DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil

Yu, Julian; Pavia, Michael J.; Deem, Lauren M.; Crow, Susan E.; Deenik, Jonathan; Penton, C. Ryan

doi:10.3389/fmicb.2020.587972

Cited by 12 publications

(7 citation statements)

References 115 publications

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“…The tRNA gene count was used as a proxy for rrn copy number as described in text. The data sets are RefSoil genomes (a), Diamond et al ( 101 ) MAGs recovered from drought-simulated meadow soils (b), Yu et al ( 102 ) MAGs recovered from heavy DNA extracted from agricultural soils supplied with 13 C-labeled ryegrass (c), Wilhelm et al ( 103 ) MAGs recovered from heavy DNA extracted from forest soils treated with either 13 C-labeled cellulose or lignin (d), Wilhelm et al ( 104 ) phylobins recovered from heavy DNA fractions extracted from agricultural soil supplied with 13 C-labeled cellulose (e), Zhalnina et al ( 105 ) genomes isolated from Avena barbata rhizosphere (f), and Li et al ( 106 ) MAGs recovered from rhizospheres of Zea mays , Triticum aestivum , and Arabidopsis thaliana (g). Red or gray lines represent the linear relationships, with shading indicating the 95% confidence intervals.…”

Section: Resultsmentioning

confidence: 99%

“…We analyzed publicly available soil microbiome data sets to determine whether the genomic relationships we observed in 13 C-labeled MAGs were representative of soil-dwelling bacteria. Seven data sets were chosen, RefSoil ( 100 ), Diamond et al ( 101 ), Yu et al ( 102 ), Wilhelm et al ( 103 ), Wilhelm et al ( 104 ), Zhalnina et al ( 105 ), and Li et al ( 106 ). Assemblies from references 101 , 102 , and 105 were downloaded from GenBank on 21 June 2021 (NCBI accession numbers given in in Data Set S1 ).…”

Section: Methodsmentioning

confidence: 99%

“…Seven data sets were chosen, RefSoil ( 100 ), Diamond et al ( 101 ), Yu et al ( 102 ), Wilhelm et al ( 103 ), Wilhelm et al ( 104 ), Zhalnina et al ( 105 ), and Li et al ( 106 ). Assemblies from references 101 , 102 , and 105 were downloaded from GenBank on 21 June 2021 (NCBI accession numbers given in in Data Set S1 ). Assemblies from 103 and 104 were acquired from the authors.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing

Barnett

Egan

Foster

et al. 2023

mBio

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing

Barnett

Egan

Foster

et al. 2023

mBio

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“…Fibrobacteraceae have also been well-documented in many wheat production systems ( Prudence et al, 2021 ), but while they are known to efficiently utilize wheat root exudates, their exact role in plant–soil systems is not yet clear. Limnochordia and Polyangiales have been linked with organic management practices commonly used to improve soil health in saline soils ( Shang et al, 2020 ; Yu et al, 2020 ). Polyangiales are suspected to play an important role in cellulose degradation and carbon cycles ( Braga et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Diversity and functional traits of indigenous soil microbial flora associated with salinity and heavy metal concentrations in agricultural fields within the Indus Basin region, Pakistan

et al. 2022

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Soil salinization and heavy metal (HM) contamination are major challenges facing agricultural systems worldwide. Determining how soil microbial communities respond to these stress factors and identifying individual phylotypes with potential to tolerate these conditions while promoting plant growth could help prevent negative impacts on crop productivity. This study used amplicon sequencing and several bioinformatic programs to characterize differences in the composition and potential functional capabilities of soil bacterial, fungal, and archaeal communities in five agricultural fields that varied in salinity and HM concentrations within the Indus basin region of Pakistan. The composition of bacteria with the potential to fix atmospheric nitrogen (N) and produce the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase were also determined. Microbial communities were dominated by: Euryarchaeota (archaea), Actinobacteria, Proteobacteria, Planctomycetota, Firimicutes, Patescibacteria and Acidobacteria (bacteria), and Ascomycota (fungi), and all soils contained phylotypes capable of N-fixation and ACC-deaminase production. Salinity influenced bacterial, but not archaeal or fungal communities. Both salinity and HM altered the relative abundance of many phylotypes that could potentially promote or harm plant growth. These stress factors also appeared to influence the potential functional capabilities of the microbial communities, especially in their capacity to cycle phosphorous, produce siderophores, and act as symbiotrophs or pathotrophs. Results of this study confirm that farms in this region are at risk due to salinization and excessive levels of some toxic heavy metals, which could negatively impact crop and human health. Changes in soil microbial communities and their potential functional capabilities are also likely to affect several critical agroecosystem services related to nutrient cycling, pathogen suppression, and plant stress tolerance. Many potentially beneficial phylotypes were identified that appear to be salt and HM tolerant and could possibly be exploited to promote these services within this agroecosystem. Future efforts to isolate these phylotypes and determine whether they can indeed promote plant growth and/or carry out other important soil processes are recommended. At the same time, identifying ways to promote the abundance of these unique phylotypes either through modifying soil and crop management practices, or developing and applying them as inoculants, would be helpful for improving crop productivity in this region.

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“…In recent years, multiple SIP studies have used metagenome sequencing in addition to, or in place of, 16S rRNA gene amplicon sequencing (16)(17)(18)(19)(20)(21). We refer to this general approach as "SIP metagenomics" from here on to distinguish it from traditional 16S rRNA-based DNA-SIP.…”

Section: Introductionmentioning

confidence: 99%

A standardized quantitative analysis strategy for stable isotope probing metagenomics

Vyshenska

Sampara

Singh

et al. 2022

Preprint

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Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids. Many SIP studies rely on 16S rRNA sequences to identify active taxa but connecting these sequences to specific bacterial genomes is often challenging. Here, we describe a standardized laboratory and analysis framework to quantify isotopic enrichment on a per-genome basis using shotgun metagenomics instead of 16S rRNA sequencing. To develop this framework, we explored various sample processing and analysis approaches using a designed microbiome where the identity of labeled genomes, and their level of isotopic enrichment, were experimentally controlled. With this ground truth dataset, we empirically assessed the accuracy of different analytic models for identifying active taxa, and examined how sequencing depth impacts the detection of isotopically labeled genomes. We also demonstrate that using synthetic DNA internal standards to measure absolute genome abundances in SIP density fractions improves estimates of isotopic enrichment. In addition, our study illustrates the utility of internal standards to reveal anomalies in sample handling that could negatively impact SIP metagenomic analyses if left undetected. Finally, we present SIPmg, an R package to facilitate the estimation of absolute abundances and perform statistical analyses for identifying labeled genomes within SIP metagenomic data. This experimentally validated analysis framework strengthens the foundation of DNA-SIP metagenomics as a tool for accurately measuring the in situ activity of environmental microbial populations and assessing their genomic potential.

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DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil

Cited by 12 publications

References 115 publications

Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing

Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing

Diversity and functional traits of indigenous soil microbial flora associated with salinity and heavy metal concentrations in agricultural fields within the Indus Basin region, Pakistan

A standardized quantitative analysis strategy for stable isotope probing metagenomics

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