Abstract
Microbial-driven organic matter (OM) degradation is a cornerstone of benthic community functioning, but little is known about the relation between OM and community composition. Here we use Rhône prodelta sediments to test the hypothesis that OM quality and source are fundamental structuring factors for bacterial communities in benthic environments. Sampling was performed on four occasions corresponding to contrasting river-flow regimes, and bacterial communities from seven different depths were analyzed by pyrosequencing of 16S rRNA gene amplicons. The sediment matrix was characterized using over 20 environmental variables including bulk parameters (for example, total nitrogen, carbon, OM, porosity and particle size), as well as parameters describing the OM quality and source (for example, pigments, total lipids and amino acids and δ13C), and molecular-level biomarkers like fatty acids. Our results show that the variance of the microbial community was best explained by δ13C values, indicative of the OM source, and the proportion of saturated or polyunsaturated fatty acids, describing OM lability. These parameters were traced back to seasonal differences in the river flow, delivering OM of different quality and origin, and were directly associated with several frequent bacterial operational taxonomic units. However, the contextual parameters, which explained at most 17% of the variance, were not always the key for understanding the community assembly. Co-occurrence and phylogenetic diversity analysis indicated that bacteria–bacteria interactions were also significant. In conclusion, the drivers structuring the microbial community changed with time but remain closely linked with the river OM input.
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Acknowledgements
We thank Christophe Rabouille, chief scientist of the MESURHOBENT cruises and coordinator of the MERMEX-RIVERS program. We thank the captain and crew of the RV Tethys II, as well as numerous colleagues, for their hard work at sea and in the laboratory. In particular, we thank Béatrice Rivière and Lionel Feuillassier from LECOB for their help with pigment and grain size analyses. Pigment concentration calculations were made using the calibration developed by François Lantoine (LECOB). We are grateful to Matthew Oliver (University of Delaware, USA) for help with R scripts for the MIC analysis, to Jeff Ghiglione and Dimitri Kalenitchenko for help with statistical analysis and Marcelino T Suzuki for his help with installing and updating QIIME and Mothur on local computer servers. Access to molecular biology instrumentation and facilities were provided through the BIO2MAR platform (http://bio2mar.obs-banyuls.fr). This research was funded by the French program MISTRALS/MERMEX, the CNRS, UPMC and in part by the ECOPOP project led by FC in the framework of ‘EC2CO/CNRS-INSU’. SB was supported by a grant from the French Ministry of Research. PEG and SKF were supported by the Agence Nationale de la Recherche (ANR) project MICADO (ANR-11JSV7-003-01). Rhône River discharge data were provided by the server Inforhône of the “Compagnie Nationale du Rhône” (CNR). The material is original work and has not been submitted for publication elsewhere.
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Fagervold, S., Bourgeois, S., Pruski, A. et al. River organic matter shapes microbial communities in the sediment of the Rhône prodelta. ISME J 8, 2327–2338 (2014). https://doi.org/10.1038/ismej.2014.86
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