Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India
<p>Abstract</p> <p>Background</p> <p>Soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to CO<sub>2</sub> dynamics in soil. In this study, we used culture dependent and independent met...
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BMC
2012-07-01
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| Series: | BMC Microbiology |
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| Online Access: | http://www.biomedcentral.com/1471-2180/12/150 |
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| author | Yousuf Basit Sanadhya Payal Keshri Jitendra Jha Bhavanath |
| author_facet | Yousuf Basit Sanadhya Payal Keshri Jitendra Jha Bhavanath |
| author_sort | Yousuf Basit |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to CO<sub>2</sub> 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 <it>cbbL</it> encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and a phylogenetic marker 16S rRNA gene. The <it>cbbL</it> 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.</p> <p>Results</p> <p>In <it>cbbL</it> libraries, the <it>cbbL</it> form IA was retrieved only from high saline soil whereas form IC was found in all three soil types. The form IC <it>cbbL</it> 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 <it>cbbL</it> sequences from agroecosystem, volcanic ashes and marine environments. In 16S rRNA clone libraries, the agricultural soil was dominated by chemolithoautotrophs (<it>Betaproteobacteria</it>) whereas photoautotrophic <it>Chloroflexi</it> 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 (<it>P</it> = 0.001) and UniFrac.</p> <p>Conclusion</p> <p>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 <it>cbbL</it> 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 (<it>cbbL</it>) and phylogenetic (16S rDNA) marker genes.</p> |
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| spelling | doaj.art-f4f2c44e557d488fb4e38993c83eb73c2022-12-22T03:28:09ZengBMCBMC Microbiology1471-21802012-07-0112115010.1186/1471-2180-12-150Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, IndiaYousuf BasitSanadhya PayalKeshri JitendraJha Bhavanath<p>Abstract</p> <p>Background</p> <p>Soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to CO<sub>2</sub> 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 <it>cbbL</it> encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and a phylogenetic marker 16S rRNA gene. The <it>cbbL</it> 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.</p> <p>Results</p> <p>In <it>cbbL</it> libraries, the <it>cbbL</it> form IA was retrieved only from high saline soil whereas form IC was found in all three soil types. The form IC <it>cbbL</it> 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 <it>cbbL</it> sequences from agroecosystem, volcanic ashes and marine environments. In 16S rRNA clone libraries, the agricultural soil was dominated by chemolithoautotrophs (<it>Betaproteobacteria</it>) whereas photoautotrophic <it>Chloroflexi</it> 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 (<it>P</it> = 0.001) and UniFrac.</p> <p>Conclusion</p> <p>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 <it>cbbL</it> 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 (<it>cbbL</it>) and phylogenetic (16S rDNA) marker genes.</p>http://www.biomedcentral.com/1471-2180/12/150<it>cbbL</it>Clone libraries16S rRNA geneRuBisCOBarren soil |
| spellingShingle | Yousuf Basit Sanadhya Payal Keshri Jitendra Jha Bhavanath Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India BMC Microbiology <it>cbbL</it> Clone libraries 16S rRNA gene RuBisCO Barren soil |
| title | Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India |
| title_full | Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India |
| title_fullStr | Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India |
| title_full_unstemmed | Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India |
| title_short | Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India |
| title_sort | comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils gujarat india |
| topic | <it>cbbL</it> Clone libraries 16S rRNA gene RuBisCO Barren soil |
| url | http://www.biomedcentral.com/1471-2180/12/150 |
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