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

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.

Soil Microbial Indicators within Rotations and Tillage Systems

“…Relatively little information exists for the Holophagae (C) Subgroup 7 (O), except that RAs were found to be positively correlated with a legume treatment compared to grass [73], with pH [74], and negatively correlated to SOM [75]. Acidobacteria (P) and many of their subgroup RAs were negatively correlated to nutrient levels and associated with C degradation [76]. Navarrete et al [77] found that Subgroup 25 (C) was only found in soybean rhizospheric soil, not in their forest comparison site.…”

High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests

“…This was based on the assumption that only a small fraction would be able to grow in the synthetic VL55 medium (pH 5.5) supplemented with xylan as the only carbon source, a medium already shown to be suitable for the cultivation of Acidobacteria ( Campanharo et al, 2016 ). This medium suppresses the growth of bacteria that cannot grow on complex carbon sources at low pH, and therefore favors the growth of the majority of Acidobacteria ( Belova et al, 2018 ; de Chaves et al, 2019 ). Furthermore, Acidobacteria appear to thrive when presented with a lower concentration of trace elements than normally found in complex media ( de Chaves et al, 2019 ).…”

“…This medium suppresses the growth of bacteria that cannot grow on complex carbon sources at low pH, and therefore favors the growth of the majority of Acidobacteria ( Belova et al, 2018 ; de Chaves et al, 2019 ). Furthermore, Acidobacteria appear to thrive when presented with a lower concentration of trace elements than normally found in complex media ( de Chaves et al, 2019 ). An additional advantage of the process described here is its ability to propagate the cultures quickly in order to reduce the risk of competition from faster-growing bacteria that take longer to become established due to the chosen medium, such as certain Proteobacteria ( George et al, 2011 ; Campanharo et al, 2016 ).…”

Distribution of Microbial Generalists and Habitat Specialists in Soils Along a Climate Gradient in the Chilean Coastal Cordillera

“…The distribution of Subgroup 2 in global forest soils is well documented [90,95], but little is known about the metabolic potential. De Chaves et al [96] recently discussed that the occurrence of this group is not triggered by N fertilization, as this is a common feature of Acidobacteria, but obtained a positive correlation with aluminium. Furthermore, we obtained an endosymbiotic representative of nematodes (Candidatus Xiphinematobacter) [97], which is a well-known inhabitant of Chilean soils [98].…”