Insights into the Genomic Potential of a Methylocystis sp. from Amazonian Floodplain Sediments

Author(s)

Gontijo, Julia B. ; Paula, Fabiana S. ; Venturini, Andressa M. ; Mandro, Jessica A. ; Bodelier, Paul L. E. ; Tsai, Siu M.

• Document type: Journal article
• Source: MICROORGANISMS; v. 10, n. 9, p. 11-pg., 2022-09-01.

Abstract

Although floodplains are recognized as important sources of methane (CH4) in the Amazon basin, little is known about the role of methanotrophs in mitigating CH4 emissions in these ecosystems. Our previous data reported the genus Methylocystis as one of the most abundant methanotrophs in these floodplain sediments. However, information on the functional potential and life strategies of these organisms living under seasonal flooding is still missing. Here, we described the first metagenome-assembled genome (MAG) of a Methylocystis sp. recovered from Amazonian floodplains sediments, and we explored its functional potential and ecological traits through phylogenomic, functional annotation, and pan-genomic approaches. Both phylogenomics and pan-genomics identified the closest placement of the bin.170_fp as Methylocystis parvus. As expected for Type II methanotrophs, the Core cluster from the pan-genome comprised genes for CH4 oxidation and formaldehyde assimilation through the serine pathway. Furthermore, the complete set of genes related to nitrogen fixation is also present in the Core. Interestingly, the MAG singleton cluster revealed the presence of unique genes related to nitrogen metabolism and cell motility. The study sheds light on the genomic characteristics of a dominant, but as yet unexplored methanotroph from the Amazonian floodplains. By exploring the genomic potential related to resource utilization and motility capability, we expanded our knowledge on the niche breadth of these dominant methanotrophs in the Amazonian floodplains. (AU)

• FAPESP's process: 18/14974-0 - Dynamics of methane and sulfur microbial communities in Amazonian soils
• Grantee: Júlia Brandão Gontijo
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 14/50320-4 - Dimensions US-BIOTA - São Paulo: collaborative research: integrating dimensions of microbial biodiversity across land use change in tropical forests
• Grantee: Tsai Siu Mui
• Support Opportunities: BIOTA-FAPESP Program - Thematic Grants
• FAPESP's process: 17/26138-0 - Taxonomic and functional evaluations of microbial community involved in methane cycling of Brazilian Amazon soils
• Grantee: Fabiana da Silva Paula
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 19/25924-7 - Desvendando as interações metabólicas e ecológicas entre os ciclos do CH4 e S em áreas inundáveis da Amazônia
• Grantee: Júlia Brandão Gontijo
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• FAPESP's process: 19/25931-3 - Taxonomic and functional depiction of the microbial community involved in methane transformations in soils of the Brazilian Amazonia
• Grantee: Andressa Monteiro Venturini
• Support Opportunities: Scholarships in Brazil - Post-Doctoral