Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils

Abstract

Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (−0.80 ≥ P ≥ 0.80, adjusted P < 0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H++Al3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.

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

“…Prominent differences imposed by ecosystem conversion in the Amazon involve pathways related to energy metabolism and observed differences involve metabolisms of methane and nitrogen, which support previous observations (6,15,16,25,27,51). Our data demonstrate that Euryarchaeota, where known methanogens belong (25), and several known KO genes associated with methanogenesis are elevated following deforestation.…”

“…This observation has important implications. The temperature difference between our study sites(24.86•C in forest versus 27.14•C in pasture)(15) is similar to what is predicted by 2050 in the Amazon(68). While both soils are sources of greenhouse gases (nitrous oxide, nitric oxide, CO 2 , CH 4 ), increasing temperature have higher potential for the generation of these greenhouse gases from both ecosystems.…”

“…Ecologists have long studied the contribution of plant and animal communities to ecosystem functions in tropical forests (8)(9)(10) and the impact of deforestation on these communities (3,4). In contrast, microbial ecologists have just started to explore similar sets of questions in the Amazon, showing that ecosystem conversion alters bacterial (5,(11)(12)(13), archaeal (14)(15)(16) and fungal (17) community composition in various Amazonian land use types. While some studies showed that plant diversity increases overall microbial diversity (18,19) and activity in soil (20), others demonstrated the consequences of deforestation were restricted to specific functional groups of microbes or specific protein-coding genes such as those associated with C and N cycles (14,(21)(22)(23)(24)(25)(26).…”

Characterization of the fungal community in the canopy air of the invasive plant Ageratina adenophora and its potential to cause plant diseases

“…Co-occurrence patterns do not allow mapping of microbial interactions directly, but provide information on particular groups sharing habitats or performing similar ecological functions [46]. Therefore, to reveal the co-occurrence among airborne fungi, network analyses of the OTU matrix based on Spearman's Rho were calculated by the "psych" R package.…”

“…The co-occurrence among all the fungi was calculated for both LC and HC. These two valid co-occurrence events were considered to be robust if the correlation coefficient ρ > |0.8| and if they were statistically significant at P < 0.05 [46][47][48][49]. The network visualization was generated with Gephi v 0.9.2 [50].…”