The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes

Myrold, David D.; Zeglin, Lydia H.; Jansson, Janet

doi:10.2136/sssaj2013.07.0287dgs

Cited by 95 publications

(63 citation statements)

References 80 publications

(76 reference statements)

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“…Specifically, the analysis provides a comprehensive map of the dominant lineages involved in eight N processes. The approach also allowed us to search all known genes in a pathway, while avoiding primer biases toward particular lineages (40).…”

Section: Discussionmentioning

confidence: 99%

Global biogeography of microbial nitrogen-cycling traits in soil

Nelson

Martiny

2016

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

399

232

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Microorganisms drive much of the Earth’s nitrogen (N) cycle, but we still lack a global overview of the abundance and composition of the microorganisms carrying out soil N processes. To address this gap, we characterized the biogeography of microbial N traits, defined as eight N-cycling pathways, using publically available soil metagenomes. The relative frequency of N pathways varied consistently across soils, such that the frequencies of the individual N pathways were positively correlated across the soil samples. Habitat type, soil carbon, and soil N largely explained the total N pathway frequency in a sample. In contrast, we could not identify major drivers of the taxonomic composition of the N functional groups. Further, the dominant genera encoding a pathway were generally similar among habitat types. The soil samples also revealed an unexpectedly high frequency of bacteria carrying the pathways required for dissimilatory nitrate reduction to ammonium, a little-studied N process in soil. Finally, phylogenetic analysis showed that some microbial groups seem to be N-cycling specialists or generalists. For instance, taxa within the Deltaproteobacteria encoded all eight N pathways, whereas those within the Cyanobacteria primarily encoded three pathways. Overall, this trait-based approach provides a baseline for investigating the relationship between microbial diversity and N cycling across global soils.

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Section: Discussionmentioning

confidence: 99%

Global biogeography of microbial nitrogen-cycling traits in soil

Nelson

Martiny

2016

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

399

232

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“…Predicting the metabolic responses in a microbial community from metagenomic data is one of the greatest challenges in microbial ecology today (Myrold et al 2014). Although metagenomics can be used to generate hypotheses about microbial metabolism and lifestyle, to date no applications connect the metabolic pathways represented in metagenomes to prediction of GHG fluxes.…”

Section: Quantifying and Modeling Arctic Soil Microbial Processes In mentioning

confidence: 99%

Permafrost Meta-Omics and Climate Change

Mackelprang

Saleska²,

Jacobsen

et al. 2016

Annu. Rev. Earth Planet. Sci.

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Permanently frozen soil, or permafrost, covers a large portion of the Earth's terrestrial surface and represents a unique environment for cold-adapted microorganisms. As permafrost thaws, previously protected organic matter becomes available for microbial degradation. Microbes that decompose soil carbon produce carbon dioxide and other greenhouse gases, contributing substantially to climate change. Next-generation sequencing and other -omics technologies offer opportunities to discover the mechanisms by which microbial communities regulate the loss of carbon and the emission of greenhouse gases from thawing permafrost regions. Analysis of nucleic acids and proteins taken directly from permafrost-associated soils has provided new insights into microbial communities and their functions in Arctic environments that are increasingly impacted by climate change. In this article we review current information from various molecular -omics studies on permafrost microbial ecology and explore the relevance of these insights to our current understanding of the dynamics of permafrost loss due to climate change.

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“…Recently, several metagenomic studies could provide insights into changes of genes associated with metabolic potentials for C and N cycling in response to environmental change (Mackelprang et al, 2011;Fierer et al, 2012). A more comprehensive and complete inventory of microbial genes in soils or sediments is desired by taking advantage of pyrosequencing technique in metagenomic approach (Smith and Osborn, 2009;Myrold et al, 2013). Complementarily, metatranscriptomic approach can assess and strengthen the connections between the structure, or composition, of the microbial community with actual microbial activity (Myrold et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

“…A more comprehensive and complete inventory of microbial genes in soils or sediments is desired by taking advantage of pyrosequencing technique in metagenomic approach (Smith and Osborn, 2009;Myrold et al, 2013). Complementarily, metatranscriptomic approach can assess and strengthen the connections between the structure, or composition, of the microbial community with actual microbial activity (Myrold et al, 2013). However, the utility of soil metatranscriptomics has not yet been fully explored and current challenges in advancing metagenomics include the difficulty in adopting standard methods, data reduction and analysis, improvement in functional gene annotation and database curation (Myrold et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

“…Complementarily, metatranscriptomic approach can assess and strengthen the connections between the structure, or composition, of the microbial community with actual microbial activity (Myrold et al, 2013). However, the utility of soil metatranscriptomics has not yet been fully explored and current challenges in advancing metagenomics include the difficulty in adopting standard methods, data reduction and analysis, improvement in functional gene annotation and database curation (Myrold et al, 2013). Progress with further developments of metagenomic and metatranscriptomic methods promises to enhance our understanding about the response of active microorganisms to environmental change.…”

Section: Discussionmentioning

confidence: 99%

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Denitrification Potential and Denitrifier Abundance in Downstream of Dams in Temperate Streams

Vo¹,

Lee²,

Doan³

et al. 2014

The Korean Journal of Microbiology

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Various studies have been conducted to investigate effects of dams on river ecosystems, but less information is available regarding damming impacts on downstream denitrification. We measured denitrification enzyme activity (potential denitrification rate) and denitrifier abundances (using nirS, nirK, and nosZ as markers) in dammed headstreams of the Nakdong River in South Korea. Sediments in Phragmites-dominated riparian areas and in-stream areas across streams (dammed vs. reference) with different streambed materials (gravel and sand) were sampled occasionally. We hypothesized that (i) the higher available N and C contents in sediments downstream of dams foster larger denitrifier communities than in the reference system and (ii) differences in potential denitrification rates across the systems correspond with denitrifier abundances. Despite 30 years of different hydrological management with dams and greater inorganic N and DOC contents in sediments downstream of dams, compared to the references, abundances of denitrifier communities and potential denitrification rates within the whole sediment were not significantly different across the systems. However, nirS and nosZ denitrifier abundances and potential denitrification rates were considerably increased in specific sediments downstream of dams (gravelly riparian and sandy in-stream) with regard to flooding events and seasonal temperature variation. nirK was not amplified in all sediments. Canonical correspondence analyses (CCA) revealed that the relationship between abundances of denitrifier communities and nutrient availabilities and potential denitrification rates was a weak one.Keywords: denitrification enzyme activity, denitrifier abundance, nitrogen cycle, stream regulation *For correspondence. E-mail: hj_kang@yonsei.ac.kr; Tel.: +82-2-2123-5803; Fax: +82-2-364-5300Current uncertainty in water management strategies, namely additional dam construction versus dam removal, has raised the question whether we should reevaluate the effectiveness of management strategies of water resources in terms of economic, social and environmental costs. Hydrological transport processes and their temporal variations are ubiquitous features of running-water ecosystems across multiple spatial scales (Kondolf et al., 2006; Fisher et al., 2007). Flood control through the construction of dams on rivers or streams has intensively altered downstream flow regimes, changing the timing, magnitude, frequency and current velocity of high and low flows (Grant et al., 2003); consequently, restricted the exchangeable flows of substrates and energy between subsystems, for example between the main channel and floodplain or riparian zones (Gergel et al., 2005). Thus, the damming of rivers necessarily results in downstream changes in water quality (temperature, oxygen and nutrient concentrations), energy sources (organic matters of both riverine and in situ origin), physical habitats (sedimentation and the expansion of nonnative riparian plants) and biotic interactions (Friedl and Wüest, 2002...

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The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes

Cited by 95 publications

References 80 publications

Global biogeography of microbial nitrogen-cycling traits in soil

Global biogeography of microbial nitrogen-cycling traits in soil

Permafrost Meta-Omics and Climate Change

Denitrification Potential and Denitrifier Abundance in Downstream of Dams in Temperate Streams

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