Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study

Steven, Blaire; Gallegos‐Graves, La Verne; Starkenburg, Shawn R.; Chain, Patrick; Kuske, Cheryl R.

doi:10.1111/j.1758-2229.2012.00328.x

Cited by 52 publications

(46 citation statements)

References 45 publications

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“…Sequences were quality checked and processed according to previously described protocols (32,33). Taxonomic classification of the 16S rRNA sequences was performed with the Bayesian classifier against the SILVA (34) bacterial taxonomy (31,32) as imple-mented in mothur.…”

Section: Methodsmentioning

confidence: 99%

Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

Steven

Kuske

Gallegos‐Graves

et al. 2015

Appl Environ Microbiol

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bBiological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remains poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2°C soil warming, altered summer precipitation [wetting], and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional changes. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in the cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreased Cyanobacteria abundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities, and the communities' functional profiles can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands.

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Section: Methodsmentioning

confidence: 99%

Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

Steven

Kuske

Gallegos‐Graves

et al. 2015

Appl Environ Microbiol

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“…Pleurocapsales were highly prevalent in the thrombolites (Myshrall et al 2010;Mobberley et al 2012). This discrepancy between gene-centered surveys and whole metagenomic sequencing may result from biases in ribosomal primer design, variation in copies of the 16S rRNA genes between organisms, as well as database differences and limitations (Liu et al 2007;Steven et al 2012). In general, most complete cyanobacterial genomes found in genomic databases, including those used by MG-RAST, are from ubiquitous aquatic ecotypes such as Nostoc spp.…”

Section: Cyanobacterial Molecular Pathways Dominate the Thrombolite Mmentioning

confidence: 99%

Metabolic potential of lithifying cyanobacteria-dominated thrombolitic mats

2013

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Thrombolites are unlaminated carbonate deposits formed by the metabolic activities of microbial mats and can serve as potential models for understanding the molecular mechanisms underlying the formation of lithifying communities. To assess the metabolic complexity of these ecosystems, high throughput DNA sequencing of a thrombolitic mat metagenome was coupled with phenotypic microarray analysis. Functional protein analysis of the thrombolite community metagenome delineated several of the major metabolic pathways that influence carbonate mineralization including cyanobacterial photosynthesis, sulfate reduction, sulfide oxidation, and aerobic heterotrophy. Spatial profiling of metabolite utilization within the thrombolite-forming microbial mats suggested that the top 5 mm contained a more metabolically diverse and active community than the deeper within the mat. This study provides evidence that despite the lack of mineral layering within the clotted thrombolite structure there is a vertical gradient of metabolic activity within the thrombolitic mat community. This metagenomic profiling also serves as a foundation for examining the active role individual functional groups of microbes play in coordinating metabolisms that lead to mineralization.

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“…The 16S rRNA gene data obtained from both the amplicon and shotgun sequencing were used to directly compare the taxonomic results obtained using these two very different methods. We conducted this comparison to determine whether biases introduced by both approaches may influence the determination of bacterial community structure, as suggested previously (26). Such biases may be derived from the PCR process itself or because the 16S rRNA gene regions recovered from the metagenomic data can span the entire length of the gene, whereas the PCR-based amplicon approach only targets the V4 region.…”

mentioning

confidence: 99%

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

Fierer

Leff

Adams

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.shotgun metagenomics | soil microbial ecology | 16S rRNA gene sequencing | biogeography

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Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study

Cited by 52 publications

References 45 publications

Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

Metabolic potential of lithifying cyanobacteria-dominated thrombolitic mats

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

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