Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities

Abstract

Land use change in the Amazon rainforest alters the taxonomic structure of soil microbial communities, but whether it alters their functional gene composition is unknown. We used the highly parallel microarray technology GeoChip 4.0, which contains 83,992 probes specific for genes linked nutrient cycling and other processes, to evaluate how the diversity, abundance and similarity of the targeted genes responded to forest-to-pasture conversion. We also evaluated whether these parameters were reestablished with secondary forest growth. A spatially nested scheme was employed to sample a primary forest, two pastures (6 and 38 years old) and a secondary forest. Both pastures had significantly lower microbial functional genes richness and diversity when compared to the primary forest. Gene composition and turnover were also significantly modified with land use change. Edaphic traits associated with soil acidity, iron availability, soil texture and organic matter concentration were correlated with these gene changes. Although primary and secondary forests showed similar functional gene richness and diversity, there were differences in gene composition and turnover, suggesting that community recovery was not complete in the secondary forest. Gene association analysis revealed that response to ecosystem conversion varied significantly across functional gene groups, with genes linked to carbon and nitrogen cycling mostly altered. This study indicates that diversity and abundance of numerous environmentally important genes respond to forest-to-pasture conversion and hence have the potential to affect the related processes at an ecosystem scale.

Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH

“…This was further supported by the diversity indices H= and J=, which differed significantly between continuous-corn soils (G1) and soils also currently under corn but with a different crop in preceding years (G4). Land use change alters not only free-living nitrogen-fixing microorganisms (29) but also soil ammonia oxidizer communities in agricultural systems (30), as well as the overall bacterial (31,32) and other functional gene diversity (33).…”

Power plant fuel switching and air quality in a tropical, forested environment

“…The Amazon region is of vital importance for the functioning of both regional ecosystems and climate (Fisch et al, 1998;Nobre et al, 2016). Topics for research in recent years have included the relationship between the biosphere and the atmosphere in the Amazon (Fan et al, 1990;Stark et al, 2015); the impacts of land use change (Dickinson and Kennedy, 1992;Fearnside, 2003;Paula et al, 2014;WertzKanounnikoff et al, 2016); and the consequences of urbanization, population growth, and increased anthropogenic emissions to the composition of the atmosphere (Shukla et al, 1990;Potter et al, 2001;Wright, 2005;Malhi et al, 2008;Martin et al, 2016).…”

Loss of Microbiome Ecological Niches and Diversity by Global Change and Trophic Downgrading

“…are known to alter microbiome diversity and functional traits (e.g., nitrogen (N) fixation, etc.) (Rodrigues et al 2013;Paula et al 2014). For instance, the loss of microbial diversity may reduce nitrogen cycling (Philippot et al 2013b) and other soil functions (Singh et al 2014).…”