Unravelling the Carbon and Sulphur Metabolism in Coastal Soil Ecosystems Using Comparative Cultivation-Independent Genome-Level Characterisation of Microbial Communities

Abstract

Bacterial autotrophy contributes significantly to the overall carbon balance, which stabilises atmospheric CO2 concentration and decelerates global warming. Little attention has been paid to different modes of carbon/sulphur metabolism mediated by autotrophic bacterial communities in terrestrial soil ecosystems. We studied these pathways by analysing the distribution and abundance of the diagnostic metabolic marker genes cbbM, apsA and soxB, which encode for ribulose-1,5-bisphosphate carboxylase/oxygenase, adenosine phosphosulphate reductase and sulphate thiohydrolase, respectively, among different contrasting soil types. Additionally, the abundance of community members was assessed by quantifying the gene copy numbers for 16S rRNA, cbbL, cbbM, apsA and soxB. Distinct compositional differences were observed among the clone libraries, which revealed a dominance of phylotypes associated with carbon and sulphur cycling, such as Gammaproteobacteria (Thiohalomonas, Allochromatium, Chromatium, Thiomicrospira) and Alphaproteobacteria (Rhodopseudomonas, Rhodovulum, Paracoccus). The rhizosphere soil was devoid of sulphur metabolism, as the soxB and apsA genes were not observed in the rhizosphere metagenome, which suggests the absence or inadequate representation of sulphur-oxidising bacteria. We hypothesise that the novel Gammaproteobacteria sulphur oxidisers might be actively involved in sulphur oxidation and inorganic carbon fixation, particularly in barren saline soil ecosystems, suggesting their significant putative ecological role and contribution to the soil carbon pool.

Differential distribution and abundance of diazotrophic bacterial communities across different soil niches using a gene-targeted clone library approach

“…In our previous studies, we have analysed the comparative community structure across these habitats based on 16S rRNA and functional genes (Yousuf et al ., , b, ). Here, we envisaged the differential distribution of diazotrophs across these habitats by targeting the nifH gene.…”

“…Four distinct sites, comprising three bulk soil types, namely low saline (SS1), high saline (SS2), agriculture (AS) and one rhizospheric (RS) soil, were selected along the Arabian Sea coast, Gujarat, India, and the composite soil samples were collected in triplicate (Supporting Information, Data S1). Physicochemical characteristics (Table S1) were analysed as described previously (Yousuf et al ., , b, ).…”

“…In this study, the comparative molecular analysis of diazotrophs was performed by targeting key nitrogenase reductase enzymes of the biogeochemical nitrogen cycling pathway from coastal–saline, agricultural and rhizosphere soils. These soil niches were previously assessed for chemolithoautotrophic metabolism, using gene‐targeted metagenomics (Yousuf et al ., , b, ). The aim of the present work was to broaden our view of the diversity and abundance of nitrogen‐fixing bacterial communities and their comparative distribution among these environmental niches.…”

Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities

“…For organic sulfur assimilation, genes and pathways related to alkanesulfonate assimilation, DMSP breakdown, L-Cystine uptake/metabolism, and utilization of taurine and glutathione as a sulfur source were identified (Figure 4). Of the two sulfur oxidation pathways, the Sox is involved in complete oxidation of reduced sulfur compounds to sulphate while the APS involves adenosine-5-phosphosulphate as an intermediate [65,66]. A completely functional Sox complex includes SoxB (key component), SoxXA, SoxYZ, and SoxCD components [64,65].…”

Seasonal spatial pattern of soil respiration in a temperate urban forest in Beijing

“…Microbial sulfur oxidation is one of the vital processes for the biogeochemical sulfur cycle and is closely linked to carbon cycling (Stevenson and Cole, 1999;Yousuf et al, 2014). Sulfur addition can alter microbial allocation to enzyme production or shift the abundance of soil microbes that produce specific enzymes (Hu et al, 2013).…”