Griffiths, J. R. et al. The importance of benthic-pelagic coupling for marine ecosystem functioning in a changing world. Glob. Chang. Biol. 23, 2179–2196 (2017).
Google Scholar
Graf, G., Bengtsson, W., Diesner, U., Schulz, R. & Theede, H. Benthic response to sedimentation of a spring phytoplankton bloom: Process and budget. Mar. Biol. 67, 201–208 (1982).
Campanyà-llovet, N., Snelgrove, P. V. R. & Parrish, C. C. Rethinking the importance of food quality in marine benthic food webs. Prog. Oceanogr. 156, 240–251 (2017).
Blomqvist, S. & Heiskanen, A.-S. The challenge of sedimentation in the Baltic Sea. In A Systems Analysis of the Baltic Sea. Ecological Studies (Analysis and Synthesis) Vol. 148 (eds Wulff, F. V. et al.) 211–227 (Springer, Berlin, 2001).
Elmgren, R. Trophic dynamics in the enclosed, brackish Baltic Sea. Rapp. P.-V. Réun. Cons. int. Explor. Mer. 183, 152–169 (1984).
Kahru, M., Elmgren, R., Di Lorenzo, E. & Savchuk, O. Unexplained interannual oscillations of cyanobacterial blooms in the Baltic Sea. Sci. Rep. 8, 6–10 (2018).
Google Scholar
BACC II Author Team. Second Assessment of Climate Change for the Baltic Sea Basin. (SpringerOpen, 2015) https://doi.org/10.1007/978-3-319-16006-1.
Spilling, K. & Lindström, M. Phytoplankton life cycle transformations lead to species-specific effects on sediment processes in the Baltic Sea. Cont. Shelf Res. 28, 2488–2495 (2008).
Google Scholar
Suikkanen, S. et al. Climate change and eutrophication induced shifts in northern summer plankton communities. PLoS ONE 8, e66475 (2013).
Google Scholar
Tamelander, T., Spilling, K. & Winder, M. Organic matter export to the seafloor in the Baltic Sea: Drivers of change and future projections. Ambio 46, 842–851 (2017).
Google Scholar
Giere, O. Meiobenthology: The Microscopic Motile Fauna of Aquatic Sediments (Springer, 2009).
Schratzberger, M. & Ingels, J. Meiofauna matters: The roles of meiofauna in benthic ecosystems. J. Exp. Mar. Biol. Ecol. 502, 12–25 (2018).
Bonaglia, S., Nascimento, F. J. A., Bartoli, M., Klawonn, I. & Brüchert, V. Meiofauna increases bacterial denitrification in marine sediments. Nat. Commun. 5, 5133 (2014).
Google Scholar
Nascimento, F. J. A., Näslund, J. & Elmgren, R. Meiofauna enhances organic matter mineralization in soft sediment ecosystems. Limnol. Oceanogr. 57, 338–346 (2012).
Google Scholar
Nealson, K. H. Sediment bacteria: Who’s there, what are they doing, and what’s new?. Annu. Rev. Earth Planet Sci. 25, 403–434 (1997).
Google Scholar
Meyer-Reil, L.-A. Seasonal and spatial distribution of extracellular enzymatic activities and microbial incorporation of dissolved organic substrates in marine sediments. Appl. Environ. Microbiol. 53, 1748–1755 (1987).
Google Scholar
Ólafsson, E. & Elmgren, R. Seasonal dynamics of sublittoral meiobenthos in relation to phytoplankton sedimentation in the Baltic Sea. Estuar. Coast. Shelf Sci. 45, 149–164 (1997).
Google Scholar
Pfannkuche, O. Benthic response to the sedimentation of particulate organic matter at the BIOTRANS station, 47°N, 20°W. Deep. Res. Part II 40, 135–149 (1993).
Hoffmann, K., Hassenrück, C., Salman-Carvalho, V., Holtappels, M. & Bienhold, C. Response of bacterial communities to different detritus compositions in Arctic deep-sea sediments. Front. Microbiol. 8, 266 (2017).
Google Scholar
Stoeck, T., Kochems, R., Forster, D., Lejzerowicz, F. & Pawlowski, J. Metabarcoding of benthic ciliate communities shows high potential for environmental monitoring in salmon aquaculture. Ecol. Indic. 85, 153–164 (2018).
Rudnick, D. T. Time lags between the deposition and meiobenthic assimilation of phytodetritus. Mar. Ecol. Prog. Ser. 50, 231–240 (1989).
Google Scholar
van der Heijden, L. H. et al. How do food sources drive meiofauna community structure in soft-bottom coastal food webs?. Mar. Biol. 165, 166 (2018).
Schratzberger, M., Forster, R. M., Goodsir, F. & Jennings, S. Nematode community dynamics over an annual production cycle in the central North Sea. Mar. Environ. Res. 66, 508–519 (2008).
Google Scholar
Wieser, W. Die beziehung zwischen mundhöhlengestalt, ernährungsweise und vorkommen bei freilebenden marinen nematoden. Ark Zool 2, 439–484 (1953).
Moens, T., Van Gansbeke, D. & Vincx, M. Linking estuarine nematodes to their suspected food. A case study from the Westerschelde Estuary (south-west Netherlands). J. Mar. Biol. Assoc. UK 79, 1017–1027 (1999).
Nascimento, F. J. A., Karlson, A. M. L. & Elmgren, R. Settling blooms of filamentous cyanobacteria as food for meiofauna assemblages. Limnol. Oceanogr. 53, 2636–2643 (2008).
Google Scholar
Nascimento, F. J. A., Karlson, A. M. L., Näslund, J. & Gorokhova, E. Settling cyanobacterial blooms do not improve growth conditions for soft bottom meiofauna. J. Exp. Mar. Biol. Ecol. 368, 138–146 (2009).
Groendahl, S. & Fink, P. High dietary quality of non-toxic cyanobacteria for a benthic grazer and its implications for the control of cyanobacterial biofilms. BMC Ecol. 17, 20 (2017).
Google Scholar
Broman, E. et al. Spring and late summer phytoplankton biomass impact on the coastal sediment microbial community structure. Microb. Ecol. 77, 288–303 (2019).
Google Scholar
Fagervold, S. K. et al. River organic matter shapes microbial communities in the sediment of the Rhône prodelta. ISME J. 8, 2327–2338 (2014).
Google Scholar
Reed, H. E. & Martiny, J. B. H. Microbial composition affects the functioning of estuarine sediments. ISME J. 7, 868–879 (2013).
Google Scholar
Tuominen, L. et al. Nutrient fluxes, porewater profiles and denitrification in sediment influenced by algal sedimentation and bioturbation by Monoporeia affinis. Estuar. Coast. Shelf Sci. 49, 83–97 (1999).
Google Scholar
Zilius, M., De Wit, R. & Bartoli, M. Response of sedimentary processes to cyanobacteria loading. J. Limnol. 75, 236–247 (2016).
Blazewicz, S. J., Barnard, R. L., Daly, R. A. & Firestone, M. K. Evaluating rRNA as an indicator of microbial activity in environmental communities: Limitations and uses. ISME J. 7, 2061–2068 (2013).
Google Scholar
Guardiola, M. et al. Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA. PeerJ 4, e2807 (2016).
Google Scholar
Soto, E., Quiroga, E., Ganga, B. & Alarcón, G. Influence of organic matter inputs and grain size on soft-bottom macrobenthic biodiversity in the upwelling ecosystem of central Chile. Mar. Biodivers. 47, 433–450 (2017).
Broman, E., Bonaglia, S., Norkko, A., Creer, S. & Nascimento, F. J. A. High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient. Mol. Ecol. 00, 1–17 (2020).
Google Scholar
Ingels, J., Tchesunov, A. V. & Vanreusel, A. Meiofauna in the Gollum Channels and the Whittard Canyon, Celtic Margin—How local environmental conditions shape nematode structure and function. PLoS ONE 6, e20094 (2011).
Google Scholar
Albert, S. et al. Influence of settling organic matter quantity and quality on benthic nitrogen cycling. Limnol. Oceanogr. 66, 1882–1895 (2021).
Google Scholar
Modig, H. & Ólafsson, E. Responses of Baltic benthic invertebrates to hypoxic events. J. Exp. Mar. Biol. Ecol. 229, 133–148 (1998).
Ankar, S. Annual dynamics of a Northern Baltic Soft Bottom. In Cyclic Phenomena in Marine Plants and Animals (eds Naylor, E. & Hartnoll, R. G.) 29–36 (Pergamon Press, 1979). https://doi.org/10.1016/b978-0-08-023217-1.50011-4.
Google Scholar
Karlson, A. M. L., Nascimento, F. J. A. & Elmgren, R. Incorporation and burial of carbon from settling cyanobacterial blooms by deposit-feeding macrofauna. Limnol. Oceanogr. 53, 2754–2758 (2008).
Google Scholar
Hedberg, P., Albert, S., Nascimento, F. J. A. & Winder, M. Effects of changing phytoplankton species composition on carbon and nitrogen uptake in benthic invertebrates. Limnol. Oceanogr. 66, 469–480 (2021).
Google Scholar
Ólafsson, E., Modig, H. & van de Bund, W. J. Species specific uptake of radio-labelled phytodetritus by benthic meiofauna from the Baltic Sea. Mar. Ecol. Prog. Ser. 177, 63–72 (1999).
Google Scholar
Guden, R. M., Vafeiadou, A., De Meester, N., Derycke, S. & Moens, T. Living apart-together: Microhabitat differentiation of cryptic nematode species in a saltmarsh habitat. PLoS ONE 13, e0204750 (2018).
Google Scholar
Rudnick, D. T. & Oviatt, C. A. Seasonal lags between organic carbon deposition and mineralization in marine sediments. J. Mar. Res. 44, 815–837 (1986).
Google Scholar
Moens, T. et al. Diatom feeding across trophic guilds in tidal flat nematodes, and the importance of diatom cell size. J. Sea Res. 92, 125–133 (2014).
Google Scholar
Schuelke, T., Pereira, T. J., Hardy, S. M. & Bik, H. M. Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats. Mol. Ecol. 27, 1930–1951 (2018).
Google Scholar
Fenchel, T. & Jansson, B.-O. On the vertical distribution of the microfauna in the sediments of a brackish-water beach. Ophelia 3, 161–177 (1966).
Fenchel, T. The ecology of marine microbenthos II. The food of marine benthic ciliates. Ophelia 5, 73–121 (1968).
Shimeta, J., Starczak, V. R., Ashiru, O. M. & Zimmer, C. A. Influences of benthic boundary-layer flow on feeding rates of ciliates and flagellates at the sediment-water interface. Limnol. Oceanogr. 46, 1709–1719 (2001).
Google Scholar
Nagata, T. Organic matter–bacteria interactions in seawater. In Microbial Ecology of the Oceans 2nd edn (ed. Kirchman, D. L.) 207–241 (Wiley, 2008).
De Mesel, I. et al. Top-down impact of bacterivorous nematodes on the bacterial community structure: A microcosm study. Environ. Microbiol. 6, 733–744 (2004).
Google Scholar
Landa, M. et al. Phylogenetic and structural response of heterotrophic bacteria to dissolved organic matter of different chemical composition in a continuous culture study. Environ. Microbiol. 16, 1668–1681 (2014).
Google Scholar
Izabel-Shen, D., Albert, S., Winder, M., Farnelid, H. & Nascimento, F. J. A. Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface. Mol. Ecol. 30, 3515–3529 (2021).
Google Scholar
Bowen, J. L., Babbin, A. R., Kearns, P. J. & Ward, B. B. Connecting the dots: Linking nitrogen cycle gene expression to nitrogen fluxes in marine sediment mesocosms. Front. Microbiol. 5, 429 (2014).
Google Scholar
Broman, E. et al. Denitrification responses to increasing cadmium exposure in Baltic Sea sediments. Aquat. Toxicol. 217, 105328 (2019).
Google Scholar
van der Loos, L. M. & Nijland, R. Biases in bulk: DNA metabarcoding of marine communities and the methodology involved. Mol. Ecol. 30, 3270–3288 (2021).
Google Scholar
Zinger, L. et al. DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions. Mol. Ecol. 28, 1857–1862 (2019).
Google Scholar
Prokopowich, C. D., Gregory, T. R. & Crease, T. J. The correlation between rDNA copy number and genome size in eukaryotes. Genome 46, 48–50 (2003).
Google Scholar
Nascimento, F. J. A., Lallias, D., Bik, H. M. & Creer, S. Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing. Sci. Rep. 8, 11737 (2018).
Google Scholar
Brannock, P. M. & Halanych, K. M. Meiofaunal community analysis by high-throughput sequencing: Comparison of extraction, quality filtering, and clustering methods. Mar. Genomics 23, 67–75 (2015).
Google Scholar
Wallenstein, M. D., Myrold, D. D., Firestone, M. & Voytek, M. Environmental controls on denitrifying communities and denitrification rates: Insights from molecular methods. Ecol. Appl. 16, 2143–2152 (2006).
Google Scholar
Höglander, H., Larsson, U. & Hajdu, S. Vertical distribution and settling of spring phytoplankton in the offshore NW Baltic Sea proper. Mar. Ecol. Prog. Ser. 283, 15–27 (2004).
Google Scholar
Walsby, A. E. Gas vesicles. Annu. Rev. Plant Physiol. 26, 427–439 (1975).
Google Scholar
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Google Scholar
Benson, D. A. et al. GenBank. Nucleic Acids Res. 41, 36–42 (2013).
Huson, D. H. et al. MEGAN community edition—Interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 12, e1004957 (2016).
Google Scholar
Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, 590–596 (2013).
Murali, A., Bhargava, A. & Wright, E. S. IDTAXA: A novel approach for accurate taxonomic classification of microbiome sequences. Microbiome 6, 1–14 (2018).
Urban-Malinga, B., Warzocha, J. & Zalewski, M. Effects of the invasive polychaete Marenzelleria spp. on benthic processes and meiobenthos of a species-poor brackish system. J. Sea Res. 80, 25–34 (2013).
Google Scholar
McMurdie, P. J. & Holmes, S. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
Google Scholar
Oksanen, J. et al. Vegan: Community ecology package. version 2.5-7, 1–298 (2020).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
Google Scholar
Alberdi, A., Aizpurua, O., Gilbert, M. T. P. & Bohmann, K. Scrutinizing key steps for reliable metabarcoding of environmental samples. Methods Ecol. Evol. 9, 134–147 (2017).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 1–21 (2014).
Source: Ecology - nature.com
