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List of works by James M. Tiedje

2,4-Dichlorophenoxyacetic acid-degrading bacteria contain mosaics of catabolic genes.

scientific article

2-Bromoethanesulfonate, sulfate, molybdate, and ethanesulfonate inhibit anaerobic dechlorination of polychlorobiphenyls by pasteurized microorganisms

scientific article

A CCD-based fluorescence imaging system for real-time loop-mediated isothermal amplification-based rapid and sensitive detection of waterborne pathogens on microchips

article

A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation

A critical role of a eubiotic microbiota in gating proper immunocompetence in Arabidopsis

scientific article published on 17 August 2023

A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community

scientific article

A general framework for quantitatively assessing ecological stochasticity

scientific article published on 07 August 2019

A large gene cluster in Burkholderia xenovorans encoding abietane diterpenoid catabolism

scientific article

A novel means to develop strain-specific DNA probes for detecting bacteria in the environment ⬇️

scientific article published on July 1, 1997

A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification

scientific article published in August 2012

A proteomic analysis of Psychrobacter articus 273-4 adaptation to low temperature and salinity using a 2-D liquid mapping approach

scientific article published on 01 February 2007

A reappraisal of the habitability of planets around M dwarf stars

scientific article

ARGs-OAP v2.0 with an Expanded SARG Database and Hidden Markov Models for Enhancement Characterization and Quantification of Antibiotic Resistance Genes in Environmental Metagenomes

scientific article

ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database

scientific article

Acetate inhibition of methanogenic, syntrophic benzoate degradation

scientific article

Acetate versus hydrogen as direct electron donors to stimulate the microbial reductive dechlorination process at chloroethene-contaminated sites

scientific article published in September 2002

Advantages of the metagenomic approach for soil exploration: reply from Vogel et al

scientific article published in 2009

Agreia bicolorata gen. nov., sp. nov., to accommodate actinobacteria isolated from narrow reed grass infected by the nematode Heteroanguina graminophila ⬇️

scientific article published on November 1, 2001

Agromyces albus sp. nov., isolated from a plant (Androsace sp.).

scientific article published in September 2003

Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease

scientific article published on 18 May 2015

An automated technique for sampling the contents of stoppered gas-collection vials

Anaerobic biodegradation of phenolic compounds in digested sludge.

scientific article published on July 1983

Anaerobic dechlorination of polychlorobiphenyls (Aroclor 1242) by pasteurized and ethanol-treated microorganisms from sediments.

scientific article

Anaerobic microbial reductive dechlorination of tetrachloroethene to predominately trans-1,2-dichloroethene

scientific article published in August 2004

Analysis of competition in soil among 2,4-dichlorophenoxyacetic acid-degrading bacteria

scientific article

Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming

scientific article

Antibiotic Resistance Gene Detection in the Microbiome Context

scientific article

Antibiotic Resistome Associated with Small-Scale Poultry Production in Rural Ecuador

scientific article published on 10 July 2018

Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence

article

Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens

scientific article published on 4 February 2016

Application of a recA gene-based identification approach to the maize rhizosphere reveals novel diversity in Burkholderia species

scientific article published in June 2006

Application of magnetic biochar/quaternary phosphonium salt to combat the antibiotic resistome in livestock wastewater

scientific article published in 2022

Aquaculture changes the profile of antibiotic resistance and mobile genetic element associated genes in Baltic Sea sediments.

scientific article published on 13 March 2016

Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach

scientific article

Assessing Nitrogen Transformations in a Flooded Agroecosystem Using the Isotope Pairing Technique and Nitrogen Functional Gene Abundances

article

Associative nitrogen fixation (ANF) in switchgrass (Panicum virgatum) across a nitrogen input gradient.

scientific article published in June 2018

Author Correction: Global diversity and biogeography of bacterial communities in wastewater treatment plants

scientific article published on 01 December 2019

Author Correction: Roadmap for naming uncultivated Archaea and Bacteria

scientific article published on 12 November 2020

BEsTRF: a tool for optimal resolution of terminal-restriction fragment length polymorphism analysis based on user-defined primer-enzyme-sequence databases

scientific article published on 15 April 2009

BSD: the Biodegradative Strain Database

scientific article published on January 2003

Bacillus cabrialesii sp. nov., an endophytic plant growth promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico

scientific article published in December 2019

Bacillus-Dominant Airborne Bacterial Communities Identified During Asian Dust Events

scientific article published on 23 March 2019

Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in A Bioreduced Uranium Contaminated Site after Reoxidation

scientific article published on 16 February 2018

Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering

scientific article (publication date: 30 August 2011)

Bacterial community composition of anthropogenic biochar and Amazonian anthrosols assessed by 16S rRNA gene 454 pyrosequencing ⬇️

scientific article published on June 7, 2013

Bacterial community in ancient Siberian permafrost as characterized by culture and culture-independent methods

scientific article published in June 2006

Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica

scientific article

Behavior of Pollutant-Degrading Microorganisms in Aquifers: Predictions for Genetically Engineered Organisms ⬇️

scientific article published on June 1, 1994

Bioavailability of Soil-Sorbed Tetracycline to Escherichia coli under Unsaturated Conditions.

scientific article

Bioavailability of clay-adsorbed dioxin to Sphingomonas wittichii RW1 and its associated genome-wide shifts in gene expression

scientific article published on 21 November 2019

Bioavailability of tetracycline to antibiotic resistant Escherichia coli in water-clay systems

scientific article published on 15 September 2018

Biodegradation of Metal-Nitrilotriacetate Complexes by a Pseudomonas Species: Mechanism of Reaction1 ⬇️

scholarly article

Biodiversity of cryopegs in permafrost

scientific article

Bioenergetic conditions of butyrate metabolism by a syntrophic, anaerobic bacterium in coculture with hydrogen-oxidizing methanogenic and sulfidogenic bacteria

scientific article

Biofilm formation by Psychrobacter arcticus and the role of a large adhesin in attachment to surfaces

scientific article published on 19 April 2013

Biogeography of two cold-adapted genera: Psychrobacter and Exiguobacterium

scientific article

Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution

scientific article

Biomass and biofuel crop effects on biodiversity and ecosystem services in the North Central US

scholarly article by Douglas A. Landis et al published July 2018 in Biomass and Bioenergy

Biotic responses buffer warming-induced soil organic carbon loss in Arctic tundra

article

Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs).

scientific article published on 24 May 2007

Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility

scholarly article

Carbon dioxide fixation and mixotrophic metabolism by strain DCB-1, a dehalogenating anaerobic bacterium

scientific article published on December 1988

Cellulosic biofuel contributions to a sustainable energy future: Choices and outcomes

scientific article

Changes in land use alter the structure of bacterial communities in Western Amazon soils

scientific article

Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium

scientific article

Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov.

scientific article

Characterization of Two Tetrachloroethene-Reducing, Acetate-Oxidizing Anaerobic Bacteria and Their Description as Desulfuromonas michiganensis sp. nov ⬇️

scientific article published on May 1, 2003

Characterization of a bacterial community from a Northeast Siberian seacoast permafrost sample

scientific article

Characterization of potential stress responses in ancient Siberian permafrost psychroactive bacteria

scientific article published on 11 January 2005

Characterization of the Dominant and Rare Members of a Young Hawaiian Soil Bacterial Community with Small-Subunit Ribosomal DNA Amplified from DNA Fractionated on the Basis of Its Guanine and Cytosine Composition

scientific article published on 19 December 2019

Characterization of the acclimation period before anaerobic dehalogenation of halobenzoates

scientific article

Characterization of the structural gene encoding a copper-containing nitrite reductase and homology of this gene to DNA of other denitrifiers

scientific article

Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400T and relatives as Burkholderia xenovorans sp. nov.

scientific article

Climate warming accelerates temporal scaling of grassland soil microbial biodiversity

scientific article published on 25 March 2019

Climate warming enhances microbial network complexity and stability

scientific article published in 2021

Climate warming leads to divergent succession of grassland microbial communities

scholarly article

Climate warming restructures seasonal dynamics of grassland soil microbial communities

scientific article published in 2022

Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture

scientific article published on 12 April 2016

Comment on "The whole-soil carbon flux in response to warming".

scientific article published in February 2018

Community shift of microbial ammonia oxidizers in air-dried rice soils after 22 years of nitrogen fertilization

scholarly article

Comparative Metagenomics of Freshwater Microbial Communities

Comparative analysis of differentially expressed genes in Shewanella oneidensis MR-1 following exposure to UVC, UVB, and UVA radiation

scientific article

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

scientific article published on 31 October 2015

Comparative systems biology across an evolutionary gradient within the Shewanella genus.

scientific article published in September 2009

Comparing the bacterial diversity of acute and chronic dental root canal infections

scientific article

Comparison of the Specificities and Efficacies of Primers for Aromatic Dioxygenase Gene Analysis of Environmental Samples ⬇️

scientific article published on April 15, 2011

Complete genome sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b

scientific article

Complete reductive dechlorination of 1,2-dichloropropane by anaerobic bacteria

scientific article

Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history

scientific article published on 24 June 2019

Consent insufficient for data release-Response

scientific article published on 01 May 2019

Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection.

scientific article published on 21 July 2018

Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms

scientific article

Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities ⬇️

scientific article published on December 27, 2012

Coping with our cold planet

scientific article

Coping with polychlorinated biphenyl (PCB) toxicity: Physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress

scientific article

Correction to: The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation

scientific article published on 2 December 2017

Correction: Recently Deglaciated High-Altitude Soils of the Himalaya: Diverse Environments, Heterogenous Bacterial Communities and Long-Range Dust Inputs from the Upper Troposphere.

scientific article published on 14 January 2014

Correspondence between community structure and function during succession in phenol- and phenol-plus-trichloroethene-fed sequencing batch reactors

scientific article

Corrigendum: The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms

scientific article published on 2 August 2017

Cryptic lineages of the genus Escherichia

scientific article (publication date: October 2009)

DNA Probe Method for the Detection of Specific Microorganisms in the Soil Bacterial Community

scientific article

DNA encoding for an efficient 'Omics processing

scientific article published on 4 May 2010

DNA-DNA hybridization values and their relationship to whole-genome sequence similarities

scientific article (publication date: 2007)

DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment

scientific article published on 31 July 2009

Dechlorination of Four Commercial Polychlorinated Biphenyl Mixtures (Aroclors) by Anaerobic Microorganisms from Sediments.

scientific article published on August 1990

Dechlorination of chloroethenes is inhibited by 2-bromoethanesulfonate in the absence of methanogens

scientific article

Deforestation alters denitrification in a lowland tropical rain forest

scientific article published in Nature

Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils

scientific article published in 2019

Degradation of aroclor 1242 dechlorination products in sediments by Burkholderia xenovorans LB400(ohb) and Rhodococcus sp. strain RHA1(fcb).

scientific article published on April 2006

Degradation of ethylene glycol and polyethylene glycols by methanogenic consortia

scientific article published on July 1983

Degradation of polychlorinated biphenyl mixtures (Aroclors 1242, 1254, and 1260) by the white rot fungus Phanerochaete chrysosporium as evidenced by congener-specific analysis.

scientific article published on July 1995

Dehalogenation: a novel pathway for the anaerobic biodegradation of haloaromatic compounds

scientific article published on 01 December 1982

Denitrification and Nitrous Oxide Production in Successional and Old-Growth Michigan Forests1

article

Denitrification and dissimilatory nitrate reduction to ammonium in digested sludge

scientific article published in September 1981

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

scientific article

Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site

scientific article

Desulfomonile limimaris sp. nov., an anaerobic dehalogenating bacterium from marine sediments

scientific article

Detection in soil of a deletion in an engineered DNA sequence by using DNA probes

scientific article

Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications

scientific article published in December 2004

Development and experimental validation of a predictive threshold cycle equation for quantification of virulence and marker genes by high-throughput nanoliter-volume PCR on the OpenArray platform

scientific article published on 18 April 2008

Development and use of genetic system to identify genes required for efficient low-temperature growth of Psychrobacter arcticus 273-4.

scientific article published on 26 September 2008

Development, operation, and long-term performance of a full-scale biocurtain utilizing bioaugmentation

scientific article

Diagnostic microarray for 14 water and foodborne pathogens using a flatbed scanner

scientific article published on 21 April 2017

Diazotroph Diversity and Nitrogen Fixation in Summer Active Perennial Grasses in a Mediterranean Region Agricultural Soil

scientific article published on 05 November 2019

Diazotrophs show sign of restoration in Amazon rainforest soils with ecosystem rehabilitation

scientific article published on 13 March 2020

Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia

scientific article

Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon

scientific article

Divergence in gene regulation contributes to sympatric speciation of Shewanella baltica strains

scientific article published on 8 December 2017

Diverse and abundant antibiotic resistance genes in Chinese swine farms ⬇️

scientific article published on February 11, 2013

Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments

scientific article

Diversity of deep-sea hydrothermal vent Archaea from Loihi Seamount, Hawaii

Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils

scientific article

Does anaerobic condition play a more positive role in dissipation of antibiotic resistance genes in soil?

scientific article published on 14 November 2020

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction.

scientific article published on 10 April 2015

Dynamics of Microbial Community Composition and Function duringIn SituBioremediation of a Uranium-Contaminated Aquifer

article

Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer

scientific article

Early Spring Nitrogen Dynamics in a Temperate Forest Landscape

article

Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool ⬇️

scientific article published on 17 September 2013

Editorial overview: Ecology and industrial microbiology

scientific article published in June 2014

Editorial: Environmental aspects of antibiotic resistance

scientific article published on 01 April 2019

Editorial: Special section of FEMS Microbiology Ecology on the environmental dimension of antibiotic resistance

scientific article published on 7 September 2016

Editorial: The Environmental Dimension of Antibiotic Resistance

scientific article published on 01 August 2020

Effect of LSU and ITS genetic markers and reference databases on analyses of fungal communities

scholarly article

Effect of low temperature and culture media on the growth and freeze-thawing tolerance of Exiguobacterium strains

scientific article published on 6 February 2007

Effect of storage conditions on the stability and fermentability of enzymatic lignocellulosic hydrolysate

scientific article

Effect of sugarcane burning or green harvest methods on the Brazilian Cerrado soil bacterial community structure

scientific article

Emerging contaminants: A One Health perspective

scientific article published in July 2024

Environmental Risk Assessment of Trifluoroacetic Acid

scientific article published in 1999

Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderia xenovorans LB400.

scientific article published on 12 August 2009

Erratum: Changes in land use alter the structure of bacterial communities in Western Amazon soils

scholarly article published in The ISME Journal

Establishment of denitrification capacity in soil: Effects of carbon, nitrate and moisture

Evaluating the performance of oligonucleotide microarrays for bacterial strains with increasing genetic divergence from the reference strain

scientific article

Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection

scientific article published on 12 December 2017

Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH

scientific article published on 24 April 2015

Evidence for para dechlorination of polychlorobiphenyls by methanogenic bacteria.

scientific article published in June 1995

Experimental warming accelerates positive soil priming in a temperate grassland ecosystem

scientific article published in 2024

Factors controlling the rate of DDE dechlorination to DDMU in Palos Verdes margin sediments under anaerobic conditions

scientific article published in January 2001

Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1.

scientific article

Frequent freeze-thaw cycles yield diminished yet resistant and responsive microbial communities in two temperate soils: a laboratory experiment ⬇️

scientific article published on August 23, 2010

FunGene: the functional gene pipeline and repository

scientific article published on October 2013

Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter

scientific article published on 17 September 2013

Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1.

scientific article

Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing

scientific article

Fungal diversity in permafrost and tallgrass prairie soils under experimental warming conditions

scientific article

Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors

scientific article published in January 2002

Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification

scientific article published on 24 October 2014

Gene-Z: a device for point of care genetic testing using a smartphone

scientific article

Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming

scientific article published on 29 September 2020

Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment

scientific article published on 24 September 2009

General method for determining anaerobic biodegradation potential

scientific article published on April 1984

Genetic and phenotypic diversity of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria isolated from 2,4-D-treated field soils

scientific article

Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction ⬇️

scientific article published on February 8, 2012

Genome sequences of Burkholderia sp. strains CCGE1002 and H160, isolated from legume nodules in Mexico and Brazil

scientific article

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species ⬇️

scientific article published on April 11, 2011

Genome sequencing of five Shewanella baltica strains recovered from the oxic-anoxic interface of the Baltic Sea.

scientific article published on March 2012

Genome-wide examination of the natural solar radiation response in Shewanella oneidensis MR-1.

scientific article

Genomic Insights into Cold Adaptation of Permafrost Bacteria

scholarly article

Genomic Variations Underlying Speciation and Niche Specialization of Shewanella baltica

scientific article published on 15 October 2019

Genomic analysis of the phenylacetyl-CoA pathway in Burkholderia xenovorans LB400

scientific article published on 26 April 2011

Genomic and Expression Analyses of Cold-Adapted Microorganisms

Genomic diversity of Escherichia isolates from diverse habitats

scientific article

Genomic insights that advance the species definition for prokaryotes

scientific article

GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer

scientific article published on 14 July 2009

Global diversity and biogeography of bacterial communities in wastewater treatment plants

scientific article published on 13 May 2019

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations

scientific article

Glucose addition increases the magnitude and decreases the age of soil respired carbon in a long-term permafrost incubation study

scholarly article

H218O isotope exchange studies on the mechanism of reduction of nitric oxide and nitrite to nitrous oxide by denitrifying bacteria. Evidence for an electrophilic nitrosyl during reduction of nitric oxide.

scientific article published in July 1991

High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant.

scientific article published on 31 January 2016

History and impact of RDP: a legacy from Carl Woese to microbiology

scientific article

How much do rRNA gene surveys underestimate extant bacterial diversity?

scientific article published on 5 January 2018

Hydrogen cycling in a three-tiered food web growing on the methanogenic conversion of 3-chlorobenzoate

scientific article (publication date: November 1986)

Hypoxia and Inactivity Related Physiological Changes (Constipation, Inflammation) Are Not Reflected at the Level of Gut Metabolites and Butyrate Producing Microbial Community: The PlanHab Study

scientific article

Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study

scientific article

Identification of Bacterial Isolates Obtained from Intestinal Contents Associated with 12,000-Year-Old Mastodon Remains ⬇️

scientific article published on February 1, 1998

Identification of functionally active aerobic methanotrophs in sediments from an arctic lake using stable isotope probing

scientific article published on 20 March 2012

Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves ⬇️

scientific article published on April 17, 2012

Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics

scientific article

Identifying the genetic basis of ecologically and biotechnologically useful functions of the bacterium Burkholderia vietnamiensis

scientific article published in April 2007

Immunological identification and distribution of dissimilatory heme cd1 and nonheme copper nitrite reductases in denitrifying bacteria

scientific article

Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration

scientific article published on July 2010

Importance of sub-surface rhizosphere-mediated coupled nitrification–denitrification in a flooded agroecosystem in Hawaii

scholarly article by C. Ryan Penton et al published February 2013 in Soil Biology and Biochemistry

In situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen

scientific article published in August 2007

In situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water

scientific article published on February 2008

In-feed antibiotic effects on the swine intestinal microbiome

scientific article published on 17 January 2012

Increased nitrous oxide accumulation by bioelectrochemical denitrification under autotrophic conditions: kinetics and expression of denitrification pathway genes

scientific article

Influence of Manure Application on the Environmental Resistome under Finnish Agricultural Practice with Restricted Antibiotic Use.

scientific article published on 28 April 2017

Influence of Soil Characteristics and Proximity to Antarctic Research Stations on Abundance of Antibiotic Resistance Genes in Soils

scientific article published on 31 October 2016

Influence of dangling ends and surface-proximal tails of targets on probe-target duplex formation in 16S rRNA gene-based diagnostic arrays

scientific article published on 17 November 2006

Influence of substituents on reductive dehalogenation of 3-chlorobenzoate analogs

scientific article published on March 1991

Inhibition by sulfide of nitric and nitrous oxide reduction by denitrifying Pseudomonas fluorescens

scientific article

Initial Characterization of a Reductive Dehalogenase from Desulfitobacterium chlororespirans Co23.

scientific article published on October 1996

Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations

scientific article

Intestinal microbial communities associated with acute enteric infections and disease recovery

scientific article published on 22 September 2015

Involvement of a Collar Structure in Polar Growth and Cell Division of Strain DCB-1.

scientific article published on May 1990

Isolation and characterization of a novel bacterium growing via reductive dehalogenation of 2-chlorophenol

scientific article

Isolation and partial characterization of bacteria in an anaerobic consortium that mineralizes 3-chlorobenzoic Acid.

scientific article

Isolation of Acidophilic Methane-Oxidizing Bacteria from Northern Peat Wetlands ⬇️

scientific article published on October 9, 1998

Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers

scientific article published on 28 April 2017

Isotope labeling studies on the mechanism of N-N bond formation in denitrification.

scientific article published in July 1986

Isotopic evidence for episodic nitrogen fixation in switchgrass (Panicum virgatum L.)

scholarly article

Kinetics of hydrogen consumption by rumen fluid, anaerobic digestor sludge, and sediment

scientific article published on December 1982

Kinetics of microbial dehalogenation of haloaromatic substrates in methanogenic environments.

scientific article published on May 1983

Kinetics of phenol biodegradation by an immobilized methanogenic consortium.

scientific article

Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities

scientific article published on 6 June 2014

Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria

scientific article

Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of shewanella species and identify metabolic pathways conserved at the genus level

scientific article

Leifsonia poae gen. nov., sp. nov., isolated from nematode galls on Poa annua, and reclassification of 'Corynebacterium aquaticum' Leifson 1962 as Leifsonia aquatica (ex Leifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyli Davis et al

scientific article

Localization of the cytochrome cd1 and copper nitrite reductases in denitrifying bacteria

scientific article

Long-Term Effect of Different Fertilization and Cropping Systems on the Soil Antibiotic Resistome

scientific article published on 08 November 2018

Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils

article

Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces

scientific article published on 14 June 2021

Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil

scientific article published on 31 December 2014

Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution

scientific article

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

scholarly article

Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness

scientific article

Metabolic activity of Siberian permafrost isolates, Psychrobacter arcticus and Exiguobacterium sibiricum, at low water activities

scientific article

Metabolism of polyethylene glycol by two anaerobic bacteria, Desulfovibrio desulfuricans and a Bacteroides sp.

scientific article published on October 1986

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces

scientific article published on 9 December 2015

Metagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota

scientific article published in 2018

Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems

scientific article published on 14 May 2021

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes

scientific article

Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community

scientific article

Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

scientific article (publication date: 2016)

Metagenomics: The Paths Forward

Methane-derived carbon flow through microbial communities in arctic lake sediments

scientific article published on 11 January 2015

Methodologies for probing the metatranscriptome of grassland soil

scientific article

Methods for estimating temperature sensitivity of soil organic matter based on incubation data: A comparative evaluation

article

Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog.

scientific article

Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs

scientific article

MicroRNAs-Based Inter-Domain Communication between the Host and Members of the Gut Microbiome

scientific article published on 27 September 2017

Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico

scientific article

Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness

article

Microbes and Climate Change: a Research Prospectus for the Future

scientific article published in 2022

Microbes in the energy grid

scientific article (publication date: 23 May 2008)

Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses

scientific article published on 01 May 2012

Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes

scientific article

Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States

scientific article published in 2018

Microbial Degradation of Ethylenediaminetetraacetate in Soils and Sediments1 ⬇️

scholarly article

Microbial Succession during a Field Evaluation of Phenol and Toluene as the Primary Substrates for Trichloroethene Cometabolism.

scientific article published on April 1997

Microbial communities biostimulated by ethanol during uranium (VI) bioremediation in contaminated sediment as shown by stable isotope probing

scholarly article published 24 June 2014

Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels

scientific article

Microbial dehalorespiration with 1,1,1-trichloroethane

scientific article published in November 2002

Microbial diversity and heterogeneity in sandy subsurface soils

scientific article published in March 2004

Microbial diversity of a Mediterranean soil and its changes after biotransformed dry olive residue amendment

scientific article

Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil

scientific article

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

scientific article

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB.

scientific article

Modulatory Influence of Segmented Filamentous Bacteria on Transcriptomic Response of Gnotobiotic Mice Exposed to TCDD.

scientific article published on 7 September 2017

Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater

scientific article published in January 2003

Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico

scientific article

Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments

scientific article

More replenishment than priming loss of soil organic carbon with additional carbon input

scientific article published in Nature Communications

Most probable number - loop mediated isothermal amplification (MPN-LAMP) for quantifying waterborne pathogens in <25min

scientific article published on 14 November 2016

Multi-locus real-time PCR for quantitation of bacteria in the environment reveals Exiguobacterium to be prevalent in permafrost

scientific article published on 7 December 2006

Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis

scientific article published on 04 March 2013

Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem

scholarly article

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

scientific article (publication date: August 2007)

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes

scientific article published in 2018

New tools for discovering and characterizing microbial diversity

scientific article

NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient

scientific article

Nitrate-stimulated mineralization of ammonium in anaerobic soils

scientific article published on 01 August 1979

Nitric oxide reductase (norB) genes from pure cultures and environmental samples

scientific article

Nitrous oxide from soil denitrification: factors controlling its biological production

scientific article published on 01 May 1980

Nitrous oxide reductase (nosZ) gene fragments differ between native and cultivated Michigan soils

scientific article

Nocardiopsis tropica sp. nov., Nocardiopsis trehalosi sp. nov., nom. rev. and Nocardiopsis dassonvillei subsp. albirubida subsp. nov., comb. nov.

scientific article

Nonlinear estimation of Monod growth kinetic parameters from a single substrate depletion curve.

scientific article published on May 1983

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

scientific article published on 10 April 2018

Novel 2,4-dichlorophenoxyacetic acid degradation genes from oligotrophic Bradyrhizobium sp. strain HW13 isolated from a pristine environment.

scientific article

Novel biphenyl-oxidizing bacteria and dioxygenase genes from a korean tidal mudflat

scientific article

On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes

scientific article

Opening the black box of soil microbial diversity

article published in 1999

Organic acids enhance bioavailability of tetracycline in water to Escherichia coli for uptake and expression of antibiotic resistance

scientific article published on 22 July 2014

Oxygen control prevents denitrifiers and barley plant roots from directly competing for nitrate

article

Pathway of degradation of nitrilotriacetate by a Pseudomonas species

scientific article

Peat-based gnotobiotic plant growth systems for Arabidopsis microbiome research

scientific article published in 2021

Permafrost thaw with warming reduces microbial metabolic capacities in subsurface soils

scientific article published in 2021

Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce

scientific article published on 20 July 2019

Phases of denitrification following oxygen depletion in soil

scientific article published on 28 December 2002

Phenol- and toluene-degrading microbial populations from an aquifer in which successful trichloroethene cometabolism occurred

scientific article published on April 1997

Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth of toluene and description of Azoarcus tolulyticus sp. nov.

scientific article

Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA ⬇️

scientific article published on December 1, 1997

Physiological characterization of strain DCB-1, a unique dehalogenating sulfidogenic bacterium

scientific article published on December 1988

Pilot-Scale Evaluation of Bioaugmentation for In-Situ Remediation of a Carbon Tetrachloride-Contaminated Aquifer

Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs

scientific article published in November 2004

Presence of two different active nirS nitrite reductase genes in a denitrifying Thauera sp. from a high-nitrate-removal-rate reactor

scientific article

Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements

scientific article published on 01 September 2018

Pristine environments harbor a new group of oligotrophic 2,4-dichlorophenoxyacetic acid-degrading bacteria

scientific article

Pristine soils mineralize 3-chlorobenzoate and 2,4-dichlorophenoxyacetate via different microbial populations

scientific article

Probing the functional diversity of global pristine soil communities with 3-chlorobenzoate reveals that communities of generalists dominate catabolic transformation

scientific article published on 30 August 2013

Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead

scientific article published on 17 October 2007

Proteomic analysis of Psychrobacter cryohalolentis K5 during growth at subzero temperatures

scientific article published on 23 November 2006

Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR

scientific article

Psychrobacter arcticus 273-4 uses resource efficiency and molecular motion adaptations for subzero temperature growth

scientific article

Psychrobacter cryohalolentis sp. nov. and Psychrobacter arcticus sp. nov., isolated from Siberian permafrost

scientific article

Purification of cytochrome cd1 nitrite reductase from Pseudomonas stutzeri JM300 and reconstitution with native and synthetic heme d1.

scientific article published in April 1991

Pyrosequencing reveals higher impact of silver nanoparticles than Ag+ on the microbial community structure of activated sludge

scientific article published on 5 October 2013

Quantification of microRNAs directly from body fluids using a base-stacking isothermal amplification method in a point-of-care device

scientific article

Quantitative detection of microbial genes by using DNA microarrays

scientific article published on March 2002

Rathayibacter caricis sp. nov. and Rathayibacter festucae sp. nov., isolated from the phyllosphere of Carex sp. and the leaf gall induced by the nematode Anguina graminis on Festuca rubra L., respectively

scientific article

Recently deglaciated high-altitude soils of the Himalaya: diverse environments, heterogenous bacterial communities and long-range dust inputs from the upper troposphere

scientific article

Reduction of microbial diversity in grassland soil is driven by long-term climate warming

scientific article published in 2022

Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA to NapA.

scientific article published on 23 April 2009

Reductive Dechlorination of DDE to DDMU in Marine Sediment Microcosms ⬇️

scientific article published on May 1, 1998

Reductive dehalogenations of halobenzoates by anaerobic lake sediment microorganisms.

scientific article

Respiratory nitrate ammonification by Shewanella oneidensis MR-1.

scientific article published on 10 November 2006

Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation

scientific article published on 18 March 2010

Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths

scientific article published on 08 July 2019

Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data

scientific article

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes

scientific article published on 15 October 2019

Ribosomal Database Project: data and tools for high throughput rRNA analysis

scientific article

Roadmap for naming uncultivated Archaea and Bacteria

scientific article published on 08 June 2020

Role of tetracycline speciation in the bioavailability to Escherichia coli for uptake and expression of antibiotic resistance

scientific article published on 23 April 2014

Root-Associated Microbiome of Maize Genotypes with Contrasting Phosphorus Use Efficiency

scholarly article

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

scientific article

Selection of fluorescent DNA dyes for real-time LAMP with portable and simple optics.

scientific article

Shewanella baltica Ecotypes Have Wide Transcriptional Variation under the Same Growth Conditions

scientific article (publication date: 19 October 2016)

Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean

scientific article

Shewanella oneidensis MR-1 chemotaxis in a diffusion gradient chamber

scientific article published on 21 December 2010

Shewanella--the environmentally versatile genome

scientific article published in November 2002

Shifts in identity and activity of methanotrophs in arctic lake sediments in response to temperature changes

scientific article

Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska

scientific article

Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach

scientific article

Simultaneous estimation of several nitrogen cycle rates using 15N: Theory and application

article

Simultaneous recovery of RNA and DNA from soils and sediments

scientific article

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

scientific article published on 2 June 2016

Soil microbial community responses to a decade of warming as revealed by comparative metagenomics

scientific article

Soil microbial residue storage linked to soil legacy under biofuel cropping systems in southern Wisconsin, USA

scientific article published in 2013

Soluble Electron Shuttles Can Mediate Energy Taxis toward Insoluble Electron Acceptors ⬇️

scientific article published on February 24, 2012

Spatial Variability in a Successional Plant Community: Patterns of Nitrogen Availability

article

Spatial and resource factors influencing high microbial diversity in soil

scientific article

Spatial controls of methane uptake in upland soils across climatic and geological regions in Greenland

scientific article published on 7 December 2023

Species abundance and diversity of Burkholderia cepacia complex in the environment

scientific article

Spectroscopic and mechanistic studies of Achromobacter cycloclastes nitrite reductase ⬇️

scholarly article

Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay

scientific article

Stability, genotypic and phenotypic diversity of Shewanella baltica in the redox transition zone of the Baltic Sea.

scientific article

Static self-directed sample dispensing into a series of reaction wells on a microfluidic card for parallel genetic detection of microbial pathogens

scientific article

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

scientific article

Strategies to improve reference databases for soil microbiomes

scientific article published on 09 December 2016

Survival of Shewanella oneidensis MR-1 after UV radiation exposure

scientific article

Syntrophy of bacteria and archaea in the anaerobic catabolism of hydrocarbon contaminants

scientific article published on 20 October 2022

TCDD administered on activated carbon eliminates bioavailability and subsequent shifts to a key murine gut commensal

scientific article published on 15 August 2017

TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome

scientific article published on 4 May 2017

Tackling soil diversity with the assembly of large, complex metagenomes

scientific article

Targeted assemblies of cas1 suggest CRISPR-Cas's response to soil warming

scientific article published on 27 March 2020

Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass.

scientific article

Taxonomic characterization of denitrifying bacteria that degrade aromatic compounds and description of Azoarcus toluvorans sp. nov. and Azoarcus toluclasticus sp. nov.

scientific article

Temperature sensitivity of organic matter decomposition of permafrost-region soils during laboratory incubations

article

Temporal change in nitrous oxide and dinitrogen from denitrification following onset of anaerobiosis

scientific article published on October 1979

TerraGenome: a consortium for the sequencing of a soil metagenome

scientific article published in 2009

Tetracycline accumulation in biofilms enhances the selection pressure on Escherichia coli for expression of antibiotic resistance

scientific article published in 2023

The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010.

scientific article

The Exiguobacterium genus: biodiversity and biogeography

scientific article

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.

scientific article published in July 2018

The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation

scientific article published on 21 June 2017

The Planned Introduction of Genetically Engineered Organisms: Ecological Considerations and Recommendations

scientific article published in 1989

The RDP-II (Ribosomal Database Project).

scientific article

The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms

scientific article published on January 2016

The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis

scientific article

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

scientific article (publication date: 2009)

The Vernal Dam: Plant-Microbe Competition for Nitrogen in Northern Hardwood Forests

article

The bacterial species definition in the genomic era.

scientific article

The chemical mechanism of microbial denitrification

scientific article published in February 1982

The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth

scientific article

The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data

scientific article

The soil microbial carbon pump: from conceptual insights to empirical assessments

scientific article published on 25 August 2020

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Thousands of small, novel genes predicted in global phage genomes

scientific article published in 2022

Toward a more robust assessment of intraspecies diversity, using fewer genetic markers

scientific article

Toward unrestricted use of public genomic data:

scientific article

Towards a genome-based taxonomy for prokaryotes

scientific article

Towards environmental systems biology of Shewanella

scientific article published on 07 July 2008

Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress

scientific article

Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation

scientific article

Trends between gene content and genome size in prokaryotic species with larger genomes

scholarly article

Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon

scientific article published on 05 August 2019

Use of both 16S rRNA and engineered functional genes with real-time PCR to quantify an engineered, PCB-degrading Rhodococcus in soil

scientific article

Use of gene probes to aid in recovery and identification of functionally dominant 2,4-dichlorophenoxyacetic acid-degrading populations in soil

scientific article

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

scientific article published on 12 December 2014

Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities

scientific article published in October 2003

Viability, diversity and composition of the bacterial community in a high Arctic permafrost soil from Spitsbergen, Northern Norway

scientific article published in November 2007

Virulence factor activity relationships (VFARs): a bioinformatics perspective

scientific article

Warming enhances old organic carbon decomposition through altering functional microbial communities

scientific article

Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community

scientific article published on 17 January 2020

Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria

scientific article published on 05 June 2020

Winter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: potential consequences on carbon stability

scientific article published on 10 December 2020

Workshop: Graph compression approaches in assembly

Worldwide prevalence of class 2 integrases outside the clinical setting is associated with human impact

scientific article

Xander: employing a novel method for efficient gene-targeted metagenomic assembly

scientific article published on 5 August 2015

tfdA-like genes in 2,4-dichlorophenoxyacetic acid-degrading bacteria belonging to the Bradyrhizobium-Agromonas-Nitrobacter-Afipia cluster in alpha-Proteobacteria

scientific article

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