The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

Molecular Chemodiversity of Dissolved Organic Matter in Paddy Soils

(2018) Xiao-Ming Li et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Paddy soil microbial communities driven by environment- and microbe-microbe interactions: A case study of elevation-resolved microbial communities in a rice terrace

(2018) Weimin Sun et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Effect of past peat cultivation practices on present dynamics of dissolved organic carbon

(2017) S. Frank et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Feed in summer, rest in winter: microbial carbon utilization in forest topsoil

(2017) Lucia Žifčáková et al.   Microbiome

Comparative study of organic matter chemical characterization using negative and positive mode electrospray ionization ultrahigh-resolution mass spectrometry

(2016) Tsutomu Ohno et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system

(2016) Helena Osterholz et al.   ISME Journal

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Effects of Land Use Changes from Paddy Fields on Soil Bacterial Communities in a Hilly and Mountainous Area

(2016) Md Rokunuzzaman et al.   MICROBES AND ENVIRONMENTS

Comparing molecular composition of dissolved organic matter in soil and stream water: Influence of land use and chemical characteristics

(2016) Anne-Gret Seifert et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Temperature mediates continental-scale diversity of microbes in forest soils

(2016) Jizhong Zhou et al.   Nature Communications

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

(2016) James C. Stegen et al.   Nature Communications

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

(2016) Cynthia M. Kallenbach et al.   Nature Communications

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Bacterial succession in paddy soils derived from different parent materials

(2015) Rong Sheng et al.   JOURNAL OF SOILS AND SEDIMENTS

Understanding the incremental value of novel diagnostic tests for tuberculosis

(2015) Nimalan Arinaminpathy et al.   NATURE

The Pfam protein families database: towards a more sustainable future

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

Linking dissolved organic carbon cycling to organic carbon fluxes in rice paddies under different water management practices

(2015) Daniel Said-Pullicino et al.   PLANT AND SOIL

The links between ecosystem multifunctionality and above- and belowground biodiversity are mediated by climate

(2015) Xin Jing et al.   Nature Communications

The Molecular Composition of Dissolved Organic Matter in Forest Soils as a Function of pH and Temperature

(2015) Vanessa-Nina Roth et al.   PLoS One

Changes in soil microbial community composition in response to fertilization of paddy soils in subtropical China

(2014) Wen-Yi Dong et al.   APPLIED SOIL ECOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus

(2014) Emmanuel Prestat et al.   NUCLEIC ACIDS RESEARCH

Plant species diversity affects infiltration capacity in an experimental grassland through changes in soil properties

(2014) Christine Fischer et al.   PLANT AND SOIL

Chemodiversity of dissolved organic matter in lakes driven by climate and hydrology

(2014) Anne M. Kellerman et al.   Nature Communications

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Hailstones: A Window into the Microbial and Chemical Inventory of a Storm Cloud

(2013) Tina Šantl-Temkiv et al.   PLoS One

Iron traps terrestrially derived dissolved organic matter at redox interfaces

(2013) T. Riedel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Concentration dynamics and biodegradability of dissolved organic matter in wetland soils subjected to experimental warming

(2013) Hang Wang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Does the chemical nature of soil carbon drive the structure and functioning of soil microbial communities?

(2013) E.-L. Ng et al.   SOIL BIOLOGY & BIOCHEMISTRY

Molecular characterization of dissolved organic matter (DOM): a critical review

(2012) Antonio Nebbioso et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Beyond biogeographic patterns: processes shaping the microbial landscape

(2012) China A. Hanson et al.   NATURE REVIEWS MICROBIOLOGY

TIGRFAMs and Genome Properties in 2013

(2012) Daniel H. Haft et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Biogeochemistry of paddy soils

(2010) Ingrid Kögel-Knabner et al.   GEODERMA

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct Exchange of Electrons Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria

(2010) Z. M. Summers et al.   SCIENCE

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing

(2009) Tomoyuki Hori et al.   ISME Journal

Farming the planet: 2. Geographic distribution of crop areas, yields, physiological types, and net primary production in the year 2000

(2008) Chad Monfreda et al.   GLOBAL BIOGEOCHEMICAL CYCLES

The earliest stages of ecosystem succession in high-elevation (5000 metres above sea level), recently deglaciated soils

(2008) S.K Schmidt et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES