Long-term excess nitrogen fertilizer increases sensitivity of soil microbial community to seasonal change revealed by ecological network and metagenome analyses

Climate warming enhances microbial network complexity and stability

(2021) Mengting Maggie Yuan et al.   Nature Climate Change

Network analysis reveals the strengthening of microbial interaction in biological soil crust development in the Mu Us Sandy Land, northwestern China

(2020) Hong Zhou et al.   SOIL BIOLOGY & BIOCHEMISTRY

Perennial Bioenergy Crop Yield and Quality Response to Nitrogen Fertilization

(2019) Sichao Wang et al.   BioEnergy Research

Inorganic N addition replaces N supplied to switchgrass ( Panicum virgatum ) by arbuscular mycorrhizal fungi

(2019) Laura C. Jach‐Smith et al.   ECOLOGICAL APPLICATIONS

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

(2018) Mara A. Freilich et al.   ECOLOGY

Associative nitrogen fixation (ANF) in switchgrass (Panicum virgatum) across a nitrogen input gradient

(2018) Sarah S. Roley et al.   PLoS One

N addition undermines N supplied by arbuscular mycorrhizal fungi to native perennial grasses

(2018) Laura C. Jach-Smith et al.   SOIL BIOLOGY & BIOCHEMISTRY

Switchgrass nitrogen response and estimated production costs on diverse sites

(2017) John H. Fike et al.   Global Change Biology Bioenergy

Tracing the fate of nitrogen with 15N isotope considering suitable fertilizer rate related to yield and environment impacts in paddy field

(2017) Yiming Zhong et al.   Paddy and Water Environment

Effects of different nitrogen additions on soil microbial communities in different seasons in a boreal forest

(2017) Guoyong Yan et al.   Ecosphere

Microbial Taxa Distribution Is Associated with Ecological Trophic Cascades along an Elevation Gradient

(2017) Fei Yao et al.   Frontiers in Microbiology

Seasonal soil microbial responses are limited to changes in functionality at two Alpine forest sites differing in altitude and vegetation

(2017) José A. Siles et al.   Scientific Reports

Comparative productivity of alternative cellulosic bioenergy cropping systems in the North Central USA

(2016) Gregg R. Sanford et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

(2016) Shengjing Shi et al.   ECOLOGY LETTERS

Nitrogen fertilization challenges the climate benefit of cellulosic biofuels

(2016) Leilei Ruan et al.   Environmental Research Letters

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

(2016) Bin Ma et al.   ISME Journal

A watering manipulation in a semiarid grassland induced changes in fungal but not bacterial community composition

(2016) Theresa A. McHugh et al.   PEDOBIOLOGIA

Global biogeography of microbial nitrogen-cycling traits in soil

(2016) Michaeline B. Nelson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Jun Zeng 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

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

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL 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

Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation

(2015) Ye Deng et al.   ENVIRONMENTAL MICROBIOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

The bacterial community inhabiting temperate deciduous forests is vertically stratified and undergoes seasonal dynamics

(2015) Rubén López-Mondéjar et al.   SOIL BIOLOGY & BIOCHEMISTRY

Seasonal Variation in Soil Bulk Density, Organic Nitrogen, Available Phosphorus, and pH

(2015) Stewart B. Wuest   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons

(2015) Shengjing Shi et al.   mBio

Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere

(2015) Chanyarat Paungfoo-Lonhienne et al.   Scientific Reports

Xander: employing a novel method for efficient gene-targeted metagenomic assembly

(2015) Qiong Wang et al.   Microbiome

A reassessment of the contribution of soybean biological nitrogen fixation to reactive N in the environment

(2014) Ilya Gelfand et al.   BIOGEOCHEMISTRY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Impact of fertilization on the abundance of nitrifiers and denitrifiers at the root–soil interface of plants with different uptake strategies for nitrogen

(2014) Eva-Maria Kastl et al.   BIOLOGY AND FERTILITY OF SOILS

Bacillus subtilisattachment toAspergillus nigerhyphae results in mutually altered metabolism

(2014) Isabelle Benoit et al.   ENVIRONMENTAL 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

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

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

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

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Seasonal dynamics of fungal communities in a temperate oak forest soil

(2013) Jana Voříšková et al.   NEW PHYTOLOGIST

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

Impact of nitrogen fertilization and soil tillage on arbuscular mycorrhizal fungal communities in a Mediterranean agroecosystem

(2013) Luciano Avio et al.   SOIL BIOLOGY & BIOCHEMISTRY

Fungal networks in yield-invigorating and -debilitating soils induced by prolonged potato monoculture

(2013) Lihua Lu et al.   SOIL BIOLOGY & BIOCHEMISTRY

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC 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

Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes

(2012) Kelly S. Ramirez et al.   GLOBAL CHANGE BIOLOGY

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

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

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

(2011) Noah Fierer et al.   ISME Journal

Validation and Application of a PCR Primer Set to Quantify Fungal Communities in the Soil Environment by Real-Time Quantitative PCR

(2011) Nicolas Chemidlin Prévost-Bouré et al.   PLoS One

Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2

(2011) J. Zhou et al.   mBio

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Effects of Plant Genotype and Growth Stage on the Betaproteobacterial Communities Associated with Different Potato Cultivars in Two Fields

(2010) O. Inceoglu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

(2010) Johannes Rousk et al.   ISME Journal

Improving indicator species analysis by combining groups of sites

(2010) Miquel De Cáceres et al.   OIKOS

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

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

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

Microbial processes influencing performance of treatment wetlands: A review

(2009) Jennifer L. Faulwetter et al.   ECOLOGICAL ENGINEERING

Regulation and function of root exudates

(2009) DAYAKAR V. BADRI et al.   PLANT CELL AND ENVIRONMENT

The genomic basis of trophic strategy in marine bacteria

(2009) F. M. Lauro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Universal and species-specific bacterial ‘fungiphiles’ in the mycospheres of different basidiomycetous fungi

(2008) J. A. Warmink et al.   ENVIRONMENTAL MICROBIOLOGY

Links between plant litter chemistry, species diversity, and below-ground ecosystem function

(2008) C. L. Meier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA