Assembly of functional microbial communities in paddy soil with long-term application of pig manure under rice-rape cropping system

Assembly of abundant and rare bacterial and fungal sub-communities in different soil aggregate sizes in an apple orchard treated with cover crop and fertilizer

(2021) Wei Zheng et al.   SOIL BIOLOGY & BIOCHEMISTRY

Bridging Rare and Abundant Bacteria with Ecosystem Multifunctionality in Salinized Agricultural Soils: from Community Diversity to Environmental Adaptation

(2021) Wenjie Wan et al.   mSystems

Responses of nitrification and bacterial community in three size aggregates of paddy soil to both of initial fertility and biochar addition

(2021) Qiong Hou et al.   APPLIED SOIL ECOLOGY

Fertilization regime has a greater effect on soil microbial community structure than crop rotation and growth stage in an agroecosystem

(2020) Zhibin Guo et al.   APPLIED SOIL ECOLOGY

Abundant fungi adapt to broader environmental gradients than rare fungi in agricultural fields

(2020) Shuo Jiao et al.   GLOBAL CHANGE BIOLOGY

Heavy nitrogen application increases soil nitrification through ammonia-oxidizing bacteria rather than archaea in acidic tea (Camellia sinensis L.) plantation soil

(2020) Xiangde Yang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Effects of soil physicochemical properties on microbial communities in different ecological niches in coastal area

(2020) Tianyun Shao et al.   APPLIED SOIL ECOLOGY

Biogeography and diversity patterns of abundant and rare bacterial communities in rice paddy soils across China

(2020) Jinyu Hou et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Soil microbial diversity and composition: Links to soil texture and associated properties

(2020) Qing Xia et al.   SOIL BIOLOGY & BIOCHEMISTRY

Effect of biogas slurry addition on soil properties, yields, and bacterial composition in the rice-rape rotation ecosystem over 3 years

(2019) Min Xu et al.   JOURNAL OF SOILS AND SEDIMENTS

Structural equation modeling of a winnowed soil microbiome identifies how invasive plants re-structure microbial networks

(2019) Steven D. Mamet et al.   ISME Journal

Microbial community structure and microbial networks correspond to nutrient gradients within coastal wetlands of the Laurentian Great Lakes.

(2019) Dean J Horton et al.   FEMS MICROBIOLOGY ECOLOGY

Microbial functional diversity and carbon use feedback in soils as affected by heavy metals

(2019) Yilu Xu et al.   ENVIRONMENT INTERNATIONAL

Microbial community diversity during fermentative hydrogen production inoculating various pretreated cultures

(2019) Guang Yang et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

Mediation of functional gene and bacterial community profiles in the sediments of eutrophic Chaohu Lake by total nitrogen and season

(2019) Yang-Yang Fan et al.   ENVIRONMENTAL POLLUTION

Benefits and trade‐offs of replacing synthetic fertilizers by animal manures in crop production in China: a meta‐analysis

(2019) Xiaoying Zhang et al.   GLOBAL CHANGE BIOLOGY

The responses of extracellular enzyme activities and microbial community composition under nitrogen addition in an upland soil

(2019) Sami Ullah et al.   PLoS One

Soil Microbial Communities and Enzyme Activities after Long-Term Application of Inorganic and Organic Fertilizers at Different Depths of the Soil Profile

(2019) Ladislav Holík et al.   Sustainability

Stoichiometric analyses of soil nutrients and enzymes in a Cambisol soil treated with inorganic fertilizers or manures for 26 years

(2019) YuLan Zhang et al.   GEODERMA

Diversity-triggered deterministic bacterial assembly constrains community functions

(2019) Weibing Xun et al.   Nature Communications

Soil health indicators impacted by long-term cattle manure and inorganic fertilizer application in a corn-soybean rotation of South Dakota

(2019) Ekrem Ozlu et al.   Scientific Reports

Bacterial community succession in paddy soil depending on rice fertilization

(2019) Weitao Li et al.   APPLIED SOIL ECOLOGY

Rare rather than abundant microbial communities drive the effects of long-term greenhouse cultivation on ecosystem functions in subtropical agricultural soils

(2019) Mengdi Xue et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Effects of long-term organic material applications on soil carbon and nitrogen fractions in paddy fields

(2019) Qiaogang Yu et al.   SOIL & TILLAGE RESEARCH

Application of organic fertilizer improves microbial community diversity and alters microbial network structure in tea (Camellia sinensis) plantation soils

(2019) Songsong Gu et al.   SOIL & TILLAGE RESEARCH

Rare microbial taxa as the major drivers of ecosystem multifunctionality in long-term fertilized soils

(2019) Qing-Lin Chen et al.   SOIL BIOLOGY & BIOCHEMISTRY

Changes in the soil bacterial community structure and enzyme activities after intercrop mulch with cover crop for eight years in an orchard

(2018) Wei Zheng et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria

(2018) Binu M. Tripathi et al.   ISME Journal

Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom

(2018) Yuanyuan Xue et al.   ISME Journal

Soil microbial biomass size and soil carbon influence the priming effect from carbon inputs depending on nitrogen availability

(2018) Lu-Jun Li et al.   SOIL BIOLOGY & BIOCHEMISTRY

Responses of fungal–bacterial community and network to organic inputs vary among different spatial habitats in soil

(2018) Wei Zheng et al.   SOIL BIOLOGY & BIOCHEMISTRY

Long-term application of manure over plant residues mitigates acidification, builds soil organic carbon and shifts prokaryotic diversity in acidic Ultisols

(2018) Guiping Ye et al.   APPLIED SOIL ECOLOGY

Increased rice yield in long-term crop rotation regimes through improved soil structure, rhizosphere microbial communities, and nutrient bioavailability in paddy soil

(2018) Sheng Lu et al.   BIOLOGY AND FERTILITY OF SOILS

Functional Gut Microbiota Remodeling Contributes to the Caloric Restriction-Induced Metabolic Improvements

(2018) Salvatore Fabbiano et al.   Cell Metabolism

Metabolic Syndrome During Perinatal Period in Sows and the Link With Gut Microbiota and Metabolites

(2018) Chuanshang Cheng et al.   Frontiers in Microbiology

Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions

(2018) Youzhi Feng et al.   MOLECULAR ECOLOGY

Soil C/N and pH together as a comprehensive indicator for evaluating the effects of organic substitution management in subtropical paddy fields after application of high-quality amendments

(2018) Xianglin Dai et al.   GEODERMA

Diversity and co-occurrence network of soil fungi are more responsive than those of bacteria to shifts in precipitation seasonality in a subtropical forest

(2017) Dan He et al.   SOIL BIOLOGY & BIOCHEMISTRY

Strategies for feeding the world more sustainably with organic agriculture

(2017) Adrian Muller et al.   Nature Communications

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

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

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

(2016) Bin Ma et al.   ISME Journal

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

Bacterial communities in oil contaminated soils: Biogeography and co-occurrence patterns

(2016) Shuo Jiao et al.   SOIL BIOLOGY & BIOCHEMISTRY

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Ecology and exploration of the rare biosphere

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

Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw

(2015) Ruibo Sun et al.   SOIL BIOLOGY & BIOCHEMISTRY

Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants

(2013) Feng Ju et al.   ENVIRONMENTAL MICROBIOLOGY

Quantifying community assembly processes and identifying features that impose them

(2013) James C Stegen et al.   ISME Journal

Patterns and Processes of Microbial Community Assembly

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

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

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

High-throughput Fluorometric Measurement of Potential Soil Extracellular Enzyme Activities

(2013) Colin W. Bell et al.   Jove-Journal of Visualized Experiments

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

(2013) Laura A Hug et al.   Microbiome

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

Beyond biogeographic patterns: processes shaping the microbial landscape

(2012) China A. Hanson et al.   NATURE REVIEWS MICROBIOLOGY

Effect of Different Fertilizer Application on the Soil Fertility of Paddy Soils in Red Soil Region of Southern China

(2012) Wenyi Dong et al.   PLoS One

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

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

Picante: R tools for integrating phylogenies and ecology

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

A global perspective on belowground carbon dynamics under nitrogen enrichment

(2010) Lingli Liu et al.   ECOLOGY LETTERS

Microbial functional diversity, metabolic quotient, and invertase activity of a sandy loam soil as affected by long-term application of organic amendment and mineral fertilizer

(2010) Junli Hu et al.   JOURNAL OF SOILS AND SEDIMENTS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Long-term fertilizer effects on organic carbon and total nitrogen and coupling relationships of C and N in paddy soils in subtropical China

(2009) Chengli Tong et al.   SOIL & TILLAGE RESEARCH

The influence of time, storage temperature, and substrate age on potential soil enzyme activity in acidic forest soils using MUB-linked substrates and l-DOPA

(2009) Jared L. DeForest   SOIL BIOLOGY & BIOCHEMISTRY

Soil enzymatic activity as affected by long term application of farm yard manure and mineral fertilizer under a rainfed soybean–wheat system in N-W Himalaya

(2008) Supradip Saha et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY