Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India

Abstract

BackgroundSoils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to CO2 dynamics in soil. In this study, we used culture dependent and independent methods to assess the community structure and diversity of chemolithoautotrophs in agricultural and coastal barren saline soils (low and high salinity). We studied the composition and distribution of chemolithoautotrophs by means of functional marker gene cbbL encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and a phylogenetic marker 16S rRNA gene. The cbbL form IA and IC genes associated with carbon fixation were analyzed to gain insight into metabolic potential of chemolithoautotrophs in three soil types of coastal ecosystems which had a very different salt load and sulphur content.ResultsIn cbbL libraries, the cbbL form IA was retrieved only from high saline soil whereas form IC was found in all three soil types. The form IC cbbL was also amplified from bacterial isolates obtained from all soil types. A number of novel monophyletic lineages affiliated with form IA and IC phylogenetic trees were found. These were distantly related to the known cbbL sequences from agroecosystem, volcanic ashes and marine environments. In 16S rRNA clone libraries, the agricultural soil was dominated by chemolithoautotrophs (Betaproteobacteria) whereas photoautotrophic Chloroflexi and sulphide oxidizers dominated saline ecosystems. Environmental specificity was apparently visible at both higher taxonomic levels (phylum) and lower taxonomic levels (genus and species). The differentiation in community structure and diversity in three soil ecosystems was supported by LIBSHUFF (P = 0.001) and UniFrac.ConclusionThis study may provide fundamentally new insights into the role of chemolithoautotrophic and photoautotrophic bacterial diversity in biochemical carbon cycling in barren saline soils. The bacterial communities varied greatly among the three sites, probably because of differences in salinity, carbon and sulphur contents. The cbbL form IA-containing sulphide-oxidizing chemolithotrophs were found only in high saline soil clone library, thus giving the indication of sulphide availability in this soil ecosystem. This is the first comparative study of the community structure and diversity of chemolithoautotrophic bacteria in coastal agricultural and saline barren soils using functional (cbbL) and phylogenetic (16S rDNA) marker genes.

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

“…This study is complementary to a previously performed determination of community structure at these sites based on 16S rRNA and cbbL genes [22]–[23]. The aim of the present work was to broaden our view on the diversity and abundance of alternative modes of autotrophic metabolism.…”

Production and Characterization of Melanin from Streptomyces Cavourensis Strain RD8 Using Response Surface Optimization

“…GoK is an exclusive niche which nurtures diverse microorganisms with unique properties that can survive under stress conditions (Yousuf et al, 2012). Many reports are available on the marine actinomycetes isolated from the west coast of India, however, according to our knowledge; this is the first investigation reporting on the melanin production from actinomycetes isolated from GoK.…”

Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China

“…Shannon and Simpson diversity indices, as well as Chao and ACE richness estimators, were calculated using Mothur software to estimate bacterial diversity and richness. Rarefaction curves and diversity indices including microbial community diversity, phylogenetic diversity (Faith's PD) and coverage were calculated in Mothur (Yousuf et al, 2012).…”