Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils

Abstract

Amazonian soil microbial communities are known to be affected by the forest-to-pasture conversion, but the identity and metabolic potential of most of their organisms remain poorly characterized. To contribute to the understanding of these communities, here we describe metagenome-assembled genomes (MAGs) recovered from 12 forest and pasture soil metagenomes of the Brazilian Eastern Amazon. We obtained 11 forest and 30 pasture MAGs (≥50% of completeness and ≤10 % of contamination), distributed among two archaeal and 11 bacterial phyla. The taxonomic classification results suggest that most MAGs may represent potential novel microbial taxa. MAGs selected for further evaluation included members of Acidobacteriota, Actinobacteriota, Desulfobacterota_B, Desulfobacterota_F, Dormibacterota, Eremiobacterota, Halobacteriota, Proteobacteria, and Thermoproteota, thus revealing their roles in carbohydrate degradation and mercury detoxification as well as in the sulphur, nitrogen, and methane cycles. A methane-producing Archaea of the genus Methanosarcina was almost exclusively recovered from pasture soils, which can be linked to a sink-to-source shift after the forest-to-pasture conversion. The novel MAGs constitute an important resource to help us unravel the yet-unknown microbial diversity in Amazonian soils and its functional potential and, consequently, the responses of these microorganisms to land-use change.

Keywords: land-use change; forest-to-pasture conversion; metagenome-assembled genomes; methane cycle; nitrogen cycle; soil microbial communities.

Fig. 1.

Taxonomic classification (at the domain and phylum levels) and quality (based on completeness and contamination scores) of the metagenome-assembled genomes (MAGs) from the merged forest and pasture metagenomes.

Fig. 2.

Relative abundance (%) of each selected metagenome-assembled genome (MAG) in the merged forest and pasture metagenomes. The MAGs were selected based on their completeness (>90 %) and contamination (<5 %) scores. Bin.006_Pasture and Bin.035_Pasture were also included due to their environmental relevance.

Fig. 3.

DRAM annotations of the selected forest and pasture metagenome-assembled genomes (MAGs). The MAGs were selected based on their completeness (>90 %) and contamination (<5 %) scores. Bin.006_Pasture and Bin.035_Pasture were also included due to their environmental relevance. The colours in the heatmap represent the completeness of relevant pathways and electron transport chain complexes in each MAG. The heatmap was created based on the DRAM output figure and only depicts modules that were present in at least one MAG. The list of genes associated with each module is available at https://www.doi.org/10.25982/91640.61/1870603.

Fig. 4.

DRAM annotations of the selected forest and pasture metagenome-assembled genomes (MAGs). The MAGs were selected based on their completeness (>90 %) and contamination (<5 %) scores. Bin.006_Pasture and Bin.035_Pasture were also included due to their environmental relevance. The colours in the heatmap represent the presence or absence of relevant metabolic functions in each MAG. The heatmap was created based on the DRAM output figure and only depicts modules that were present in at least one MAG. The list of genes associated with each module is available at https://www.doi.org/10.25982/91640.61/1870603. CAZy, carbohydrate-active enzymes; metab., metabolism; red., reductases; SCFA, short-chain fatty acids.