Ward, J. V & Stanford, J. A. Serial discontinuity concept of lotic ecosystems. In Dynamics of Lotic Systems, Ann Arbor Science, Ann Arbor 29–42 (1983).
Bouwman, A. F. et al. Nutrient dynamics, transfer and retention along the aquatic continuum from land to ocean: towards integration of ecological and biogeochemical models. Biogeosciences 10, 1–22 (2013).
Proia, L. et al. Microbial carbon processing along a river discontinuum. Freshw. Sci. 35, 1133–1147 (2016).
Casas-Ruiz, J. P. et al. A tale of pipes and reactors: Controls on the in-stream dynamics of dissolved organic matter in rivers. Limnol. Oceanogr. 62, S85–S94 (2017).
Artigas, J. et al. Phosphorus use by planktonic communities in a large regulated Mediterranean river. Sci. Total Environ. 426, 180–187 (2012).
Gómez-Gener, L., Gubau, M., von Schiller, D., Marcé, R. & Obrador, B. Effect of small water retention structures on diffusive CO2 and CH4 emissions along a highly impounded river. Inl. Waters 8, 449–460 (2018).
Irriberri, J., Unanue, M., Barcina, I. & Egea, L. Seasonal variation in population density and heterotrophic activity of attached and free-living bacteria in coastal waters. Appl. Environ. Microbiol. 53, 2308–2314 (1987).
Grossart, H. & Simon, M. Bacterial colonization and microbial decomposition of limnetic organic aggregates (lake snow). Aquat. Microb. Ecol. 15, 1127–1140 (1998).
Simon, M., Grossart, H. P., Schweitzer, B. & Ploug, H. Microbial ecology of organic aggregates in aquatic ecosystems. Aquat. Microb. Ecol. 28, 175–211 (2002).
Wilczek, S., Wörner, U., Pusch, M. T. & Fischer, H. Role of suspended particles for extracellular enzyme activity and biotic control of pelagic bacterial populations in the large lowland river Elbe. Fundam. Appl. Limnol./Arch. für Hydrobiol. 169, 153–168 (2007).
Rieck, A., Herlemann, D. P. R., Jürgens, K. & Grossart, H. P. Particle-associated differ from free-living bacteria in surface waters of the baltic sea. Front. Microbiol. 6, 1297 (2015).
Ruiz-González, C., Proia, L., Ferrera, I., Gasol, J. M. & Sabater, S. Effects of large river dam regulation on bacterioplankton community structure. FEMS Microbiol. Ecol. 84, 316–331 (2013).
Salazar, G. et al. Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Mol. Ecol. 24, 5692–5706 (2015).
López-Pérez, M., Kimes, N. E., Haro-Moreno, J. M. & Rodriguez-Valera, F. Not all particles are equal: The selective enrichment of particle-associated bacteria from the mediterranean sea. Front. Microbiol. 7, 996 (2016).
Mestre, M., Borrull, E., Sala, M. & Gasol, J. M. Patterns of bacterial diversity in the marine planktonic particulate matter continuum. ISME J. 11, 999–1010 (2017).
Zeglin, L. H. Stream microbial diversity in response to environmental changes: Review and synthesis of existing research. Front. Microbiol. 6, 1–15 (2015).
Galand, P. E., Lovejoy, C., Pouliot, J. & Vincent, W. F. Heterogeneous archaeal communities in the particle-rich environment of an arctic shelf ecosystem. J. Mar. Syst. 74, 774–782 (2008).
Orsi, W. D. et al. Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter. ISME J. 9, 1747–1763 (2015).
Crump, B. C. & Baross, J. A. Archaeaplankton in the Columbia River, its estuary and the adjacent coastal ocean, USA. FEMS Microbiol. Ecol. 31, 231–239 (2000).
Dumestre, J., Casamayor, E. O., Massana, R. & Pedrós-alió, C. Changes in bacterial and archaeal assemblages in an equatorial river induced by the water eutrophication of Petit Saut dam reservoir (French Guiana). Aquat. Microb. Ecol. 26, 209–221 (2001).
Galand, P. E., Lovejoy, C. & Vincent, W. F. Remarkably diverse and contrasting archaeal communities in a large arctic river and the coastal Arctic Ocean. Aquat. Microb. Ecol. 44, 115–126 (2006).
Leibold, M. A. & Chase, J. M. Metacommunity Ecology (Princeton University Press, Princeton, 2018).
Lindström, E. S. & Langenheder, S. Local and regional factors influencing bacterial community assembly. Environ. Microbiol. Rep. 4, 1–9 (2012).
Staley, C. et al. Species sorting and seasonal dynamics primarily shape bacterial communities in the Upper Mississippi River. Sci. Total Environ. 505, 435–445 (2015).
Ruiz-González, C. et al. Weak coherence in abundance patterns between bacterial classes and their constituent OTUs along a regulated river. Front. Microbiol. 6, 1–13 (2015).
Grossart, H. P. Ecological consequences of bacterioplankton lifestyles: Changes in concepts are needed. Environ. Microbiol. Rep. 2, 706–714 (2010).
Azam, F. & Malfatti, F. Microbial structuring of marine ecosystems. Nat. Rev. Microbiol. 5, 782–791 (2007).
Böckelmann, U., Manz, W., Neu, T. R. & Szewzyk, U. Characterization of the microbial community of lotic organic aggregates (‘river snow’) in the Elbe River of Germany by cultivation and molecular methods. FEMS Microbiol. Ecol. 33, 157–170 (2000).
Ghiglione, J. F. et al. Diel and seasonal variations in abundance, activity, and community structure of particle-attached and free-living bacteria in NW Mediterranean Sea. Microb. Ecol. 54, 217–231 (2007).
Rösel, S. & Grossart, H. P. Contrasting dynamics in activity and community composition of free-living and particle-associated bacteria in spring. Aquat. Microb. Ecol. 66, 169–181 (2012).
Crespo, B. G., Pommier, T., Fernández-Gómez, B. & Pedrós-Alió, C. Taxonomic composition of the particle-attached and free-living bacterial assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of the 16S rRNA. Microbiologyopen 2, 541–552 (2013).
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).
Hollibaughl, J. T., Wongl, P. S. & Michael, C. Similarity of particle-associated and free-living bacterial communities in northern San Francisco. Water 21, 103–114 (2000).
Moeseneder, M. M., Winter, C. & Herndl, G. J. Horizontal and vertical complexity of attached and free-living bacteria of the eastern Mediterranean Sea, determined by 16S rDNA and 16S rRNA fingerprints. Limnol. Oceanogr. 46, 95–107 (2001).
Eloe, E. A. et al. Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment. Environ. Microbiol. Rep. 3, 449–458 (2011).
Zhang, R., Liu, B., Lau, S., Ki, J.-S. & Qian, P.-Y. Particle-attached and free-living bacterial communities in a contrasting marine environment: Victoria Harbor, Hong Kong. FEMS Microbiol. Ecol. 61, 496–508 (2007).
Mestre, M. et al. Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum. Mol. Ecol. 26, 6827–6840 (2017).
Ivars-Martinez, E. et al. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME J. 2, 1194–1212 (2008).
Fernández-Gómez, B. et al. Ecology of marine Bacteroidetes: A comparative genomics approach. ISME J. 7, 1026–1037 (2013).
Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75, 14–49 (2011).
Kasalický, V., Jezbera, J., Hahn, M. W. & Šimek, K. The diversity of the Limnohabitans genus, an important group of freshwater bacterioplankton, by characterization of 35 isolated strains. PLoS ONE 8, e58209 (2013).
Simek, K. et al. Broad habitat range of the phylogenetically narrow R-BT065 cluster, representing a core group of the Betaproteobacterial genus Limnohabitans. Appl. Environ. Microbiol. 76, 631–639 (2010).
Jezberová, J., Šimek, K., Hahn, M. W., Jezbera, J. & Kasalický, V. Patterns of Limnohabitans microdiversity across a large set of freshwater habitats as revealed by reverse line blot hybridization. PLoS ONE 8, e58527 (2013).
Shade, A. et al. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. MBio 5, 1–9 (2014).
Castelle, C. J. et al. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr. Biol. 25, 690–701 (2015).
Stahl, D. A. & de la Torre, J. R. Physiology and diversity of ammonia-oxidizing archaea. Annu. Rev. Microbiol. 66, 83–101 (2012).
Liu, X. et al. Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages. Microbiome 6, 1–16 (2018).
Ortiz-Alvarez, R. & Casamayor, E. O. High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes. Environ. Microbiol. Rep. 8, 210–217 (2016).
Fillol, M., Auguet, J.-C., Casamayor, E. O. & Borrego, C. M. Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage. ISME J. 10, 653–677 (2016).
Durbin, A. M. & Teske, A. Archaea in organic-lean and organic-rich marine subsurface sediments: an environmental gradient reflected in distinct phylogenetic lineages. Front. Microbiol. 3, 168 (2012).
Fillol, M., Sànchez-Melsió, A., Gich, F. & Borrego, M. C. Diversity of Miscellaneous Crenarchaeotic Group archaea in freshwater karstic lakes and their segregation between planktonic and sediment habitats. FEMS Microbiol. Ecol. 91, fiv20 (2015).
Compte-Port, S. et al. Abundance and Co-Distribution of Widespread Marine Archaeal Lineages in Surface Sediments of Freshwater Water Bodies across the Iberian Peninsula. Microb. Ecol. 74, 776–787 (2017).
Allgaier, M. & Grossart, H. Diversity and seasonal dynamics of actinobacteria populations in four lakes in Northeastern Germany. Appl. Environ. Microbiol. 72, 3489–3497 (2006).
Grasshoff, K., Kremling, K. & Ehrhardt, M. Methods of Seawater Analysis (Wiley-VCH Verlag Gmbh, Weinheim, 1999).
Dowd, S. E. et al. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol. 8, 125 (2008).
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).
Desantis, T. Z. et al. Gene database and workbench compatible with ARB. (California Institute of Technology, accessed 2 October 2 2014);http://aem.asm.org/.
Desantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006).
Caporaso, J. G. et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266–267 (2010).
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).
Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996 (2018).
Lozupone, C. & Knight, R. UniFrac : A new phylogenetic method for comparing microbial communitiess. Appl. Environ. Microbiol. 71, 8228–8235 (2005).
Andersen, S. K., Kirkegaard, R. H., Karst, S. M. & Albertsen, M. ampvis2: An R package to analyse and visualise 16S rRNA amplicon data. BioRxiv https://doi.org/10.1101/299537 (2018).
R Development Core Team. R: A language and environment for statistical computing. ISBN: 3-900051-07-0 (2011).
Dufrene, M. & Legendre, P. Species assemblages and indicator species: The need for flexible asymmetrical approach. Ecol. Monogr. 67, 345–366 (1997).
De Cáceres, M. & Legendre, P. Associations between species and groups of sites: Indices and statistical inference. Ecology 90, 3566–3574 (2009).
Aßhauer, K. P., Wemheuer, B., Daniel, R. & Meinicke, P. Tax4Fun: Predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics 31, 2882–2884 (2015).
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. 57, 289–300 (1995).
Wickham, H. ggplot2. Elegant Grsaphics for Data Analysis (Springer, New York , 2009). https://doi.org/10.1007/978-0-387-98141-3.
Source: Ecology - nature.com
