Azam, F. & Malfatti, F. Microbial structuring of marine ecosystems. Nat. Rev. Microbiol. 5, 782–791 (2007).
Google Scholar
Martiny, J. B. H. et al. Microbial biogeography: Putting microorganisms on the map. Nat. Rev. Microbiol. 4, 102–112 (2006).
Google Scholar
Hanson, C. A., Fuhrman, J. A., Horner-Devine, M. C. & Martiny, J. B. H. Beyond biogeographic patterns: Processes shaping the microbial landscape. Nat. Rev. Microbiol. 10, 497–506 (2012).
Google Scholar
Grossart, H. P. Ecological consequences of bacterioplankton lifestyles: Changes in concepts are needed. Environ. Microbiol. Rep. 2, 706–714 (2010).
Google Scholar
Simon, M., Grossart, H. P., Schweitzer, B. & Ploug, H. Microbial ecology of organic aggregates in aquatic ecosystems. Aquat. Microb. Ecol. 28, 175–211 (2002).
Google Scholar
Smith, D. C., Simon, M., Alldredge, A. L. & Azam, F. Intense hydrolytic enzyme activity on marine aggregates and implication for rapid particle dissolution. Nature 359, 139–141 (1992).
Google Scholar
Grossart, H. P., Tang, K. W., Kiørboe, T. & Ploug, H. Comparison of cell-specific activity between free-living and attached bacteria using isolates and natural assemblages. FEMS Microbiol. Lett. 206, 194–200 (2007).
Google Scholar
Rieck, A., Herlemann, D. P. R., Jürgens, K. & Grossart, H. Particle-associated differ from free-living bacteria in surface waters of the Baltic Sea. Front. Microbiol. 6, 1297 (2015).
Google Scholar
Karner, M. & Herndl, G. J. Extracellular enzymatic activity and secondary production in free-living and marine-snow-associated bacteria. Mar. Biol. 113, 341–347 (1992).
Google Scholar
Lyons, M. M. & Dobbs, F. C. Differential utilization of carbon substrates by aggregate-associated and water-associated heterotrophic bacterial communities. Hydrobiologia 686, 181–193 (2012).
Google Scholar
Simon, H. M., Smith, M. W. & Herfort, L. Metagenomic insights into particles and their associated microbiota in a coastal margin ecosystem. Front. Microbiol. 5, 466 (2014).
Google Scholar
Smith, M. W., Allen, L. Z., Allen, A. E., Herfort, L. & Simon, H. M. Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem. Front. Microbiol. 4, 120 (2013).
Google Scholar
Mestre, M. et al. Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum. Mol. Ecol. 26, 6827–6840 (2017).
Google Scholar
Bižic-Ionescu, M. et al. Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization. Environ. Microbiol. 17, 3500–3514 (2015).
Google Scholar
Hollibaugh, J. T., Wong, P. S. & Murrell, M. C. Similarity of particle-associated and free-living bacterial communities in northern San Francisco Bay, California. Aquat. Microb. Ecol. 21, 103–114 (2000).
Google Scholar
Ortega-Retuerta, E., Joux, F., Jeffrey, W. H. & Ghiglione, J. F. Spatial variability of particle-attached and free-living bacterial diversity in surface waters from the Mackenzie River to the Beaufort Sea (Canadian Arctic). Biogeosciences 10, 2747–2759 (2013).
Google Scholar
Noble, P. A., Bidle, K. D. & Fletcher, M. Natural microbial community compositions compared by a back-propagating neural network and cluster analysis of 5S rRNA. Appl. Environ. Microbiol. 63, 1762–1770 (1997).
Google Scholar
Zhou, J. & Ning, D. Stochastic community assembly: Does it matter in microbial ecology?. Microbiol. Mol. Biol. Rev. 81, e00002-17 (2017).
Google Scholar
Jain, A., Balmonte, J. P., Singh, R., Bhaskar, P. V. & Krishnan, K. P. Spatially resolved assembly, connectivity and structure of particle-associated and free-living bacterial communities in a high Arctic fjord. FEMS Microbiol. Ecol. 97, 1–12 (2021).
Google Scholar
Yao, Z. et al. Bacterial community assembly in a typical estuarine marsh. Appl. Environ. Microbiol. 85, e02602-18 (2019).
Google Scholar
Wang, J. et al. Assembly processes and source tracking of planktonic and benthic bacterial communities in the Yellow River estuary. Environ. Microbiol. 23, 2578–2591 (2021).
Google Scholar
Balmonte, J. P. et al. Sharp contrasts between freshwater and marine microbial enzymatic capabilities, community composition, and DOM pools in a NE Greenland fjord. Limnol. Oceanogr. 65, 77–95 (2019).
Google Scholar
Fortunato, C. S., Herfort, L., Zuber, P., Baptista, A. M. & Crump, B. C. Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient. ISME J. 6, 554–563 (2012).
Google Scholar
Yawata, Y., Carrara, F., Menolascina, F. & Stocker, R. Constrained optimal foraging by marine bacterioplankton on particulate organic matter. Proc. Natl. Acad. Sci. USA 117, 25571–25579 (2020).
Google Scholar
Hu, Y. et al. The relationships between the free-living and particle-attached bacterial communities in response to elevated eutrophication. Front. Microbiol. 11, 423 (2020).
Google Scholar
Lima-Mendez, G. et al. Determinants of community structure in the grobal plankton interactome. Science (80-) 348, 1262073-1–10 (2015).
Google Scholar
Milici, M. et al. Co-occurrence analysis of microbial taxa in the Atlantic ocean reveals high connectivity in the free-living bacterioplankton. Front. Microbiol. 7, 649 (2016).
Google Scholar
Herren, C. M. & McMahon, K. D. Cohesion: A method for quantifying the connectivity of microbial communities. ISME J. 11, 2426–2438 (2017).
Google Scholar
Friedman, J. & Alm, E. J. Inferring correlation networks from genomic survey data. PLoS Comput. Biol. 8, e1002687 (2012).
Google Scholar
Deng, Y. et al. Molecular ecological network analyses. BMC Bioinform. 13, 113 (2012).
Google Scholar
Labry, C. et al. High alkaline phosphatase activity in phosphate replete waters: The case of two macrotidal estuaries. Limnol. Oceanogr. 61, 1513–1529 (2016).
Google Scholar
Crump, B. C. et al. Quantity and quality of particulate organic matter controls bacterial production in the Columbia River estuary. Limnol. Oceanogr. 62, 2713–2731 (2017).
Google Scholar
Canuel, E. A. & Hardison, A. K. Sources, ages, and alteration of organic matter in Estuaries. Ann. Rev. Mar. Sci. 8, 409–434 (2016).
Google Scholar
He, W., Chen, M., Schlautman, M. A. & Hur, J. Dynamic exchanges between DOM and POM pools in coastal and inland aquatic ecosystems: A review. Sci. Total Environ. 551–552, 415–428 (2016).
Google Scholar
Bianchi, T. S. The role of terrestrially derived organic carbon in the coastal ocean: A changing paradigm and the priming effect. Proc. Natl. Acad. Sci. 108, 19473–19481 (2011).
Google Scholar
Auffret, G. A. Dynamique sédimentaire de la marge continentale celtique-Evolution Cénozoïque-Spécificité du Pleistocène supérieur et de l’Holocène (Université de Bordeaux I, 1983).
Delmas, R. & Tréguer, P. Évolution saisonnière des nutriments dans un écosystème eutrophe d’Europe occidentale (la rade de Brest). Interactions marines et terrestres. Oceanol. Acta 6, 345–356 (1983).
Google Scholar
Bassoullet, P. Etude de la dynamique des sédiments en suspension dans l’estuaire de l’Aulne (rade de Brest) (Université de Bretagne Occidentale, 1979).
Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41, e1 (2013).
Google Scholar
Bolyen, E. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).
Google Scholar
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Google Scholar
Olesen, S. W., Duvallet, C. & Alm, E. J. dbOTU3: A new implementation of distribution-based OTU calling. PLoS ONE 12, 1–13 (2017).
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).
Google Scholar
R Core Team. R: A Language and Environment for Statistical Computing (2013).
Whickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
Google Scholar
Lê, S., Josse, J. & Husson, F. FactoMineR: An R package for multivariate analysis. J. Stat. Softw. 25, 1–18 (2008).
Google Scholar
Wei, T. & Simko, V. R package ‘corrplot’: Visualization of a Correlation Matrix (2011).
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 (2022).
Liu, C., Cui, Y., Li, X. & Yao, M. Microeco: An R package for data mining in microbial community ecology. FEMS Microbiol. Ecol. 97, fiaa255 (2021).
Google Scholar
Kandlikar, G. ranacapa: Utility Functions and ‘shiny’ App for Simple Environmental DNA Visualizations and Analyses (2021).
Cao, Y. microbiomeMarker: microbiome biomarker analysis toolkit (2021).
Tsirogiannis, C. & Brody, S. PhyloMeasures: Fast and Exact Algorithms for Computing Phylogenetic Biodiversity Measures (2017).
McKnight, D. T. et al. Methods for normalizing microbiome data: An ecological perspective. Methods Ecol. Evol. 10, 389–400 (2019).
Google Scholar
Paradis, E. & Schliep, K. Ape 50: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics https://doi.org/10.1093/bioinformatics/bty633 (2019).
Google Scholar
Legendre, P. & Legendre, L. Numerical Ecology (Third English Edition) (Elsevier, 2012).
Google Scholar
Stegen, J. C., Lin, X., Fredrickson, J. K. & Konopka, A. E. Estimating and mapping ecological processes influencing microbial community assembly. Front. Microbiol. 6, 370 (2015).
Google Scholar
Stegen, J. C., Lin, X., Konopka, A. E. & Fredrickson, J. K. Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J. 6, 1653–1664 (2012).
Google Scholar
Naimi, B. usdm: Uncertainty Analysis for Species Distribution Models (2017).
Wu, W., Xu, Z., Dai, M., Gan, J. & Liu, H. Homogeneous selection shapes free-living and particle-associated bacterial communities in subtropical coastal waters. Divers. Distrib. 00, 1–14 (2020).
Wang, Y. et al. Patterns and processes of free-living and particle-associated bacterioplankton and archaeaplankton communities in a subtropical river-bay system in South China. Limnol. Oceanogr. 65, 161–179 (2020).
Zhou, L. et al. Environmental filtering dominates bacterioplankton community assembly in a highly urbanized estuarine ecosystem. Environ. Res. 196, 110934 (2021).
Google Scholar
Graham, E. B. & Stegen, J. C. Dispersal-based microbial community assembly decreases biogeochemical function. Processes 5, 65 (2017).
Google Scholar
Campbell, B. J. & Kirchman, D. L. Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient. ISME J. 7, 210–220 (2013).
Google Scholar
Herlemann, D. P. R. et al. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 5, 1571–1579 (2011).
Google Scholar
Fuhrman, J. A., Cram, J. A. & Needham, D. M. Marine microbial community dynamics and their ecological interpretation. Nat. Rev. Microbiol. 13, 133–146 (2015).
Google Scholar
Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science (80-) 348, 1261359 (2015).
Google Scholar
Buchan, A., LeCleir, G. R., Gulvik, C. A. & González, J. M. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat. Rev. Microbiol. 12, 686–698 (2014).
Google Scholar
Martinez-Garcia, M. et al. Capturing single cell genomes of active polysaccharide degraders: An unexpected contribution of verrucomicrobia. PLoS ONE 7, e35314 (2012).
Google Scholar
Reintjes, G., Arnosti, C., Fuchs, B. M. & Amann, R. An alternative polysaccharide uptake mechanism of marine bacteria. ISME J. 11, 1640–1650 (2017).
Google Scholar
Gralka, M., Szabo, R., Stocker, R. & Cordero, O. X. Trophic interactions and the drivers of microbial community assembly. Curr. Biol. 30, R1176–R1188 (2020).
Google Scholar
Liu, J., Meng, Z., Liu, X. & Zhang, X. H. Microbial assembly, interaction, functioning, activity and diversification: a review derived from community compositional data. Mar. Life Sci. Technol. 1, 112–128 (2019).
Google Scholar
Hernandez, D. J., David, A. S., Menges, E. S., Searcy, C. A. & Afkhami, M. E. Environmental stress destabilizes microbial networks. ISME J. 15, 1722–1734 (2021).
Google Scholar
Herren, C. M. & McMahon, K. D. Keystone taxa predict compositional change in microbial communities. Environ. Microbiol. 20, 2207–2217 (2018).
Google Scholar
Liénart, C. et al. Dynamics of particulate organic matter composition in coastal systems: A spatio-temporal study at multi-systems scale. Prog. Oceanogr. 156, 221–239 (2017).
Google Scholar
Fraisse, S., Bormans, M. & Lagadeuc, Y. Morphofunctional traits reflect differences in phytoplankton community between rivers of contrasting flow regime. Aquat. Ecol. 47, 315–327 (2013).
Google Scholar
Treguer, P. & Queguiner, B. Seasonal variations in conservative and nonconservative mixing of nitrogen compounds in a West European macrotidal estuary. Oceanol. Acta 12, 371–380 (1989).
Google Scholar
Grossart, H. P. & Tang, K. W. Communicative & integrative biology. Commun. Integr. Biol. 3, 491–494 (2010).
Google Scholar
Source: Ecology - nature.com
