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

Metagenomic and metatranscriptomic responses of natural oil degrading bacteria in the presence of dispersants

(2019) Julien Tremblay et al.   ENVIRONMENTAL MICROBIOLOGY

Distinct pattern of nitrogen functional gene abundances in top- and subsoils along a 120,000-year ecosystem development gradient

(2019) Stephanie Turner et al.   SOIL BIOLOGY & BIOCHEMISTRY

The microbial nitrogen-cycling network

(2018) Marcel M. M. Kuypers et al.   NATURE REVIEWS MICROBIOLOGY

Decreasing soil microbial diversity is associated with decreasing microbial biomass under nitrogen addition

(2018) Chao Wang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Responses of the soil microbial community to nitrogen fertilizer regimes and historical exposure to extreme weather events: Flooding or prolonged-drought

(2018) Linh T.T. Nguyen et al.   SOIL BIOLOGY & BIOCHEMISTRY

The role of nitrifier denitrification in the production of nitrous oxide revisited

(2018) Nicole Wrage-Mönnig et al.   SOIL BIOLOGY & BIOCHEMISTRY

Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop

(2018) Késia S. Lourenço et al.   Frontiers in Microbiology

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

Long-Term Nitrogen Fertilization Elevates the Activity and Abundance of Nitrifying and Denitrifying Microbial Communities in an Upland Soil: Implications for Nitrogen Loss From Intensive Agricultural Systems

(2018) Fenghua Wang et al.   Frontiers in Microbiology

Biocrust moss populations differ in growth rates, stress response, and microbial associates

(2017) Kyle D. Doherty et al.   PLANT AND SOIL

Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase

(2017) Jonathan D. Caranto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

pH drives ammonia oxidizing bacteria rather than archaea thereby stimulate nitrification under Ageratina adenophora colonization

(2017) Haifeng Xiao et al.   SOIL BIOLOGY & BIOCHEMISTRY

Contrasting effects of nitrogen forms and soil pH on ammonia oxidizing microorganisms and their responses to long-term nitrogen fertilization in a typical steppe ecosystem

(2017) Jiaoyan Ying et al.   SOIL BIOLOGY & BIOCHEMISTRY

Effect of fertilization on soil microorganisms in paddy rice systems – A meta-analysis

(2017) Daniel Geisseler et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil Complexity and Pedogenesis

(2017) Jonathan D. Phillips   SOIL SCIENCE

Survey of methanotrophic diversity in various ecosystems by degenerate methane monooxygenase gene primers

(2017) Mohammad Ghashghavi et al.   AMB Express

Bacterial community composition is shaped by soil secondary salinization and acidification brought on by high nitrogen fertilization rates

(2016) Weishou Shen et al.   APPLIED SOIL ECOLOGY

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

(2016) Ravi Ranjan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Least-Squares Means: TheRPackagelsmeans

(2016) Russell V. Lenth   Journal of Statistical Software

16S metagenomics reveals changes in the soil bacterial community driven by soil organic C, N-fertilizer and tillage-crop residue management

(2016) Yosef Chávez-Romero et al.   SOIL & TILLAGE RESEARCH

Nitrogen fertilization directly affects soil bacterial diversity and indirectly affects bacterial community composition

(2016) Jun Zeng et al.   SOIL BIOLOGY & BIOCHEMISTRY

Ammonia-oxidizing bacteria are more responsive than archaea to nitrogen source in an agricultural soil

(2016) Yang Ouyang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Impacts of nitrogen and phosphorus additions on the abundance and community structure of ammonia oxidizers and denitrifying bacteria in Chinese fir plantations

(2016) Yuqian Tang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Nitrogen fertilization induced changes in ammonia oxidation are attributable mostly to bacteria rather than archaea in greenhouse-based high N input vegetable soil

(2016) Wenhui Zhong et al.   SOIL BIOLOGY & BIOCHEMISTRY

Meta-analysis reveals ammonia-oxidizing bacteria respond more strongly to nitrogen addition than ammonia-oxidizing archaea

(2016) Chelsea J. Carey et al.   SOIL BIOLOGY & BIOCHEMISTRY

Anthropogenic N Deposition Slows Decay by Favoring Bacterial Metabolism: Insights from Metagenomic Analyses

(2016) Zachary B. Freedman et al.   Frontiers in Microbiology

Measuring and Modeling the Long-Term Impact of Crop Management on Soil Carbon Sequestration in the Semiarid Canadian Prairies

(2015) K. A. Congreves et al.   AGRONOMY JOURNAL

Soil microbial community structure and function relationships: A heat stress experiment

(2015) Wassila Riah-Anglet et al.   APPLIED SOIL ECOLOGY

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

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

Complete nitrification by Nitrospira bacteria

(2015) Holger Daims et al.   NATURE

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

(2015) Jonathan W. Leff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of 44 years of chronic nitrogen fertilization on the soil nitrifying community of permanent grassland

(2015) Xue Zhou et al.   SOIL BIOLOGY & BIOCHEMISTRY

Long term tillage, cover crop, and fertilization effects on microbial community structure, activity: Implications for soil quality

(2015) Lilian Wanjiru Mbuthia et al.   SOIL BIOLOGY & BIOCHEMISTRY

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

(2015) Marcel Huntemann et al.   Standards in Genomic Sciences

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Investigation of Soil Legacy Phosphorus Transformation in Long-Term Agricultural Fields Using Sequential Fractionation, P K-edge XANES and Solution P NMR Spectroscopy

(2014) Jin Liu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil

(2014) Yao Pan et al.   FEMS MICROBIOLOGY ECOLOGY

Interactive effects of C, N and P fertilization on soil microbial community structure and function in an Amazonian rain forest

(2014) Nicolas Fanin et al.   FUNCTIONAL ECOLOGY

pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils

(2014) Barbara Stempfhuber et al.   MICROBIAL ECOLOGY

Long-term effects of mineral fertilizers on soil microorganisms – A review

(2014) Daniel Geisseler et al.   SOIL BIOLOGY & BIOCHEMISTRY

Thermal acclimation of organic matter decomposition in an artificial forest soil is related to shifts in microbial community structure

(2014) Hui Wei et al.   SOIL BIOLOGY & BIOCHEMISTRY

Influence of nitrogen fertilization on soil ammonia oxidizer and denitrifier abundance, microbial biomass, and enzyme activities in an alpine meadow

(2013) Xiao-Fang Tian et al.   BIOLOGY AND FERTILITY OF SOILS

Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm

(2013) Andrea K. Bartram et al.   FEMS MICROBIOLOGY ECOLOGY

Patterns and trends in nitrogen use and nitrogen recovery efficiency in world agriculture

(2013) Richard T. Conant et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways

(2013) Feng-Ping Wang et al.   ISME Journal

Nitric oxide: an effective weapon of the plant or the pathogen?

(2013) Magdalena Arasimowicz-Jelonek et al.   MOLECULAR PLANT PATHOLOGY

Changes in Fungal Community Composition in Response to Elevated Atmospheric CO2 and Nitrogen Fertilization Varies with Soil Horizon

(2013) Carolyn F. Weber et al.   Frontiers in Microbiology

Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials

(2012) Anne E Taylor et al.   ISME Journal

The Divergent AmoC3 Subunit of Ammonia Monooxygenase Functions as Part of a Stress Response System in Nitrosomonas europaea

(2012) P. M. Berube et al.   JOURNAL OF BACTERIOLOGY

Direct and indirect influences of 8 yr of nitrogen and phosphorus fertilization on Glomeromycota in an alpine meadow ecosystem

(2012) Yongjun Liu et al.   NEW PHYTOLOGIST

Green Revolution: Impacts, limits, and the path ahead

(2012) P. L. Pingali   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation

(2012) James I. Prosser et al.   TRENDS IN MICROBIOLOGY

Ammonium Availability Affects the Ratio of Ammonia-Oxidizing Bacteria to Ammonia-Oxidizing Archaea in Simulated Creek Ecosystems

(2011) Martina Herrmann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantitative analyses of ammonia-oxidizing Archaea and bacteria in the sediments of four nitrogen-rich wetlands in China

(2011) Shanyun Wang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Phosphorus use efficiency and long-term trends in soil available phosphorus in wheat production systems with and without nitrogen fertilizer

(2011) F. Selles et al.   CANADIAN JOURNAL OF SOIL SCIENCE

The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology

(2011) Michael Pester et al.   CURRENT OPINION IN MICROBIOLOGY

Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms

(2011) Daniel T Verhamme et al.   ISME Journal

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

(2011) Noah Fierer et al.   ISME Journal

Nitrogen loading levels affect abundance and composition of soil ammonia oxidizing prokaryotes in semiarid temperate grassland

(2011) Xin-Yi Shen et al.   JOURNAL OF SOILS AND SEDIMENTS

Niche specialization of terrestrial archaeal ammonia oxidizers

(2011) C. Gubry-Rangin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Soil moisture is the major factor influencing microbial community structure and enzyme activities across seven biogeoclimatic zones in western Canada

(2011) Beth F.T. Brockett et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil beneficial bacteria and their role in plant growth promotion: a review

(2010) Rifat Hayat et al.   ANNALS OF MICROBIOLOGY

Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management

(2010) Ella Wessén et al.   APPLIED SOIL ECOLOGY

Soil organic matter quality as a link between microbial community structure and vegetation composition along a successional gradient in a boreal forest

(2010) Päivi Merilä et al.   APPLIED SOIL ECOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Johannes Rousk et al.   ISME Journal

Examining the global distribution of dominant archaeal populations in soil

(2010) Scott T Bates et al.   ISME Journal

Characteristics of the Microbial Community Associated with Ammonia Oxidation in a Full-Scale Rockwool Biofilter Treating Malodors from Livestock Manure Composting

(2010) Tomoko Yasuda et al.   MICROBES AND ENVIRONMENTS

Impact of Long-Term Fertilization on the Composition of Denitrifier Communities Based on Nitrite Reductase Analyses in a Paddy Soil

(2010) Zhe Chen et al.   MICROBIAL ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses

(2009) Ryan T Jones et al.   ISME Journal

Long-Term Phosphorus Fertilization Impacts Soil Fungal and Bacterial Diversity but not AM Fungal Community in Alfalfa

(2009) M. S. Beauregard et al.   MICROBIAL ECOLOGY

Environment: The disappearing nutrient

(2009) Natasha Gilbert   NATURE

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY

Short-term competition between crop plants and soil microbes for inorganic N fertilizer

(2009) Erich Inselsbacher et al.   SOIL BIOLOGY & BIOCHEMISTRY

Nitrogen additions and microbial biomass: a meta-analysis of ecosystem studies

(2008) Kathleen K. Treseder   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

The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria

(2008) Graeme W. Nicol et al.   ENVIRONMENTAL MICROBIOLOGY

Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam

(2008) Ju-pei Shen et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California

(2008) J Michael Beman et al.   ISME Journal

Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota

(2008) Céline Brochier-Armanet et al.   NATURE REVIEWS MICROBIOLOGY

Thirty-seven years of soil nitrogen and phosphorus fertility management shapes the structure and function of the soil microbial community in a Brown Chernozem

(2008) Andre Freire Cruz et al.   PLANT AND SOIL