Metagenomic insights into nitrogen and phosphorus cycling at the soil aggregate scale driven by organic material amendments

Peat-vermiculite alters microbiota composition towards increased soil fertility and crop productivity

(2021) Xingjie Wu et al.   PLANT AND SOIL

Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining

(2020) Jie-Liang Liang et al.   ISME Journal

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

(2020) Bin Ma et al.   Microbiome

Soil Carbon, Nitrogen, and Phosphorus Cycling Microbial Populations and Their Resistance to Global Change Depend on Soil C:N:P Stoichiometry

(2020) Gongwen Luo et al.   mSystems

Response of N2O emission to manure application in field trials of agricultural soils across the globe

(2020) Fang Xia et al.   SCIENCE OF THE TOTAL ENVIRONMENT

DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems

(2020) C.B. Pandey et al.   SCIENCE OF THE TOTAL ENVIRONMENT

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

Long term combined fertilization and soil aggregate size on the denitrification and community of denitrifiers

(2020) Pei-Pei Li et al.   APPLIED SOIL ECOLOGY

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

Dissimilatory nitrate reduction to ammonium dominates nitrate reduction in long-term low nitrogen fertilized rice paddies

(2019) Arjun Pandey et al.   SOIL BIOLOGY & BIOCHEMISTRY

Saving the face of soil aggregates

(2019) Anna Yudina et al.   GLOBAL CHANGE BIOLOGY

Indications for enzymatic denitrification to N2O at low pH in an ammonia-oxidizing archaeon

(2019) Man-Young Jung et al.   ISME Journal

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

Comammox Nitrospira play an active role in nitrification of agricultural soils amended with nitrogen fertilizers

(2019) Chaoyu Li et al.   SOIL BIOLOGY & BIOCHEMISTRY

Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning

(2019) Cameron Wagg et al.   Nature Communications

Suppressed N fixation and diazotrophs after four decades of fertilization

(2019) Kunkun Fan et al.   Microbiome

Long-term nutrient inputs shift soil microbial functional profiles of phosphorus cycling in diverse agroecosystems

(2019) Zhongmin Dai et al.   ISME Journal

Improving soil quality for higher grain yields in Chinese wheat and maize production

(2019) Junxiao Pan et al.   LAND DEGRADATION & DEVELOPMENT

The soil microbiome — from metagenomics to metaphenomics

(2018) Janet K Jansson et al.   CURRENT OPINION IN MICROBIOLOGY

The microbial nitrogen-cycling network

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

Greatest soil microbial diversity found in micro-habitats

(2018) Elizabeth M. Bach et al.   SOIL BIOLOGY & BIOCHEMISTRY

Bacterial potentials for uptake, solubilization and mineralization of extracellular phosphorus in agricultural soils are highly stable under different fertilization regimes

(2018) Martin Grafe et al.   Environmental Microbiology Reports

Distinct Microbial Community Performing Dissimilatory Nitrate Reduction to Ammonium (DNRA) in a High C/NO3− Reactor

(2018) Pokchat Chutivisut et al.   MICROBES AND ENVIRONMENTS

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems

(2018) Shuo Jiao et al.   Microbiome

Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil

(2018) Jingjing Peng et al.   Microbiome

Soil aggregates as biogeochemical reactors and implications for soil-atmosphere exchange of greenhouse gases-A concept

(2018) Bin Wang et al.   GLOBAL CHANGE BIOLOGY

Heterotrophic nitrification and denitrification are the main sources of nitrous oxide in two paddy soils

(2018) Haiyang Liu et al.   PLANT AND SOIL

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Organic Residue Amendments to Modulate Greenhouse Gas Emissions From Agricultural Soils

(2018) Kristof Brenzinger et al.   Frontiers in Microbiology

Soil aggregate size and long-term fertilization effects on the function and community of ammonia oxidizers

(2018) Pei-Pei Li et al.   GEODERMA

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

(2017) Pankaj Trivedi et al.   ENVIRONMENTAL MICROBIOLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Soil aggregates as massively concurrent evolutionary incubators

(2017) Matthias C Rillig et al.   ISME Journal

Below-ground connections underlying above-ground food production: a framework for optimising ecological connections in the rhizosphere

(2017) Franciska T. de Vries et al.   JOURNAL OF ECOLOGY

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Cross-biome assessment of gross soil nitrogen cycling in California ecosystems

(2017) Wendy H. Yang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial Phosphorus Solubilization and Its Potential for Use in Sustainable Agriculture

(2017) Elizabeth T. Alori et al.   Frontiers in Microbiology

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

(2017) Manoeli Lupatini et al.   Frontiers in Microbiology

Urbanization erodes ectomycorrhizal fungal diversity and may cause microbial communities to converge

(2017) Dietrich J. Epp Schmidt et al.   Nature Ecology & Evolution

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

(2016) Leighton Pritchard et al.   Analytical Methods

Dissimilatory nitrate reduction to ammonium and N2O flux: effect of soil redox potential and N fertilization in loblolly pine forests

(2016) K. J. Minick et al.   BIOLOGY AND FERTILITY OF SOILS

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

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

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

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

(2015) Dinghua Li et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Influence of organic carbon and nitrate loading on partitioning between dissimilatory nitrate reduction to ammonium (DNRA) and N 2 production

(2015) Amber K. Hardison et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Complete nitrification by a single microorganism

(2015) Maartje A. H. J. van Kessel et al.   NATURE

Complete nitrification by Nitrospira bacteria

(2015) Holger Daims et al.   NATURE

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

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

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

Hydration and diffusion processes shape microbial community organization and function in model soil aggregates

(2015) Ali Ebrahimi et al.   WATER RESOURCES RESEARCH

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Soil biodiversity and soil community composition determine ecosystem multifunctionality

(2014) C. Wagg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pathways of litter C by formation of aggregates and SOM density fractions: Implications from 13C natural abundance

(2014) Anna Gunina et al.   SOIL BIOLOGY & BIOCHEMISTRY

Can the isotopic exchange kinetic method be used in soils with a very low water extractable phosphate content and a high sorbing capacity for phosphate ions?

(2013) Lalajaona Randriamanantsoa et al.   GEODERMA

Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils

(2013) Man-Young Jung et al.   ISME Journal

Effect of long-term compost and inorganic fertilizer application on background N2O and fertilizer-induced N2O emissions from an intensively cultivated soil

(2012) Weixin Ding et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Microbial mediation of carbon-cycle feedbacks to climate warming

(2011) Jizhong Zhou et al.   Nature Climate Change

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Carbon and oxygen controls on N2O and N2 production during nitrate reduction

(2010) N. Morley et al.   SOIL BIOLOGY & BIOCHEMISTRY

Small-scale heterogeneity in carbon dioxide, nitrous oxide and methane production from aggregates of a cultivated sandy-loam soil

(2008) Benjamin K. Sey et al.   SOIL BIOLOGY & BIOCHEMISTRY