We acknowledge the Molecular Core Facility and the Cytometry Core Facility at the University of La Rochelle. Authors are grateful to A. Leynaert (LEMAR, Brest, ...
C3 group: a rare but active Thaumarchaeal group in intertidal muddy sediment Agogué Hélène 1, Hugoni Mylène2, Dupuy Christine1 and Lavergne Céline1 1
2
Littoral, Environnement et Sociétés (LIENSS) UMR 7266 CNRS – Université de La Rochelle, La Rochelle, France ‘Microorganismes: Génome et Environnement’ laboratory (LMGE) UMR 6023 CNRS- Université Blaise Pascal, 63000 Clermont-Ferrand, France
Prokaryotic communities in coastal zones vary greatly in space and time because of sharp gradients in salinity and nutrients (1, 2). In these benthic coastal systems, fluctuations in composition vary temporally and spatially, with a vertical-related depth influence (1, 3). During low tide, the vertical stratification of prokaryotic communities is under strong pressures : stochastic events such as storms, rain or hail; deterministic parameters as organic carbon availability (1), inorganic nutrient enrichment (4) or microphytobenthic activity (primary production, production of labile organic matter and nutrient uptake) (5). Additionally, the overall sedimentary stratification could be disturbed by bioturbation (6). Finally, sediment stability should be modified by hydrodynamic pressures such as wind or wave action (7).
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Experimental procedures • Sampling site : Brouage mudflat located in the Bay of Marennes-Oléron
Field survey
Sampling strategy
Pyrosequencing 16S rRNA gene
D1: Biofilm D2: 0.5-1 cm D3: 1-2 cm
Mesocosm experiment
D4: 2-5 cm
D5: 5-10 cm
Macrofaune removal No resuspension Irradiance control (Day/Night: 15h/9h) Tide control (6h:6h)
Pyrosequencing 16S rRNA transcripts
Among vertical sediment depth, do Archaea have different ecological niches ?
Total archaeal communities
Depth stratification Thaum
Eury
C3 group abundance stable throughout all the sediment depths (13 %) Archaea were distributed among specific ecological niches defined by depth stratification and associated with major biogeochemical cycles such as nitrogen, sulphur and carbon.
Active archaeal communities
VS Eury
Thaum
C3
Clear vertical-depth pattern : 2 horizons (shift Thaum (MGI)/C3 group at 5 cm depth) C3 group : 72 % at 5-10 cm depth (10 % at sediment surface) Suggesting drastic modification in sediment properties (as C3 group supposed to be specific to anoxic sediment)
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Phylogenetic tree of the 16S rRNA transcript sequences derived from the 454 pyrosequencing from samples of muddy sediments in mesocosm experiment. Sequences were analysed using the ARB software package (version July 2014) (8) and the corresponding SILVA SSUREF 99 database (9). The tree was first generated with 1050 sequences (>1200 bp) using Neighbour-joining (1000 bootstraps) and maximum likelyhood (100 runs) techniques. The final tree was calculated with 361 sequences (300-400 bp) using a variable position filter with Neighbour joining (model: kimura), bootstrapping method (1000 replications). The final topology of the tree was in accordance with initial tree topology.
C3 = rare but active
Conclusion
This C3 group is considered as Miscellaneous Crenarchaeotic Group (MCG) (10, 11), it is also specifically named “MCG-15 group” by Kubo et al. (12). Our study show that C3 group is putatively affiliated to Thaumarchaea but seems not belonging to MCG cluster. No member has been cultivated until now and no functional role was assigned to this group. Our work show that they may not express archaeal amoA (data not shown). Specific habitat = anoxic sediment Fine phylogenetic analyses of full-length 16S clones sequences of the C3 group should be done in order to taxonomically classify this group in the archaeal phylum.
References 1.Böer SI, et al (2009) Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. ISME J 3: 780-791. 2.Herlemann DPR, et al (2011) Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J 5: 1571-1579. 3.Gobet A, et al (2012) Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME J 6: 542-553. 4.Hewson I, et al (2003) Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: effects of virus infection, containment, and nutrient enrichment. Microb Ecol 46: 322-336. 5.Risgaard-Petersen N (2003) Coupled nitrification-denitrification in autotrophic and heterotrophic estuarine sediments: On the influence of benthic microalgae. Limnol Oceanogr 48: 93-105. 6.Laverock B, et al (2011) Bioturbation: Impact on the marine nitrogen cycle. Biochemical Society Transactions 39: 315-320. 7.Friend P, et al (2005) Day–night variation of cohesive sediment stability. Estuarine, Coastal and Shelf Science 64: 407-418. 8.Ludwig W, et al (2004) ARB: a software environment for sequence data. Nucleic Acids Research 32: 1363-1371. 9.Yilmaz P, et al (2014) The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Research 42: D643-D648. 10.Inagaki F, et al (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc Natl Acad Sci USA 103: 2815-2820. 11.Hirayama H, et al (2007) Culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off Taketomi Island, Japan. Appl Environ Microbiol 73: 7642-7656. 12.Kubo K, et al (2012) Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments. ISME J. 6: 1949-1965.
Acknowledgements This research was supported by a PhD grant from the Charente Maritime Department to C. L. and by the national program CPER 2007-2013 (Contrat Projet Etat Région) of Charente Maritime, the French national program EC2CO (CAPABIOC, 2012-2014), and the CNRS organism. We acknowledge the Molecular Core Facility and the Cytometry Core Facility at the University of La Rochelle. Authors are grateful to A. Leynaert (LEMAR, Brest, France) for the rhizons technique, to P. Pineau (LIENSs, La Rochelle, France) for the nutrient measurement and to N. Lachaussée, L. Beaugeard, V. Becquet, M. Bréret (LIENSs, La Rochelle, France) for sampling. Authors are also grateful to M. Prineau (LIENSs, La Rochelle, France) for electricity improvement. We want to thank N. Taib and JC. Charvy (LMGE, Clermont-Ferrand, France) for their help during PANAM data analysis. Authors also received help for genetic dataset manipulation from E. Panté (LIENSs, La Rochelle, France).
