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Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities

https://doi.org/10.1128/mbio.01157-14
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Denaturing Gradient Gel Electrophoresis (DGGE) for Microbial Community Analysis
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Advances in Fungal Biotechnology for Industry, Agriculture, and Medicine
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Methodological Considerations for the Use of Stable Isotope Probing in Microbial Ecology
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Achievements and new knowledge unraveled by metagenomic approaches
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Cloning and functional characterization of a novel endo-β-1,4-glucanase gene from a soil-derived metagenomic library
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Identification and characterization of novel cellulolytic and hemicellulolytic genes and enzymes derived from German grassland soil metagenomes
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Investigation of endoglucanase selectivity on carboxymethyl cellulose by mass spectrometric techniques
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Enhancement of gene detection frequencies by combining DNA-based stable-isotope probing with the construction of metagenomic DNA libraries
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A versatile and robust aerotolerant microbial community capable of cellulosic ethanol production
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Liquid chromatography combined with mass spectrometry for the investigation of endoglucanase selectivity on carboxymethyl cellulose
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Seasonal variations in sugar contents and microbial community in a ryegrass soil
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Isolation and characterization of novel cellulase genes from uncultured microorganisms in different environmental niches
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Nonlinear electrophoresis for purification of soil DNA for metagenomics
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Versatile broad-host-range cosmids for construction of high quality metagenomic libraries
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Decoupling of microbial glucose uptake and mineralization in soil
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Stable isotope probing in biodegradation research
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Microbial activity in response to water-filled pore space of variably eroded southern Piedmont soils
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Stable-isotope probing as a tool in microbial ecology
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High-resolution metagenomics targets specific functional types in complex microbial communities
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QIIME allows analysis of high-throughput community sequencing data
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DNA stable-isotope probing
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Stable isotope probing — linking microbial identity to function
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Microbial diversity and soil functions
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The diversity and biogeography of soil bacterial communities
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THE POPULATION FREQUENCIES OF SPECIES AND THE ESTIMATION OF POPULATION PARAMETERS
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UniProt: the Universal Protein knowledgebase
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The carbohydrate-active enzymes database (CAZy) in 2013
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An efficient one-step site-directed and site-saturation mutagenesis protocol
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Taxonomic study of Cellvibrio strains and description of Cellvibrio ostraviensis sp. nov., Cellvibrio fibrivorans sp. nov. and Cellvibrio gandavensis sp. nov.
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Spirochaeta americana sp. nov., a new haloalkaliphilic, obligately anaerobic spirochaete isolated from soda Mono Lake in California
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Salinibacterium amurskyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment
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Asticcacaulis benevestitus sp. nov., a psychrotolerant, dimorphic, prosthecate bacterium from tundra wetland soil
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Devosia soli sp. nov., isolated from greenhouse soil in Korea
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Devosia subaequoris sp. nov., isolated from beach sediment
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Salinibacterium xinjiangense sp. nov., a psychrophilic bacterium isolated from the China No. 1 glacier
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Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm
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Microbial diversity and soil functions
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Identification of a complete methane monooxygenase operon from soil by combining stable isotope probing and metagenomic analysis
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Identification of cellulolytic bacteria in soil by stable isotope probing
inferredcites →https://doi.org/10.1111/j.1462-2920.2006.01197.xopenalex-snapshot
Dynamics and identification of soil microbial populations actively assimilating carbon from 13 C‐labelled wheat residue as estimated by DNA‐ and RNA‐SIP techniques
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Marine methylotrophs revealed by stable‐isotope probing, multiple displacement amplification and metagenomics
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Revealing the uncultivated majority: combining DNA stable‐isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands
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Metabolic responses of novel cellulolytic and saccharolytic agricultural soil Bacteria to oxygen
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Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers
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Characterization of a gene encoding cellulase from uncultured soil bacteria
inferredcites →https://doi.org/10.1111/j.1742-4658.2010.07585.xopenalex-snapshot
Cellulose crystallinity – a key predictor of the enzymatic hydrolysis rate
inferredcites →https://doi.org/10.1128/aem.00023-11openalex-snapshot
Novel Biphenyl-Oxidizing Bacteria and Dioxygenase Genes from a Korean Tidal Mudflat
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DNA-Stable Isotope Probing Integrated with Metagenomics for Retrieval of Biphenyl Dioxygenase Genes from Polychlorinated Biphenyl-Contaminated River Sediment
inferredcites →https://doi.org/10.1128/aem.00335-09openalex-snapshot
Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale
inferredcites →https://doi.org/10.1128/aem.00523-11openalex-snapshot
Novel Family of Carbohydrate-Binding Modules Revealed by the Genome Sequence of Spirochaeta thermophila DSM 6192
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Contamination of Soil by Copper Affects the Dynamics, Diversity, and Activity of Soil Bacterial Communities Involved in Wheat Decomposition and Carbon Storage
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Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads
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Identification of Cellulose-Responsive Bacterial and Fungal Communities in Geographically and Edaphically Different Soils by Using Stable Isotope Probing
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Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
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DNA recovery from soils of diverse composition
inferredcites →https://doi.org/10.1128/jb.00235-12openalex-snapshot
Genome Sequence of a Salinibacterium sp. Isolated from Antarctic Soil
inferredcites →https://doi.org/10.1128/jb.00295-11openalex-snapshot
Genome Sequence of Chthoniobacter flavus Ellin428, an Aerobic Heterotrophic Soil Bacterium
inferredcites →https://doi.org/10.1128/jb.01348-05openalex-snapshot
Complete Cellulase System in the Marine BacteriumSaccharophagus degradansStrain 2-40T
inferredcites →https://doi.org/10.1128/jb.05709-11openalex-snapshot
Complete Genome Sequence of Alicyclobacillus acidocaldarius Strain Tc-4-1
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Phylogenetic identification and in situ detection of individual microbial cells without cultivation
inferredcites →https://doi.org/10.1139/cjm-2014-0193openalex-snapshot
Recovering glycoside hydrolase genes from active tundra cellulolytic bacteria
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Bacterium organizes hierarchical amorphous structure in microbial cellulose
inferredcites →https://doi.org/10.1146/annurev.mi.49.100195.002151openalex-snapshot
CELLULOSE DEGRADATION IN ANAEROBIC ENVIRONMENTS
inferredcites →https://doi.org/10.1159/000142892openalex-snapshot
Advances in Recovery of Novel Biocatalysts from Metagenomes
inferredcites →https://doi.org/10.1159/000142898openalex-snapshot
Metagenomics for Mining New Genetic Resources of Microbial Communities
inferredcites →https://doi.org/10.1186/1471-2105-13-31openalex-snapshot
PANDAseq: paired-end assembler for illumina sequences
inferredcites →https://doi.org/10.1186/1471-2105-9-386openalex-snapshot
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
inferredcites →https://doi.org/10.1186/1754-6834-4-24openalex-snapshot
Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses
inferredcites →https://doi.org/10.1186/2047-217x-2-3openalex-snapshot
AXIOME: automated exploration of microbial diversity
inferredcites →https://doi.org/10.1201/9781420015201openalex-snapshot
Modern Soil Microbiology
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SPECIES ASSEMBLAGES AND INDICATOR SPECIES:THE NEED FOR A FLEXIBLE ASYMMETRICAL APPROACH
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Effect of Water‐Filled Pore Space on Carbon Dioxide and Nitrous Oxide Production in Tilled and Nontilled Soils
inferredcites →https://doi.org/10.3791/2027openalex-snapshot
DNA Stable-Isotope Probing (DNA-SIP)
inferredcites →https://doi.org/10.4056/sigs.19262openalex-snapshot
Complete genome sequence of Dyadobacter fermentans type strain (NS114T)
inferredcites →https://doi.org/10.4056/sigs.1974654openalex-snapshot
Open resource metagenomics: a model for sharing metagenomic libraries

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1038/s41467-019-10542-0openalex-snapshot
Probing the active fraction of soil microbiomes using BONCAT-FACS
inferred← citeshttps://doi.org/10.1038/s41467-024-46254-3openalex-snapshot
Nonpathogenic Pseudomonas syringae derivatives and its metabolites trigger the plant “cry for help” response to assemble disease suppressing and growth promoting rhizomicrobiome
inferred← citeshttps://doi.org/10.1038/s41598-017-01126-3openalex-snapshot
Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments
inferred← citeshttps://doi.org/10.1038/s41598-017-02506-5openalex-snapshot
Revealing the insoluble metasecretome of lignocellulose-degrading microbial communities
inferred← citeshttps://doi.org/10.1038/s41598-017-11678-zopenalex-snapshot
Impacts of aquaculture wastewater irrigation on soil microbial functional diversity and community structure in arid regions
inferred← citeshttps://doi.org/10.1038/s41598-024-72796-zopenalex-snapshot
Glucose addition in natural forest soils has higher biological nitrogen fixation capacity than other types of soils
inferred← citeshttps://doi.org/10.1038/s42003-020-1106-yopenalex-snapshot
Rapid detection of microbiota cell type diversity using machine-learned classification of flow cytometry data
inferred← citeshttps://doi.org/10.1080/10408398.2019.1632790openalex-snapshot
Mixed-species biofilms in the food industry: Current knowledge and novel control strategies
inferred← citeshttps://doi.org/10.1080/1040841x.2017.1337713openalex-snapshot
Bioprospecting of functional cellulases from metagenome for second generation biofuel production: a review
inferred← citeshttps://doi.org/10.1080/15226514.2016.1216076openalex-snapshot
Phytoremediation: State-of-the-art and a key role for the plant microbiome in future trends and research prospects
inferred← citeshttps://doi.org/10.1093/femsec/fiw177openalex-snapshot
Bacterial succession on decomposing leaf litter exhibits a specific occurrence pattern of cellulolytic taxa and potential decomposers of fungal mycelia
inferred← citeshttps://doi.org/10.1093/femsec/fiz192openalex-snapshot
Arctic tundra soil bacterial communities active at subzero temperatures detected by stable isotope probing
inferred← citeshttps://doi.org/10.1093/femsle/fnw151openalex-snapshot
A novel isolate and widespread abundance of the candidate alphaproteobacterial order (Ellin 329), in southern Appalachian peatlands
inferred← citeshttps://doi.org/10.1093/femsle/fnx211openalex-snapshot
Metagenomics: novel enzymes from non-culturable microbes
inferred← citeshttps://doi.org/10.1098/rsif.2016.0627openalex-snapshot
Constraint-based stoichiometric modelling from single organisms to microbial communities
inferred← citeshttps://doi.org/10.1099/ijsem.0.001681openalex-snapshot
Micropepsis pineolensis gen. nov., sp. nov., a mildly acidophilic alphaproteobacterium isolated from a poor fen, and proposal of Micropepsaceae fam. nov. within Micropepsales ord. nov.
inferred← citeshttps://doi.org/10.1101/022483openalex-snapshot
Unearthing the microbial ecology of soil carbon cycling with DNA-SIP
inferred← citeshttps://doi.org/10.1101/2021.05.12.443848openalex-snapshot
Conservation of isolate substrate preferences in mixed communities revealed through ribosomal marker protein profiling
inferred← citeshttps://doi.org/10.1101/404087openalex-snapshot
Study of Oak Ridge soils using BONCAT-FACS-Seq reveals that a large fraction of the soil microbiome is active
inferred← citeshttps://doi.org/10.1111/1462-2920.13643openalex-snapshot
Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity
inferred← citeshttps://doi.org/10.1111/1751-7915.12309openalex-snapshot
Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends
inferred← citeshttps://doi.org/10.1111/aab.12546openalex-snapshot
Effect of long‐term mineral fertilisation on soil microbial abundance, community structure and diversity in a Typic Hapludoll under intensive farming systems
inferred← citeshttps://doi.org/10.1111/gcb.16321openalex-snapshot
Microbial community shifts correspond with suppression of decomposition 25 years after liming of acidic forest soils
inferred← citeshttps://doi.org/10.1111/gcbb.12371openalex-snapshot
Biochar alters the soil microbiome and soil function: results of next‐generation amplicon sequencing across Europe
inferred← citeshttps://doi.org/10.1128/aem.00055-15openalex-snapshot
Stable-Isotope Probing Identifies Uncultured Planctomycetes as Primary Degraders of a Complex Heteropolysaccharide in Soil
inferred← citeshttps://doi.org/10.1128/genomea.00514-15openalex-snapshot
Genome Assemblies of Three Soil-Associated Devosia species: D. insulae , D. limi , and D. soli
inferred← citeshttps://doi.org/10.1128/mbio.03099-20openalex-snapshot
Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil
inferred← citeshttps://doi.org/10.1128/msphere.00085-21openalex-snapshot
Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil
inferred← citeshttps://doi.org/10.1128/msystems.01039-25openalex-snapshot
Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes
inferred← citeshttps://doi.org/10.1139/cjm-2019-0384openalex-snapshot
Changes in rhizosphere bacterial communities associated with tree decline: grapevine esca syndrome case study
inferred← citeshttps://doi.org/10.1186/s12859-020-3372-6openalex-snapshot
Simulating metagenomic stable isotope probing datasets with MetaSIPSim
inferred← citeshttps://doi.org/10.1186/s12864-016-2404-0openalex-snapshot
A multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveils novel thermoalkaliphilic enzymes
inferred← citeshttps://doi.org/10.1186/s13068-020-01869-8openalex-snapshot
Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues
inferred← citeshttps://doi.org/10.1186/s40168-020-00836-7openalex-snapshot
Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer
inferred← citeshttps://doi.org/10.1371/journal.pone.0240559openalex-snapshot
Effects of organic fertilizer on soil nutrient status, enzyme activity, and bacterial community diversity in Leymus chinensis steppe in Inner Mongolia, China
inferred← citeshttps://doi.org/10.1371/journal.pone.0262691openalex-snapshot
Glucose addition promotes C fixation and bacteria diversity in C-poor soils, improves root morphology, and enhances key N metabolism in apple roots
inferred← citeshttps://doi.org/10.18331/brj2017.4.2.5openalex-snapshot
Genetic modification: a tool for enhancing cellulase secretion
inferred← citeshttps://doi.org/10.21203/rs.3.rs-3235026/v1openalex-snapshot
The Properties of Soilless Culture Substrates Determine the Evolutionary Direction of Rhizosphere Microbial Communities in Potato Breeding, Having Potential Impact on Breeding
inferred← citeshttps://doi.org/10.2217/fmb-2016-0079openalex-snapshot
Metabolic Competition as a Driver of Bacterial Population Structure
inferred← citeshttps://doi.org/10.3109/07388551.2015.1083939openalex-snapshot
Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development
inferred← citeshttps://doi.org/10.31219/osf.io/esdp2openalex-snapshot
Using bio-manipulation to optimise nutrient management within intensive farm systems
inferred← citeshttps://doi.org/10.32920/ryerson.14646525openalex-snapshot
A corynecaterium glutamicum expression system for glycoside hydrolase analysis
inferred← citeshttps://doi.org/10.32920/ryerson.14646525.v1openalex-snapshot
A corynecaterium glutamicum expression system for glycoside hydrolase analysis
inferred← citeshttps://doi.org/10.3389/fmicb.2016.00703openalex-snapshot
Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil
inferred← citeshttps://doi.org/10.3389/fmicb.2016.01366openalex-snapshot
Interspecific Bacterial Interactions are Reflected in Multispecies Biofilm Spatial Organization
inferred← citeshttps://doi.org/10.3389/fmicb.2016.01524openalex-snapshot
Resource Partitioning between Bacteria, Fungi, and Protists in the Detritusphere of an Agricultural Soil
inferred← citeshttps://doi.org/10.3389/fmicb.2017.00537openalex-snapshot
Long-Term Enrichment of Stress-Tolerant Cellulolytic Soil Populations following Timber Harvesting Evidenced by Multi-Omic Stable Isotope Probing
inferred← citeshttps://doi.org/10.3389/fmicb.2017.00606openalex-snapshot
Bacterial and Fungal Community Structures in Loess Plateau Grasslands with Different Grazing Intensities
inferred← citeshttps://doi.org/10.3389/fmicb.2017.02293openalex-snapshot
Resource Legacies of Organic and Conventional Management Differentiate Soil Microbial Carbon Use
inferred← citeshttps://doi.org/10.3389/fmicb.2020.587972openalex-snapshot
DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil
inferred← citeshttps://doi.org/10.3389/fmicb.2023.1283675openalex-snapshot
Rice straw increases microbial nitrogen fixation, bacterial and nifH genes abundance with the change of land use types
inferred← citeshttps://doi.org/10.3389/fmicb.2025.1656448openalex-snapshot
Top-down enrichment of oil-degrading microbial consortia reveals functional streamlining and novel degraders
inferred← citeshttps://doi.org/10.3390/agronomy13071897openalex-snapshot
Changes in Physicochemical Properties and Bacterial Communities of Tropical Soil in China under Different Soil Utilization Types
inferred← citeshttps://doi.org/10.3390/ecologies7030069openalex-snapshot
Distinct Bacterial Communities Among Halimeda Thalli, Seawater, Sediment, and Sea Cucumber Feces in a Halimeda-Dominated Habitat
inferred← citeshttps://doi.org/10.3390/horticulturae10030236openalex-snapshot
The Effect of Bacillus velezensis LJ02 Compounded with Different Fungi on the Growth of Watermelon Seedlings and Microbial Community Structure
inferred← citeshttps://doi.org/10.3390/md20020108openalex-snapshot
Understanding Interaction Patterns within Deep-Sea Microbial Communities and Their Potential Applications
inferred← citeshttps://doi.org/10.3390/microorganisms10091763openalex-snapshot
Land-Use Change and Management Intensification Is Associated with Shifts in Composition of Soil Microbial Communities and Their Functional Diversity in Coffee Agroecosystems
inferred← citeshttps://doi.org/10.3390/microorganisms12030584openalex-snapshot
Exploring the Impact of Coconut Peat and Vermiculite on the Rhizosphere Microbiome of Pre-Basic Seed Potatoes under Soilless Cultivation Conditions
inferred← citeshttps://doi.org/10.3390/microorganisms12102034openalex-snapshot
Are Changes Occurring in Bacterial Taxa Community and Diversity with the Utilization of Different Substrates within SIR Measurements?
inferred← citeshttps://doi.org/10.3390/microorganisms13020263openalex-snapshot
Microbiota Involved in the Degradation of Tremella fuciformis Polysaccharide and Microbial Enzymatic Potential Revealed by Microbiome and Metagenome
inferred← citeshttps://doi.org/10.3390/w15020271openalex-snapshot
Comparative Analysis of Metagenomic (Amplicon and Shotgun) DNA Sequencing to Characterize Microbial Communities in Household On-Site Wastewater Treatment Systems
inferred← citeshttps://doi.org/10.4018/979-8-3693-0448-8.ch015openalex-snapshot
Bacterial Exopolysaccharides-Based Nanomaterials for Targeting Biofilm-Associated Infections
inferred← citeshttps://doi.org/10.4314/njtd.v19i2.3openalex-snapshot
Analysis of decomposing wood wastes in the Lagos Lagoon using terminal-restriction fragment length polymorphism and illumina sequencing platform
inferred← citeshttps://doi.org/10.70675/c28304d8z958cz4fc7z8799zc58846460599openalex-snapshot
Effets des biostimulants sur le fonctionnement biologique de sols d’agrosystèmes : réponses des communautés microbiennes et dynamique de minéralisation du carbone organique
inferred← citeshttps://doi.org/10.7287/peerj.2687v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.2687v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.2687v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone (v0.2)"
inferred← citeshttps://doi.org/10.7717/peerj.2687openalex-snapshot
Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.