T. V?trovský and P. Baldrian, The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses, PLoS ONE, vol.8, issue.e57923, 2013.

J. Pollock, L. Glendinning, T. Wisedchanwet, and M. Watson, The madness of microbiome: Attempting to find consensus "best practice" for 16S microbiome studies, Appl. Environ. Microbiol, vol.84, pp.2627-2644, 2018.

P. Hugon, J. Lagier, P. Colson, F. Bittar, and D. Raoult, Repertoire of human gut microbes, vol.106, pp.103-112, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01478556

J. Lagier, S. Khelaifia, M. T. Alou, S. Ndongo, N. Dione et al., Culture of previously uncultured members of the human gut microbiota by culturomics, Nat. Microbiol, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01453324

M. L. Sogin, H. G. Morrison, J. A. Huber, D. Mark-welch, S. M. Huse et al., Microbial diversity in the deep sea and the underexplored "rare biosphere, Proc. Natl. Acad. Sci, vol.103, pp.12115-12120, 2006.

, Microorganisms 2020, vol.8, p.1129

M. D. Lynch and J. D. Neufeld, Ecology and exploration of the rare biosphere, Nat. Rev. Microbiol, vol.13, pp.217-229, 2015.

N. Khammar, L. Malhautier, V. Degrange, R. Lensi, and J. Fanlo, Evaluation of dispersion methods for enumeration of microorganisms from peat and activated carbon biofilters treating volatile organic compounds, Chemosphere, vol.54, pp.243-254, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02569669

E. O. King, M. K. Ward, and D. E. Raney, Two simple media for the demonstration of pyocyanin and fluorescin, J. Lab. Clin. Med, vol.44, pp.301-307, 1954.

N. W. Schaad, Serological identification of plant pathogenic bacteria, Ann. Rev. Phytopathol, vol.17, pp.123-147, 1979.

P. Faye, C. Bertrand, J. Pédron, and M. Barny, Draft genomes of "Pectobacterium peruviense" strains isolated from fresh water in France, Stand. Genom. Sci, vol.13, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01922694

J. Cigna, P. Dewaegeneire, A. Beury, V. Gobert, and D. Faure, A gapA PCR-sequencing Assay for Identifying the Dickeya and Pectobacterium Potato Pathogens, Plant. Disease, vol.101, pp.1278-1282, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02192067

M. Mulet and J. Lalucat, García-Valdés, E. DNA sequence-based analysis of the Pseudomonas species, Environ. Microbiol, vol.12, pp.1513-1530, 2010.

B. Borschinger, C. Bartoli, C. Chandeysson, C. Guilbaud, L. Parisi et al., A set of PCRs for rapid identification and characterization of Pseudomonas syringae phylogroups, J. Appl. Microbiol, vol.121, p.903, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01444672

C. Guilbaud, C. E. Morris, M. Barakat, P. Ortet, and O. Berge, Isolation and identification of Pseudomonas syringae facilitated by a PCR targeting the whole P. syringae group, FEMS Microbiol. Ecol, vol.92, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02632676

E. Rochelle-newall, F. D. Hulot, J. L. Janeau, and A. Merroune, CDOM fluorescence as a proxy of DOC concentration in natural waters: A comparison of four contrasting tropical systems, Environ. Monit. Assess, vol.186, pp.589-596, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02633861

C. Fasching, A. J. Ulseth, J. Schelker, G. Steniczka, and T. J. Battin, Hydrology controls dissolved organic matter export and composition in an Alpine stream and its hyporheic zone, Limnol. Oceanogr, vol.61, pp.558-571, 2016.

C. G. Fichot and R. Benner, The spectral slope coefficient of chromophoric dissolved organic matter (S 275-295 ) as a tracer of terrigenous dissolved organic carbon in river-influenced ocean margins, Limnol. Oceanogr, vol.57, pp.1453-1466, 2012.

P. D. Schloss, S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities, Appl. Environ. Microbiol, vol.75, pp.7537-7541, 2009.

J. J. Kozich, S. L. Westcott, N. T. Baxter, S. K. Highlander, and P. D. Schloss, Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the miSeq illumina sequencing platform, Appl. Environ. Microbiol, vol.79, pp.5112-5120, 2013.

Q. Wang, G. M. Garrity, J. M. Tiedje, and J. R. Cole, Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microbiol, vol.73, pp.5261-5267, 2007.

Ø. Hammer, D. A. Harper, and D. R. Paul, Past: Paleontological Statistics Software Package for Education and Data Analysis, Palaeontol. Electron, vol.4, p.9, 2001.

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.

A. Baselga, D. Orme, S. Villger, J. Bortoli, and F. Leprieur, Partitioning Beta Diversity into Turnover and Nestedness Components, p.27, 2020.

A. Baselga, Partitioning the turnover and nestedness components of beta diversity: Partitioning beta diversity, Glob. Ecol. Biogeogr, vol.19, pp.134-143, 2010.

A. Baselga, The relationship between species replacement, dissimilarity derived from nestedness, and nestedness: Species replacement and nestedness, Glob. Ecol. Biogeogr, vol.21, pp.1223-1232, 2012.

J. J. Minich, J. G. Sanders, A. Amir, G. Humphrey, J. A. Gilbert et al., Quantifying and understanding well-to-well contamination in microbiome research, vol.4, pp.186-205, 2019.

L. Wilhelm, G. A. Singer, C. Fasching, T. J. Battin, and K. Besemer, Microbial biodiversity in glacier-fed streams, ISME J, vol.7, pp.1651-1660, 2013.

N. Hassell, K. A. Tinker, T. Moore, and E. A. Ottesen, Temporal and spatial dynamics in microbial community composition within a temperate stream network: Microbial community assembly in streams, Environ. Microbiol, vol.20, pp.3560-3572, 2018.

H. T. Le, E. Rochelle-newall, Y. Auda, O. Ribolzi, O. Sengtaheuanghoung et al., Vicinal land use change strongly drives stream bacterial community in a tropical montane catchment, FEMS Microbiol. Ecol, vol.94, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02479068

K. E. Judd, B. C. Crump, and G. W. Kling, Variation in dissolved organic matter controls bacterial production and community composition, Ecology, vol.87, pp.2068-2079, 2006.

M. Llirós, Ö. Inceoglu, 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, 2014.

O. Berge, C. L. Monteil, C. Bartoli, C. Chandeysson, C. Guilbaud et al., A user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex, PLoS ONE, vol.9, 2014.

J. Pédron, C. Bertrand, G. Taghouti, P. Portier, and M. Barny, Pectobacterium aquaticum sp. nov., isolated from waterways, Int. J. Syst. Evol. Microbiol, vol.69, pp.745-751, 2019.

P. Portier, J. Pédron, G. Taghouti, M. Fischer-le-saux, E. Caullireau et al., Elevation of Pectobacterium carotovorum subsp. odoriferum to species level as Pectobacterium odoriferum sp. nov., proposal of Pectobacterium brasiliense sp. nov. and Pectobacterium actinidiae sp. nov., emended description of Pectobacterium carotovorum and description of Pectobacterium versatile sp. nov., isolated from streams and symptoms on diverse plants, Int. J. Syst. Evol. Microbiol, vol.69, pp.3207-3216, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02335217