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Luis P, Saint-Genis G, Vallon L, Bourgeois C, Bruto M, Marchand C, Record E, Hugoni M. Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments. Environ Microbiol 2019; 21:1407-1424. [PMID: 30807675 DOI: 10.1111/1462-2920.14571] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/20/2019] [Accepted: 02/23/2019] [Indexed: 11/29/2022]
Abstract
Mangroves are forest ecosystems located at the interface between land and sea where sediments presented a variety of contrasted environmental conditions (i.e. oxic/anoxic, non-sulfidic/sulfidic, organic matter content) providing an ideal ecosystem to study microbial communities with niche differentiation and distinct community structures. In this work, prokaryotic and fungal compositions were investigated during both wet and dry seasons in New Caledonian mangrove sediments, from the surface to deeper horizons under the two most common tree species in this region (Avicennia marina and Rhizophora stylosa), using high-throughput sequencing. Our results showed that Bacteria and Archaea communities were mainly shaped by sediment depth while the fungal community was almost evenly distributed according to sediment depth, vegetation cover and season. A detailed analysis of prokaryotic and fungal phyla showed a dominance of Ascomycota over Basidiomycota whatever the compartment, while there was a clear shift in prokaryotic composition. Some prokaryotic phyla were enriched in surface layers such as Proteobacteria, Euryarchaeota while others were mostly associated with deeper layers as Chloroflexi, Bathyarchaeota, Aminicenantes. Our results highlight the importance of considering fungal and prokaryotic counterparts for a better understanding of the microbial succession involved in plant organic matter decomposition in tropical coastal sediments.
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Affiliation(s)
- Patricia Luis
- CNRS, UMR5557; Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
| | - Geoffroy Saint-Genis
- CNRS, UMR5557; Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
| | - Laurent Vallon
- CNRS, UMR5557; Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
| | - Carine Bourgeois
- IMPMC, Institut de Recherche pour le Développement (IRD), UPMC, CNRS, MNHN, Noumea, New Caledonia, France
| | - Maxime Bruto
- UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, CS 90074, F-29688, Roscoff Cedex, France
| | - Cyril Marchand
- IMPMC, Institut de Recherche pour le Développement (IRD), UPMC, CNRS, MNHN, Noumea, New Caledonia, France.,ISEA, EA, Université de la Nouvelle-Calédonie (UNC), 3325, BP R4, 98851, Noumea, New Caledonia, France
| | - Eric Record
- INRA, Aix-Marseille Université, UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France
| | - Mylène Hugoni
- CNRS, UMR5557; Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
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Liu CH, Huang X, Xie TN, Duan N, Xue YR, Zhao TX, Lever MA, Hinrichs KU, Inagaki F. Exploration of cultivable fungal communities in deep coal-bearing sediments from ∼1.3 to 2.5 km below the ocean floor. Environ Microbiol 2017; 19:803-818. [DOI: 10.1111/1462-2920.13653] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 12/14/2016] [Accepted: 12/19/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Chang-Hong Liu
- State Key of Pharmaceutical Biotechnology, School of Life Science; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Xin Huang
- State Key of Pharmaceutical Biotechnology, School of Life Science; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Tian-Ning Xie
- State Key of Pharmaceutical Biotechnology, School of Life Science; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Ning Duan
- State Key of Pharmaceutical Biotechnology, School of Life Science; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Ya-Rong Xue
- State Key of Pharmaceutical Biotechnology, School of Life Science; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Tan-Xi Zhao
- State Key of Pharmaceutical Biotechnology, School of Life Science; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Mark A. Lever
- Department of Environmental Systems Science, ETH Zürich; Institute of Biogeochemistry and Pollutant Dynamics; Zürich CH-8092 Switzerland
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences; University of Bremen; Bremen D-28359 Germany
| | - Fumio Inagaki
- Kochi Institute for Core Sample Research; Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Nankoku Kochi 783-8502 Japan
- Research and Development Center for Ocean Drilling Science, JAMSTEC; Yokohama 236-0061 Japan
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