Land-use and forest floor explain prokaryotic metacommunity structuring and spatial turnover in Amazonian forest-to-pasture conversion areas

ABSTRACTAdvancing extensive cattle production shifts the forest landscape and is considered one of the main drivers against biodiversity conservation in the Brazilian Amazonia. Considering soil as an ecosystem it becomes vital to identify the effects of land-use changes on soil microbial communities, structure, as well as its ecological functions and services. Herein, we explored relationships between land-use, soil types and forest floor (i.e., association between litter, root layer and bulk soil) on the prokaryotic metacommunity structuring in the Western Amazonia. Sites under high anthropogenic pressure were evaluated along a gradient of ± 800 km. Prokaryotic metacommunity are synergistically affected by soil types and land-use systems. Especially, the gradient of soil fertility and land-use shapes the structuring of the metacommunity and determines its composition. Forest-to-pasture conversion increases alpha, beta, and gamma diversities when considering only the prokaryotes from the bulk soil. Beta diversity was significantly higher in all forests when the litter and root layer were taken into account with the bulk soil. Our argumentation is that the forest floor harbors a prokaryotic metacommunity that adds at the regional scale of diversity a spatial turnover hitherto underestimated. Our findings highlight the risks of biodiversity loss and, consequently, the soil microbial diversity maintenance in tropical forests.

Amazonian soil metagenomes indicate different physiological strategies of microbial communities in response to land use change

ABSTRACTDespite the global importance in ecological processes, the Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. In this study, we used a combination of deep shotgun metagenomics and a machine learning approach to compare physiological strategies of microbial communities between contrasting forest and pasture soils. We showed that microbial communities (bacteria, archaea and viruses), and the composition of protein-coding genes are distinct in each ecosystem. The diversities of these metagenomic datasets are strongly correlated, indicating that the protein-coding genes found in any given sample of these soil types are predictable from their taxonomic lineages. Shifts in metagenome profiles reflected potential physiological differences caused by forest-to-pasture conversion with alterations in gene abundances related to carbohydrate and energy metabolisms. These variations in these gene contents are associated with several soil factors including C/N, temperature and H++Al3+ (exchangeable acidity). These data underscore that microbial community taxa and protein-coding genes co-vary. Differences in gene abundances for carbohydrate utilization, energy, amino acid, and xenobiotic metabolisms indicate alterations of physiological strategy with forest-to-pasture conversion, with potential consequences to C and N cycles. Our analysis also indicated that soil virome was altered and shifts in the viral community provide insights into increased health risks to human and animal populations.

The natural recovery of soil microbial community and nitrogen functions after pasture abandonment in the Amazon region

ABSTRACT We assessed the impacts of forest-to-pasture conversion on the dynamic of soil microbial communities, especially those involved in the N-cycle, and their potential functions, using DNA-metagenomic sequencing coupled with the quantification of marker genes for N-cycling. We also evaluated whether the community's dynamic was reestablished with secondary forest growth. In general, the microbial community structure was influenced by changes in soil chemical properties. Aluminum and nitrate significantly correlated to community structure and with 12 out of 21 microbial phyla. The N-related microbial groups and their potential functions were also affected by land-use change, with pasture being clearly different from primary and secondary forest systems. The microbial community analysis demonstrated that forest-to-pasture conversion increased the abundance of different microbial groups related to nitrogen fixation, including Bacteroidetes, Chloroflexi and Firmicutes. In contrast, after pasture abandonment and with the secondary forest regeneration, there was an increase in the abundance of Proteobacteria taxa and denitrification genes. Our multi-analytical approach indicated that the secondary forest presented some signs of resilience, suggesting that the N-related microbial groups and their potential functions can be recovered over time with implications for future ecological restoration programs.