Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers.

Miriam Gonçalves De Chaves,Siu Mui Tsai,Genivaldo Gueiros Z Silva,Raffaella Rossetto,Acacio Aparecido Navarrete,Robert Alan Edwards

doi:10.3389/fmicb.2019.01680

Abstract

Acidobacteria is a predominant bacterial phylum in tropical agricultural soils, including sugarcane cultivated soils. The increased need for fertilizers due to the expansion of sugarcane production is a threat to the ability of the soil to maintain its potential for self-regulation in the long term, in witch carbon degradation has essential role. In this study, a culture-independent approach based on high-throughput DNA sequencing and microarray technology was used to perform taxonomic and functional profiling of the Acidobacteria community in a tropical soil under sugarcane (Saccharum spp.) that was supplemented with nitrogen (N) combined with vinasse. These analyses were conducted to identify the subgroup-level responses to chemical changes and the carbon (C) degradation potential of the different Acidobacteria subgroups. Eighteen Acidobacteria subgroups from a total of 26 phylogenetically distinct subgroups were detected based on high-throughput DNA sequencing, and 16 gene families associated with C degradation were quantified using Acidobacteria-derived DNA microarray probes. The subgroups Gp13 and Gp18 presented the most positive correlations with the gene families associated with C degradation, especially those involved in hemicellulose degradation. However, both subgroups presented low abundance in the treatment containing vinasse. In turn, the Gp4 subgroup was the most abundant in the treatment that received vinasse, but did not present positive correlations with the gene families for C degradation analyzed in this study. The metabolic potential for C degradation of the different Acidobacteria subgroups in sugarcane soil amended with N and vinasse can be driven in part through the increase in soil nutrient availability, especially calcium (Ca), magnesium (Mg), potassium (K), aluminum (Al), boron (B) and zinc (Zn). This soil management practice reduces the abundance of Acidobacteria subgroups, including those potentially involved with C degradation in this agricultural soil.

Highlights

Acidobacteria are among the most widespread bacterial phyla that occur in soils around the world, including the tropical soils under sugarcane Saccharum spp. (Rachid et al, 2013; Navarrete et al, 2015a; Val-Moraes et al, 2016)
The presence of membrane transporters and the use of carbon (C) sources ranging from simple sugars to more complex substrates, such as hemicellulose, cellulose and chitin, are among the genomic and physiological characteristics that may contribute to the survival and growth of Acidobacteria in soil (Ward et al, 2009; Rawat et al, 2012)
Kielak et al (2016) recently reviewed the genomic and physiological characteristics of Acidobacteria and showed that there are still many gaps to understanding the functional role of this bacterial phylum in the soil C degradation process. Despite of this lack of biological and ecological information for Acidobacteria, previous studies in agricultural soils have shown that both microbial C degradation processes and acidobacterial community can be affected by soil management (Craine et al, 2007; Navarrete et al, 2015a; Omori et al, 2016; Wang et al, 2018; Lian et al, 2019)

Summary

Introduction

Acidobacteria are among the most widespread bacterial phyla that occur in soils around the world, including the tropical soils under sugarcane Saccharum spp. (Rachid et al, 2013; Navarrete et al, 2015a; Val-Moraes et al, 2016). Kielak et al (2016) recently reviewed the genomic and physiological characteristics of Acidobacteria and showed that there are still many gaps to understanding the functional role of this bacterial phylum in the soil C degradation process. Despite of this lack of biological and ecological information for Acidobacteria, previous studies in agricultural soils have shown that both microbial C degradation processes and acidobacterial community can be affected by soil management (Craine et al, 2007; Navarrete et al, 2015a; Omori et al, 2016; Wang et al, 2018; Lian et al, 2019). Studies from the 1980s have recommended the use of N fertilizer in combination with vinasse in sugarcane fields with high productivity

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