Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado?

Abstract

BackgroundThe Cerrado—an edaphic type of savannah— comprises the second largest biome of the Brazilian territory and is the main area for grain production in the country, but information about the impact of land conversion to agriculture on microbial diversity is still scarce. We used a shotgun metagenomic approach to compare undisturbed (native) soil and soils cropped for 23 years with soybean/maize under conservation tillage—“no-till” (NT)—and conventional tillage (CT) systems in the Cerrado biome.ResultsSoil management and fertilizer inputs with the introduction of agriculture improved chemical properties, but decreased soil macroporosity and microbial biomass of carbon and nitrogen. Principal coordinates analyses confirmed different taxonomic and functional profiles for each treatment. There was predominance of the Bacteria domain, especially the phylum Proteobacteria, with higher numbers of sequences in the NT and CT treatments; Archaea and Viruses also had lower numbers of sequences in the undisturbed soil. Within the Alphaproteobacteria, there was dominance of Rhizobiales and of the genus Bradyrhizobium in the NT and CT systems, attributed to massive inoculation of soybean, and also of Burkholderiales. In contrast, Rhizobium, Azospirillum, Xanthomonas, Pseudomonas and Acidobacterium predominated in the native Cerrado. More Eukaryota, especially of the phylum Ascomycota were detected in the NT. The functional analysis revealed lower numbers of sequences in the five dominant categories for the CT system, whereas the undisturbed Cerrado presented higher abundance.ConclusionHigh impact of agriculture in taxonomic and functional microbial diversity in the biome Cerrado was confirmed. Functional diversity was not necessarily associated with taxonomic diversity, as the less conservationist treatment (CT) presented increased taxonomic sequences and reduced functional profiles, indicating a strategy to try to maintain soil functioning by favoring taxa that are probably not the most efficient for some functions. Our results highlight that underneath the rustic appearance of the Cerrado vegetation there is a fragile soil microbial community.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0657-z) contains supplementary material, which is available to authorized users.

Microbial energy and matter transformation in agricultural soils

“…Conversion of forest to agriculture, pasture or deforestation all lead to significant changes in the abundance of functional genes associated with respiration (Mendes et al, 2015). In regard to agricultural management practices, the relative abundance of respiratory functional genes increases in no tillage cropping systems compared to native ecosystem (Souza et al, 2016). However, where SOM and MBC had significantly decreased under 23 years of conventional tillage, decreases in the relative abundance of respiratory functional genes compared to native ecosystem occurred (Souza et al, 2016).…”

“…In regard to agricultural management practices, the relative abundance of respiratory functional genes increases in no tillage cropping systems compared to native ecosystem (Souza et al, 2016). However, where SOM and MBC had significantly decreased under 23 years of conventional tillage, decreases in the relative abundance of respiratory functional genes compared to native ecosystem occurred (Souza et al, 2016). Increasing N fertilisation (across gradients of 0e291 kg N ha À1 year À1 ) increases the relative abundance of ubiquinonecytochrome reductase complexes and F 0 F 1 ATP synthase (Fierer et al, 2012), similar to shifts observed in Table 2.…”

Microbiome engineering: Current applications and its future

“…Navarrete et al [7] reported taxonomic and functional adaptations in soil microbiome after deforestation in the Amazon region and these adaptations typically result in increased soil fertility. Other agricultural practices, such as logging [43], tillage [44] and cropping systems [45,46], also play roles in effecting structural and functional changes in soil microbiome that lead to changes in soil functions. As many of the discussed agricultural management practices have been implemented for decades with success, recent efforts in understanding their effects on soil microbiota composition would enable rational engineering of the soil microbiome to optimize these practices for improved crops.…”

“…Agricultural management Soil Organic farming, changing land usage, logging, tillage, cropping [7,[41][42][43][44][45][46] Improve soil fertility • Alter structure and function of soil microbiome;…”

Surveying the sweetpotato rhizosphere, endophyte, and surrounding soil microbiomes at two North Carolina farms reveals underpinnings of sweetpotato microbiome community assembly

“…The Alphaproteobacteria clade of balance 'n138' also possesses a number of Sphingomonadales ASVs. BothSphingomonadales and Rhizobiales have been shown to increase in relative abundance when land is used for agriculture(Souza et al 2016) and Sphingomonadales was among a number of groups shown to previously increase in relative abundance in the sweetpotato rhizosphere(Marques et al 2014) .…”