Selected Bacteria Are Critical for Karst River Carbon Sequestration via Integrating Multi-omics and Hydrochemistry Data

Carbonate Mineral Dissolution and Its Carbon Sink Effect in Chinese Loess

(2023) Mingyu Shao et al.   Land

Karst carbon sink processes and effects: A review

(2023) Lvfan Chen et al.   QUATERNARY INTERNATIONAL

Methods, progress and prospect for diagnosis of karst ecosystem health in China—An overview

(2023) Xiaoyong Bai et al.   Kexue Tongbao/Chinese Science Bulletin

Carbon dioxide partial pressure and its diffusion flux in karst surface aquatic ecosystems: a review

(2023) Xingxing Cao et al.   Acta Geochimica

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

(2022) Zhichao Zhou et al.   Microbiome

The impact of heterotrophic bacteria on recalcitrant dissolved organic carbon formation in a typical karstic river

(2022) Qiufang He et al.   SCIENCE OF THE TOTAL ENVIRONMENT

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

(2022) Changfei He et al.   WATER RESEARCH

Deep ocean microbial communities produce more stable dissolved organic matter through the succession of rare prokaryotes

(2022) Richard LaBrie et al.   Science Advances

Excitation-emission matrix fluorescence spectra of chromophoric dissolved organic matter reflected the composition and origination of dissolved organic carbon in Lijiang River, Southwest China

(2021) Qiufang He et al.   JOURNAL OF HYDROLOGY

Metagenomics and metatranscriptomics uncover the microbial community associated with high S0 production in a denitrifying desulfurization granular sludge reactor

(2021) Wei Li et al.   WATER RESEARCH

Structural and Catalytic Characterization of TsBGL, a β-Glucosidase From Thermofilum sp. ex4484_79

(2021) Anke Chen et al.   Frontiers in Microbiology

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

(2020) Qiang Zheng et al.   mBio

Sources and transformations of nitrate constrained by nitrate isotopes and Bayesian model in karst surface water, Guilin, Southwest China

(2020) Haijuan Zhao et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Transformation of DIC into POC in a karst river system: evidence from δ13CDIC and δ13CPOC in Lijiang, Southwest China

(2020) Haijuan Zhao et al.   Environmental Earth Sciences

Particulate Organic Carbon Deconstructed: Molecular and Chemical Composition of Particulate Organic Carbon in the Ocean

(2020) Jenan J. Kharbush et al.   Frontiers in Marine Science

Coupled carbon-nitrogen cycling controls the transformation of dissolved inorganic carbon into dissolved organic carbon in karst aquatic systems

(2020) Haijuan Zhao et al.   JOURNAL OF HYDROLOGY

Top‐down controls on nutrient cycling and population dynamics in a model estuarine photoautotroph–heterotroph co‐culture system

(2020) Qiang Zheng et al.   MOLECULAR ECOLOGY

Dynamics in riverine inorganic and organic carbon based on carbonate weathering coupled with aquatic photosynthesis in a karst catchment, Southwest China

(2020) Ping'an Sun et al.   WATER RESEARCH

Effects of aquatic phototrophs on seasonal hydrochemical, inorganic, and organic carbon variations in a typical karst basin, Southwest China

(2019) Ping’an Sun et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Biogeochemical and physical controls on the evolution of dissolved inorganic carbon (DIC) and δ13CDIC in karst spring-waters exposed to atmospheric CO2(g): Insights from laboratory experiments

(2019) Yongjun Jiang et al.   JOURNAL OF HYDROLOGY

OUP accepted manuscript

(2018)   BIOINFORMATICS

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Xiaoqin Wu et al.   Frontiers in Microbiology

Evolving Paradigms in Biological Carbon Cycling in the Ocean

(2018) Chuanlun Zhang et al.   National Science Review

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

(2018) Gherman V. Uritskiy et al.   Microbiome

How environment selects: Resilience and survival of microbial mat community within intermittent karst spring Krčić (Croatia)

(2018) Anamarija Kolda et al.   Ecohydrology

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Carbon sequestration processes and mechanisms in coastal mariculture environments in China

(2017) YongYu Zhang et al.   Science China-Earth Sciences

Organic carbon source tracing and DIC fertilization effect in the Pearl River: Insights from lipid biomarker and geochemical analysis

(2016) Mingxing Yang et al.   APPLIED GEOCHEMISTRY

The Size-Reactivity Continuum of Major Bioelements in the Ocean

(2015) Ronald Benner et al.   Annual Review of Marine Science

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

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

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels

(2013) Yu Peng et al.   BIOINFORMATICS

Bacterial chitin degradation—mechanisms and ecophysiological strategies

(2013) Sara Beier et al.   Frontiers in Microbiology

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

Squalene-Hopene Cyclases

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

The Microbial Carbon Pump: from Genes to Ecosystems

(2011) Nianzhi Jiao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast and precise method for HPLC–size exclusion chromatography with UV and TOC (NDIR) detection: Importance of multiple detectors to evaluate the characteristics of dissolved organic matter

(2011) Nobuyuki Kawasaki et al.   WATER RESEARCH

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

(2010) Karl Kaiser et al.   LIMNOLOGY AND OCEANOGRAPHY

Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean

(2010) Nianzhi Jiao et al.   NATURE REVIEWS MICROBIOLOGY

Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation

(2008) Stephen W. Ragsdale et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS