Embracing the unknown: disentangling the complexities of the soil microbiome

Survey of corticioid fungi in North American pinaceous forests reveals hyperdiversity, underpopulated sequence databases, and species that are potentially ectomycorrhizal

(2017) Lisa M. Rosenthal et al.   MYCOLOGIA

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

(2017) Frédéric Mahé et al.   Nature Ecology & Evolution

Rapidly restoring biological soil crusts and ecosystem functions in a severely disturbed desert ecosystem

(2016) Lindsay P. Chiquoine et al.   ECOLOGICAL APPLICATIONS

Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs

(2016) A. Ö. C. Dupont et al.   ENVIRONMENTAL MICROBIOLOGY

Spatial scale drives patterns in soil bacterial diversity

(2016) Sarah L. O'Brien et al.   ENVIRONMENTAL MICROBIOLOGY

What drives differences in arbuscular mycorrhizal fungal communities among plant species?

(2016) Ylva Lekberg et al.   Fungal Ecology

Phylogenetic organization of bacterial activity

(2016) Ember M Morrissey et al.   ISME Journal

Strategies to improve reference databases for soil microbiomes

(2016) Jinlyung Choi et al.   ISME Journal

Diversity is the question, not the answer

(2016) Ashley Shade   ISME Journal

Mobile genes in the human microbiome are structured from global to individual scales

(2016) I. L. Brito et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces

(2016) Cheryl P. Andam et al.   mBio

Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

(2016) Charles Pepe-Ranney 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

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

(2016) Tess E. Brewer et al.   Nature Microbiology

Diversity and Ecology of Viruses in Hyperarid Desert Soils

(2015) Olivier Zablocki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest

(2015) Albert Barberán et al.   ECOLOGY LETTERS

Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter

(2015) Lucia Žifčáková et al.   ENVIRONMENTAL MICROBIOLOGY

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

(2015) Leho Tedersoo et al.   ISME Journal

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

(2015) Jenni Hultman et al.   NATURE

Ecology and exploration of the rare biosphere

(2015) Michael D. J. Lynch et al.   NATURE REVIEWS MICROBIOLOGY

Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology

(2015) James I. Prosser   NATURE REVIEWS MICROBIOLOGY

Microbial hotspots and hot moments in soil: Concept & review

(2015) Yakov Kuzyakov et al.   SOIL BIOLOGY & BIOCHEMISTRY

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes

(2015) Kathryn M. Docherty et al.   PLoS One

Effects of Fertilization and Sampling Time on Composition and Diversity of Entire and Active Bacterial Communities in German Grassland Soils

(2015) Sarah Herzog et al.   PLoS One

Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla

(2014) Harald Cederlund et al.   APPLIED SOIL ECOLOGY

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

(2014) Suzanne M. Prober et al.   ECOLOGY LETTERS

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

(2014) Uli Klümper et al.   ISME Journal

Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

(2014) Jennifer D Rocca et al.   ISME Journal

Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally

(2014) K. S. Ramirez et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Community structure of prokaryotes and their functional potential in subsoils is more affected by spatial heterogeneity than by temporal variations

(2014) Marie Uksa et al.   SOIL BIOLOGY & BIOCHEMISTRY

A theoretical analysis of microbial eco-physiological and diffusion limitations to carbon cycling in drying soils

(2014) S. Manzoni et al.   SOIL BIOLOGY & BIOCHEMISTRY

Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

(2014) Sascha Krause et al.   Frontiers in Microbiology

Estimates of viral abundance in soils are strongly influenced by extraction and enumeration methods

(2013) Kurt E. Williamson et al.   BIOLOGY AND FERTILITY OF SOILS

Global drivers and patterns of microbial abundance in soil

(2013) Hector M. Serna-Chavez et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

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

(2013) Steven J Blazewicz et al.   ISME Journal

Temporal variability in soil microbial communities across land-use types

(2013) Christian L Lauber et al.   ISME Journal

Strong coupling of plant and fungal community structure across western Amazonian rainforests

(2013) Kabir G Peay et al.   ISME Journal

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Going back to the roots: the microbial ecology of the rhizosphere

(2013) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Advances in plant growth-promoting bacterial inoculant technology: formulations and practical perspectives (1998–2013)

(2013) Yoav Bashan et al.   PLANT AND SOIL

Back to the basics: The need for ecophysiological insights to enhance our understanding of microbial behaviour in the rhizosphere

(2013) Francisco Dini-Andreote et al.   PLANT AND SOIL

Micrometer-scale physical structure and microbial composition of soil macroaggregates

(2013) Vanessa L. Bailey et al.   SOIL BIOLOGY & BIOCHEMISTRY

Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon

(2013) Woo Jun Sul et al.   SOIL BIOLOGY & BIOCHEMISTRY

Active microorganisms in soil: Critical review of estimation criteria and approaches

(2013) Evgenia Blagodatskaya et al.   SOIL BIOLOGY & BIOCHEMISTRY

Perspectives of plant-associated microbes in heavy metal phytoremediation

(2012) M. Rajkumar et al.   BIOTECHNOLOGY ADVANCES

Estimation of fungal biomass in forest litter and soil

(2012) Petr Baldrian et al.   Fungal Ecology

Sizing up metatranscriptomics

(2012) Mary Ann Moran et al.   ISME Journal

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

(2012) Davide Bulgarelli et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

Digging deeper to find unique microbial communities: The strong effect of depth on the structure of bacterial and archaeal communities in soil

(2012) Kathryn G. Eilers et al.   SOIL BIOLOGY & BIOCHEMISTRY

Cultivation of unculturable soil bacteria

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

Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies

(2012) Adrian Ho et al.   Environmental Microbiology Reports

Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition

(2012) Nicholas J. Bouskill et al.   Frontiers in Microbiology

The generation and maintenance of diversity in microbial communities

(2011) Noah Fierer et al.   AMERICAN JOURNAL OF BOTANY

A Coevolutionary Framework for Managing Disease-Suppressive Soils

(2011) Linda L. Kinkel et al.   Annual Review of Phytopathology

The bacterial biogeography of British soils

(2011) Robert I. Griffiths et al.   ENVIRONMENTAL MICROBIOLOGY

Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH

(2011) Eiko Kuramae et al.   FEMS MICROBIOLOGY ECOLOGY

Soil characteristics more strongly influence soil bacterial communities than land-use type

(2011) Eiko E. Kuramae et al.   FEMS MICROBIOLOGY ECOLOGY

Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning

(2011) Ella Wessén et al.   ISME Journal

Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions

(2011) Roey Angel et al.   ISME Journal

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

(2011) Gaddy T. Bergmann et al.   SOIL BIOLOGY & BIOCHEMISTRY

Exploring the viral world through metagenomics

(2011) Karyna Rosario et al.   Current Opinion in Virology

Effect of DNA Extraction Method on the Apparent Microbial Diversity of Soil

(2010) O. Inceoglu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Horizontal arsC gene transfer among microorganisms isolated from arsenic polluted soil

(2010) Maria F. Villegas-Torres et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale

(2010) D Bru et al.   ISME Journal

Examining the global distribution of dominant archaeal populations in soil

(2010) Scott T Bates et al.   ISME Journal

Are preferential flow paths perpetuated by microbial activity in the soil matrix? A review

(2010) Verónica L. Morales et al.   JOURNAL OF HYDROLOGY

The Path to Personalized Medicine

(2010) Margaret A. Hamburg et al.   NEW ENGLAND JOURNAL OF MEDICINE

Conceptual Synthesis in Community Ecology

(2010) Mark Vellend   QUARTERLY REVIEW OF BIOLOGY

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

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

Ecology of viruses in soils: Past, present and future perspectives

(2010) Makoto Kimura et al.   SOIL SCIENCE AND PLANT NUTRITION

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

(2010) Sara Vieira-Silva et al.   PLoS Genetics

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

Global patterns in belowground communities

(2009) Noah Fierer et al.   ECOLOGY LETTERS

Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere

(2009) Gabriele Berg et al.   FEMS MICROBIOLOGY ECOLOGY

Carbon flow in the rhizosphere: carbon trading at the soil–root interface

(2009) D. L. Jones et al.   PLANT AND SOIL

The genomic basis of trophic strategy in marine bacteria

(2009) F. M. Lauro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

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

Quantitative assessment of the fungal contribution to microbial tissue in soil

(2008) R JOERGENSEN et al.   SOIL BIOLOGY & BIOCHEMISTRY