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. 2012 Jul 26:12:150.
doi: 10.1186/1471-2180-12-150.

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

Basit Yousuf  1 , Payal Sanadhya, Jitendra Keshri, Bhavanath Jha
Affiliations

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

Basit Yousuf et al. BMC Microbiol. .

Abstract

Background: Soils 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.

Results: In 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.

Conclusion: This 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.

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Figures

Figure 1
Figure 1
Phylogenetic analysis of green likecbbLclones. Neighbour-joining tree (Jukes–Cantor correction) was constructed from saline soil (SS2) clone library partial cbbL (form IA) nucleic acid sequences (phylotypes) with closely related cbbL-gene sequences from known organisms and environmental clones. Clone sequences of form IA cbbL sequence are coded as ‘RG’. One representative phylotype is shown followed by phylotype number and the number of clones within each phylotype is shown at the end. One thousand bootstrap analyses were performed and percentages are shown at nodes. The scale bar indicates 0.05 substitutions per site. The red-like cbbL sequence of Xanthobacter autotrophicus was used as outgroup for tree calculations.
Figure 2
Figure 2
Phylogenetic analysis of red likecbbLclones. A composite neighbour joining tree (Jukes-Cantor correction) was constructed from aligned nucleotide sequences (phylotypes) of form IC cbbL-gene obtained from agricultural soil ‘AS’ and barren saline soils ‘SS1 & SS2’ with closely related cbbL-gene sequences from known organisms and environmental clones. Bootstrap values are shown as percentages of 1000 bootstrap replicates. The bar indicates 5% estimated sequence divergence. One representative phylotype is shown followed by phylotype number and the number of clones within each phylotype is shown at the end. Clone sequences from this study are coded as ‘BS’ (AS), ‘HS’ (SS1) and ‘R’ (SS2). The cbbL-gene sequences of the isolates from this study are denoted as ‘BSC’, ‘HSC’ and ‘RSC’ from AS, SS1 and SS2 respectively. The green-like cbbL-gene sequence of Methylococcus capsulatus was used as outgroup for tree calculations.
Figure 3
Figure 3
Taxonomic distribution of different bacterial phylogenetic groups in agricultural soil (AS) and saline soils (SS1, SS2). Analysis of amplified 16S rRNA gene sequences was done in comparison with the RDP II database (match length >1200 nucleotides). The percentages of the phylogenetically classified sequences are plotted on y-axis.
Figure 4
Figure 4
UniFrac PCA ofcbbLand 16S rRNA clone libraries. The ordination plots for the first two dimensions to show the relationship between agricultural and the saline soils for (a) cbbL and (b) 16S rRNA gene assemblages. Agricultural soil (AS) is represented by square and saline soils is represented by diamond (SS1) and circle (SS2). Each axis indicates the fraction of the variance in the data that the axis accounts for.
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