Abstract
Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change.
Highlights
The Amazon Basin contains the largest continuous tropical rainforest on the planet (Laurance et al, 2001) and is home to unparalleled levels of plant and animal diversity (Da Silva et al, 2005)
The sequence alignment map (SAM) files were converted to a binary format (BAM) that were imported into the Anvi’o 2.0 pipeline along with the metagenomic co-assembly for genomic binning using sequence composition and differential mean coverage (Li et al, 2009; Eren et al, 2015)
With land-use change from rainforest to pasture there was a significant change in soil geochemistry with increases in acidic potential, and in organic matter, copper, iron, and zinc concentrations in the cattle pasture, while boron and aluminum concentrations were significantly higher in rainforest soil (Supplementary Table S3)
Summary
The Amazon Basin contains the largest continuous tropical rainforest on the planet (Laurance et al, 2001) and is home to unparalleled levels of plant and animal diversity (Da Silva et al, 2005). Few studies have successfully performed genome-resolved metagenomics on soil and among those, some have perturbed the community composition prior to sampling to lower the complexity of the microbial communities (Delmont et al, 2015; Yeoh et al, 2015), while others have assembled MAGs without manipulation (Butterfield et al, 2016; White et al, 2016; Tas et al, 2018). Despite these recent metagenomic accomplishments, the genomic content of most microbial populations inhabiting soil from the Amazon basin and elsewhere have yet to be characterized. Does our study begin to depict the genomic and functional potential of poorly understood phyla, but it increases our understanding of understudied tropical microbial biodiversity
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