Current Challenges and Pitfalls in Soil Metagenomics

Potassium phosphite enhanced the suppressive capacity of the soil microbiome against the tomato pathogen Ralstonia solanacearum

(2022) Lv Su et al.   BIOLOGY AND FERTILITY OF SOILS

Many researchers were not compliant with their published data sharing statement: mixed-methods study

(2022) Mirko Gabelica et al.   JOURNAL OF CLINICAL EPIDEMIOLOGY

From diversity to complexity: Microbial networks in soils

(2022) Ksenia Guseva et al.   SOIL BIOLOGY & BIOCHEMISTRY

Ammonia-oxidizing bacteria and fungal denitrifier diversity are associated with N2O production in tropical soils

(2022) Késia Silva Lourenço et al.   SOIL BIOLOGY & BIOCHEMISTRY

Unearthing Shifts in Microbial Communities Across a Soil Disturbance Gradient

(2022) Taylor J. Seitz et al.   Frontiers in Microbiology

Trends in Microbial Community Composition and Function by Soil Depth

(2022) Dan Naylor et al.   Microorganisms

Eucalypt species drive rhizosphere bacterial and fungal community assembly but soil phosphorus availability rearranges the microbiome

(2022) R.G. Bulgarelli et al.   SCIENCE OF THE TOTAL ENVIRONMENT

On the link between tree size and ecosystem carbon sequestration capacity across continental forests

(2022) Meifang Zhao et al.   Ecosphere

Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production

(2022) Christophe Djemiel et al.   Frontiers in Microbiology

Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases

(2021) Gerhard Mayer et al.   BRIEFINGS IN BIOINFORMATICS

Global projections of the soil microbiome in the Anthropocene

(2021) Carlos A. Guerra et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Mitigation of yield-scaled greenhouse gas emissions from irrigated rice through Azolla, Blue-green algae, and plant growth–promoting bacteria

(2021) Sandeep K. Malyan et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Modulation of the soil microbiome by long-term Ca-based soil amendments boosts soil organic carbon and physicochemical quality in a tropical no-till crop rotation system

(2021) João W. Bossolani et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil microbial communities in the face of changing farming practices: A case study in an agricultural landscape in France

(2021) Laurie Dunn et al.   PLoS One

Quantifying the spatiotemporal characteristics of ecosystem services and livelihoods in China’s poverty-stricken counties

(2021) Lilei Zhou et al.   Frontiers of Earth Science

Can We Estimate Functionality of Soil Microbial Communities from Structure-Derived Predictions? A Reality Test in Agricultural Soils

(2021) Claudia Breitkreuz et al.   Microbiology Spectrum

Forage Grasses Steer Soil Nitrogen Processes, Microbial Populations, and Microbiome Composition in A Long-term Tropical Agriculture System

(2021) Letusa Momesso et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Diversity of archaea and niche preferences among putative ammonia‐oxidizing Nitrososphaeria dominating across European arable soils

(2021) Aurélien Saghaï et al.   ENVIRONMENTAL MICROBIOLOGY

The Sequence Read Archive: a decade more of explosive growth

(2021) Kenneth Katz et al.   NUCLEIC ACIDS RESEARCH

Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input

(2021) Marcio F.A. Leite et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Advances in monitoring soil microbial community dynamic and function

(2020) K. K. Nkongolo et al.   JOURNAL OF APPLIED GENETICS

Putting science back into microbial ecology: a question of approach

(2020) James I. Prosser   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Soil Microbial Biogeography in a Changing World: Recent Advances and Future Perspectives

(2020) Haiyan Chu et al.   mSystems

Effects of different management approaches on the stoichiometric characteristics of soil C, N, and P in a mature Chinese fir plantation

(2020) Yanfeng Bai et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Modern Climate and Soil Properties Explain Functional Structure Better Than Phylogenetic Structure of Plant Communities in Northern China

(2020) Yabo Shi et al.   Frontiers in Ecology and Evolution

The archives are half-empty: an assessment of the availability of microbial community sequencing data

(2020) Stephanie D. Jurburg et al.   Communications Biology

Spatial distribution of soil organic carbon and total nitrogen in disturbed Carex tussock wetland

(2020) Qing Qi et al.   ECOLOGICAL INDICATORS

You must choose, but choose wisely: Model-based approaches for microbial community analysis

(2020) Márcio F.A. Leite et al.   SOIL BIOLOGY & BIOCHEMISTRY

Reproducible big data science: A case study in continuous FAIRness

(2019) Ravi Madduri et al.   PLoS One

Drivers of soil bacterial community structure and diversity in tropical agroforestry systems

(2019) Chenggang Liu et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Effects of Agricultural Management on Rhizosphere Microbial Structure and Function in Processing Tomato Plants

(2019) Jennifer E. Schmidt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantitative assessment of microbial necromass contribution to soil organic matter

(2019) Chao Liang et al.   GLOBAL CHANGE BIOLOGY

Microbial communities in top- and subsoil of repacked soil columns respond differently to amendments but their diversity is negatively correlated with plant productivity

(2019) Corinne Celestina et al.   Scientific Reports

Advances and Challenges in Metatranscriptomic Analysis

(2019) Migun Shakya et al.   Frontiers in Genetics

Vertical distribution and influencing factors of soil organic carbon in the Loess Plateau, China

(2019) Haiyan Yu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

The FAIR guiding principles for data stewardship: fair enough?

(2018) Martin Boeckhout et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Data sharing in PLOS ONE: An analysis of Data Availability Statements

(2018) Lisa M. Federer et al.   PLoS One

Resource Availability Drives Responses of Soil Microbial Communities to Short-term Precipitation and Nitrogen Addition in a Desert Shrubland

(2018) Weiwei She et al.   Frontiers in Microbiology

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences

(2018) Adithya Murali et al.   Microbiome

Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion

(2018) Késia Silva Lourenço et al.   Microbiome

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Opinion: Why we need a National Living Soil Repository

(2017) Daniel K. Manter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Successive DNA extractions improve characterization of soil microbial communities

(2017) Mauricio R. Dimitrov et al.   PeerJ

Reproducible and reusable research: are journal data sharing policies meeting the mark?

(2017) Nicole A. Vasilevsky et al.   PeerJ

The metagenomic data life-cycle: standards and best practices

(2017) Petra ten Hoopen et al.   GigaScience

The importance of anabolism in microbial control over soil carbon storage

(2017) Chao Liang et al.   Nature Microbiology

Toward Accurate and Quantitative Comparative Metagenomics

(2016) Stephen Nayfach et al.   CELL

The challenges of big data

(2016) Elaine R. Mardis   Disease Models & Mechanisms

Long-term fertilizer and crop-rotation treatments differentially affect soil bacterial community structure

(2016) Chinmay Soman et al.   PLANT AND SOIL

Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland

(2016) Noriko A. Cassman et al.   Scientific Reports

Unravelling Linkages between Plant Community Composition and the Pathogen-Suppressive Potential of Soils

(2016) Ellen Latz et al.   Scientific Reports

Response of Soil Properties and Microbial Communities to Agriculture: Implications for Primary Productivity and Soil Health Indicators

(2016) Pankaj Trivedi et al.   Frontiers in Plant Science

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

(2015) Alejandra Escobar-Zepeda et al.   Frontiers in Genetics

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

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

Soil-Borne Microbial Functional Structure across Different Land Uses

(2014) Eiko E. Kuramae et al.   TheScientificWorldJOURNAL

Manipulating the soil microbiome to increase soil health and plant fertility

(2012) Jacqueline M. Chaparro et al.   BIOLOGY AND FERTILITY OF SOILS

Soil characteristics more strongly influence soil bacterial communities than land-use type

(2011) Eiko E. Kuramae et al.   FEMS MICROBIOLOGY ECOLOGY

The Genomic Standards Consortium

(2011) Dawn Field et al.   PLOS BIOLOGY

Microbial secondary succession in a chronosequence of chalk grasslands

(2010) Eiko E Kuramae et al.   ISME Journal

Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology

(2010) Stefano Mocali et al.   RESEARCH IN MICROBIOLOGY

Fungi mediate long term sequestration of carbon and nitrogen in soil through their priming effect

(2010) S. Fontaine et al.   SOIL BIOLOGY & BIOCHEMISTRY

TerraGenome: a consortium for the sequencing of a soil metagenome

(2009) Timothy M. Vogel et al.   NATURE REVIEWS MICROBIOLOGY