facilitates increased productivity in M marinum, algal contact competitively inhibits sponge condition.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\INLPSCKE\\Eassonetal2014.pdf}
}

@article{ellison1996,
  title = {Facultative Mutualism between Red Mangroves and Root-Fouling Sponges in {{Belizean}} Mangal},
  author = {Ellison, A. M. and Farnsworth, E. J. and Twilley, R. R.},
  year = {1996},
  month = dec,
  journal = {Ecology},
  volume = {77},
  number = {8},
  pages = {2431--2444},
  issn = {0012-9658},
  doi = {10.2307/2265744},
  abstract = {We report results of transplant experiments that examined direct interactions between red mangrove (Rhizophora mangle) roots and two common root-fouling sponges (Tedania ignis and Haliclona implexiformis) on carbonate-based, oligotrophic mangrove cays in Belize, Central America. On these cays, subtidal prop roots of mangroves at water's edge often extend 1-2 m below lowest low water before anchoring in the substrate and host a community of algal and invertebrate epibionts dominated by massive sponges. Live sponges transplanted onto otherwise bare roots increased root growth rate two- to fourfold relative to controls. Roots fouled naturally by these and other massive sponges produce adventitious fine rootlets that ramify throughout sponge tissue; these rootlets structurally resemble underground rootlets that function in nutrient uptake. Sponges transplanted onto bare mangrove roots induced rootlet proliferation within 4 wk. Only live sponges elicited this response, indicating that adventitious rootlet production is not simply a by-product of anoxia or darkness. Sponges transplanted onto bare roots grew 1.4-10 times faster than did sponges grown on polyvinyl chloride (PVC) tubes at identical depths and locations. Relative abundances of N-15 (expressed as delta(15)N parts per thousand) and C-13 (delta(13)C parts per thousand) in Tedania, Haliclona, an additional sponge, Ulosa ruetzleri, and rootlets, roots, stems, twigs, and leaves of mangrove hosts suggest that mangrove roots obtain dissolved inorganic nitrogen from sponges, and that sponges obtain carbon from mangrove roots. No transfer of N or C was observed in similar analyses of roots fouled by the red alga Acanthophora spicifera. We conclude that where they co-occur, massive sponges and mangroves are facultative mutualists. In mangrove forests, as in other marginal habitats, facilitations may enable increased growth and production of component species.},
  langid = {english},
  keywords = {Belize,BIOLOGICAL INVASION,ecosystem dynamics,ENGLAND SALT-MARSH,facilitations,FRENCH,Haliclona implexiformis,mangle,mangroves,mutualisms,NITROGEN-FIXATION,NUTRIENT STATUS,ORGANIC-CARBON,plant-animal interactions,Porifera,Rhizophora,RHIZOPHORA-MANGLE,SOUTHWEST FLORIDA,SPARTINA-ALTERNIFLORA PRODUCTION,STABLE ISOTOPES,Tedania ignis,WEST-INDIES},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\DY8LWG4U\\ellisonetal1996.pdf}
}

@article{erwin2012,
  title = {Stability of Sponge-Associated Bacteria over Large Seasonal Shifts in Temperature and Irradiance},
  author = {Erwin, P. M. and Pita, L. and {Lopez-Legentil}, S. and Turon, X.},
  year = {2012},
  month = oct,
  journal = {Applied and environmental microbiology},
  volume = {78},
  number = {20},
  pages = {7358--7368},
  issn = {0099-2240},
  doi = {10.1128/aem.02035-12},
  abstract = {Complex microbiomes reside in marine sponges and consist of diverse microbial taxa, including functional guilds that may contribute to host metabolism and coastal marine nutrient cycles. Our understanding of these symbiotic systems is based primarily on static accounts of sponge microbiota, while their temporal dynamics across seasonal cycles remain largely unknown. Here, we investigated temporal variation in bacterial symbionts of three sympatric sponges (Ircinia spp.) over 1.5 years in the northwestern (NW) Mediterranean Sea, using replicated terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses of bacterial 16S rRNA gene sequences. Bacterial symbionts in Ircinia spp. exhibited host species-specific structure and remarkable stability throughout the monitoring period, despite large fluctuations in temperature and irradiance. In contrast, seawater bacteria exhibited clear seasonal shifts in community structure, indicating that different ecological constraints act on free-living and on symbiotic marine bacteria. Symbiont profiles were dominated by persistent, sponge-specific bacterial taxa, notably affiliated with phylogenetic lineages capable of photosynthesis, nitrite oxidation, and sulfate reduction. Variability in the sponge microbiota was restricted to rare symbionts and occurred most prominently in warmer seasons, coincident with elevated thermal regimes. Seasonal stability of the sponge microbiota supports the hypothesis of host-specific, stable associations between bacteria and sponges. Further, the core symbiont profiles revealed in this study provide an empirical baseline for diagnosing abnormal shifts in symbiont communities. Considering that these sponges have suffered recent, episodic mass mortalities related to thermal stresses, this study contributes to the development of model sponge-microbe symbioses for assessing the link between symbiont fluctuations and host health.},
  langid = {english},
  keywords = {alpha-proteobacterium,aplysina-aerophoba,chondrilla-nucula,clone libraries,cyanobacteria symbioses,diversity,in-situ,marine sponges,microbial communities,rhopaloeides-odorabile},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\GTIJ7IYH\\Erwinetal_stability_2012.pdf}
}

@article{ferdie2004,
  title = {Responses of Seagrass Communities to Fertilization along a Gradient of Relative Availability of Nitrogen and Phosphorus in a Carbonate Environment},
  author = {Ferdie, M. and Fourqurean, J. W.},
  year = {2004},
  month = nov,
  journal = {Limnology and Oceanography},
  volume = {49},
  number = {6},
  pages = {2082--2094},
  issn = {0024-3590},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\HXX5A7KC\\FerdieandFourqurean.pdf}
}

@article{Folmer2012,
  ids = {folmer2012a},
  title = {Seagrass-{{Sediment Feedback}}: {{An Exploration Using}} a {{Non-recursive Structural Equation Model}}},
  shorttitle = {Seagrass\textendash{{Sediment Feedback}}},
  author = {Folmer, Eelke O. and {van der Geest}, Matthijs and Jansen, Erik and Olff, Han and Michael Anderson, T. and Piersma, Theunis and {van Gils}, Jan A.},
  year = {2012},
  month = dec,
  journal = {Ecosystems},
  volume = {15},
  number = {8},
  pages = {1380--1393},
  issn = {1432-9840, 1435-0629},
  doi = {10.1007/s10021-012-9591-6},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\2PK4ZQGP\\Folmer et al. - 2012 - Seagrass–Sediment Feedback An Exploration Using a.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\GTKSMYUE\\Folmaretal2012.pdf}
}

@article{Fonseca1992,
  ids = {fonseca1992a},
  title = {A Preliminary Evaluation of Wave Attenuation by Four Species of Seagrass},
  author = {Fonseca, Mark S. and Cahalan, Jennifer A.},
  year = {1992},
  month = dec,
  journal = {Estuarine, Coastal and Shelf Science},
  volume = {35},
  number = {6},
  pages = {565--576},
  issn = {02727714},
  doi = {10.1016/S0272-7714(05)80039-3},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\VX629JBM\\Fonseca and Cahalan - 1992 - A preliminary evaluation of wave attenuation by fo.pdf}
}

@article{fourqurean1992,
  title = {Phosphorus Limitation of Primary Production in {{Florida Bay}}: {{Evidence}} from {{C}}: {{N}}: {{P}} Ratios of the Dominant Seagrass {\emph{ }}{{{\emph{Thalassia}}}}{\emph{ Testudinum}}},
  author = {Fourqurean, James W and Zieman, Joseph C and Powell, George VN},
  year = {1992},
  journal = {Limnology and Oceanography},
  volume = {37},
  number = {1},
  pages = {162--171},
  issn = {0024-3590},
  doi = {10.4319/lo.1992.37.1.0162},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\4H5PV3L6\\Fourqurean1992.pdf}
}

@article{fourqurean1995,
  title = {The {{Effects}} of {{Long-Term Manipulation}} of {{Nutrient Supply}} on {{Competition}} between the {{Seagrasses}} {{{\emph{Thalassia}}}}{\emph{ Testudinum}} and {{{\emph{Halodule}}}}{\emph{ Wrightii}} in {{Florida Bay}}},
  author = {Fourqurean, James W. and Powell, George V. N. and Kenworthy, W. Judson and Zieman, Joseph C.},
  year = {1995},
  journal = {Oikos},
  volume = {72},
  number = {3},
  pages = {349--358},
  issn = {00301299},
  doi = {10.2307/3546120},
  abstract = {Long term (8 yr) continuous fertilization (via application of bird feces) of established seagrass beds in Florida Bay, FL, USA caused a change in the dominant seagrass species. Before fertilization, the seagrass beds were a Thalassia testudinum monoculture; after 8 yr of fertilization the seagrass Halodule wrightii made up 97\% of the aboveground biomass. Fertilization had a positive effect on the standing crop of T. testudinum for the first two years of the experiment. The transition from T. testudinum-dominated to H. wrightii-dominated was dependent on the timing of colonization of the sites by H. wrightii; the decrease in T. testudinum standing crop and density at the fertilized sites occurred only after the colonization of the sites by H. wrightii. There were no trends in the standing crop or density of T. testudinum at control sites, and none of the control sites were colonized by H. wrightii. The effects of fertilization on these seagrass beds persisted at least 8 yr after the cessation of nutrient addition, suggesting that these systems retain and recycle acquired nutrients efficiently. Results of these experiments suggest that Halodule wrightii, the normal early-successional seagrass during secondary succession in Caribbean seagrass communities, has a higher nutrient demand than Thalassia testudinum, the normal late successional species, and that the replacement of H. wrightii by T. testudinum during secondary succession is due to the ability of T. testudinum to draw nutrient availability below the requirements of H. wrightii.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\MQE2E8E3\\fourqureanetal1995.pdf}
}

@article{Fourqurean2012,
  ids = {fourqurean2012a},
  title = {Seagrass Ecosystems as a Globally Significant Carbon Stock},
  author = {Fourqurean, James W. and Duarte, Carlos M. and Kennedy, Hilary and Marb{\`a}, N{\'u}ria and Holmer, Marianne and Mateo, Miguel Angel and Apostolaki, Eugenia T. and Kendrick, Gary A. and {Krause-Jensen}, Dorte and McGlathery, Karen J. and Serrano, Oscar},
  year = {2012},
  month = jul,
  journal = {Nature Geoscience},
  volume = {5},
  number = {7},
  pages = {505--509},
  issn = {1752-0894, 1752-0908},
  doi = {10.1038/ngeo1477},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\A5X385CS\\Fourqurean et al 2012 Nature Geoscience online.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\FK4RBBDP\\Fourqurean et al. - 2012 - Seagrass ecosystems as a globally significant carb.pdf}
}

@article{gagnon2020,
  title = {Facilitating Foundation Species: {{The}} Potential for Plant-Bivalve Interactions to Improve Habitat Restoration Success},
  shorttitle = {Facilitating Foundation Species},
  author = {Gagnon, Karine and Rinde, Eli and Bengil, Elizabeth G. T. and Carugati, Laura and Christianen, Marjolijn J. A. and Danovaro, Roberto and Gambi, Cristina and Govers, Laura L. and Kipson, Silvija and Meysick, Lukas and Pajusalu, Liina and T{\"u}ney K{\i}z{\i}lkaya, {\.I}nci and Koppel, Johan and Heide, Tjisse and Katwijk, Marieke M. and Bostr{\"o}m, Christoffer},
  editor = {Pinto, Rute},
  year = {2020},
  month = jun,
  journal = {Journal of Applied Ecology},
  volume = {57},
  number = {6},
  pages = {1161--1179},
  issn = {0021-8901, 1365-2664},
  doi = {10.1111/1365-2664.13605},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\GZFAHWC3\\Gagnon et al. - 2020 - Facilitating foundation species The potential for.pdf}
}

@article{gutierrez2020,
  title = {Ecosystem {{Engineers}} in the {{World Coasts}}: {{Case Studies}} and {{Conceptual Linkages}}},
  shorttitle = {Ecosystem {{Engineers}} in the {{World Coasts}}},
  author = {Guti{\'e}rrez, Jorge L.},
  year = {2020},
  month = jun,
  journal = {Diversity},
  volume = {12},
  number = {6},
  pages = {243},
  issn = {1424-2818},
  doi = {10.3390/d12060243},
  abstract = {Research on physical ecosystem engineering\textemdash i.e., the structural modification of environments by organisms\textemdash has flourished during the last two decades. At present, the importance of physical ecosystem engineers for the biodiversity and the functioning of ecosystems is well recognized by scientists. This Special Issue contains fifteen papers that illustrate the diversity of physical ecosystem engineering processes that occur in the world coastal habitats\textemdash from coastal dunes to the shallow subtidal zone. It includes 2 reviews comparing ecosystem engineering attributes and impacts across taxa and 13 case studies that inform our general understanding of the variation in engineering impacts, compound engineering effects, novel engineering interactions, and engineered structural legacies.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\UZINAWY2\\Gutiérrez - 2020 - Ecosystem Engineers in the World Coasts Case Stud.pdf}
}

@article{hao2013,
  title = {Facilitation and Competition among Foundation Species of Submerged Macrophytes Threatened by Severe Eutrophication and Implications for Restoration},
  author = {Hao, Beibei and Wu, Haoping and Shi, Qiao and Liu, Guihua and Xing, Wei},
  year = {2013},
  journal = {Ecological Engineering},
  volume = {60},
  number = {0},
  pages = {76--80},
  issn = {0925-8574},
  doi = {10.1016/j.ecoleng.2013.07.067},
  keywords = {Competition,Ecological stoichiometry,Eutrophication,Facilitation,Foundation species,Restoration,Stress gradient hypothesis,Submerged macrophyte},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\7CSELE96\\Haoetal.pdf}
}

@article{Heck2003,
  ids = {heck2003},
  title = {Critical Evaluation of the Nursery Role Hypothesis for Seagrass Meadows},
  author = {Heck, Kl and Hays, G and Orth, Rj},
  year = {2003},
  journal = {Marine Ecology Progress Series},
  volume = {253},
  pages = {123--136},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps253123},
  abstract = {The vast majority of published papers concerning seagrass meadows contain statements to the effect that seagrass beds serve as important nurseries for many species. We reviewed more than 200 papers that were relevant to the nursery role hypothesis. We used both vote counting and meta-analytic techniques to evaluate whether the body of previous studies that report seagrass meadows to be nursery grounds actually contain data that support this proposition. We restricted our analyses to papers that compared seagrass beds to other habitats, and examined data on a variety of well-studied species concerning their density, growth, survival and migration to adult habitat. Within this group of papers, we considered potential factors that could influence the nursery function (e.g. location, or laboratory vs field studies). We also evaluated case histories of well-documented largescale seagrass losses on the nursery function. Major results were consistent with the expectations that abundance, growth and survival were greater in seagrass than in unstructured habitats. Abundance data also suggested that seagrass beds in the Northern Hemisphere might be more important as nursery areas than those in the Southern Hemisphere. Surprisingly, few significant differences existed in abundance, growth or survival when seagrass meadows were compared to other structured habitats, such as oyster or cobble reefs, or macroalgal beds. Nor were there decreases in harvests of commercially important species that could clearly be attributed to significant seagrass declines in 3 wellstudied areas. However, there were decreased abundances of juveniles of commercially important species in these areas, suggesting a strong link between seagrass abundance and those of juvenile finfish and shellfish. One important implication of these results is that structure per se, rather than the type of structure, appears to be an important determinant of nursery value. Clearly, more rigorous studies that test all aspects of the nursery role hypothesis are clearly needed for seagrass meadows as well as other structured habitats. The results of such studies will allow better decisions to be made concerning the conservation and restoration of marine habitats.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\9XXLDDV6\\Heck Hay et al. - 2003 - Critical evaluation of the nursery role hypothesis.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\JD8IR5XP\\Heck et al 2003.pdf}
}

@article{Hemminga1991,
  type = {Journal {{Article}}},
  ids = {hemminga1991a},
  title = {The Balance of Nutrient Losses and Gains in Seagrass Meadows},
  author = {Hemminga, MA and Harrison, PG and Van Lent, F.},
  year = {1991},
  journal = {Marine Ecology Progress Series},
  volume = {71},
  number = {1},
  pages = {85--96},
  doi = {10.3354/meps071085},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\DCSHUB4J\\Heminga1991.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\GZVESFGV\\Heminga1991.pdf}
}

@article{holzapfel1999,
  title = {Bidirectional Facilitation and Interference between Shrubs and Annuals in the {{Mojave Desert}}},
  author = {Holzapfel, Claus and Mahall, Bruce E},
  year = {1999},
  journal = {Ecology},
  volume = {80},
  number = {5},
  pages = {1747--1761},
  issn = {0012-9658},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\LYTN6VJD\\3516-Bidirectional.PDF}
}

@article{hughes2014,
  title = {Additive and Site-Specific Effects of Two Foundation Species on Invertebrate Community Structure},
  author = {Hughes, A Randall and Gribben, Paul E and Kimbro, David L and Bishop, Melanie J},
  year = {2014},
  journal = {Marine Ecology Progress Series},
  volume = {508},
  pages = {129--138},
  issn = {0171-8630},
  doi = {10.3354/meps10867},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\ALZLU9HS\\hughesetal2014.pdf}
}

@article{jones1994,
  title = {Organisms as Ecosystem Engineers},
  author = {Jones, Clive G and Lawton, John H and Shachak, Moshe},
  year = {1994},
  journal = {Oikos},
  pages = {373--386},
  issn = {0030-1299},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\CU7GQ24Y\\Jones_et_al_1994_Organisms_as_Oikos_69_373-386.pdf}
}

@article{jones2021,
  title = {Seagrass {{Structural Traits Drive Fish Assemblages}} in {{Small-Scale Fisheries}}},
  author = {Jones, Benjamin L. and Nordlund, Lina M. and Unsworth, Richard K. F. and Jiddawi, Narriman S. and Ekl{\"o}f, Johan S.},
  year = {2021},
  month = apr,
  journal = {Frontiers in Marine Science},
  volume = {8},
  pages = {640528},
  issn = {2296-7745},
  doi = {10.3389/fmars.2021.640528},
  abstract = {Seagrasses \textendash{} a group of foundation species in coastal ecosystems \textendash{} provide key habitat for diverse and abundant faunal assemblages and support numerous ecosystem functions and services. However, whether the habitat role of seagrasses is influenced by seagrass diversity, by dominant species or both, remains unclear. To that end, we sought to investigate the specific seagrass characteristics (e.g., species diversity, seagrass traits) that influence tropical fish assemblages, and place this in the context of small-scale fishery use. We surveyed seagrass variables at 55 plots, nested within 12 sites around Zanzibar (Tanzania) in the Western Indian Ocean, and used Baited Remote Underwater Video (BRUV) systems to assess fish assemblages across plots. Using linear mixed models, we reveal that seagrass structural complexity and depth were the best predictors of fish abundance, with higher abundance occurring in deeper meadows or meadows with high canopy, leaf length and number of leaves per shoot. Moreover, an interaction between seagrass cover and land-use was the best predictor of fish species richness, where sites closer to human impacts were less affected by cover than sites with lower human impact. Overall, models with seagrass species richness or functional diversity as predictors poorly explained fish assemblages. Fish taxa that were important for small-scale fishery sectors (e.g., emperors, snappers, rabbitfish, and parrotfish) were primarily driven by seagrass structural complexity. Our results provide a unique analysis of the relationship between seagrass habitat and its associated fish assemblages in that we show that seagrass species diversity had little effect on seagrass fish assemblages, which instead appear driven by specific seagrass traits and seagrass cover. If conserving high value species that support adjacent fisheries is the priority for protecting seagrass meadows, then seagrass areas should be chosen with high cover and structural complexity that are in deeper waters. Any conservation measures also need to balance the needs of fishers that use the resources supported by seagrasses.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\SWRTCSM3\\Jones et al. - 2021 - Seagrass Structural Traits Drive Fish Assemblages .pdf}
}

@article{karplus2006,
  title = {Predator Recognition and Social Facilitation of Predator Avoidance in Coral Reef Fish {{Dascyllus}} Marginatus Juveniles},
  author = {Karplus, I. and Katzenstein, R. and Goren, M.},
  year = {2006},
  journal = {Marine Ecology Progress Series},
  volume = {319},
  pages = {215--223},
  issn = {0171-8630},
  abstract = {Predator recognition was studied in Dascyllus marginatus, a small Red Sea pomacentrid that forms mixed-size schools associated with branching corals of the genera Acropora and Stylophora. The reactions of variously sized D. marginatus to sudden exposure to a live predatory fish (Epinephelus fasciatus), a non-predatory fish (Acanthurus nigrofuscus), and an empty cell were monitored in the laboratory. Adult fish (49 to 60 mm) discriminated between predatory and non-predatory fish, whereas juveniles (13 to 17 mm) could not. The responses of single juveniles, pairs of juveniles, and juvenile/adult pairs to sudden exposure to a predator were compared. Juveniles paired with adults avoided the predator more than single or paired juveniles. A mechanism in the reef habitat of social facilitation of predator recognition and avoidance among mixed-sized school pomacentrids is suggested. The relevance of the findings of this study to the low survival of reef fishes shortly after settlement and their preference for coral heads inhabited by conspecifics is discussed.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\K6JIADFU\\Karplus2006.pdf}
}

@article{kennish2014,
  title = {Drivers of {{Change}} in {{Shallow Coastal Photic Systems}}: {{An Introduction}} to a {{Special Issue}}},
  shorttitle = {Drivers of {{Change}} in {{Shallow Coastal Photic Systems}}},
  author = {Kennish, Michael J. and Brush, Mark J. and Moore, Kenneth A.},
  year = {2014},
  month = mar,
  journal = {Estuaries and Coasts},
  volume = {37},
  number = {S1},
  pages = {3--19},
  issn = {1559-2723, 1559-2731},
  doi = {10.1007/s12237-014-9779-4},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\MHA4XT4F\\Kennish et al. - 2014 - Drivers of Change in Shallow Coastal Photic System.pdf}
}

@article{layman2013,
  title = {Thresholds of {{Ecosystem Response}} to {{Nutrient Enrichment}} from {{Fish Aggregations}}},
  author = {Layman, Craig A. and Allgeier, Jacob Edward and Yeager, Lauren A. and Stoner, Elizabeth W.},
  year = {2013},
  journal = {Ecology},
  volume = {94},
  number = {2},
  pages = {530--536},
  issn = {0012-9658},
  doi = {10.1890/12-0705.1},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\YCAA5482\\LaymanAllgierYeagerStoner2012.pdf}
}

@article{Layman2016,
  title = {Mechanistic Evidence of Enhanced Production on Artificial Reefs: {{A}} Case Study in a {{Bahamian}} Seagrass Ecosystem},
  shorttitle = {Mechanistic Evidence of Enhanced Production on Artificial Reefs},
  author = {Layman, Craig A. and Allgeier, Jacob E. and Monta{\~n}a, Carmen G.},
  year = {2016},
  month = oct,
  journal = {Ecological Engineering},
  volume = {95},
  pages = {574--579},
  issn = {09258574},
  doi = {10.1016/j.ecoleng.2016.06.109},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\HR558KE2\\Layman et al. - 2016 - Mechanistic evidence of enhanced production on art.pdf}
}

@article{lohrer2016,
  title = {Influence of {{New Zealand}} Cockles ( {{{\emph{Austrovenus}}}}{\emph{ Stutchburyi}} ) on Primary Productivity in Sandflat-Seagrass ( {{{\emph{Zostera}}}}{\emph{ Muelleri}} ) Ecotones},
  author = {Lohrer, Andrew M. and Townsend, Michael and Hailes, Sarah F. and Rodil, Iv{\'a}n F. and Cartner, Katie and Pratt, Daniel R. and Hewitt, Judi E.},
  year = {2016},
  month = nov,
  journal = {Estuarine, Coastal and Shelf Science},
  volume = {181},
  pages = {238--248},
  issn = {02727714},
  doi = {10.1016/j.ecss.2016.08.045},
  abstract = {New Zealand cockles (Austrovenus stutchburyi) are ecologically important, intertidal bivalves that have been shown to influence nutrient cycles and the productivity of microphytobenthos on sandflats. Here, we investigated the potential for cockles to impact the productivity of seagrass, Zostera muelleri, and examined interactions between these habitat-defining species where they co-occur. We sampled bivalve densities and sizes, sediment properties, and seagrass shoot densities across the boundaries of two seagrass patches on an intertidal sandflat in northern New Zealand, and measured dissolved oxygen and nutrient fluxes in light and dark benthic incubation chambers in conjunction with a 0e97\% gradient in seagrass cover. Although gross primary production (GPP, mmol O2 m\`A2 h\`A1) increased predictably with the cover of live seagrass, the density of cockles and sediment properties also contributed directly and indirectly. Seagrass cover was positively correlated with cockle density (ranging from 225 to 1350 individuals per m2), sediment mud percentage (0.5e9.5\%), and organic matter content (0.5e2.2\%), all of which can affect the efflux of ammonium (readily utilisable inorganic nitrogen) from sediments. Moreover, the cover of green seagrass blades plateaued (never exceeded 70\%) in the areas of highest total seagrass cover, adding complexity to cockle-seagrass interactions and contributing to a unimodal cockleGPP relationship.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\DQCL6PVT\\Lohrer et al. - 2016 - Influence of New Zealand cockles ( Austrovenus stu.pdf}
}

@article{lortie2016,
  title = {Functional Assessment of Animal Interactions with Shrub-facilitation Complexes: A Formal Synthesis and Conceptual Framework},
  author = {Lortie, Christopher J and Filazzola, Alessandro and Sotomayor, Diego A},
  year = {2016},
  journal = {Functional Ecology},
  volume = {30},
  number = {1},
  pages = {41--51},
  issn = {1365-2435},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\SHJMXBIH\\Loriteetal.pdf}
}

@article{maestre2009,
  title = {Refining the Stress-Gradient Hypothesis for Competition and Facilitation in Plant Communities},
  author = {Maestre, Fernando T. and Callaway, Ragan M. and Valladares, Fernando and Lortie, Christopher J.},
  year = {2009},
  journal = {Journal of Ecology},
  volume = {97},
  number = {2},
  pages = {199--205},
  issn = {1365-2745},
  doi = {10.1111/j.1365-2745.2008.01476.x},
  keywords = {abiotic stress,competition,environmental gradients,facilitation,plant–plant interactions,stress-gradient hypothesis},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\953N596X\\Maestre.pdf}
}

@article{medina-gomez2016,
  title = {Response of {{Thalassia Testudinum Morphometry}} and {{Distribution}} to {{Environmental Drivers}} in a {{Pristine Tropical Lagoon}}},
  author = {{Medina-G{\'o}mez}, Israel and Madden, Christopher J. and {Herrera-Silveira}, Jorge and Kjerfve, Bj{\"o}rn},
  editor = {Bianchi, Carlo Nike},
  year = {2016},
  month = oct,
  journal = {PLOS ONE},
  volume = {11},
  number = {10},
  pages = {e0164014},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0164014},
  abstract = {This study was undertaken to determine the relationships between the biomass, morphometry, and density of short shoots (SS) of the tropical seagrass Thalassia testudinum and the physical-environmental forcing in the region. Seasonal sampling surveys were undertaken four times in Bahia de la Ascension, a shallow estuary in the western Mexican Caribbean, to measure plant morphology and environmental variables. The estuary has a fresh waterinfluenced inner bay, a large central basin and a marine zone featuring a barrier reef at the seaward margin. Leaf size was positively correlated with increasing salinity, but total biomass was not, being similar across most of the sites. Aboveground biomass exhibited seasonal differences in dry and rainy seasons along the bay, most markedly in the brackish inner bay where an abrupt decline in biomass coincided with the rainy season. The relationship between nutrients and biomass indicates that the aboveground/belowground biomass ratio increases as nutrient availability increases. Areal cover was inversely correlated with SS density during both dry and rainy seasons. Maximum SS recruitment coincided with the rainy season. Peaks in SS density were recorded in the freshwater-influenced inner bay during an ENSO cold phase in 2007 (``La Ni\~na'') which is associated with a wetter dry season and following a strong storm (Hurricane Dean). The onset of the rainy season influences both shoot density and T. testudinum biomass by controlling the freshwater input to the bay and thus, the system's salinity gradient and external nutrients supply from the coastal wetland.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\M23M5S7D\\Medina-Gómez et al. - 2016 - Response of Thalassia Testudinum Morphometry and D.pdf}
}

@article{Meyer1983,
  ids = {meyer1983a},
  title = {Fish {{Schools}}: {{An Asset}} to {{Corals}}},
  author = {Meyer, Judy L. and Schultz, Eric T. and Helfman, Gene S.},
  year = {1983},
  journal = {Science, New Series},
  volume = {220},
  number = {4601},
  pages = {1047--1049},
  doi = {10.1126/science.220.4601.1047},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\IJ8YM2EU\\meyerschultzandhelfman.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\SQG8PRDC\\Meyer et al. - 1983 - Fish Schools An Asset to Corals.pdf}
}

@article{meysick2020,
  title = {Context-Dependency of Eelgrass-Clam Interactions: Implications for Coastal Restoration},
  shorttitle = {Context-Dependency of Eelgrass-Clam Interactions},
  author = {Meysick, L and Norkko, A and Gagnon, K and Gr{\"a}fnings, M and Bostr{\"o}m, C},
  year = {2020},
  month = aug,
  journal = {Marine Ecology Progress Series},
  volume = {647},
  pages = {93--108},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps13408},
  abstract = {Facilitative interactions between co-occurring species sustain diverse communities and constitute a vital functional component of coastal marine ecosystems. In seagrass ecosystems, facilitation ensures the survival and resilience of this important habitat. As seagrass meadows are in decline, innovative restoration strategies incorporating facilitative interactions could open new avenues in marine restoration. Here, we investigated the interactions between eelgrass Zostera marina and the Baltic clam Macoma balthica, and tested whether clams could enhance early survival and biomass increase of transplanted eelgrass shoots in the northern Baltic Sea. We measured eelgrass responses to differing densities of clams, as well as porewater ammonium (NH4+) and phosphate (PO43-) concentrations in field and aquarium experiments. Overall, survival of transplanted plots was high, independent of clam density. Specifically, we found that clams facilitated eelgrass above- and below-ground biomass in low porewater nutrient conditions, potentially through nutrient release, but inhibited growth in high-nutrient conditions, particularly where clams were added at high densities. Our results show the important role of infaunal bivalves for nutrient fluxes within seagrass meadows. Most notably, we highlight the importance of considering and testing context- and density-dependency when studying interspecific interactions, as clams could both benefit and hamper Zostera biomass increase. This becomes particularly crucial when incorporating such interactions in a restoration context.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\HXMUBCFK\\Meysick et al. - 2020 - Context-dependency of eelgrass-clam interactions .pdf}
}

@article{michalet2016,
  title = {Facilitation in Communities: Underlying Mechanisms, Community and Ecosystem Implications},
  author = {Michalet, Richard and Pugnaire, Francisco I.},
  year = {2016},
  journal = {Functional Ecology},
  volume = {30},
  number = {1},
  pages = {3--9},
  issn = {1365-2435},
  doi = {10.1111/1365-2435.12602},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\6VTM7VHY\\Michalet_et_al-2016-Functional_Ecology.pdf}
}

@article{orth2006,
  title = {A Global Crisis for Seagrass Ecosystems},
  author = {Orth, R. J. and Carruthers, T. J. B. and Dennison, W. C. and Duarte, C. M. and Fourqurean, J. W. and Heck, K. L. and Hughes, A. R. and Kendrick, G. A. and Kenworthy, W. J. and Olyarnik, S. and Short, F. T. and Waycott, M. and Williams, S. L.},
  year = {2006},
  month = dec,
  journal = {Bioscience},
  volume = {56},
  number = {12},
  pages = {987--996},
  issn = {0006-3568},
  doi = {10.1641/0006-3568(2006)56[987:agcfse]2.0.co;2},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\QWUH5KW2\\orthetal.pdf}
}

@article{pawlik2020,
  title = {The {{Emerging Ecological}} and {{Biogeochemical Importance}} of {{Sponges}} on {{Coral Reefs}}},
  author = {Pawlik, Joseph R. and McMurray, Steven E.},
  year = {2020},
  month = jan,
  journal = {Annual Review of Marine Science},
  volume = {12},
  number = {1},
  pages = {315--337},
  issn = {1941-1405, 1941-0611},
  doi = {10.1146/annurev-marine-010419-010807},
  abstract = {With the decline of reef-building corals on tropical reefs, sponges have emerged as an important component of changing coral reef ecosystems. Seemingly simple, sponges are highly diverse taxonomically, morphologically, and in terms of their relationships with symbiotic microbes, and they are one of nature's richest sources of novel secondary metabolites. Unlike most other benthic organisms, sponges have the capacity to disrupt boundary flow as they pump large volumes of seawater into the water column. This seawater is chemically transformed as it passes through the sponge body as a consequence of sponge feeding, excretion, and the activities of microbial symbionts, with important effects on carbon and nutrient cycling and on the organisms in the water column and on the adjacent reef. In this review, we critically evaluate developments in the recently dynamic research area of sponge ecology on tropical reefs and provide a perspective for future studies.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\4GE6ZKII\\Pawlik and McMurray - 2020 - The Emerging Ecological and Biogeochemical Importa.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\TQ87FM5Q\\Pawlik_McMurray2019.pdf}
}

@article{peterson1999,
  title = {The Potential for Suspension Feeding Bivalves to Increase Seagrass Productivity},
  author = {Peterson, Bradley J. and Heck, Kenneth L.},
  year = {1999},
  month = jul,
  journal = {Journal of Experimental Marine Biology and Ecology},
  volume = {240},
  number = {1},
  pages = {37--52},
  issn = {00220981},
  doi = {10.1016/S0022-0981(99)00040-4},
  abstract = {Suspension feeding bivalves are commonly associated with seagrass habitats in the Gulf of Mexico and Caribbean Sea. Biodeposits of some suspension feeding bivalves have been shown to be high in nitrogen and phosphorus. Consequently, filter feeding bivalves may act as a benthopelagic couple bringing planktonic production to the benthos, thereby elevating submerged aquatic vegetation growth by increasing the nutrients available to the rhizosphere. Laboratory feeding experiments were used to calculate the filtration rate of a typical suspension feeding bivalve Modiolus americanus. Filtration rates were estimated to be 2.8760.82 l h21 g tissue dry weight21. Consumption rates were estimated to be 9.4162.62 mg Chl a h21 g tissue dry weight21. In addition, field experiments were used to calculate mean biodeposition rates. Biodeposition rates were estimated to be 2.2560.36 g dry wt material g tissue dry weight day21. Therefore, at mean field densities M. americanus are capable of depositing 218 kg dry weight material m22 annually. These deposits will contain 215 g N and 7.1 g P. A flower pot experiment demonstrated that the biodeposits of M. americanus were capable of increasing the pore water nutrient content and a mussel density manipulation in the field revealed that the presence of mussels significantly reduced leaf tissue C:N and C:P ratios. Pore water ammonium and phosphate concentrations were four times greater in the highest mussel density than in the control treatments and the lower leaf tissue C:N and C:P ratios in the presence of mussels established that this increased pore water nutrient was available to the seagrass, Thalassia testudinum. Collectively, these experiments suggest that suspension feeding bivalves may be important resource conduits converting inaccessible PON and POP in the water column to elevated sediment nutrient levels within the rhizosphere available for absorption by submerged aquatic vegetation. \textcopyright{} 1999 Elsevier Science B.V. All rights reserved.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\8VKCAVZ2\\Peterson and Heck - 1999 - The potential for suspension feeding bivalves to i.pdf}
}

@article{peterson2013,
  title = {The Snapper\textendash Grunt Pump: {{Habitat}} Modification and Facilitation of the Associated Benthic Plant Communities by Reef-Resident Fish},
  author = {Peterson, Bradley J. and Valentine, John F. and Heck Jr, Kenneth L.},
  year = {2013},
  journal = {Journal of Experimental Marine Biology and Ecology},
  volume = {441},
  number = {0},
  pages = {50--54},
  issn = {0022-0981},
  doi = {10.1016/j.jembe.2013.01.015},
  keywords = {Facilitation,Haemulon flavolineatum,Herbivory,Lutjanus synagris,Thalassia testudinum,Whole community mutualism},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\BX2DUDNH\\Petersonetal2013.pdf}
}

@article{powell1989,
  title = {Experimental Evidence for Nutrient Limitation of Seagrass Growth in a Tropical Estuary with Restricted Circulation},
  author = {Powell, George V. N. and Kenworthy, Judson W. and Fourqurean, James W.},
  year = {1989},
  journal = {Bulletin of Marine Science},
  volume = {44},
  number = {1},
  pages = {324--340},
  abstract = {We studied the impacts of additions of nutrients to a seagrass community on a carbonate mud bank in Florida Bay. Shallow mud banks dampen lunar tide in Florida Bay, and empoundment and channelization of the upland watershed (the Everglades) have reduced freshwater imput, resulting in restricted circulation and reduced nutrient availability. Nutrients were supplied by seabirds defecating from experimental roosts. Seabirds used the roosts 87\% of the time so the input of nutrients was constant and quantifiable. The birds delivered approximately 2-4 g of excrement per day, resulting in an average loading rate of 0.052 gN and 0.009 gP\&\#8901;m\textsuperscript{-2}\&\#8901;d\textsuperscript{-1}. Only a portion of the excrement is immediately released as inorganic NH\textsubscript{3} and PO\textsubscript{4}; about 80\% reaches the sediment surface in a relatively insoluble form. There was a significant buildup of phosphate and ammonium in the pore water at the enriched, sites. The ammonium profile of low concentrations at the surface and then increasing with a steep slope through 20 em suggests a rapid uptake and demand for mineralized nitrogen. Phosphorus in contrast had relatively high levels at the surface. Nutrient addition significantly increased areal leaf production and standing crop of \emph{Thafassia testudinum} and \emph{Halodufe wrightii}. Above ground biomass at enriched sites averaged twice controls while below grounc biomass was not significantly different between fertilized and control plots. Increased standing crop was produced primarily through longer, wider blades by \emph{Thalassia} and longer blades and increased short shoot density by \emph{Halodufe. Thalassia} areal leaf production was 60\% greater at enriched sites than at controls. \emph{Halodule} areal leaf production increased by three orders of magnitude at enriched sites. Tissue nutrient content and nitrogen fixation assays suggest that phosphorus availability limits seagrass growth in unenriched conditions, but that nitrogen becomes limiting with the addition of bird excrement.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\AETWBGJX\\Powelletal1989.pdf}
}

@misc{rcoreteam2020,
  title = {R: {{A}} Language and Environment for Statistical Computing.},
  author = {{R Core Team}},
  year = {2020},
  address = {{Vienna, Austria}},
  howpublished = {R Foundation for Statistical Computing}
}

@article{reiswig1971,
  title = {Particle Feeding in Natural Populations of 3 Marine {{Demosponges}}},
  author = {Reiswig, H. M.},
  year = {1971},
  journal = {Biological Bulletin},
  volume = {141},
  number = {3},
  pages = {568--591},
  issn = {0006-3185},
  doi = {10.2307/1540270},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\P2RZJADL\\Reiswig1971.pdf}
}

@article{reiswig1974,
  title = {Water Transport, Respiration and Energetics of Three Tropical Marine Sponges},
  author = {Reiswig, H.M.},
  year = {1974},
  journal = {Journal of Experimental Marine Biology and Ecology},
  volume = {14},
  number = {3},
  pages = {231--249},
  issn = {0022-0981},
  doi = {10.1016/0022-0981(74)90005-7},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\VLYU84LY\\Reiswig1974.pdf}
}

@article{reusch1994,
  title = {Blue Mussels{\emph{ }}{{{\emph{Mytilus}}}}{\emph{ Edulis }} Do Not Interfere with Eelgrass {{{\emph{Zostera}}}}{\emph{ Marina}} but Fertilize Shoot Growth through Biodeposition},
  author = {Reusch, Tbh and Chapman, Aro and Groger, Jp},
  year = {1994},
  journal = {Marine Ecology Progress Series},
  volume = {108},
  pages = {265--282},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps108265},
  abstract = {Blue mussels Mytilus eduljs L. and eelgrass Zostera marina L. commonly CO-occurin mlxed stands at sheltered sites of the Western Baltic. The effects of mussels on density, vegetative propagation and growth of eelgrass were tested experimentally. Mussels were either added to 2. marina patches or removed from existing Zostera/Mytilus associations. We found no effect of these experimental manipulations on the shoot density of Z. marina from April to October L \textasciitilde{} k e w i s eo, bservatlons on a series of permanent plots over 1 growth period showed that adjacent mussel patches did not impede the vegetative propagat\textasciitilde onof eelgrass patches. Instead of damaging eelgrass by interference competition, mussels enhance eelgrass growth. At the end of August, plants in the M. edulis addition treatment had a 36\% higher leaf area than the controls, whereas mussel removal led to an area decrease of 16 "10compared to the controls Since, at the same time, the sedlment porewater concentrations of amrnonlum and phosphate doubled in presence of M. edulis, we infer that 2.marina is nutrient-limited in the sandy, organically poor sediments of the shallow subtidal zone. M. edulis facilitates Z. marina by the biodeposition of organic material via faeces and pseudofaeces. A correlation between porewater ammonium concentration and plant size supports the contention that nitrogen is growth limiting. In contrast, no relationship was found between porewater phosphate concentration and plant size.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\IJUTZM2X\\Reusch et al. - 1994 - Blue mussels Mytilus edulis do not interfere with .pdf}
}

@article{silliman2011,
  title = {Whole-{{Community Facilitation Regulates Biodiversity}} on {{Patagonian Rocky Shores}}},
  author = {Silliman, B. R. and Bertness, M. D. and Altieri, A. H. and Griffin, J. N. and Bazterrica, M. C. and Hidalgo, F. J. and Crain, C. M. and Reyna, M. V.},
  year = {2011},
  month = oct,
  journal = {PLoS ONE},
  volume = {6},
  number = {10},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0024502},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\9RAYG6KH\\Sillimanetalplos.pdf}
}

@article{slattery2013,
  title = {Facilitation of Coral Reef Biodiversity and Health by Cave Sponge Communities},
  author = {Slattery, M. and Gochfeld, D. J. and Easson, C. G. and O'Donahue, L. R. K.},
  year = {2013},
  journal = {Marine Ecology Progress Series},
  volume = {476},
  pages = {71-+},
  issn = {0171-8630},
  doi = {10.3354/meps10139},
  abstract = {Marine caves are understudied ecosystems that are frequently associated with coral reef communities; many are tidally influenced and may host a highly diverse sponge fauna. Although each cave represents a distinct habitat likely structured by site-specific hydrographic processes, a more complete understanding of the ecology of these communities requires comparative studies. Based on a gradient of sponge cover within 5 Bahamian caves, we conducted a natural experiment in sponge-derived nutrient enrichment of nearby patch reefs. We tested the hypothesis that water exiting the cave during low tide provides a nutrient-rich resource that facilitates the diversity and health of nearby reef communities. The percent cover and diversity of corals surrounding the openings of caves were significantly higher than in similar habitats farther removed from these communities. There was a significant correlation between percent sponge cover within the caves and nitrate concentrations in seawater flowing out of the caves, and delta N-15 stable isotope signatures indicated enrichment of the nearby reefs by sponge-derived nitrate. Zooxanthellae abundance and total protein concentration were higher in corals from reefs near cave entrances, suggesting that those corals benefited more from cave nutrients than did corals farther from cave openings. In addition to corals, percent algal cover increased near cave entrances, but these potential competitors of corals were kept in check by increased levels of herbivory relative to sites removed from cave mouths. As global environmental changes continue to impact coral reef ecosystems, diversity 'hot spots', such as these marine caves, could serve as refuges and 'seed-banks' for nearby dwindling reef habitats.},
  langid = {english},
  keywords = {Biodiversity,caribbean reef,Caves,cavity sponges,climate-change,Coral health,Facilitation,facultative,growth,Herbivory,marine sponges,mutualism,nutrient enrichment,Nutrients,phase-shifts,positive interactions,Sponges,submarine cave},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\MTDGSQII\\Slatteryetal2013.pdf}
}

@article{soluk1997,
  title = {The Role of Stoneflies in Enhancing Growth of Trout: A Test of the Importance of Predator-Predator Facilitation within a Stream Community},
  author = {Soluk, D. A. and Richardson, J. S.},
  year = {1997},
  month = nov,
  journal = {Oikos},
  volume = {80},
  number = {2},
  pages = {214--219},
  issn = {0030-1299},
  abstract = {Failure to understand subtle behavioral mechanisms can lead to mischaracterization of interactions within food webs. Laboratory studies indicating increased prey capture by fish when predatory invertebrates are present suggested a field experiment to evaluate the effect of stonefly removal on growth rare of fish. Individually marked juvenile cutthroat trout (Oncorynchus clarki) were introduced into replicate experimental stream channels beside a coastal Pacific rainforest stream. In stream channels with large perlid stoneflies (Doroneuria and Calineuria sp.) trout gained mass, whereas in channels without stoneflies trout lost body mass. There was no significant effect of stoneflies on trout mortality over the month-long experiments. Although total predator number and biomass were higher in channels with stoneflies (trout and stonefly biomass combined), trout apparently gained more from the way prey behavior was altered by the presence of stoneflies, than they lost from any effects of competition far common prey resources. The presence of significant facilitation amongst predators complicates our view of trophic structuring in stream communities, requiring that such nun-intuitive interactions be more explicitly considered both by modelers and experimentalists seeking to evaluate the role of predators in these and in other communities.}
}

@article{southwell2008a,
  title = {In Situ Fluxes of Dissolved Inorganic Nitrogen from the Sponge Community on {{Conch Reef}}, {{Key Largo}}, {{Florida}}},
  author = {Southwell, M. W. and Weisz, J. B. and Martens, C. S. and Lindquist, N.},
  year = {2008},
  month = may,
  journal = {Limnology and Oceanography},
  volume = {53},
  number = {3},
  pages = {986--996},
  issn = {0024-3590},
  doi = {10.4319/lo.2008.53.3.0986},
  abstract = {We measured ammonium and nitrate plus nitrite fluxes from 14 common sponge species on a Florida Keys reef (Conch Reef) using a combination of incubation experiments and an in situ method that requires no manipulation of the sponge. On a 600- m(2) section of Conch Reef, species-specific biomass for all nonencrusting sponges was measured. The biomass data combined with species-specific dissolved inorganic nitrogen ( DIN) flux rates yielded the benthic DIN flux from 14 species, and allowed us to extrapolate these data to the total nonencrusting sponge community. The species for which we measured DIN fluxes represented 85\% of the nonencrusting sponge biomass in the study area and released a combined 480 +/- 93 mu mol m(-2) h(-1) of nitrate plus nitrite, and 57 +/- 73 mu mol m(-2) h(-1) of ammonium. Approximately 73\% of the measured DIN flux was produced by Xestospongia muta, a massive barrel sponge. Of the 14 species studied, 10 hosted active nitrifying communities, and 8 hosted photosynthetic microbial associates. However, the presence of these microbial communities had no apparent effect on the magnitude of the total DIN flux. We estimate that the DIN flux for the entire nonencrusting sponge community is 640 +/- 130 mu mol m(-2) h(-1).},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\7U9FDYFP\\Southwell.pdf}
}

@article{stachowicz2001,
  title = {Mutualism, Facilitation, and the Structure of Ecological Communities},
  author = {Stachowicz, J. J.},
  year = {2001},
  month = mar,
  journal = {Bioscience},
  volume = {51},
  number = {3},
  pages = {235--246},
  issn = {0006-3568},
  doi = {10.1641/0006-3568(2001)051[0235:mfatso]2.0.co;2},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\WFEDLIGM\\stacowicz.pdf}
}

@article{thomsen2010,
  title = {Habitat Cascades: {{The}} Conceptual Context and Global Relevance of Facilitation Cascades via Habitat Formation and Modification},
  author = {Thomsen, M. S. and Wernberg, T. and Altieri, A. H. and Tuya, F. and Gulbransen, D. and McGlathery, K. J. and Holmer, M. and Silliman, B. R.},
  year = {2010},
  month = aug,
  journal = {Integrative and Comparative Biology},
  volume = {50},
  number = {2},
  pages = {158--175},
  issn = {1540-7063},
  doi = {10.1093/icb/icq042},
  abstract = {The importance of positive interactions is increasingly acknowledged in contemporary ecology. Most research has focused on direct positive effects of one species on another. However, there is recent evidence that indirect positive effects in the form of facilitation cascades can also structure species abundances and biodiversity. Here we conceptualize a specific type of facilitation cascade-the habitat cascade. The habitat cascade is defined as indirect positive effects on focal organisms mediated by successive facilitation in the form of biogenic formation or modification of habitat. Based on a literature review, we demonstrate that habitat cascades are a general phenomenon that enhances species abundance and diversity in forests, salt marshes, seagrass meadows, and seaweed beds. Habitat cascades are characterized by a hierarchy of facilitative interactions in which a basal habitat former (typically a large primary producer, e.g., a tree) creates living space for an intermediate habitat former (e.g., an epiphyte) that in turn creates living space for the focal organisms (e.g., spiders, beetles, and mites). We then present new data on a habitat cascade common to soft-bottom estuaries in which a relatively small invertebrate provides basal habitat for larger intermediate seaweeds that, in turn, generate habitat for focal invertebrates and epiphytes. We propose that indirect positive effects on focal organisms will be strongest when the intermediate habitat former is larger and different in form and function from the basal habitat former. We also discuss how humans create, modify, and destroy habitat cascades via global habitat destruction, climatic change, over-harvesting, pollution, or transfer of invasive species. Finally, we outline future directions for research that will lead to a better understanding of habitat cascades.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\L2WBQVSC\\Thomsenetal.pdf}
}

@article{thomsen2019,
  title = {Communities and {{Attachment Networks Associated}} with {{Primary}}, {{Secondary}} and {{Alternative Foundation Species}}; {{A Case Study}} of {{Stressed}} and {{Disturbed Stands}} of {{Southern Bull Kelp}}},
  author = {Thomsen, Mads S. and South, Paul M.},
  year = {2019},
  month = apr,
  journal = {Diversity},
  volume = {11},
  number = {4},
  pages = {56},
  issn = {1424-2818},
  doi = {10.3390/d11040056},
  abstract = {Southern bull kelps (Durvillaea spp., Fucales) are `primary' foundation species that control community structures and ecosystem functions on temperate wave-exposed rocky reefs. However, these large foundation species are threatened by disturbances and stressors, including invasive species, sedimentation and heatwaves. It is unknown whether `alternative' foundation species can replace lost southern bull kelps and its associated communities and networks. We compared community structure (by quantifying abundances of different species) and attachment-interaction networks (by quantifying which species were attached to other species) among plots dominated by Durvillaea spp. and plots where Durvillaea spp. were lost either through long-term repeated experimental removals or by recent stress from a marine heatwave. Long-term experimental removal plots were dominated by `alternative' foundation species, the canopy-forming Cystophora spp. (Fucales), whereas the recent heatwave stressed plots were dominated by the invasive kelp Undaria pinnatifida (Laminariales). A network analysis of attachment interactions showed that communities differed among plots dominated by either Durvillaea spp., Cystophora spp. or U. pinnatifida, with different relationships between the primary, or alternative, foundation species and attached epiphytic `secondary' foundation species. For example, native Cystophora spp. were more important as hosts for secondary foundation species compared to Durvillaea spp. and U. pinnatifida. Instead, Durvillaea spp. facilitated encrusting algae, which in turn provided habitat for gastropods. We conclude that (a) repeated disturbances and strong stressors can reveal ecological differences between primary and alternative foundation species, (b) analyses of abundances and attachment-networks are supplementary methods to identify linkages between primary, alternative and secondary foundation species, and (c) interspersed habitats dominated by different types of foundation species increase system-level biodiversity by supporting different species-abundance patterns and species-attachment networks.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\W5Y3LLR4\\Thomsen and South - 2019 - Communities and Attachment Networks Associated wit.pdf}
}

@article{valdez2020,
  title = {Positive {{Ecological Interactions}} and the {{Success}} of {{Seagrass Restoration}}},
  author = {Valdez, Stephanie R. and Zhang, Y. Stacy and {van der Heide}, Tjisse and Vanderklift, Mathew A. and Tarquinio, Flavia and Orth, Robert J. and Silliman, Brian R.},
  year = {2020},
  month = feb,
  journal = {Frontiers in Marine Science},
  volume = {7},
  pages = {91},
  issn = {2296-7745},
  doi = {10.3389/fmars.2020.00091},
  abstract = {Seagrasses provide multiple ecosystem services including nursery habitat, improved water quality, coastal protection, and carbon sequestration. However, seagrasses are in crisis as global coverage is declining at an accelerating rate. With increased focus on ecological restoration as a conservation strategy, methods that enhance restoration success need to be explored. Decades of work in coastal plant ecosystems, including seagrasses, has shown that positive species relationships and feedbacks are critical for ecosystem stability, expansion, and recovery from disturbance. We reviewed the restoration literature on seagrasses and found few studies have tested for the beneficial effects of including positive species interactions in seagrass restoration designs. Here we review the full suite of positive species interactions that have been documented in seagrass ecosystems, where they occur, and how they might be integrated into seagrass restoration. The few studies in marine plant communities that have explicitly incorporated positive species interactions and feedbacks have found an increase in plant growth with little additional resource investment. As oceans continue to change and stressors become more prevalent, harnessing positive interactions between species through innovative approaches will likely become key to successful seagrass restoration.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\QRRUJHKJ\\Valdez et al. - 2020 - Positive Ecological Interactions and the Success o.pdf}
}

@article{vanderheide2011,
  title = {Positive {{Feedbacks}} in {{Seagrass Ecosystems}} - {{Evidence}} from {{Large-Scale Empirical Data}}},
  author = {{van der Heide}, Tjisse and {van Nes}, Egbert H. and {van Katwijk}, Marieke M. and Olff, Han and Smolders, Alfons J. P.},
  year = {2011},
  month = jan,
  journal = {PLoS ONE},
  volume = {6},
  number = {1},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0016504},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\BAECS8R8\\van der Heideetal2011.pdf}
}

@article{vanderheide2012,
  title = {A {{Three-Stage Symbiosis Forms}} the {{Foundation}} of {{Seagrass Ecosystems}}},
  author = {{van der Heide}, T. and Govers, L. L. and {de Fouw}, J. and Olff, H. and {van der Geest}, M. and {van Katwijk}, M. M. and Piersma, T. and {van de Koppel}, J. and Silliman, B. R. and Smolders, A. J. P. and {van Gils}, J. A.},
  year = {2012},
  month = jun,
  journal = {Science},
  volume = {336},
  number = {6087},
  pages = {1432--1434},
  issn = {0036-8075},
  doi = {10.1126/science.1219973},
  abstract = {Seagrasses evolved from terrestrial plants into marine foundation species around 100 million years ago. Their ecological success, however, remains a mystery because natural organic matter accumulation within the beds should result in toxic sediment sulfide levels. Using a meta-analysis, a field study, and a laboratory experiment, we reveal how an ancient three-stage symbiosis between seagrass, lucinid bivalves, and their sulfide-oxidizing gill bacteria reduces sulfide stress for seagrasses. We found that the bivalve-sulfide-oxidizer symbiosis reduced sulfide levels and enhanced seagrass production as measured in biomass. In turn, the bivalves and their endosymbionts profit from organic matter accumulation and radial oxygen release from the seagrass roots. These findings elucidate the long-term success of seagrasses in warm waters and offer new prospects for seagrass ecosystem conservation.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\TBSF5SZP\\vanderHeideetal2012.pdf}
}

@article{vanderheide2020,
  title = {Facultative Mutualisms: {{A}} Double-edged Sword for Foundation Species in the Face of Anthropogenic Global Change},
  author = {{van der Heide}, Tjisse and Angelini, Christine and {de Fouw}, Jimmy and Ekl{\"o}f, Johan S.},
  year = {2020},
  journal = {Ecology and Evolution},
  volume = {00},
  pages = {16},
  doi = {10.1002/ece3.7044},
  abstract = {Ecosystems worldwide depend on habitat-forming foundation species that often facilitate themselves with increasing density and patch size, while also engaging in facultative mutualisms. Anthropogenic global change (e.g., climate change, eutrophication, overharvest, land-use change), however, is causing rapid declines of foundation species-structured ecosystems, often typified by sudden collapse. Although disruption of obligate mutualisms involving foundation species is known to precipitate collapse (e.g., coral bleaching), how facultative mutualisms (i.e., context-dependent, nonbinding reciprocal interactions) affect ecosystem resilience is uncertain. Here, we synthesize recent advancements and combine these with model analyses supported by real-world examples, to propose that facultative mutualisms may pose a doubleedged sword for foundation species. We suggest that by amplifying self-facilitative feedbacks by foundation species, facultative mutualisms can increase foundation species' resistance to stress from anthropogenic impact. Simultaneously, however, mutualism dependency can generate or exacerbate bistability, implying a potential for sudden collapse when the mutualism's buffering capacity is exceeded, while recovery requires conditions to improve beyond the initial collapse point (hysteresis). Thus, our work emphasizes the importance of acknowledging facultative mutualisms for conservation and restoration of foundation species-structured ecosystems, but highlights the potential risk of relying on mutualisms in the face of global change. We argue that significant caveats remain regarding the determination of these feedbacks, and suggest empirical manipulation across stress gradients as a way forward to identify related nonlinear responses.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\4LTJAU3X\\Facultative mutualisms A double‐edged sword for f.pdf}
}

@article{vinther2012,
  title = {Effects of Coexistence between the Blue Mussel and Eelgrass on Sediment Biogeochemistry and Plant Performance},
  author = {Vinther, Hf and Norling, P and Kristensen, Ps and Dolmer, P and Holmer, M},
  year = {2012},
  month = feb,
  journal = {Marine Ecology Progress Series},
  volume = {447},
  pages = {139--149},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps09505},
  abstract = {The habitat-modifying suspension-feeding mussel Mytilus edulis may have facilitating or inhibiting effects on seagrass meadows depending on the environmental conditions. We investigated the effects of M. edulis on sediment biogeochemistry in Zostera marina meadows under eutrophic conditions in Flensborg fjord, Denmark. Sediment and plant samples were collected at 5 stations with Z. marina (Eelgrass), 5 with Z. marina and M. edulis (Mixed), and at 2 unvegetated ones, 1 with mussels (Mussel) and 1 with sand (Sand). The Mixed sediment was enriched in fine particles (2 to 3 times), nutrients and sulphides compared to Eelgrass stations. Increased sediment nutrient availability at the Mixed stations was reflected in increased N and P content in eelgrass. However, the plant biomass did not differ significantly between stations, while shoot features (number of leaves and leaf area) were significantly reduced at Mixed stations, suggesting an inhibiting effect of M. edulis on Z. marina. Negative correlations between eelgrass measures and sediment sulphide at Mixed stations indicate that the presence of mussels increases sulphide invasion in the plants. A survey of 318 stations in Danish fjords suggests a threshold of 1.6 kg M. edulis m-2 beyond which no coexistence between Z. marina and M. edulis was found.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\AZHVA3VD\\Vinther et al. - 2012 - Effects of coexistence between the blue mussel and.pdf}
}

@article{wall2008,
  title = {Facilitation of Seagrass {{{\emph{Zostera}}}}{\emph{ Marina}} Productivity by Suspension-Feeding Bivalves},
  author = {Wall, Cc and Peterson, Bj and Gobler, Cj},
  year = {2008},
  month = apr,
  journal = {Marine Ecology Progress Series},
  volume = {357},
  pages = {165--174},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps07289},
  abstract = {Seagrasses and suspension feeders are both critical ecosystem engineers in estuaries. Seagrass beds are important structural habitats, and suspension feeders, when abundant, can regulate phytoplankton densities. Furthermore, there may be mutual facilitation of growth and recruitment between seagrasses and suspension-feeding bivalves. In a series of mesocosm experiments, the effects of environmentally realistic densities of 3 different suspension-feeding bivalves (Mercenaria mercenaria, Crassostrea virginica, Mytilus edulis) on the growth of eelgrass Zostera marina in a eutrophied environment were examined. Experimental treatments with bivalves consistently yielded significantly lower chlorophyll a concentrations (p {$<$} 0.05), and most bivalve treatments also showed significant increases in light penetration (p {$<$} 0.05). Eelgrass productivity was measured by leaf area growth, and varied from 0.318 {$\pm$} 0.018 to 0.832 {$\pm$} 0.036 cm2 shoot\textendash 1 d\textendash 1 (mean {$\pm$} SE); leaf area productivity was always significantly higher (on average, 48 {$\pm$} 9.3\% higher) in the treatments with the highest density of bivalves compared to a control without bivalves (p {$<$} 0.05). The data indicate that clearance of the water column, and the subsequent increase in light penetration, was the primary mechanism by which suspension-feeding bivalves facilitated the growth of eelgrass. These findings suggest that healthy populations of suspension-feeding bivalves can mitigate the effects of estuarine eutrophication and can facilitate the growth of seagrass in degraded, light-limited habitats.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\DK5ZKJ5E\\Wall et al. - 2008 - Facilitation of seagrass Zostera marina productivi.pdf}
}

@article{waycott2009,
  title = {Accelerating Loss of Seagrasses across the Globe Threatens Coastal Ecosystems},
  author = {Waycott, Michelle and Duarte, Carlos M. and Carruthers, Tim J. B. and Orth, Robert J. and Dennison, William C. and Olyarnik, Suzanne and Calladine, Ainsley and Fourqurean, James W. and Heck, Jr., Kenneth L. and Hughes, A. Randall and Kendrick, Gary A. and Kenworthy, W. Judson and Short, Frederick T. and Williams, Susan L.},
  year = {2009},
  month = jul,
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {106},
  number = {30},
  pages = {12377--12381},
  issn = {0027-8424},
  doi = {10.1073/pnas.0905620106},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\I7EXTMXP\\Waycottetal2009.pdf}
}

@article{weisz2008,
  title = {Do Associated Microbial Abundances Impact Marine Demosponge Pumping Rates and Tissue Densities?},
  author = {Weisz, J. B. and Lindquist, N. and Martens, C. S.},
  year = {2008},
  month = mar,
  journal = {Oecologia},
  volume = {155},
  number = {2},
  pages = {367--376},
  issn = {0029-8549},
  doi = {10.1007/s00442-007-0910-0},
  abstract = {The evolution of marine demosponges has led to two basic life strategies: one involving close associations with large and diverse communities of microorganisms, termed high microbial abundance (HMA) species, and one that is essentially devoid of associated microorganisms, termed low microbial abundance (LMA) species. This dichotomy has previously been suggested to correlate with morphological differences, with HMA species having a denser mesohyl and a more complex aquiferous systems composed of longer and narrower water canals that should necessitate slower seawater filtration rates. We measured mesohyl density for a variety of HMA and LMA sponges in the Florida Keys, and seawater pumping rates for a select group of these sponges using an in situ dye technique. HMA sponges were substantially denser than LMA species, and had per unit volume pumping rates 52-94\% slower than the LMA sponges. These density and pumping rate differences suggest that evolutionary differences between HMA and LMA species may have resulted in profound morphological and physiological differences between the two groups. The LMA sponge body plan moves large quantities of water through their porous tissues allowing them to rapidly acquire the small particulate organic matter (POM) that supplies the majority of their nutritional needs. In contrast, the HMA sponge body plan is suited to host large and tightly packed communities of microorganisms and has an aquiferous system that increases contact time between seawater and the sponge/microbial consortium that feeds on POM, dissolved organic matter and the raw inorganic materials for chemolithotrophic sponge symbionts. The two evolutionary patterns represent different, but equally successful patterns and illustrate how associated microorganisms can potentially have substantial effects on host evolution.},
  langid = {english},
  keywords = {aquiferous systems,bacteria,baikal littoral-zone,current-induced flow,ecology,evolution,filtration,food,halichondria-panicea,mutualism,natural diet,reef sponges,sponge,symbiosis},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\SKTIWD52\\weiszetal2008.pdf}
}

@article{williams1990,
  title = {Experimental Studies of {{Caribbean}} Seagrass Bed Development},
  author = {Williams, Susan L},
  year = {1990},
  journal = {Ecological monographs},
  pages = {449--469},
  issn = {0012-9615},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\96B8JJ7H\\williams1990.pdf}
}

@article{wright2014,
  title = {Engineering or Food? Mechanisms of Facilitation by a Habitat-Forming Invasive Seaweed},
  author = {Wright, Jeffrey T and Byers, James E and DeVore, Jayna L and Sotka, Erik E},
  year = {2014},
  journal = {Ecology},
  volume = {95},
  number = {10},
  pages = {2699--2706},
  issn = {0012-9658},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\JKXJDR2U\\Wright-et-al-Grac-2014.pdf}
}

@article{wulff2008,
  title = {Collaboration among Sponge Species Increases Sponge Diversity and Abundance in a Seagrass Meadow},
  author = {Wulff, J. L.},
  year = {2008},
  month = jun,
  journal = {Marine Ecology-an Evolutionary Perspective},
  volume = {29},
  number = {2},
  pages = {193--204},
  issn = {0173-9565},
  doi = {10.1111/j.1439-0485.2008.00224.x},
  abstract = {Caribbean sponge species typical of coral reefs are generally inhibited from living in seagrass meadows by their vulnerability to predation by the large starfish Oreaster reticulatus (Linnaeus 1758). Although readily consumed by Oreaster, the conspicuous coral reef sponge species Lissodendoryx colombiensis Zea \& van Soest, 1986 has expanded its habitat distribution to include a seagrass (Thalassia testudinum Banks ex Konig, 1805) meadow in Belize, where individuals grow to volumes of nearly 7 l. By simple observation, L. colombiensis appears to be an inferior competitor in this system, because portions of many individuals are overgrown by seagrass sponge species. However, experimentally clustering seagrass sponges around L. colombiensis individuals deterred starfish from feeding on them, suggesting an advantage to being overgrown. Sizes of individual L. colombiensis can fluctuate widely over short time intervals, reflecting both a relatively fast growth rate and the high rate at which starfish consume this species. At the population level these fluctuations are not evident, as losses of L. colombiensis due to Oreaster are balanced by a combination of efficient recruitment, rapid regeneration and growth, and protection of portions of many individuals by the overgrowth of seagrass sponge species that are unpalatable to Oreaster. In turn, the seagrass sponges acquire stable perches on L. colombiensis individuals in this sediment-dominated habitat. Community ecology theory relating to diversity patterns in sessile organisms has focused on competition between space-requiring neighbors as the underlying process that inevitably decreases diversity unless curtailed. Sponges, with their propensity for engaging in beneficial interactions with neighbors, demand expansion of the theory to acknowledge how collaboration can increase abundance and species diversity within a community.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\498JY87X\\wulff.pdf}
}

@article{Yeager2012,
  ids = {yeager2012a},
  title = {Effects of Seascape Context on Condition, Abundance, and Secondary Production of a Coral Reef Fish, {{{\emph{Haemulon}}}}{\emph{ Plumierii}}},
  author = {Yeager, La and Acevedo, Cl and Layman, Ca},
  year = {2012},
  month = aug,
  journal = {Marine Ecology Progress Series},
  volume = {462},
  pages = {231--240},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps09855},
  abstract = {Variation in seascape composition has the potential to impact habitat quality for fishes, and characteristics of the surrounding seascape have been correlated with abundance of organisms in many systems. Less studied is how seascape context may affect other aspects of habitat quality including growth, condition, or production of focal species. Juvenile white grunts Haemulon plumierii are known to rest on patch reefs during the day and move into seagrass habitat at night to feed, linking multiple habitats through these daily foraging migrations. We created artificial reefs across a gradient of seagrass cover and determined how juvenile white grunt condition, growth, abundance, and secondary production were related to seagrass cover within the seascape. White grunt abundance was positively correlated with the cover of seagrass within the seascape, while condition (relative condition factor, Kn) and growth rate (measured using the ratio of RNA to DNA) did not vary among reefs within different seascapes. Secondary production of white grunts was found to be highest on reefs in seascapes with more seagrass. Our results are consistent with the hypothesis that increased food resources associated with higher seagrass cover contribute to increased grunt production. Differences in habitat quality among reefs in different seascapes were manifest at the population (abundance) and ecosystem function (secondary production) levels and not at the individual level (individual growth rate or condition factor). These results highlight the importance of considering multiple levels of individual and population responses in assessments of habitat quality, and add evidence that seascape composition should be considered in spatially explicit management strategies.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\BVPDXX6W\\Yeager et al. - 2012 - Effects of seascape context on condition, abundanc.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\PI3GETUG\\yeageretal2012.pdf}
}

@article{zhang2019,
  title = {A {{Facilitation Cascade Enhances Local Biodiversity}} in {{Seagrass Beds}}},
  author = {Zhang, Y. and Silliman, Brian},
  year = {2019},
  month = feb,
  journal = {Diversity},
  volume = {11},
  number = {3},
  pages = {30},
  issn = {1424-2818},
  doi = {10.3390/d11030030},
  abstract = {Invertebrate diversity can be a key driver of ecosystem functioning, yet understanding what factors influence local biodiversity remains uncertain. In many marine and terrestrial systems, facilitation cascades where primary foundation and/or autogenic ecosystem engineering species promote the settlement and survival of a secondary foundation/engineering species have been shown to enhance local biodiversity and ecosystem functioning. We experimentally tested if a facilitation cascade occurs among eelgrass (Zostera marina), pen clams (Atrina rigida), and community diversity in temperate seagrass beds in North Carolina, U.S.A., and if this sequence of direct positive interactions created feedbacks that affected various metrics of seagrass ecosystem function and structure. Using a combination of surveys and transplant experiments, we found that pen clam density and survivorship was significantly greater in seagrass beds, indicating that eelgrass facilitates pen clams. Pen clams in turn enhanced local diversity and increased both the abundance and species richness of organisms (specifically, macroalgae and fouling invertebrate fauna)\textemdash the effect of which scaled with increasing clam density. However, we failed to detect an impact of pen clams on other seagrass functions and hypothesize that functioning may more likely be enhanced in scenarios where secondary foundation species specifically increase the diversity of key functional groups such as epiphyte grazers and/or when bivalves are infaunal rather than epifaunal. Our findings add to the growing amount of literature that demonstrates that secondary foundation species are important drivers of local biodiversity in marine ecosystems. Further experimentation is needed that directly examines (i) the role of functional versus overall diversity on seagrass functions and (ii) the relative importance of life-history strategy in determining when and where engineering bivalves increase biodiversity and/or functioning of seagrass beds.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\4HC5B7NP\\Zhang and Silliman - 2019 - A Facilitation Cascade Enhances Local Biodiversity.pdf}
}

@article{zieman1974,
  title = {Methods for the Study of the Growth and Production of Turtle Grass, {{{\emph{Thalassia}}}}{\emph{ Testudinum}} {{K\"onig}}},
  author = {Zieman, Joseph C.},
  year = {1974},
  journal = {Aquaculture},
  volume = {4},
  number = {0},
  pages = {139--143},
  issn = {0044-8486},
  doi = {10.1016/0044-8486(74)90029-5},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\Z4K2ELS9\\zieman1974.pdf}
}

@article{zieman1999,
  title = {Seagrass {{Die-Off}} in {{Florida Bay}}: {{Long-Term Trends}} in {{Abundance}} and {{Growth}} of {{Turtle Grass}}, {{Thalassia}} Testudinum},
  shorttitle = {Seagrass {{Die-Off}} in {{Florida Bay}}},
  author = {Zieman, Joseph C. and Fourqurean, James W. and Frankovich, Thomas A.},
  year = {1999},
  month = jun,
  journal = {Estuaries},
  volume = {22},
  number = {2},
  pages = {460},
  issn = {01608347},
  doi = {10.2307/1353211},
  abstract = {Beginning in late 1987 Florida Bay experienced a large and unprecedented die-off of Tha/ass/a testudinum. The die-off occurred only in stands o f d e n s e T. testudinum. We initiated an experimental monitoring e f f o r t in 1989 to attempt to ascertain the causes o f this die-off p h e n o m e n o n . From 1989 to 1995 the abundance ;rod productivity o f T. testudinum was measured at five stations associated with the seagrass die-off and three stations where no die-off had occurred (including one on the seaside of Key Largo, outside of Florida Bay). Early in the stu\textasciitilde r the salinity was very high, exceeding 46 psu, but it has decreased to 29-38 psu in recent years. Seagrass standing crop and either short-shoot density or mass per short shoot declined at nearly all stations, including the stations without die-off (unaffected stations). Over the course of the study, areal productivity declined at three die-off stations; but mass-specific productivity increased at all die-off stations and one unaffected station. Seasonality was pronounced; detrended standardized residuals showed responses for all of the seagrass parameters to be greater than the yearly mean in spring and summer and less than the mean in fall and winter. Detrended residuals also showed decreased productivity to be correlated with increased salinities in the summer despite a long-term record of declining salinities. We propose a conceptual model of the seagrass die-off p h e n o m e n o n . We d o c u m e n t that salinity d o e s contribute to stress on T. testudinum in Florida Bay, 'but salinity is believed to be only one contributing factor to the loss of seagrasses. The documented increase in the mass-specific productivity o f T. testudinum over the p e r i o d 1989-1995 suggests seagrasses are growing rapidly in Florida Bay by 1995; we predict that the loss o f T. testudinum may be slowing down and that recovery is possible.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\F46UF6BB\\Zieman et al. - 1999 - Seagrass Die-Off in Florida Bay Long-Term Trends .pdf}
}