Direct cell extraction from fresh and stored soil samples: Impact on microbial viability and community compositions

Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

(2019) Alexander Burkert et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil

(2019) Alan W. Bowsher et al.   mSystems

High proportions of bacteria and archaea across most biomes remain uncultured

(2019) Andrew D. Steen et al.   ISME Journal

Optimization of a Method To Quantify Soil Bacterial Abundance by Flow Cytometry

(2019) Banafshe Khalili et al.   mSphere

Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens

(2018) Bradley M. Hover et al.   Nature Microbiology

Climate warming leads to divergent succession of grassland microbial communities

(2018) Xue Guo et al.   Nature Climate Change

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems

(2017) Joanne B. Emerson et al.   Microbiome

A pipeline for developing and testing staining protocols for flow cytometry, demonstrated with SYBR Green I and propidium iodide viability staining

(2016) Alina Nescerecka et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Flow Cytometric Assessment of Bacterial Abundance in Soils, Sediments and Sludge

(2016) Aline Frossard et al.   Frontiers in Microbiology

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

(2016) Paul Carini et al.   Nature Microbiology

A rapid flow cytometry method to assess bacterial abundance in agricultural soil

(2015) Mélanie Bressan et al.   APPLIED SOIL ECOLOGY

Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis

(2015) Liyou Wu et al.   BMC MICROBIOLOGY

Mass and Density Measurements of Live and Dead Gram-Negative and Gram-Positive Bacterial Populations

(2014) Christina L. Lewis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evaluation of soil storage methods for soil microbial community using genetic and metabolic fingerprintings

(2014) Hang Cui et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption

(2014) Benjamin L Wang et al.   NATURE BIOTECHNOLOGY

Cell Size Distributions of Soil Bacterial and Archaeal Taxa

(2013) Maria C. Portillo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples

(2013) Benjamin E. R. Rubin et al.   PLoS One

Cultivation of unculturable soil bacteria

(2012) Van H.T. Pham et al.   TRENDS IN BIOTECHNOLOGY

Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies

(2011) Yong Kong   GENOMICS

An improved method for extracting bacteria from soil for high molecular weight DNA recovery and BAC library construction

(2011) Juan Liu et al.   JOURNAL OF MICROBIOLOGY

Bias in bacterial diversity as a result of Nycodenz extraction from bulk soil

(2011) Peter N. Holmsgaard et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial mediation of carbon-cycle feedbacks to climate warming

(2011) Jizhong Zhou et al.   Nature Climate Change

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples

(2010) Christian L. Lauber et al.   FEMS MICROBIOLOGY LETTERS

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

The impacts of climate change on water resources and agriculture in China

(2010) Shilong Piao et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Optimizing the indirect extraction of prokaryotic DNA from soils

(2010) Kurt. E. Williamson et al.   SOIL BIOLOGY & BIOCHEMISTRY

Complete genome sequence of Haliangium ochraceum type strain (SMP-2T)

(2010) Natalia Ivanova et al.   Standards in Genomic Sciences

Variability of soil microbial properties: Effects of sampling, handling and storage

(2009) Jitka Černohlávková et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Reappraisal of drying and wetting effects on C and N mineralization and fluxes in soils

(2008) WERNER BORKEN et al.   GLOBAL CHANGE BIOLOGY

Tumebacillus permanentifrigoris gen. nov., sp. nov., an aerobic, spore-forming bacterium isolated from Canadian high Arctic permafrost

(2008) B. Steven et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Recovery and quantification of bacterial cells associated with streambed sediments

(2008) Stefano Amalfitano et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity

(2008) Vesela A. Tzeneva et al.   RESEARCH IN MICROBIOLOGY