Birkeland, C. & Grosenbaugh, D. Ecological interactions between tropical coastal ecosystems. in UNEP Regional Seas Reports and Studies, Vol. 73 (PNUMA, 1985).
Moberg, F. & Rönnbäck, P. Ecosystem services of the tropical seascape: interactions, substitutions and restoration. Ocean Coast. Manag.46, 27–46 (2003).
Gladstone, W. Conservation and management of tropical coastal ecosystems. In Ecological Connectivity Among Tropical Coastal Ecosystems (ed. Nagelkerken, I.) 565–605 (Springer, Dordrecht, 2009). https://doi.org/10.1007/978-90-481-2406-0_16.
Berkström, C. et al. Exploring ‘knowns’ and ‘unknowns’ in tropical seascape connectivity with insights from East African coral reefs. Estuar. Coast. Shelf Sci.107, 1–21 (2012).
Ogden, J. C. The influence of adjacent systems on the structure and function of coral reefs. In Proceedings of the 6th International Coral Reef Symposium, Vol. 1, 123–129 (1988).
Nagelkerken, I. et al. Importance of mangroves, seagrass beds and the shallow coral reef as a nursery for important coral reef fishes, using a visual census technique. Estuar. Coast. Shelf Sci.51, 31–44 (2000).
Grober-Dunsmore, R., Pittman, S. J., Caldow, C., Kendall, M. S. & Frazer, T. K. A landscape ecology approach for the study of ecological connectivity across tropical marine seascapes. In Ecological Connectivity Among Tropical Coastal Ecosystems (ed. Nagelkerken, I.) 493–530 (Springer, Dordrecht, 2009). https://doi.org/10.1007/978-90-481-2406-0_14.
Hemminga, M. A. & Duarte, C. M. Seagrass ecology (Cambridge University Press, Cambridge, 2000). https://doi.org/10.1017/CBO9780511525551.
Short, F., Carruthers, T., Dennison, W. & Waycott, M. Global seagrass distribution and diversity: a bioregional model. J. Exp. Mar. Biol. Ecol.350, 3–20 (2007).
Knowles, L. L. & Bell, S. S. The influence of habitat structure in faunal-habitat associations in a Tampa Bay seagrass system Florida. Bull. Mar. Sci.62, 781–794 (1998).
Connolly, R. M. & Hindell, J. S. Review of nekton patterns and ecological processes in seagrass landscapes. Estuar. Coast. Shelf Sci.68, 433–444 (2006).
Horinouchi, M. Review of the effects of within-patch scale structural complexity on seagrass fishes. J. Exp. Mar. Biol. Ecol.350, 111–129 (2007).
Gacia, E., Duarte, C. M. & Middelburg, J. J. Carbon and nutrient deposition in a Mediterranean seagrass (Posidonia oceanica) meadow. Limnol. Oceanogr.47, 23–32 (2002).
Hendriks, I. E., Sintes, T., Bouma, T. J. & Duarte, C. M. Experimental assessment and modeling evaluation of the effects of the seagrass Posidonia oceanica on flow and particle trapping. Mar. Ecol. Prog. Ser.356, 163–173 (2008).
Beck, M. W. et al. The identification, conservation, and management of estuarine and marine nurseries for fish and invertebrates: a better understanding of the habitats that serve as nurseries for marine species and the factors that create site-specific variability in nursery quality will improve conservation and management of these areas. AIBS Bull.51, 633–641 (2001).
Heck, K. L. Jr., Hays, G. & Orth, R. J. Critical evaluation of the nursery role hypothesis for seagrass meadows. Mar. Ecol. Prog. Ser.253, 123–136 (2003).
Boström, C., Jackson, E. L. & Simenstad, C. A. Seagrass landscapes and their effects on associated fauna: a review. Estuar. Coast. Shelf Sci.68, 383–403 (2006).
Unsworth, R. K. F. & Cullen, L. C. Recognising the necessity for Indo-Pacific seagrass conservation. Conserv. Lett.3, 63–73 (2010).
Leopardas, V., Uy, W. & Nakaoka, M. Benthic macrofaunal assemblages in multispecific seagrass meadows of the southern Philippines: variation among vegetation dominated by different seagrass species. J. Exp. Mar. Biol. Ecol.457, 71–80 (2014).
Waycott, M. et al. Accelerating loss of seagrasses across the globe threatens coastal ecosystems. PNAS106, 12377–12381 (2009).
Short, F. T. & Wyllie-Echeverria, S. Natural and human-induced disturbance of seagrasses. Environ. Conserv.23, 17–27 (1996).
Short, F. T. et al. Extinction risk assessment of the world’s seagrass species. Biol. Conserv.144, 1961–1971 (2011).
Duarte, C. M. The future of seagrass meadows. Environ. Conserv.29, 192–206 (2002).
Hastings, K., Hesp, P. & Kendrick, G. A. Seagrass loss associated with boat moorings at Rottnest Island, Western Australia. Ocean Coast. Manag.26, 225–246 (1995).
Orth, R. J., Luckenbach, M. L., Marion, S. R., Moore, K. A. & Wilcox, D. J. Seagrass recovery in the Delmarva Coastal Bays, USA. Aquat. Bot.84, 26–36 (2006).
Ruiz, J. M. & Romero, J. Effects of in situ experimental shading on the Mediterranean seagrass Posidonia oceanica. Mar. Ecol. Prog. Ser.215, 107–120 (2001).
Frost, M. T., Rowden, A. A. & Attrill, M. J. Effect of habitat fragmentation on the macroinvertebrate infaunal communities associated with the seagrass Zostera marina L. Aquat. Conserv. Mar. Freshw. Ecosyst.9, 255–263 (1999).
Hovel, K. A. Habitat fragmentation in marine landscapes: relative effects of habitat cover and configuration on juvenile crab survival in California and North Carolina seagrass beds. Biol. Conserv.110, 401–412 (2003).
Hovel, K. A. & Lipcius, R. N. Effects of seagrass habitat fragmentation on juvenile blue crab survival and abundance. J. Exp. Mar. Biol. Ecol.271, 75–98 (2002).
Thomas, C. D. & Mallorie, H. C. Rarity, species richness and conservation: butterflies of the Atlas Mountains in Morocco. Biol. Conserv.33, 95–117 (1985).
Fahrig, L. Effects of habitat fragmentation on biodiversity. Ann. Rev. Ecol. Evol. Syst.34, 487–515 (2003).
Fischer, J. & Lindenmayer, D. B. Landscape modification and habitat fragmentation: a synthesis. Glob. Ecol. Biogeogr.16, 265–280 (2007).
Link, J. Does food web theory work for marine ecosystems?. Mar. Ecol. Prog. Ser.230, 1–9 (2002).
Peterson, B. J., Thompson, K. R., Cowan, J. H. Jr. & Heck, K. L. Jr. Comparison of predation pressure in temperate and subtropical seagrass habitats based on chronographic tethering. Mar. Ecol. Prog. Ser.224, 77–85 (2001).
Sweatman, J. L., Layman, C. A. & Fourqurean, J. W. Habitat fragmentation has some impacts on aspects of ecosystem functioning in a sub-tropical seagrass bed. Mar. Environ. Res.126, 95–108 (2017).
Williams, J. A. et al. Seagrass fragmentation impacts recruitment dynamics of estuarine-dependent fish. J. Exp. Mar. Biol. Ecol.479, 97–105 (2016).
Bell, S. S., Brooks, R. A., Robbins, B. D., Fonseca, M. S. & Hall, M. O. Faunal response to fragmentation in seagrass habitats: implications for seagrass conservation. Biol. Conserv.100, 115–123 (2001).
McCloskey, R. M. & Unsworth, R. K. F. Decreasing seagrass density negatively influences associated fauna. PeerJ3, e1053 (2015).
Ubertini, M. et al. Spatial variability of benthic-pelagic coupling in an estuary ecosystem: consequences for microphytobenthos resuspension phenomenon. PLoS ONE7, e44155 (2012).
Welsh, D. T. Nitrogen fixation in seagrass meadows: regulation, plant–bacteria interactions and significance to primary productivity. Ecol. Lett.3, 58–71 (2000).
Alongi, D. M. The role of bacteria in nutrient recycling in tropical mangrove and other coastal benthic ecosystems. Hydrobiologia285, 19–32 (1994).
Harrison, P. G. Detrital processing in seagrass systems: a review of factors affecting decay rates, remineralization and detritivory. Aquat. Bot.35, 263–288 (1989).
Mateo, M. A. & Romero, J. Detritus dynamics in the seagrass Posidonia oceanica: elements for an ecosystem carbon and nutrient budget. Mar. Ecol. Prog. Ser.151, 43–53 (1997).
Barrón, C., Apostolaki, E. T. & Duarte, C. M. Dissolved organic carbon fluxes by seagrass meadows and macroalgal beds. Front. Mar. Sci.1, 42 (2014).
Wetzel, R. G. & Penhale, P. A. Transport of carbon and excretion of dissolved organic carbon by leaves and roots/rhizomes in seagrasses and their epiphytes. Aquat. Bot.6, 149–158 (1979).
Martin, B. C. et al. Low light availability alters root exudation and reduces putative beneficial microorganisms in seagrass roots. Front. Microbiol.8, 2667 (2018).
Danovaro, R. Detritus-Bacteria-Meiofauna interactions in a seagrass bed (Posidonia oceanica) of the NW Mediterranean. Mar. Biol.127, 1–13 (1996).
Lohrer, A. M., Thrush, S. F. & Gibbs, M. M. Bioturbators enhance ecosystem function through complex biogeochemical interactions. Nature431, 1092–1095 (2004).
Rosenberg, R. Marine benthic faunal successional stages and related sedimentary activity. Sci. Marina65, 107–119 (2001).
Austen, M. C. et al. Biodiversity links above and below the marine sediment–water interface that may influence community stability. Biodivers. Conserv.11, 113–136 (2002).
Fanjul, E., Bazterrica, M. C., Escapa, M., Grela, M. A. & Iribarne, O. Impact of crab bioturbation on benthic flux and nitrogen dynamics of Southwest Atlantic intertidal marshes and mudflats. Estuar. Coast. Shelf Sci.92, 629–638 (2011).
Forster, S. & Graf, G. Impact of irrigation on oxygen flux into the sediment: intermittent pumping by Callianassa subterranea and “piston-pumping” by Lanice conchilega. Mar. Biol.123, 335–346 (1995).
Snelgrove, P. V. R. The biodiversity of macrofaunal organisms in marine sediments. Biodivers. Conserv.7, 1123–1132 (1998).
Hyndes, G. A. & Lavery, P. S. Does transported seagrass provide an important trophic link in unvegetated, nearshore areas?. Estuar. Coast. Shelf Sci.63, 633–643 (2005).
Jones, D. A., Ghamrawy, M. & Wahbeh, M. I. Littoral and shallow subtidal environments. In Red Sea (eds Edwards, A. J. & Head, S. M.) 169–193 (Pergamon Press, London, 1987). https://doi.org/10.1016/B978-0-08-028873-4.50014-1.
Ruiz-Compean, P. et al. Baseline evaluation of sediment contamination in the shallow coastal areas of Saudi Arabian Red Sea. Mar. Pollut. Bull.123, 205–218 (2017).
Bologna, P. A. X. & Heck, K. L. Impact of habitat edges on density and secondary production of seagrass-associated fauna. Estuaries25, 1033–1044 (2002).
Calleja, M. L., Al-Otaibi, N. & Morán, X. A. G. Dissolved organic carbon contribution to oxygen respiration in the central Red Sea. Sci. Rep.9, 1–12 (2019).
Stedmon, C. A., Markager, S. & Bro, R. Tracing dissolved organic matter in aquatic environments using a new approach to fluorescence spectroscopy. Mar. Chem.82, 239–254 (2003).
Coble, P. G. Marine optical biogeochemistry: the chemistry of ocean color. Chem. Rev.107, 402–418 (2007).
Gasol, J. M. & Morán, X. A. G. Flow cytometric determination of microbial abundances and its use to obtain indices of community structure and relative activity. In Hydrocarbon and Lipid Microbiology Protocols: Single-Cell and Single-Molecule Methods (eds McGenity, T. J. et al.) 159–1870 (Springer, Berlin, 2015). https://doi.org/10.1007/8623_2015_139.
Silva, L. et al. Low abundances but high growth rates of coastal heterotrophic bacteria in the Red Sea. Front. Microbiol.9, 3244 (2019).
Leray, M. & Knowlton, N. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. PNAS112, 2076–2081 (2015).
Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucl. Acids Res.41, e1 (2013).
Oksanen, J. et al. Vegan: community ecology package. R package version 2.5-2, (2018).
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, 2018).
Lê, S., Josse, J. & Husson, F. FactoMineR: a package for multivariate analysis. J. Stat. Softw.25, 1–18 (2008).
Goslee, S. C. & Urban, D. L. The ecodist package for dissimilarity-based analysis of ecological data. J. Stat. Softw.22, 1–19 (2007).
Chen, H. VennDiagram: Generate High-Resolution Venn and Euler Plots (2018).
Clarke, K. R. & Gorley, R. N. PRIMER v7: User Manual/Tutorial, PRIMER-E: Plymouth (2015).
Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods13, 581–583 (2016).
Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl. Acids Res.35, 7188–7196 (2007).
McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE8, e61217 (2013).
Keeley, N., Wood, S. A. & Pochon, X. Development and preliminary validation of a multi-trophic metabarcoding biotic index for monitoring benthic organic enrichment. Ecol. Indic.85, 1044–1057 (2018).
Lobelle, D., Kenyon, E. J., Cook, K. J. & Bull, J. C. Local competition and metapopulation processes drive long-term seagrass-epiphyte population dynamics. PLoS ONE8, e57072 (2013).
Ávila, E., Yáñez, B. & Vazquez-Maldonado, L. E. Influence of habitat structure and environmental regime on spatial distribution patterns of macroinvertebrate assemblages associated with seagrass beds in a southern Gulf of Mexico coastal lagoon. Mar. Biol. Res.11, 755–764 (2015).
Barnes, R. S. K. & Hendy, I. W. Seagrass-associated macrobenthic functional diversity and functional structure along an estuarine gradient. Estuar. Coast. Shelf Sci.164, 233–243 (2015).
York, P. H., Hyndes, G. A., Bishop, M. J. & Barnes, R. S. K. Faunal assemblages of seagrass ecosystems. In Seagrasses of Australia: Structure, Ecology and Conservation (eds Larkum, A. W. D. et al.) 541–588 (Springer, Berlin, 2018). https://doi.org/10.1007/978-3-319-71354-0_17.
Magni, P., Como, S., Kamijo, A. & Montani, S. Effects of Zostera marina on the patterns of spatial distribution of sediments and macrozoobenthos in the boreal lagoon of Furen (Hokkaido, Japan). Mar. Environ. Res.131, 90–102 (2017).
Thomsen, M. S. et al. Secondary foundation species enhance biodiversity. Nat. Ecol. Evol.2, 634 (2018).
Attrill, M. J., Strong, J. A. & Rowden, A. A. Are macroinvertebrate communities influenced by seagrass structural complexity?. Ecography23, 114–121 (2000).
Lee, S. Y., Fong, C. W. & Wu, R. S. S. The effects of seagrass (Zostera japonica) canopy structure on associated fauna: a study using artificial seagrass units and sampling of natural beds. J. Exp. Mar. Biol. Ecol.259, 23–50 (2001).
Nakamura, Y. & Sano, M. Comparison of invertebrate abundance in a seagrass bed and adjacent coral and sand areas at Amitori Bay, Iriomote Island, Japan. Fish. Sci.71, 543–550 (2005).
Barrio Froján, C. R. S. et al. The importance of bare marine sedimentary habitats for maintaining high polychaete diversity and the implications for the design of marine protected areas. Aquat. Conserv. Mar. Freshw. Ecosyst.19, 748–757 (2009).
Barnes, R. S. K. & Barnes, M. K. S. Spatial uniformity of biodiversity is inevitable if the available species are distributed independently of each other. Mar. Ecol. Prog. Ser.516, 263–266 (2014).
Webster, P. J., Rowden, A. A. & Attrill, M. J. Effect of shoot density on the infaunal macro-invertebrate community within a Zostera marina seagrass bed. Estuar. Coast. Shelf Sci.47, 351–357 (1998).
Bowden, D. A., Rowden, A. A. & Attrill, M. J. Effect of patch size and in-patch location on the infaunal macroinvertebrate assemblages of Zostera marina seagrass beds. J. Exp. Mar. Biol. Ecol.259, 133–154 (2001).
Turner, S. J. et al. Seagrass patches and landscapes: the influence of wind-wave dynamics and hierarchical arrangements of spatial structure on macrofaunal seagrass communities. Estuaries22, 1016–1032 (1999).
Tanner, J. E. Edge effects on fauna in fragmented seagrass meadows. Austral Ecol.30, 210–218 (2005).
Włodarska-Kowalczuk, M., Jankowska, E., Kotwicki, L. & Balazy, P. Evidence of season-dependency in vegetation effects on macrofauna in temperate seagrass meadows (Baltic Sea). PLoS ONE9, e100788 (2014).
Calleja, M. L., Barrón, C., Hale, J. A., Frazer, T. K. & Duarte, C. M. Light regulation of benthic sulfate reduction rates mediated by seagrass (Thalassia testudinum) metabolism. Estuar. Coasts J ERF29, 1255–1264 (2006).
Barnes, R. S. K. & Barnes, M. K. S. Shore height and differentials between macrobenthic assemblages in vegetated and unvegetated areas of an intertidal sandflat. Estuar. Coast. Shelf Sci.106, 112–120 (2012).
Agawin, N. S. R., Duarte, C. M., Fortes, M. D., Uri, J. S. & Vermaat, J. E. Temporal changes in the abundance, leaf growth and photosynthesis of three co-occurring Philippine seagrasses. J. Exp. Mar. Biol. Ecol.260, 217–239 (2001).
Pereg, L. L., Lipkin, Y. & Sar, N. Different niches of the Halophila stipulacea seagrass bed harbor distinct populations of nitrogen fixing bacteria. Mar. Biol.119, 327–333 (1994).
Holmer, M., Duarte, C., Boschker, H. & Barrón, C. Carbon cycling and bacterial carbon sources in pristine and impacted Mediterranean seagrass sediments. Aquat. Microb. Ecol.36, 227–237 (2004).
Barberá-Cebrián, C., Sánchez-Jerez, P. & Ramos-Esplá, A. Fragmented seagrass habitats on the Mediterranean coast, and distribution and abundance of mysid assemblages. Mar. Biol.141, 405–413 (2002).
Ringold, P. Burrowing, root mat density, and the distribution of fiddler crabs in the eastern United States. J. Exp. Mar. Biol. Ecol.36, 11–21 (1979).
Ricart, A. M. et al. Variability of sedimentary organic carbon in patchy seagrass landscapes. Mar. Pollut. Bull.100, 476–482 (2015).
Samper-Villarreal, J., Lovelock, C. E., Saunders, M. I., Roelfsema, C. & Mumby, P. J. Organic carbon in seagrass sediments is influenced by seagrass canopy complexity, turbidity, wave height, and water depth. Limnol. Oceanogr.61, 938–952 (2016).
Serra, T., Oldham, C. & Colomer, J. Local hydrodynamics at edges of marine canopies under oscillatory flows. PLoS ONE13, e0201737 (2018).
Choat, J. H. & Kingett, P. D. The influence of fish predation on the abundance cycles of an algal turf invertebrate fauna. Oecologia54, 88–95 (1982).
Nakamura, Y., Horinouchi, M., Nakai, T. & Sano, M. Food habits of fishes in a seagrass bed on a fringing coral reef at Iriomote Island, southern Japan. Ichthyol. Res.50, 0015–0022 (2003).
Eklöf, J. S., de la Torre Castro, M., Adelsköld, L., Jiddawi, N. S. & Kautsky, N. Differences in macrofaunal and seagrass assemblages in seagrass beds with and without seaweed farms. Estuar. Coast. Shelf Sci.63, 385–396 (2005).
Díaz-Cárdenas, C., Patel, B. K. C. & Baena, S. Tistlia consotensisgen. nov., sp. an aerobic, chemoheterotrophic, free-living, nitrogen-fixing alphaproteobacterium, isolated from a Colombian saline spring. Int. J. Syst. Evol. Microbiol.60, 1437–1443 (2010).
Sun, F. et al. Seagrass (Zostera marina) colonization promotes the accumulation of diazotrophic bacteria and alters the relative abundances of specific bacterial lineages involved in benthic carbon and sulfur cycling. Appl. Environ. Microbiol.81, 6901–6914 (2015).
Brown, S. M. & Jenkins, B. D. Profiling gene expression to distinguish the likely active diazotrophs from a sea of genetic potential in marine sediments. Environ. Microbiol.16, 3128–3142 (2014).
Santos, R., Lirman, D. & Pittman, S. Long-term spatial dynamics in vegetated seascapes: fragmentation and habitat loss in a human-impacted subtropical lagoon. Mar. Ecol.37(1), 200–214. https://doi.org/10.1111/maec.12259 (2015).
Irlandi, E. & Crawford, M. Habitats linkages: the effect of intertidal saltmarshes and adjacent habitats on abundance, movement and growth of an estuarine fish. Oecologia110, 222–230 (1997).
Boström, C., Pittman, S. J., Simenstad, C. & Kneib, R. T. Seascape ecology of coastal biogenic habitats: advances, gaps, and challenges. Mar. Ecol. Prog. Ser.427, 191–218 (2011).
Mumby, P. J. Connectivity of reef fish between mangroves and coral reefs: algorithms for the design of marine reserves at seascape scales. Biol. Conserv.128, 215–222 (2006).
Haila, Y. A conceptual genealogy of fragmentation research: from island biogeography to landscape ecology. Ecol. Appl.12, 321–334 (2002).
Barnes, R. S. K. Distribution patterns of macrobenthic biodiversity in the intertidal seagrass beds of an estuarine system, and their conservation significance. Biodivers. Conserv.22, 357–372 (2013).
Barnes, R. S. K. & Hamylton, S. On the very edge: faunal and functional responses to the interface between benthic seagrass and unvegetated sand assemblages. Mar. Ecol. Prog. Ser.553, 33–48 (2016).
Source: Ecology - nature.com
