Advances in monitoring soil microbial community dynamic and function

Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities

(2019) Zhou Shi et al.   mSystems

NanoSIMS for biological applications: Current practices and analyses

(2018) Jamie Nuñez et al.   Biointerphases

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

(2018) Simon Ardui et al.   NUCLEIC ACIDS RESEARCH

NanoSIMS for biological applications: Current practices and analyses

(2018) Jamie Nuñez et al.   Biointerphases

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

(2018) Nicholas D. Youngblut et al.   Frontiers in Microbiology

Effects of liming on the microbial biomass and its activities in soils long-term contaminated by toxic elements

(2018) G. Mühlbachová et al.   PLANT SOIL AND ENVIRONMENT

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes

(2018) Joshua P. Earl et al.   Microbiome

Application of stable-isotope labelling techniques for the detection of active diazotrophs

(2017) Roey Angel et al.   ENVIRONMENTAL MICROBIOLOGY

Success of chemolithoautotrophic SUP05 and Sulfurimonas GD17 cells in pelagic Baltic Sea redox zones is facilitated by their lifestyles as K- and r -strategists

(2017) Andreas Rogge et al.   ENVIRONMENTAL MICROBIOLOGY

Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis

(2017) Ramon Terrado et al.   ISME Journal

DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies

(2017) Ryan M Ziels et al.   ISME Journal

Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing

(2017) Michael Tessler et al.   Scientific Reports

Microbial Response to Soil Liming of Damaged Ecosystems Revealed by Pyrosequencing and Phospholipid Fatty Acid Analyses

(2017) Ramya Narendrula-Kotha et al.   PLoS One

Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments

(2017) Salvador Lladó et al.   PLoS One

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis

(2016) Ryan S. Renslow et al.   Biointerphases

Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami

(2016) Satoshi Hiraoka et al.   BMC GENOMICS

The succession pattern of soil microbial communities and its relationship with tobacco bacterial wilt

(2016) Jiaojiao Niu et al.   BMC MICROBIOLOGY

Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond

(2016) Satoshi Hiraoka et al.   MICROBES AND ENVIRONMENTS

Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis

(2016) Ryan S. Renslow et al.   Biointerphases

Microbial Community Structure and Function of Soil Following Ecosystem Conversion from Native Forests to Teak Plantation Forests

(2016) Vidya de Gannes et al.   Frontiers in Microbiology

Identification of bacteria assimilating formaldehyde in a biological activated carbon filter by means of DNA stable isotope probing and next-generation sequencing

(2016) I. Kasuga et al.   Water Science and Technology-Water Supply

Quantifying the Sensitivity of Soil Microbial Communities to Silver Sulfide Nanoparticles Using Metagenome Sequencing

(2016) Casey L. Doolette et al.   PLoS One

Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon

(2016) Riccardo Rosselli et al.   Scientific Reports

Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease

(2016) Valentina Cappello et al.   Scientific Reports

Nitrogen addition changes grassland soil organic matter decomposition

(2015) Charlotte E. Riggs et al.   BIOGEOCHEMISTRY

Illumina MiSeq sequencing investigation on the contrasting soil bacterial community structures in different iron mining areas

(2015) Chen Hong et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

N2-fixation, ammonium release and N-transfer to the microbial and classical food web within a plankton community

(2015) Birgit Adam et al.   ISME Journal

Heterogeneous composition of key metabolic gene clusters in a vent mussel symbiont population

(2015) Tetsuro Ikuta et al.   ISME Journal

Single cell activity reveals direct electron transfer in methanotrophic consortia

(2015) Shawn E. McGlynn et al.   NATURE

Functional diversity: an overview of its history and applicability

(2015) Livia Maira Orlandi Laureto et al.   Natureza & Conservacao

Effect of metal contamination on microbial enzymatic activity in soil

(2015) Diane F. Hagmann et al.   SOIL BIOLOGY & BIOCHEMISTRY

High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats

(2015) Jizhong Zhou et al.   mBio

Illumina high-throughput sequencing and comparative analysis of bacterial communities in cherry orchard soil

(2015) Lingzhi Liu et al.   TOXICOLOGICAL AND ENVIRONMENTAL CHEMISTRY

Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research

(2015) Brendan P. Hodkinson et al.   Advances in Wound Care

Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle

(2014) Henning Seedorf et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling

(2014) Stephen J. Salipante et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

454 Pyrosequencing Analysis of Bacterial Diversity Revealed by a Comparative Study of Soils from Mining Subsidence and Reclamation Areas

(2014) Yuanyuan Li et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

16S rDNA Pyrosequencing Analysis of Bacterial Community in Heavy Metals Polluted Soils

(2014) Marcin Gołębiewski et al.   MICROBIAL ECOLOGY

The role of bacteria and mycorrhiza in plant sulfur supply

(2014) Jacinta Gahan et al.   Frontiers in Plant Science

Analysis of plant microbe interactions in the era of next generation sequencing technologies

(2014) Claudia Knief   Frontiers in Plant Science

Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing

(2013) Suparna Mitra et al.   BMC GENOMICS

Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem

(2013) Shawn P. Brown et al.   FEMS MICROBIOLOGY ECOLOGY

Fungal and bacterial utilization of organic substrates depends on substrate complexity and N availability

(2013) Marianne Koranda et al.   FEMS MICROBIOLOGY ECOLOGY

Horizontal gene transfer in plants

(2013) Caihua Gao et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Measuring carbon and N2fixation in field populations of colonial and free-living unicellular cyanobacteria using nanometer-scale secondary ion mass spectrometry1

(2013) Rachel A. Foster et al.   JOURNAL OF PHYCOLOGY

Editorial 2014

(2013) Kevin Livingstone et al.   Molecular Ecology Resources

Updating benchtop sequencing performance comparison

(2013) Sebastian Jünemann et al.   NATURE BIOTECHNOLOGY

Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing

(2013) David E. Alquezar-Planas et al.   Scientific Reports

High throughput phospholipid fatty acid analysis of soils

(2012) Jeffrey S. Buyer et al.   APPLIED SOIL ECOLOGY

Applications of functional gene microarrays for profiling microbial communities

(2012) Zhili He et al.   CURRENT OPINION IN BIOTECHNOLOGY

Viral infection ofPhaeocystis globosaimpedes release of chitinous star-like structures: quantification using single cell approaches

(2012) A. R. Sheik et al.   ENVIRONMENTAL MICROBIOLOGY

GeoChip-Based Analysis of Microbial Functional Gene Diversity in a Landfill Leachate-Contaminated Aquifer

(2012) Zhenmei Lu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Comparison of Next-Generation Sequencing Systems

(2012) Lin Liu et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Genomic approaches to studying the human microbiota

(2012) George M. Weinstock   NATURE

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

(2012) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

(2012) Chengwei Luo et al.   PLoS One

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The impact of next-generation sequencing on genomics

(2011) Jun Zhang et al.   Journal of Genetics and Genomics

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Soil Respiration, Climate Change and the Role of Microbial Communities

(2011) O. Roger Anderson   PROTIST

Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2

(2010) Zhili He et al.   ECOLOGY LETTERS

Soil bacterial and fungal communities across a pH gradient in an arable soil

(2010) Johannes Rousk et al.   ISME Journal

Assessment of soil fungal communities using pyrosequencing

(2010) Young Woon Lim et al.   JOURNAL OF MICROBIOLOGY

Microbial phylogeny and diversity: Small subunit ribosomal RNA sequence analysis and beyond

(2010) J. Rajendhran et al.   MICROBIOLOGICAL RESEARCH

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Factors affecting soil microbial community structure in tomato cropping systems

(2010) Jeffrey S. Buyer et al.   SOIL BIOLOGY & BIOCHEMISTRY

Use and misuse of PLFA measurements in soils

(2010) Åsa Frostegård et al.   SOIL BIOLOGY & BIOCHEMISTRY

Arbuscular mycorrhizal fungal community structure and diversity in response to long-term fertilization: a field case from China

(2010) Fa Yuan Wang et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

DNA Stable-Isotope Probing (DNA-SIP)

(2010) Eric A. Dunford et al.   Jove-Journal of Visualized Experiments

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms

(2009) Alan E. Richardson et al.   PLANT AND SOIL

Fixation and fate of C and N in the cyanobacterium Trichodesmium using nanometer-scale secondary ion mass spectrometry

(2009) J. A. Finzi-Hart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Advances in Imaging Secondary Ion Mass Spectrometry for Biological Samples

(2008) Steven G. Boxer et al.   Annual Review of Biophysics

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Stoichiometry of soil enzyme activity at global scale

(2008) Robert L. Sinsabaugh et al.   ECOLOGY LETTERS

Influence of temperature and soil water content on bacterial, archaeal and denitrifying microbial communities in drained fen grassland soil microcosms

(2008) Blaž Stres et al.   FEMS MICROBIOLOGY ECOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Relationships between soil respiration and soil moisture

(2008) Freeman J. Cook et al.   SOIL BIOLOGY & BIOCHEMISTRY

Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use

(2008) V. Acosta-Martínez et al.   SOIL BIOLOGY & BIOCHEMISTRY