Microbial functions and soil nitrogen mineralisation processes in the soil of a cool temperate forest in northern Japan

Evaluation of host effects on ectomycorrhizal fungal community compositions in a forested landscape in northern Japan

(2020) Shunsuke Matsuoka et al.   Royal Society Open Science

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

Abundance and functional importance of complete ammonia-oxidizing bacteria (comammox) versus canonical nitrifiers in temperate forest soils

(2020) Ernest D. Osburn et al.   SOIL BIOLOGY & BIOCHEMISTRY

The steps in the soil nitrogen transformation process vary along an aridity gradient via changes in the microbial community

(2019) Chikae Tatsumi et al.   BIOGEOCHEMISTRY

Does conversion from natural forest to plantation affect fungal and bacterial biodiversity, community structure, and co-occurrence networks in the organic horizon and mineral soil?

(2019) Masataka Nakayama et al.   FOREST ECOLOGY AND MANAGEMENT

Consequences of microbial diversity in forest nitrogen cycling: diverse ammonifiers and specialized ammonia oxidizers

(2019) Kazuo Isobe et al.   ISME Journal

Changes in soil microbial community structure and function after afforestation depend on species and age: Case study in a subtropical alluvial island

(2018) Hongzhang Kang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

High soil microbial activity in the winter season enhances nitrogen cycling in a cool-temperate deciduous forest

(2018) Kazuo Isobe et al.   SOIL BIOLOGY & BIOCHEMISTRY

Solar radiation strongly influences the quantity of forest tree root exudates

(2018) Masataka Nakayama et al.   TREES-STRUCTURE AND FUNCTION

Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

(2018) Roland C. Wilhelm et al.   ISME Journal

Soil microbial response to Rhododendron understory removal in southern Appalachian forests: Effects on extracellular enzymes

(2018) Ernest D. Osburn et al.   SOIL BIOLOGY & BIOCHEMISTRY

Geospatial variation in co-occurrence networks of nitrifying microbial guilds

(2018) Christopher M. Jones et al.   MOLECULAR ECOLOGY

The Impacts of Soil Fertility and Salinity on Soil Nitrogen Dynamics Mediated by the Soil Microbial Community Beneath the Halophytic Shrub Tamarisk

(2017) Chikae Iwaoka et al.   MICROBIAL ECOLOGY

Structure, Variation, and Co-occurrence of Soil Microbial Communities in Abandoned Sites of a Rare Earth Elements Mine

(2016) Yuanqing Chao et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Factors contributing to soil nitrogen mineralization and nitrification rates of forest soils in the Japanese archipelago

(2016) Rieko Urakawa et al.   FOREST ECOLOGY AND MANAGEMENT

Mycorrhizal and saprotrophic fungal guilds compete for the same organic substrates but affect decomposition differently

(2016) Inga T. M. Bödeker et al.   FUNCTIONAL ECOLOGY

Correlations between the composition of modular fungal communities and litter decomposition-associated ecosystem functions

(2016) Witoon Purahong et al.   Fungal Ecology

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

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

Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria

(2016) Anne E Taylor et al.   ISME Journal

Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

(2016) Pankaj Trivedi et al.   ISME Journal

Microbial recycling of dissolved organic matter confines plant nitrogen uptake to inorganic forms in a semi-arid ecosystem

(2016) D. Huygens et al.   SOIL BIOLOGY & BIOCHEMISTRY

Linking microbial communities, functional genes and nitrogen-cycling processes in forest floors under four tree species

(2016) Relena R. Ribbons et al.   SOIL BIOLOGY & BIOCHEMISTRY

Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons

(2016) Hirokazu Toju et al.   PLoS One

Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities

(2016) S. Uroz et al.   Scientific Reports

Functional screening of abundant bacteria from acidic forest soil indicates the metabolic potential of Acidobacteria subdivision 1 for polysaccharide decomposition

(2015) Salvador Lladó et al.   BIOLOGY AND FERTILITY OF SOILS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees

(2015) Michaela Urbanová et al.   SOIL BIOLOGY & BIOCHEMISTRY

Recovering glycoside hydrolase genes from active tundra cellulolytic bacteria

(2014) Lee J. Pinnell et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters

(2014) Alexandre B. de Menezes et al.   ENVIRONMENTAL MICROBIOLOGY

Taxonomical and functional microbial community selection in soybean rhizosphere

(2014) Lucas W Mendes et al.   ISME Journal

Fungi-dominant heterotrophic nitrification in a subtropical forest soil of China

(2014) Tongbin Zhu et al.   JOURNAL OF SOILS AND SEDIMENTS

Ecological Perspectives on Microbes Involved in N-Cycling

(2014) Kazuo Isobe et al.   MICROBES AND ENVIRONMENTS

Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage

(2014) Colin Averill et al.   NATURE

Soil C:N ratio is the major determinant of soil microbial community structure in subtropical coniferous and broadleaf forest plantations

(2014) Xiaohua Wan et al.   PLANT AND SOIL

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

The mycorrhizal-associated nutrient economy: a new framework for predicting carbon-nutrient couplings in temperate forests

(2013) Richard P. Phillips et al.   NEW PHYTOLOGIST

The production and turnover of extramatrical mycelium of ectomycorrhizal fungi in forest soils: role in carbon cycling

(2013) A. Ekblad et al.   PLANT AND SOIL

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples

(2012) Hirokazu Toju et al.   PLoS One

A consideration of the relative contributions of different microbial subpopulations to the soil N cycle

(2012) Peter J. Bottomley et al.   Frontiers in Microbiology

Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils

(2011) Huaiying Yao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SOM genesis: microbial biomass as a significant source

(2011) Anja Miltner et al.   BIOGEOCHEMISTRY

Ectomycorrhizal hyphae structure components of the soil bacterial community for decreased phosphatase production

(2011) Denise D. Brooks et al.   FEMS MICROBIOLOGY ECOLOGY

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

(2011) Noah Fierer et al.   ISME Journal

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors

(2011) Aline Frossard et al.   ISME Journal

Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils

(2011) Li-Mei Zhang et al.   ISME Journal

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Nitrification and nitrifying microbial communities in forest soils

(2011) Kazuo Isobe et al.   Journal of Forest Research

Change in gene abundance in the nitrogen biogeochemical cycle with temperature and nitrogen addition in Antarctic soils

(2011) Jaejoon Jung et al.   RESEARCH IN MICROBIOLOGY

Seasonal dynamics of the bacterial community in forest soils under different quantities of leaf litter

(2010) Nicolas Chemidlin Prevost-Boure et al.   APPLIED SOIL ECOLOGY

Plants control the seasonal dynamics of microbial N cycling in a beech forest soil by belowground C allocation

(2010) Christina Kaiser et al.   ECOLOGY

Archaea rather than bacteria control nitrification in two agricultural acidic soils

(2010) Cécile Gubry-Rangin et al.   FEMS MICROBIOLOGY ECOLOGY

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

(2010) Johannes Rousk et al.   ISME Journal

Belowground carbon allocation by trees drives seasonal patterns of extracellular enzyme activities by altering microbial community composition in a beech forest soil

(2010) Christina Kaiser et al.   NEW PHYTOLOGIST

Quantification of effects of season and nitrogen supply on tree below-ground carbon transfer to ectomycorrhizal fungi and other soil organisms in a boreal pine forest

(2010) Mona N. Högberg et al.   NEW PHYTOLOGIST

Tree species-mediated spatial patchiness of the composition of microbial community and physicochemical properties in the topsoils of a tropical montane forest

(2010) Masayuki Ushio et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

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

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

Testing the functional significance of microbial community composition

(2009) Michael S. Strickland et al.   ECOLOGY

Bacteriarather thanArchaeadominate microbial ammonia oxidation in an agricultural soil

(2009) Zhongjun Jia et al.   ENVIRONMENTAL MICROBIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

NITROGEN LIMITATION OF NET PRIMARY PRODUCTIVITY IN TERRESTRIAL ECOSYSTEMS IS GLOBALLY DISTRIBUTED

(2008) David S. LeBauer et al.   ECOLOGY

Plant species traits are the predominant control on litter decomposition rates within biomes worldwide

(2008) William K. Cornwell et al.   ECOLOGY LETTERS

Stoichiometry of soil enzyme activity at global scale

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

Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms

(2008) Maria Tourna et al.   ENVIRONMENTAL MICROBIOLOGY

The influence of soil properties on the structure of bacterial and fungal communities across land-use types

(2008) Christian L. Lauber et al.   SOIL BIOLOGY & BIOCHEMISTRY

Bacterial and fungal contributions to soil nitrogen cycling under Douglas fir and red alder at two sites in Oregon

(2007) Stephanie A. Boyle et al.   SOIL BIOLOGY & BIOCHEMISTRY