Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment

Microbial transformation of distinct exogenous substrates into analogous composition of recalcitrant dissolved organic matter

(2021) Jie Lian et al.   ENVIRONMENTAL MICROBIOLOGY

Correspondence between DOM molecules and microbial community in a subtropical coastal estuary on a spatiotemporal scale

(2021) Qi Chen et al.   ENVIRONMENT INTERNATIONAL

Harnessing solar energy using phototrophic microorganisms: A sustainable pathway to bioenergy, biomaterials, and environmental solutions

(2021) Rahamat Ullah Tanvir et al.   RENEWABLE & SUSTAINABLE ENERGY REVIEWS

Lepidopteran mevalonate pathway optimization in Escherichia coli efficiently produces isoprenol analogs for next-generation biofuels

(2021) Bo Pang et al.   METABOLIC ENGINEERING

Different carboxyl‐rich alicyclic molecules proxy compounds select distinct bacterioplankton for oxidation of dissolved organic matter in the mesopelagic Sargasso Sea

(2020) Shuting Liu et al.   LIMNOLOGY AND OCEANOGRAPHY

Metagenomic and Metaproteomic Insights into Photoautotrophic and Heterotrophic Interactions in a Synechococcus Culture

(2020) Qiang Zheng et al.   mBio

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics

(2020) Shunan Cao et al.   Microbiome

In-House Standard Method for Molecular Characterization of Dissolved Organic Matter by FT-ICR Mass Spectrometry

(2020) Chen He et al.   ACS Omega

Highly enriched N‐containing organic molecules of Synechococcus lysates and their rapid transformation by heterotrophic bacteria

(2020) Qiang Zheng et al.   LIMNOLOGY AND OCEANOGRAPHY

Differences in bioavailability of canonical and non-canonical D-amino acids for marine microbes

(2020) Rui Wang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

DOC dynamics and bacterial community succession during long-term degradation of Ulva prolifera and their implications for the legacy effect of green tides on refractory DOC pool in seawater

(2020) Jing Chen et al.   WATER RESEARCH

Resource aromaticity affects bacterial community successions in response to different sources of dissolved organic matter

(2020) Lei Zhou et al.   WATER RESEARCH

Amino acid enantiomers in old and young dissolved organic matter: Implications for a microbial nitrogen pump

(2019) Taylor A.B. Broek et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Microbial transformation of virus-induced dissolved organic matter from picocyanobacteria: coupling of bacterial diversity and DOM chemodiversity

(2019) Zhao Zhao et al.   ISME Journal

Stratification of dissolved organic matter in the upper 2000 m water column at the Mariana Trench

(2019) Penghui Li et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Molecular properties are a primary control on the microbial utilization of dissolved organic matter in the ocean

(2019) Yuan Shen et al.   LIMNOLOGY AND OCEANOGRAPHY

Linking metagenomics to aquatic microbial ecology and biogeochemical cycles

(2019) Hans‐Peter Grossart et al.   LIMNOLOGY AND OCEANOGRAPHY

Pyruvate cycle increases aminoglycoside efficacy and provides respiratory energy in bacteria

(2018) Yu-bin Su et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession

(2018) Xiaoqin Wu et al.   Frontiers in Microbiology

Unveiling the enigma of refractory carbon in the ocean

(2018) Nianzhi Jiao et al.   National Science Review

Universal molecular structures in natural dissolved organic matter

(2018) Maren Zark et al.   Nature Communications

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

(2018) Hong-Yi Li et al.   Microbiome

Biosynthetic studies on terpenoids produced by Streptomyces

(2017) Tomohisa Kuzuyama   JOURNAL OF ANTIBIOTICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

(2017) Zachary Landry et al.   mBio

Picocyanobacteria and deep-ocean fluorescent dissolved organic matter share similar optical properties

(2017) Zhao Zhao et al.   Nature Communications

Carotenoids are the likely precursor of a significant fraction of marine dissolved organic matter

(2017) Neal Arakawa et al.   Science Advances

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

Dissolved organic sulfur in the ocean: Biogeochemistry of a petagram inventory

(2016) K. B. Ksionzek et al.   SCIENCE

Untangling the role that microbes play in ocean carbon cycle─A new paradigm in marine biogeochemistry

(2016) ChuanLun Zhang   Science China-Earth Sciences

iGraph: an incremental data processing system for dynamic graph

(2016) Wuyang Ju et al.   Frontiers of Computer Science

Heterotrimeric NADH-Oxidizing Methylenetetrahydrofolate Reductase from the Acetogenic Bacterium Acetobacterium woodii

(2015) Johannes Bertsch et al.   JOURNAL OF BACTERIOLOGY

An ultrahigh-resolution mass spectrometry index to estimate natural organic matter lability

(2015) Juliana D'Andrilli et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Marine sequestration of carbon in bacterial metabolites

(2015) Oliver J. Lechtenfeld et al.   Nature Communications

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

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Molecular composition of dissolved organic matter from a wetland plant (Juncus effusus) after photochemical and microbial decomposition (1.25 yr): Common features with deep sea dissolved organic matter

(2013) Pamela E. Rossel et al.   ORGANIC GEOCHEMISTRY

Combination of Entner-Doudoroff Pathway with MEP Increases Isoprene Production in Engineered Escherichia coli

(2013) Huaiwei Liu et al.   PLoS One

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Evaluation method for the potential functionome harbored in the genome and metagenome

(2012) Hideto Takami et al.   BMC GENOMICS

Oxidized sterols as a significant component of dissolved organic matter: Evidence from 2D HPLC in combination with 2D and 3D NMR spectroscopy

(2012) Gwen C. Woods et al.   WATER RESEARCH

Squalene-Hopene Cyclases

(2011) Gabriele Siedenburg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A simple and efficient method for the solid-phase extraction of dissolved organic matter (SPE-DOM) from seawater

(2011) Thorsten Dittmar et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Dissolved Organic Matter in the Ocean: A Controversy Stimulates New Insights

(2011) Dennis Hansell et al.   OCEANOGRAPHY

A Methylaspartate Cycle in Haloarchaea

(2011) M. Khomyakova et al.   SCIENCE

Multivariate Statistical Approaches for the Characterization of Dissolved Organic Matter Analyzed by Ultrahigh Resolution Mass Spectrometry

(2010) Rachel L. Sleighter et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Systems-Level Metabolic Flux Profiling Elucidates a Complete, Bifurcated Tricarboxylic Acid Cycle in Clostridium acetobutylicum

(2010) D. Amador-Noguez et al.   JOURNAL OF BACTERIOLOGY

Major bacterial contribution to the ocean reservoir of detrital organic carbon and nitrogen

(2010) Karl Kaiser et al.   LIMNOLOGY AND OCEANOGRAPHY

Characterization of dissolved organic matter across the Subtropical Convergence off the South Island, New Zealand

(2010) Michael Gonsior et al.   MARINE CHEMISTRY

Unprecedented acetoacetyl-coenzyme A synthesizing enzyme of the thiolase superfamily involved in the mevalonate pathway

(2010) E. Okamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

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

Quantifying environmental adaptation of metabolic pathways in metagenomics

(2009) T. A. Gianoulis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE