Spatial Physicochemical and Metagenomic Analysis of Desert Environment
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Investigating bacterial diversity and its metabolic capabilities is crucial for interpreting the ecological patterns in a desert environment and assessing the presence of exploitable microbial resources. In this study, we evaluated the spatial heterogeneity of physicochemical parameters, soil bacterial diversity and metabolic adaptation at meter scale. Soil samples were collected from two quadrats of a desert (Thar Desert, India) with a hot, arid climate, very little rainfall and extreme temperatures. Analysis of physico-chemical parameters and subsequent variance analysis (p-values < 0.05) revealed that sulfate, potassium and magnesium ions were the most variable between the quadrats. Microbial diversity of the two quadrats was studied using Illumina bar-coded sequencing by targeting V3-V4 regions of 16S rDNA. As for the results, 702504 high-quality sequence reads, assigned to 173 operational taxonomic units (OTUs) at species level, were examined. The most abundant phyla in both quadrats were Actinobacteria (38.72%), Proteobacteria (32.94%), and Acidobacteria (9.24%). At genus level, Gaiella represented highest prevalence, followed by Streptomyces, Solirubrobacter, Aciditerrimonas, Geminicoccus, Geodermatophilus, Microvirga, and Rubrobacter. Between the quadrats, significant difference (p-values < 0.05) was found in the abundance of Aciditerrimonas, Geodermatophilus, Geminicoccus, Ilumatobacter, Marmoricola, Nakamurella, and Solirubrobacter. Metabolic functional mapping revealed diverse biological activities, and was significantly correlated with physicochemical parameters. The results revealed spatial variation of ions, microbial abundance and functional attributes in the studied quadrats, and patchy nature in local scale. Interestingly, abundance of the biotechnologically important phylum Actinobacteria, with large proposition of unclassified species in the desert, suggested that this arid environment is a promising site for bioprospection.
Abstract
Investigating bacterial diversity and its metabolic capabilities is crucial for interpreting the ecological patterns in a desert environment and assessing the presence of exploitable microbial resources. In this study, we evaluated the spatial heterogeneity of physicochemical parameters, soil bacterial diversity and metabolic adaptation at meter scale. Soil samples were collected from two quadrats of a desert (Thar Desert, India) with a hot, arid climate, very little rainfall and extreme temperatures. Analysis of physico-chemical parameters and subsequent variance analysis (p-values < 0.05) revealed that sulfate, potassium and magnesium ions were the most variable between the quadrats. Microbial diversity of the two quadrats was studied using Illumina bar-coded sequencing by targeting V3-V4 regions of 16S rDNA. As for the results, 702504 high-quality sequence reads, assigned to 173 operational taxonomic units (OTUs) at species level, were examined. The most abundant phyla in both quadrats were Actinobacteria (38.72%), Proteobacteria (32.94%), and Acidobacteria (9.24%). At genus level, Gaiella represented highest prevalence, followed by Streptomyces, Solirubrobacter, Aciditerrimonas, Geminicoccus, Geodermatophilus, Microvirga, and Rubrobacter. Between the quadrats, significant difference (p-values < 0.05) was found in the abundance of Aciditerrimonas, Geodermatophilus, Geminicoccus, Ilumatobacter, Marmoricola, Nakamurella, and Solirubrobacter. Metabolic functional mapping revealed diverse biological activities, and was significantly correlated with physicochemical parameters. The results revealed spatial variation of ions, microbial abundance and functional attributes in the studied quadrats, and patchy nature in local scale. Interestingly, abundance of the biotechnologically important phylum Actinobacteria, with large proposition of unclassified species in the desert, suggested that this arid environment is a promising site for bioprospection.
참고문헌 (43)
- Cowan DA, "Microbial ecology and biogeochemistry of continental Antarctic soils", Front. Microbiol., 5, pp.154~ (2014)
- Makhalanyane TP, "Microbial ecology of hot desert edaphic systems", FEMS Microbiol. Rev., 39, pp.203~221 (2015)[DOI]
- Jones FT, "Degradation of aflatoxin by poultry litter", Poult. Sci., 75, pp.52~58 (1996)[DOI]
- Elbert T, "Increased cortical representation of the fingers of the left hand in string players", Science, 270, pp.305~307 (1995)[DOI]
- Belap J, "Linkages between microbial and hydrologic processes in arid and semiarid watersheds", Ecology, 86, pp.298~307 (2005)[DOI]
- Housman DC, "Heterogeneity of soil nutrients and subsurface biota in a dryland ecosystem", Soil Biol. Biochem., 39, pp.2138~2149 (2007)[DOI]
- Geyer KM, "Environmental controls over bacterial communities in polar desert soils", Ecosphere, 4, pp.127~ (2013)
- Pajares S, "Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from CuatroCienegas, Mexico", PeerJ, 4, pp.e2459~ (2016)[DOI]
- Garcia-Pichel F, "Temperature drives the continental-scale distribution of key microbes in topsoil communities", Science, 340, pp.1574~1577 (2013)[DOI]
- Ben-David EA, "Assessment of the spatial distribution of soil microbial communities in patchy arid and semi-arid landscapes of the Negev Desert using combined PLFA and DGGE analyses", FEMS Microbiol. Ecol., 76, pp.492~503 (2011)[DOI]
- Maestre FT, "Does spatial pattern matter to ecosystem functioning? Insights from biological soil crusts", Funct. Ecol., 19, pp.566~573 (2005)[DOI]
- Mohammadipanah F, "Actinobacteria from arid and desert habitats: diversity and biological activity", Front Microbiol., 6, pp.1541~ (2016)
- Arocha-Garza HF, "High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis", PeerJ, 5, pp.e3247~ (2017)[DOI]
- Peel MC, "Updated world map of the Koppen-Geiger climate classification", Hydrol. Earth Syst. Sci., 11, pp.1633~1644 (2007)[DOI]
- Shyampura RL, "Soils of Rajasthan for optimizing land use. Soils of India Series", pp.51~ (1995)
- Bower CA, "Exchangeable cations of saline and alkaline soils", Soil Sci., 73, pp.251~257 (1972)
- Walkley A, "An estimation of digestion method for determining soil organic matter and a proposed modification of chromic acid titration method", Soil Sci., 37, pp.29~38 (1934)[DOI]
- Jackson ML, "Soil chemical analysis" (1973), Prentice Hall of India Private Limited
- Keeney DR, "Nitrogen-inorganic forms;Methods of soil analysis, Part 2, chemical and microbiological methods", pp.643~698 (1982)
- Pamberton H, "Estimation of total phosphorus", J Amer. Chem. Soc., 15, pp.383~395 (1945)
- Edgar RC, "UPARSE: Highly accurate OTU sequences from microbial amplicon reads", Nat. Methods, 10, pp.996~998 (2013)[DOI]
- Huson DH, "MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data", PLoS Comput. Biol., 12, pp.e1004957~ (2016)[DOI]
- Colwell RK, "Models and estimators linking individual-based and sample-based rarefaction, extrapolation, and comparison of assemblages", J. Plant Ecol., 5, pp.3~21 (2012)[DOI]
- Arndt D, "METAGENassist: A comprehensive web server for comparative metagenomics", Nucleic Acids Res., 40, pp.W88~W95 (2012)[DOI]
- Hackstadt AJ, "Filtering for increased power for microarray data analysis", BMC Bioinformatics, 10, pp.11~ (2009)[DOI]
- Rao S, "Pointing microbial diversity in soil, sand dune and rock substrates of the Thar monsoon desert, India", Indian J. Microbiol., 56, pp.35~45 (2016)[DOI]
- Perry RA, "Arid Land Ecosystems: structure, functioning and management" (2009), Cambridge University Press
- Yasir M, "Composition of soil microbiome along elevation gradients in southwestern highlands of Saudi Arabia", BMC Microbiol., 15, pp.65~ (2015)[DOI]
- Ronca S, "Namib desert dune", interdune transects exhibit habitat-specific edaphic bacterial communities, 2015, pp.6, 845~
- Wei STS, "Taxonomic and functional diversity of soil and hypolithic microbial communities in Miers Valley, McMurdo Dry Valleys, Antarctica", Front Microbiol., 7, pp.1642~ (2016)
- Le PT, "Comparative metagenomic analysis reveals mechanisms for stress response in hypoliths from extreme hyperarid deserts", Genome Biol. Evol., 8, pp.2737~2747 (2016)[DOI]
- Vikram S, "Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community", Environ. Microbiol., 18, pp.1875~1888 (2015)
- Barka EA, "Taxonomy, physiology, and natural products of Actinobacteria", Microbiol. Mol. Biol. Rev., 80, pp.1~43 (2016)[DOI]
- Parrot D, "Littoral lichens as a novel source of potentially bioactive Actinobacteria", Sci. Rep., 5, pp.15839~ (2015)[DOI]
- Guo X, "Red soils harbour diverse culturable actinomycetes that are promising sources of novel secondary metabolites", Appl. Environ. Microbiol., 81, pp.3086~3103 (2015)[DOI]
- Jose PA, "Intertidal marine sediment harbours Actinobacteria with promising bioactive and biosynthetic potential", Sci. Rep., 7, pp.10041~ (2017)[DOI]
- Maestre FT, "Increasing aridity reduces soil microbial diversity and abundance in global drylands", P. Natl. Acad. Sci. USA, 112, pp.15684~15689 (2015)
- Lupatini M, "Soil-borne bacterial structure and diversity does not reflect community activity in Pampa biome", PLoS One, 8, pp.e76465~ (2013)[DOI]
- Gorlach-Lira K, "Population dynamics and extracellular enzymes activity of mesophilic and thermophilic bacteria isolated from semi-arid soil of Northeastern Brazil", Braz. J. Microbiol., 38, pp.135~141 (2007)[DOI]
- Sharma R, "Isolation and characterization of osmotolerant bacteria from Thar desert of western Rajasthan (India)", Rev. Biol. Trop., 61, pp.1551~1562 (2013)
- Bachar A, "The effect of resource islands on abundance and diversity of bacteria in arid soils", Microbial Ecol., 63, pp.694~700 (2012)[DOI]
- Su LJ, "Comparative gut microbiomes of four species representing the higher and the lower termites", J. Insect. Sci., 16, pp.97~ (2016)[DOI]
- Llorens-Mares T, "Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics", ISME J., 9, pp.1648~1661 (2015)[DOI]