Forest conversion induces seasonal variation in microbial β-diversity

The endobacterium of an arbuscular mycorrhizal fungus modulates the expression of its toxin–antitoxin systems during the life cycle of its host

(2017) Alessandra Salvioli di Fossalunga et al.   ISME Journal

Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire

(2017) Sang-Hoon Lee et al.   ISME Journal

Feed in summer, rest in winter: microbial carbon utilization in forest topsoil

(2017) Lucia Žifčáková et al.   Microbiome

Long-lasting effects of land use history on soil fungal communities in second-growth tropical rain forests

(2016) Benedicte Bachelot et al.   ECOLOGICAL APPLICATIONS

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

(2016) Teotonio Soares de Carvalho et al.   ECOLOGY

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

(2016) Nhu H. Nguyen et al.   Fungal Ecology

Land-use intensification causes multitrophic homogenization of grassland communities

(2016) Martin M. Gossner et al.   NATURE

Biogeographic Distribution Patterns of Bacteria in Typical Chinese Forest Soils

(2016) Zongwei Xia et al.   Frontiers in Microbiology

Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes

(2015) Ximei Zhang et al.   GLOBAL CHANGE BIOLOGY

Differentiating between niche and neutral assembly in metacommunities using null models of β-diversity

(2015) Caroline M. Tucker et al.   OIKOS

Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

(2015) Francisco Dini-Andreote et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deterministic processes vary during community assembly for ecologically dissimilar taxa

(2015) Jeff R. Powell et al.   Nature Communications

Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

(2015) Morten Schostag et al.   Frontiers in Microbiology

Impact of Lowland Rainforest Transformation on Diversity and Composition of Soil Prokaryotic Communities in Sumatra (Indonesia)

(2015) Dominik Schneider et al.   Frontiers in Microbiology

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

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

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

(2014) Francisco Dini-Andreote et al.   ISME Journal

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

(2014) Fabiana S. Paula et al.   MOLECULAR ECOLOGY

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

(2014) Jizhong Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An arbuscular mycorrhizal fungus significantly modifies the soil bacterial community and nitrogen cycling during litter decomposition

(2013) Erin E. Nuccio et al.   ENVIRONMENTAL MICROBIOLOGY

Temporal variability in soil microbial communities across land-use types

(2013) Christian L Lauber et al.   ISME Journal

A meta-analysis of changes in bacterial and archaeal communities with time

(2013) Ashley Shade et al.   ISME Journal

Changes in assembly processes in soil bacterial communities following a wildfire disturbance

(2013) Scott Ferrenberg et al.   ISME Journal

Patterns and Processes of Microbial Community Assembly

(2013) D. R. Nemergut et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Revisiting the host effect on ectomycorrhizal fungal communities: implications from host–fungal associations in relict Pseudotsuga japonica forests

(2013) Masao Murata et al.   MYCORRHIZA

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

The seasonal pattern of soil microbial community structure in mesic low arctic tundra

(2013) Kate M. Buckeridge et al.   SOIL BIOLOGY & BIOCHEMISTRY

Adding unaligned sequences into an existing alignment using MAFFT and LAST

(2012) Kazutaka Katoh et al.   BIOINFORMATICS

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

Unlocking the potential of metagenomics through replicated experimental design

(2012) Rob Knight et al.   NATURE BIOTECHNOLOGY

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

(2012) J. L. M. Rodrigues et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Responses of the extracellular enzyme activities in hardwood forest to soil temperature and seasonality and the potential effects of climate change

(2012) Petr Baldrian et al.   SOIL BIOLOGY & BIOCHEMISTRY

Global Biogeography and Quantitative Seasonal Dynamics of Gemmatimonadetes in Soil

(2011) Jennifer M. DeBruyn et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Community assembly: alternative stable states or alternative transient states?

(2011) Tadashi Fukami et al.   ECOLOGY LETTERS

Temperature and biotic factors influence bacterial communities associated with the cyanobacteriumMicrocystissp.

(2011) Claudia Dziallas et al.   ENVIRONMENTAL MICROBIOLOGY

The bacterial biogeography of British soils

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

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

ggplot2: Elegant Graphics for Data Analysis

(2011) Cedric Ginestet   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY

Disentangling the importance of ecological niches from stochastic processes across scales

(2011) J. M. Chase et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Drivers of bacterial  -diversity depend on spatial scale

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

(2010) Frank Rasche et al.   ISME Journal

Decline of soil fertility during forest conversion of secondary forest to Chinese fir plantations in subtropical China

(2010) Q. Wang et al.   LAND DEGRADATION & DEVELOPMENT

Conversion of secondary broadleaved forest into Chinese fir plantation alters litter production and potential nutrient returns

(2010) Qingkui Wang et al.   PLANT ECOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Tropical forests were the primary sources of new agricultural land in the 1980s and 1990s

(2010) H. K. Gibbs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity meets decomposition

(2010) Mark O. Gessner et al.   TRENDS IN ECOLOGY & EVOLUTION

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

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Testing the functional significance of microbial community composition

(2009) Michael S. Strickland et al.   ECOLOGY

Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland

(2009) Karelyn Cruz-Martínez et al.   ISME Journal

Effect of monospecific and mixed Cunninghamia lanceolata plantations on microbial community and two functional genes involved in nitrogen cycling

(2009) Li Liu et al.   PLANT AND SOIL

Leaf litter decomposition in the pure and mixed plantations of Cunninghamia lanceolata and Michelia macclurei in subtropical China

(2008) Qingkui Wang et al.   BIOLOGY AND FERTILITY OF SOILS

Relative impacts of land-use, management intensity and fertilization upon soil microbial community structure in agricultural systems

(2008) Kamlesh Jangid et al.   SOIL BIOLOGY & BIOCHEMISTRY

Seasonal changes in the soil microbial community in a grassland plant diversity gradient four years after establishment

(2008) Maike Habekost et al.   SOIL BIOLOGY & BIOCHEMISTRY

Comparisons of litterfall, litter decomposition and nutrient return in a monoculture Cunninghamia lanceolata and a mixed stand in southern China

(2007) Qingkui Wang et al.   FOREST ECOLOGY AND MANAGEMENT