Assembly of Active Bacterial and Fungal Communities Along a Natural Environmental Gradient

Microbial response to simulated global change is phylogenetically conserved and linked with functional potential

(2015) Anthony S Amend et al.   ISME Journal

Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

(2015) Cedar N. Hesse et al.   Frontiers in Microbiology

Microbial resource utilization traits and trade-offs: implications for community structure, functioning, and biogeochemical impacts at present and in the future

(2015) Elena Litchman et al.   Frontiers in Microbiology

Resuscitation of the rare biosphere contributes to pulses of ecosystem activity

(2015) Zachary T. Aanderud et al.   Frontiers in Microbiology

Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing

(2013) Michaela Novodvorska et al.   BMC GENOMICS

Climate change alters ecological strategies of soil bacteria

(2013) Sarah E. Evans et al.   ECOLOGY LETTERS

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

Responses of soil bacterial and fungal communities to extreme desiccation and rewetting

(2013) Romain L Barnard et al.   ISME Journal

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

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

Phylogenetic Clustering of Soil Microbial Communities by 16S rRNA but Not 16S rRNA Genes

(2012) Kristen M. DeAngelis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial Mechanisms Mediating Increased Soil C Storage under Elevated Atmospheric N Deposition

(2012) Sarah D. Eisenlord et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils

(2012) Coralie Damon et al.   PLoS One

Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups

(2012) S. A. Placella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

(2011) Kuan-Liang Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fungal spores: Dormancy, germination, chemical composition, and role in biotechnology (review)

(2011) E. P. Feofilova et al.   APPLIED BIOCHEMISTRY AND MICROBIOLOGY

RNA Dynamics in Aging Bacterial Spores

(2011) Einat Segev et al.   CELL

Massive multiplication of genome and ribosomes in dormant cells (akinetes) of Aphanizomenon ovalisporum (Cyanobacteria)

(2011) Assaf Sukenik et al.   ISME Journal

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

(2011) Petr Baldrian et al.   ISME Journal

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

More closely related species are more ecologically similar in an experimental test

(2011) J. H. Burns et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Living in the Now: Physiological Mechanisms to Tolerate a Rapidly Changing Environment

(2010) Gretchen E. Hofmann et al.   Annual Review of Physiology

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Opposing effects of competitive exclusion on the phylogenetic structure of communities

(2010) Margaret M. Mayfield et al.   ECOLOGY LETTERS

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

(2010) Johannes Rousk et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

Dormancy contributes to the maintenance of microbial diversity

(2010) S. E. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Investigating the mechanisms for the opposing pH relationships of fungal and bacterial growth in soil

(2010) Johannes Rousk et al.   SOIL BIOLOGY & BIOCHEMISTRY

Considering fungal:bacterial dominance in soils – Methods, controls, and ecosystem implications

(2010) Michael S. Strickland et al.   SOIL BIOLOGY & BIOCHEMISTRY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Contrasting Soil pH Effects on Fungal and Bacterial Growth Suggest Functional Redundancy in Carbon Mineralization

(2009) J. Rousk et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests

(2009) Steven W. Kembel   ECOLOGY LETTERS

The merging of community ecology and phylogenetic biology

(2009) Jeannine Cavender-Bares et al.   ECOLOGY LETTERS

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS

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

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH