H. Sioli, The Amazon: Limnology and landscape ecology of a mighty tropical river and its basin, 1984.

W. J. Junk, P. B. Bayley, and R. E. Sparks, The flood pulse concept in river-floodplain systems, Can Spec Publ Fish Aquat Sci, vol.106, pp.110-127, 1989.

J. E. Richey, J. M. Melack, A. K. Aufdenkampe, V. M. Ballester, and L. L. Hess, Outgassing from Amazonian rivers and wetlands as a large tropical source of atmospheric CO2, Nature, vol.416, p.11948346, 2002.

J. Richey, E. Hedges, J. I. Devol, A. H. Quay, P. D. Victoria et al., Biogeochemistry of carbon in the Amazon River, Limnol Oceanogr, vol.35, pp.352-371, 1990.

J. M. Melack, Atmosphere and Human Land Use in the Amazon Basin, Interactions Between Biosphere, pp.119-167, 2016.

P. A. Raymond, J. Hartmann, R. Lauerwald, S. Sobek, C. Mcdonald et al., Global carbon dioxide emissions from inland waters, Nature, vol.503, p.24256802, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01194582

G. Abril, J. Martinez, L. F. Artigas, P. Moreira-turcq, M. F. Benedetti et al., Amazon River carbon dioxide outgassing fuelled by wetlands, Nature, vol.505, p.24336199, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00960060

M. L. De-melo, S. Bertilsson, J. Amaral, P. M. Barbosa, B. R. Forsberg et al., Flood pulse regulation of bacterioplankton community composition in an Amazonian floodplain lake, Freshw Biol, pp.1-13, 2018.

C. Ruiz-gonzá-lez, J. P. Niño-garcía, J. Lapierre, D. Giorgio, and P. A. , The quality of organic matter shapes the functional biogeography of bacterioplankton across boreal freshwater ecosystems, Glob Ecol Biogeogr, vol.24, pp.1487-1498, 2015.

C. Ruiz-gonzá-lez, J. P. Niño-garcía, D. Giorgio, and P. A. , Terrestrial origin of bacterial communities in complex boreal freshwater networks, Ecol Lett, vol.18, p.26306742, 2015.

P. Moreira-turcq, M. Bonnet, M. Amorim, M. Bernardes, C. Lagane et al., Seasonal variability in concentration, composition, age, and fluxes of particulate organic carbon exchanged between the floodplain and Amazon River, Global Biogeochem Cycles, vol.27, pp.119-130, 2013.

J. Amaral, A. V. Borges, J. M. Melack, H. Sarmento, P. M. Barbosa et al., Influence of plankton metabolism and mixing depth on CO2dynamics in an Amazon floodplain lake, Sci Total Environ, vol.630, p.29554758, 2018.

T. Silva, M. Costa, and J. M. Melack, Annual net primary production of macrophytes in the eastern Amazon floodplain, Wetlands, vol.29, pp.747-758, 2009.

J. M. Mortillaro, C. Passarelli, G. Abril, C. Hubas, P. Albé-ric et al., The fate of C 4 and C 3 macrophyte carbon in central Amazon floodplain waters: insights from a batch experiment, Limnol Manag Inl Waters, vol.59, pp.90-98, 2016.
URL : https://hal.archives-ouvertes.fr/mnhn-02283647

D. S. Read, H. S. Gweon, M. J. Bowes, L. K. Newbold, D. Field et al., Catchment-scale biogeography of riverine bacterioplankton, ISME J, vol.9, p.25238398, 2015.

D. Savio, L. Sinclair, U. Z. Ijaz, J. Parajka, G. H. Reischer et al., Bacterial diversity along a 2600 km river continuum, Environ Microbiol, vol.17, p.25922985, 2015.

C. Staley, T. J. Gould, P. Wang, J. Phillips, J. B. Cotner et al., Species sorting and seasonal dynamics primarily shape bacterial communities in the Upper Mississippi River, Sci Total Environ, vol.505, p.25461045, 2015.

R. Ghai, F. Rodriguez-valera, K. D. Mcmahon, D. Toyama, R. Rinke et al., Metagenomics of the water column in the pristine upper course of the Amazon river, PLoS One, vol.6, p.21915244, 2011.

B. M. Satinsky, C. S. Fortunato, M. Doherty, C. B. Smith, S. Sharma et al., Metagenomic and metatranscriptomic inventories of the lower Amazon River, vol.3, p.39, 2011.

M. Tessler, M. R. Brugler, R. Desalle, R. Hersch, L. Velho et al., A Global eDNA Comparison of Freshwater Bacterioplankton Assemblages Focusing on Large-River Floodplain Lakes of Brazil

, Microb Ecol, vol.73, pp.1-14, 2016.

V. Mohit, P. Archambault, N. Toupoint, and C. Lovejoy, Phylogenetic differences in attached and free-living bacterial communities in a temperate coastal lagoon during summer, revealed via high-throughput 16S rRNA gene sequencing, Appl Environ Microbiol, vol.80, p.24463966, 2014.

M. Bi?i?-ionescu, M. Zeder, D. Ionescu, S. Orli?, B. M. Fuchs et al., Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization

, Environ Microbiol, vol.17, p.24674021, 2015.

M. Mestre, E. Borrull, S. Mm, and J. M. Gasol, Patterns of bacterial diversity in the marine planktonic particulate matter continuum, ISME J, vol.11, pp.999-1010, 2017.

B. Luef, F. Aspetsberger, T. Hein, F. Huber, and P. Peduzzi, Impact of hydrology on free-living and particleassociated microorganisms in a river floodplain system, Freshw Biol, vol.52, pp.1043-1057, 2007.

C. Pedrós-alió, Marine microbial diversity: can it be determined?, Trends Microbiol, vol.14, p.16679014, 2006.

C. Pedrós-alió, The rare bacterial biosphere, Ann Rev Mar Sci, vol.4, p.22457983, 2012.

M. Bonnet, G. Barroux, J. Martinez, F. Seyler, P. Moreira-turcq et al., Floodplain hydrology in an Amazon floodplain lake (Lago Grande de Curuai), J Hydrol, vol.349, pp.18-30, 2008.
URL : https://hal.archives-ouvertes.fr/ird-00270979

M. Perez, P. Moreira-turcq, H. Gallard, T. Allard, and M. F. Benedetti, Dissolved organic matter dynamic in the Amazon basin: sorption by mineral surfaces, Chem Geol, vol.286, pp.158-168, 2011.

F. Mackereth, J. Heron, and J. F. Talling, Water Analysis: Some Revised Methods for Limnologists

. Ambleside, , 1979.

. Apha/awwa/wef, Standard Methods for the Examination of Water and Wastewater, Stand Methods, vol.541, p.9780875532356, 2012.

M. A. Schneegurt, S. Y. Dore, and C. F. Kulpa, Direct extraction of DNA from soils for studies in microbial ecology, Curr Issues Mol Biol, vol.5, p.12638659, 2003.

D. Herlemann, M. Labrenz, K. Jürgens, S. Bertilsson, J. J. Waniek et al., Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea, ISME J, vol.5, p.21472016, 2011.

R. C. Edgar, UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nat Methods, vol.10, p.23955772, 2013.

R. Logares, S. Sunagawa, G. Salazar, F. M. Cornejo-castillo, I. Ferrera et al., Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities, Environ Microbiol, vol.16, p.24102695, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01258219

R. Logares, Workflow for analysing MiSeq amplicons based on Uparse v1, 2017.

J. Zhang, K. Kobert, T. Flouri, and A. Stamatakis, PEAR: a fast and accurate Illumina Paired-End reAd mergeR, Bioinformatics, vol.30, p.24142950, 2014.

C. Quast, E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer et al., The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res, vol.41, p.23193283, 2013.

R. C. Edgar, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, vol.26, p.20709691, 2010.

Z. Zhang, S. Schwartz, L. Wagner, and W. Miller, A greedy algorithm for aligning DNA sequences, J Comput Biol, vol.7, p.10890397, 2000.

M. Lynch and J. D. Neufeld, Ecology and exploration of the rare biosphere, Nat Rev Microbiol, vol.13, p.25730701, 2015.

J. R. Bray and J. T. Curtis, An ordination of the upland forest communities of southern Wisconsin, Ecol Monogr, vol.27, pp.325-349, 1957.

M. J. Anderson and . Permanova, Permutational multivariate analysis of variance, 2005.

M. Dufrene and P. Legendre, Species assemblages and indicator species: the need for a flexible asymmetrical approach, Ecol Monogr, vol.67, pp.345-366, 1997.

. R-core-team, R: A Language and Environment for Statistical Computing, 2016.

J. Oksanen, F. G. Blanchet, M. Friendly, R. Kindt, P. Legendre et al., Community Ecology Package, 2016.

D. W. Roberts, labdsv: Ordination and multivariate analysis for ecology. R package version 1.8-0, 2007.

J. J. Wiens, R. A. Pyron, and D. S. Moen, Phylogenetic origins of local-scale diversity patterns and the causes of Amazonian megadiversity, Ecol Lett, vol.14, p.21535341, 2011.

H. Sarmento, F. Unrein, M. Isumbisho, S. Stenuite, J. M. Gasol et al., Abundance and distribution of picoplankton in tropical, Freshw Biol, vol.53, pp.756-771, 2008.

H. Sarmento, New paradigms in tropical limnology: the importance of the microbial food web. Hydrobiologia, vol.686, pp.1-14, 2012.

W. M. Lewis, Surface/volume ratio: implications for phytoplankton morphology. Science (80-), vol.192, pp.885-887, 1976.

C. S. Reynolds, The ecology of freshwater phytoplankton, 1984.

P. Dvo?ák, D. A. Casamatta, A. Poulí?ková, P. Ha?ler, V. Ond?ej et al., Synechococcus: 3 billion years of global dominance, Mol Ecol, vol.23, p.25283338, 2014.

M. Llirós, Ö. Inceo?lu, T. García-armisen, A. Anzil, B. Leporcq et al., Bacterial community composition in three freshwater reservoirs of different alkalinity and trophic status, PLoS One, vol.9, p.25541975, 2014.

L. Liu, J. Yang, Z. Yu, and D. M. Wilkinson, The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China, ISME J, vol.9, p.25748371, 2015.

R. J. Newton, S. E. Jones, A. Eiler, K. D. Mcmahon, and S. Bertilsson, A guide to the natural history of freshwater lake bacteria, Microbiol Mol Biol Rev, vol.75, p.21372319, 2011.

T. W. Ghylin, S. L. Garcia, F. Moya, B. O. Oyserman, P. Schwientek et al., Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage, ISME J, vol.8, p.25093637, 2014.

M. M. Salcher, Same same but different: ecological niche partitioning of planktonic freshwater prokaryotes, J Limnol, vol.73, pp.74-87, 2013.

H. Cai, Y. Z. Wang, A. Krumholz, L. R. Jiang, and H. , Analysis of the attached microbial community on mucilaginous cyanobacterial aggregates in the eutrophic Lake Taihu reveals the importance of Planctomycetes, Microb Ecol, vol.66, p.23571665, 2013.

J. N. Woodhouse, A. S. Kinsela, R. N. Collins, L. C. Bowling, G. L. Honeyman et al., Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake, ISME J, vol.10, p.26636552, 2016.

M. Doherty, P. L. Yager, M. A. Moran, V. J. Coles, C. S. Fortunato et al., Bacterial biogeography across the Amazon River-ocean continuum, Front Microbiol, vol.8, p.28588561, 2017.

Y. Ji, R. Angel, M. Klose, C. P. Marotta, H. Pinho et al., Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types, Environ Microbiol, vol.18, p.27507000, 2016.

M. L. Schmidt, J. D. White, and V. J. Denef, Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla, Environ Microbiol, vol.18, p.26631909, 2016.

R. L. Carney, S. M. Mitrovic, T. Jeffries, D. Westhorpe, N. Curlevski et al., River bacterioplankton community responses to a high inflow event, Aquat Microb Ecol, vol.75, pp.187-205, 2015.

L. M. Bourgoin, M. Bonnet, J. Martinez, P. Kosuth, G. Cochonneau et al., Temporal dynamics of water and sediment exchanges between the Curuaí floodplain and the Amazon River, Brazil, J Hydrol, vol.335, pp.140-156, 2007.