1
|
Tschoeke DA, Coutinho FH, Leomil L, Cavalcanti G, Silva BS, Garcia GD, Dos Anjos LC, Nascimento LB, Moreira LS, Otsuki K, Cordeiro RC, Rezende CE, Thompson FL, Thompson CC. New bacterial and archaeal lineages discovered in organic rich sediments of a large tropical Bay. Mar Genomics 2020; 54:100789. [PMID: 32563694 DOI: 10.1016/j.margen.2020.100789] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 12/15/2022]
Abstract
The nutrient and oxygen gradient present in marine sediments promotes high levels of microbial diversity. We applied metagenomics and biogeochemical tools to analyze microbial communities in different sediment depths (0-4 m below sea floor, mbsf) from Guanabara Bay, Brazil, a brackish tropical ecosystem with a history of massive anthropogenic impacts, and a largely unknown sediment microbial diversity. Methanogens (e.g. Methanosarcinales, Methanomicrobiales) were more abundant at 1 mbsf, while sulphate-reducing microbes (Desulfurococcales, Thermoprotales, and Sulfolobales) were more abundant at deeper layers (4 mbsf; corresponding to 3 K Radiocarbon years before present, Holocene Epoch). Taxonomic analyzes and functional gene identification associated with anaerobic methane oxidation (e.g. monomethylamine methyltransferase (mtmB), trimethylamine methyltransferase (mttB) and CO dehydrogenase/acetyl-CoA synthase delta subunit) and sulfate reduction indicated the dominance of Campylobacteria (Sulfurimonas) at deeper sediment layers. Gene sequences related to assimilation of inorganic sulfur increased with depth, while organic sulfur related sequences decrease, accompanying the clear reduction in the concentration of sulfur, organic carbon and chla torwards deeper layers. Analyzes of metagenome assembled genomes also led to the discovery of a novel order within the phylum Acidobacteriota, named Guanabacteria. This novel order had several in silico phenotyping features that differentiate it from closely related phylogenetic neighbors (e.g. Acidobacteria, Aminicenantes, and Thermoanaerobaculum), including several genes (carbon monoxide dehydrogenase, CO dehydrogenase/CO-methylating acetyl-CoA synthase complex subunit beta, heterodisulfide reductase, sulfite exporter TauE/SafE family protein, sulfurtransferase) that relevant for the S and C cycles. Furthermore, the recovered Bathyarchaeota genome SS9 illustrates the methanogenic potential in deeper sediment layer.
Collapse
Affiliation(s)
- Diogo A Tschoeke
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Núcleo Professor Rogerio Valle de Produção Sustentável-SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Programa de Engenharia Biomédica, COPPE, CT, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
| | - Felipe H Coutinho
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Luciana Leomil
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Núcleo Professor Rogerio Valle de Produção Sustentável-SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Giselle Cavalcanti
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Núcleo Professor Rogerio Valle de Produção Sustentável-SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Bruno S Silva
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Núcleo Professor Rogerio Valle de Produção Sustentável-SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Gizele D Garcia
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Universidade Federal do Rio de Janeiro (UFRJ), Departamento de Ensino de Graduação, Campus UFRJ - Macaé Professor Aloisio Teixeira, Macaé, RJ, Brazil
| | - Leandro Candeia Dos Anjos
- Programa de Geoquímica, Departamento de Geoquímica, Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Larissa Borges Nascimento
- Programa de Geoquímica, Departamento de Geoquímica, Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Luciane S Moreira
- Programa de Geoquímica, Departamento de Geoquímica, Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Koko Otsuki
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Núcleo Professor Rogerio Valle de Produção Sustentável-SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Renato C Cordeiro
- Programa de Geoquímica, Departamento de Geoquímica, Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Carlos E Rezende
- Laboratório de Ciências Ambientais, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, UENF, RJ, Brazil
| | - Fabiano L Thompson
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Núcleo Professor Rogerio Valle de Produção Sustentável-SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Cristiane C Thompson
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Núcleo Professor Rogerio Valle de Produção Sustentável-SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
| |
Collapse
|
2
|
Zhang CJ, Pan J, Liu Y, Duan CH, Li M. Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments. MICROBIOME 2020; 8:94. [PMID: 32552798 PMCID: PMC7302380 DOI: 10.1186/s40168-020-00876-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/26/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Methanogens are crucial to global methane budget and carbon cycling. Methanogens from the phylum Euryarchaeota are currently classified into one class and seven orders, including two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales. The relative importance of the novel methanogens to methane production in the natural environment is poorly understood. RESULTS Here, we used a combined metagenomic and metatranscriptomic approach to investigate the metabolic activity of methanogens in mangrove sediments in Futian Nature Reserve, Shenzhen. We obtained 13 metagenome-assembled genomes (MAGs) representing one class (Methanofastidiosa) and five orders (Methanomassiliicoccales, Methanomicrobiales, Methanobacteriales, Methanocellales, and Methanosarcinales) of methanogens, including the two novel methanogens. Comprehensive annotation indicated the presence of an H2-dependent methylotrophic methanogenesis pathway in Methanofastidiosa and Methanomassiliicoccales. Based on the functional gene analysis, hydrogenotrophic and methylotrophic methanogenesis are the dominant pathways in mangrove sediments. MAG mapping revealed that hydrogenotrophic Methanomicrobiales were the most abundant methanogens and that methylotrophic Methanomassiliicoccales were the most active methanogens in the analyzed sediment profile, suggesting their important roles in methane production. CONCLUSIONS Partial or near-complete genomes of two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales, in natural environments were recovered and analyzed here for the first time. The presented findings highlight the ecological importance of the two novel methanogens and complement knowledge of how methane is produced in mangrove ecosystem. This study implies that two novel methanogens play a vital role in carbon cycle. Video Abstract.
Collapse
Affiliation(s)
- Cui-Jing Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Chang-Hai Duan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
| |
Collapse
|
6
|
Yu T, Liang Q, Niu M, Wang F. High occurrence of Bathyarchaeota (MCG) in the deep-sea sediments of South China Sea quantified using newly designed PCR primers. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:374-382. [PMID: 28419783 DOI: 10.1111/1758-2229.12539] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 06/07/2023]
Abstract
The archaeal phylum Bathyarchaeota, which is composed of a large number of diverse lineages, is widespread and abundant in marine sediments. Environmental factors that control the distribution, abundance and evolution of this largely diversified archaeal phylum are currently unclear. In this study, a new pair of specific primers that target the major marine subgroups of bathyarchaeotal 16S rRNA genes was designed and evaluated to investigate the distribution and abundance of Bathyarchaeota in marine sediments. The abundance of Bathyarchaeota along two sediment cores from the deep-sea sediments of South China Sea (SCS, each from the Dongsha and Shenhu area) was determined. A strong correlation was found between the bathyarchaeotal abundance and the content of total organic carbon (TOC), suggesting an important role of Bathyarchaeota in organic matter remineralisation in the sediments of SCS. Furthermore, diversity analysis revealed that subgroups Bathy-2, Bathy-8 and Bathy-10 were dominant bathyarchaeotal members of the deep-sea sediments in the SCS. Bathy-8 was found predominantly within the reducing and deeper sediment layers, while Bathy-10 occurred preferentially in the oxidizing and shallower sediment layers. Our study lays a foundation for the further understanding of the ecological functions and niche differentiation of the important but not well-understood sedimentary archaeal group.
Collapse
Affiliation(s)
- Tiantian Yu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qianyong Liang
- Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, 510070, China
| | - Mingyang Niu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|