Manure application increases microbiome complexity in soil aggregate fractions: Results of an 18-year field experiment

Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

(2020) Antonio J. Fernández-González et al.   Microbiome

Influence mechanisms of long-term fertilizations on the mineralization of organic matter in Ultisol

(2020) Peidong Xu et al.   SOIL & TILLAGE RESEARCH

Niche differentiation of comammox Nitrospira and canonical ammonia oxidizers in soil aggregate fractions following 27-year fertilizations

(2020) Yongxin Lin et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

(2019) Samiran Banerjee et al.   ISME Journal

Visualizing the dynamics of soil aggregation as affected by arbuscular mycorrhizal fungi

(2019) E. K. Morris et al.   ISME Journal

Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales

(2019) Regina L. Wilpiszeski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Spatio-temporal microbial community dynamics within soil aggregates

(2019) Racheal N. Upton et al.   SOIL BIOLOGY & BIOCHEMISTRY

Responses of soil fungal diversity and community composition to long-term fertilization: Field experiment in an acidic Ultisol and literature synthesis

(2019) Guiping Ye et al.   APPLIED SOIL ECOLOGY

Soil aggregate size modifies the impacts of fertilization on microbial communities

(2019) Fengqiao Li et al.   GEODERMA

Linking bacterial community to aggregate fractions with organic amendments in a sandy soil

(2019) Hongcui Dai et al.   LAND DEGRADATION & DEVELOPMENT

Manure over crop residues increases soil organic matter but decreases microbial necromass relative contribution in upland Ultisols: Results of a 27-year field experiment

(2019) Guiping Ye et al.   SOIL BIOLOGY & BIOCHEMISTRY

Long-term manure application increases soil organic matter and aggregation, and alters microbial community structure and keystone taxa

(2019) Yongxin Lin et al.   SOIL BIOLOGY & BIOCHEMISTRY

Long‐term nitrogen addition modifies microbial composition and functions for slow carbon cycling and increased sequestration in tropical forest soil

(2019) Jing Tian et al.   GLOBAL CHANGE BIOLOGY

Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons

(2019) Tess E. Brewer et al.   mBio

Long-term organic fertilization improves the productivity of kiwifruit (Actinidia chinensis Planch.) through increasing rhizosphere microbial diversity and network complexity

(2019) Zhe Liu et al.   APPLIED SOIL ECOLOGY

Long‐term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production

(2019) Yunliang Li et al.   ENVIRONMENTAL MICROBIOLOGY

Fungal community demonstrates stronger dispersal limitation and less network connectivity than bacterial community in sediments along a large river

(2019) Juan Chen et al.   ENVIRONMENTAL MICROBIOLOGY

Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history

(2019) Min Xu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning

(2019) Cameron Wagg et al.   Nature Communications

Total and active soil fungal community profiles were significantly altered by six years of warming but not by grazing

(2019) Rongxiao Che et al.   SOIL BIOLOGY & BIOCHEMISTRY

Biogeographic patterns of microbial association networks in paddy soil within Eastern China

(2019) Xiaoling Wan et al.   SOIL BIOLOGY & BIOCHEMISTRY

Response of the soil microbial community to different fertilizer inputs in a wheat-maize rotation on a calcareous soil

(2018) Shuikuan Bei et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Integrated network analysis reveals the importance of microbial interactions for maize growth

(2018) Jiemeng Tao et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Plant growth stages and fertilization regimes drive soil fungal community compositions in a wheat-rice rotation system

(2018) Jichen Wang et al.   BIOLOGY AND FERTILITY OF SOILS

Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities?

(2018) Mara A. Freilich et al.   ECOLOGY

Keystone taxa predict compositional change in microbial communities

(2018) Cristina M. Herren et al.   ENVIRONMENTAL MICROBIOLOGY

Gigasporaceae versus Glomeraceae (phylum Glomeromycota): A biogeographic tale of dominance in maritime sand dunes

(2018) Sidney L. Stürmer et al.   Fungal Ecology

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

(2018) Yuanyuan Xue et al.   ISME Journal

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

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 fertilization regimes drive the abundance and composition of N-cycling-related prokaryotic groups via soil particle-size differentiation

(2018) Gongwen Luo et al.   SOIL BIOLOGY & BIOCHEMISTRY

Nitrosospira Cluster 8a Plays a Predominant Role in the Nitrification Process of a Subtropical Ultisol under Long-Term Inorganic and Organic Fertilization

(2018) Yongxin Lin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Effect of nitrogen fertilization on the abundance of nitrogen cycling genes in agricultural soils: A meta-analysis of field studies

(2018) Yang Ouyang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil bacterial networks are less stable under drought than fungal networks

(2018) Franciska T. de Vries et al.   Nature Communications

Microbial diversity and ecological networks as indicators of environmental quality

(2017) Battle Karimi et al.   Environmental Chemistry Letters

Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content

(2017) Pankaj Trivedi et al.   ENVIRONMENTAL MICROBIOLOGY

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

High temperatures inhibited the growth of soil bacteria and archaea but not that of fungi and altered nitrous oxide production mechanisms from different nitrogen sources in an acidic soil

(2017) Xiaoya Xu et al.   SOIL BIOLOGY & BIOCHEMISTRY

Generalist species drive microbial dispersion and evolution

(2017) Sira Sriswasdi 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

Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model

(2016) Ali Ebrahimi et al.   GLOBAL CHANGE BIOLOGY

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

Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis

(2016) Ning Ling et al.   SOIL BIOLOGY & BIOCHEMISTRY

Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil

(2016) Samiran Banerjee et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial diversity drives multifunctionality in terrestrial ecosystems

(2016) Manuel Delgado-Baquerizo et al.   Nature Communications

Mineral vs. Organic Amendments: Microbial Community Structure, Activity and Abundance of Agriculturally Relevant Microbes Are Driven by Long-Term Fertilization Strategies

(2016) Davide Francioli et al.   Frontiers in Microbiology

Determinants of bacterial communities in Canadian agroforestry systems

(2015) Samiran Banerjee et al.   ENVIRONMENTAL MICROBIOLOGY

Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in South China

(2015) Weibing Xun et al.   ENVIRONMENTAL MICROBIOLOGY

Soil aggregate size mediates the impacts of cropping regimes on soil carbon and microbial communities

(2015) Pankaj Trivedi et al.   SOIL BIOLOGY & BIOCHEMISTRY

Fungal and bacterial N2O production regulated by soil amendments of simple and complex substrates

(2015) Huaihai Chen et al.   SOIL BIOLOGY & BIOCHEMISTRY

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest

(2014) Neslihan Taş et al.   ISME Journal

Pathogen accumulation and long-term dynamics of plant invasions

(2013) S. Luke Flory et al.   JOURNAL OF ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Mapping the niche space of soil microorganisms using taxonomy and traits

(2012) Jay T. Lennon et al.   ECOLOGY

Comparative genomic and physiological analysis provides insights into the role ofAcidobacteriain organic carbon utilization in Arctic tundra soils

(2012) Suman R. Rawat et al.   FEMS MICROBIOLOGY ECOLOGY

Effects of organic and inorganic fertilization on soil aggregation in an Ultisol as characterized by synchrotron based X-ray micro-computed tomography

(2012) Hu Zhou et al.   GEODERMA

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

(2011) T. Magoc et al.   BIOINFORMATICS

Detecting Novel Associations in Large Data Sets

(2011) D. N. Reshef et al.   SCIENCE

The distribution of nematodes and soil microbial communities across soil aggregate fractions and farm management systems

(2011) Shabeg S. Briar et al.   SOIL BIOLOGY & BIOCHEMISTRY

Pyrosequencing and mid-infrared spectroscopy reveal distinct aggregate stratification of soil bacterial communities and organic matter composition

(2011) Marko Davinic et al.   SOIL BIOLOGY & BIOCHEMISTRY

Effects of long-term fertilization on corn productivity and its sustainability in an Ultisol of southern China

(2010) Shan Huang et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Soil aggregation and carbon sequestration are tightly correlated with the abundance of arbuscular mycorrhizal fungi: results from long-term field experiments

(2009) Gail W. T. Wilson et al.   ECOLOGY LETTERS

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