Characterization of bacterial and microbial eukaryotic communities associated with an ephemeral hypoxia event in Taihu Lake, a shallow eutrophic Chinese lake

Improved 18S rDNA amplification protocol for assessing protist diversity in oxygen-deficient marine systems

(2018) C Wylezich et al.   AQUATIC MICROBIAL ECOLOGY

Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions

(2017) Stilianos Louca et al.   ENVIRONMENTAL MICROBIOLOGY

Determination and Variation of Core Bacterial Community in a Two-Stage Full-Scale Anaerobic Reactor Treating High-Strength Pharmaceutical Wastewater

(2017) Haijun Ma et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Effect of Microcystins on Proto- and Metazooplankton Is More Evident in Artificial Than in Natural Waterbodies

(2017) J. Kosiba et al.   MICROBIAL ECOLOGY

DNA metabarcoding reveals that 200-μ m-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes

(2017) Lemian Liu et al.   Molecular Ecology Resources

Temporal dynamics of bacterial communities and predicted nitrogen metabolism genes in a full-scale wastewater treatment plant

(2017) Xiao-Yan Fan et al.   RSC Advances

Patterns and Processes in Marine Microeukaryotic Community Biogeography from Xiamen Coastal Waters and Intertidal Sediments, Southeast China

(2017) Weidong Chen et al.   Frontiers in Microbiology

Microbial communities mediating algal detritus turnover under anaerobic conditions

(2017) Jessica M. Morrison et al.   PeerJ

Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

(2017) André M. Comeau et al.   mSystems

Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation

(2017) Cindy J. Castelle et al.   Scientific Reports

Optimum dredging time for inhibition and prevention of algae-induced black blooms in Lake Taihu, China

(2016) Chao Chen et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Assessing and managing the risks of hypoxia in transitional waters: a case study in the tidal Garonne River (South-West France)

(2016) Sabine Schmidt et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Dynamics of bacterial abundance and the related environmental factors in large shallow eutrophic Lake Taihu

(2016) Yi Gong et al.   JOURNAL OF FRESHWATER ECOLOGY

SAR11 bacteria linked to ocean anoxia and nitrogen loss

(2016) Despina Tsementzi et al.   NATURE

Meteorological and hydrological conditions driving the formation and disappearance of black blooms, an ecological disaster phenomena of eutrophication and algal blooms

(2016) Yunlin Zhang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Diazotrophic bacterial community variability in a subtropical deep reservoir is correlated with seasonal changes in nitrogen

(2015) Lina Wang et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Illumina MiSeq sequencing investigation on the contrasting soil bacterial community structures in different iron mining areas

(2015) Chen Hong et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans

(2015) Massimo C Pernice et al.   ISME Journal

The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China

(2015) Lemian Liu et al.   ISME Journal

Identification and quantification of suspended algae and bacteria populations using flow cytometry: applications for algae biofuel and biochemical growth systems

(2015) G. T. Peniuk et al.   JOURNAL OF APPLIED PHYCOLOGY

Chromophoric dissolved organic matter of black waters in a highly eutrophic Chinese lake: Freshly produced from algal scums?

(2015) Yongqiang Zhou et al.   JOURNAL OF HAZARDOUS MATERIALS

Aerobic Microbial Respiration In Oceanic Oxygen Minimum Zones

(2015) Tim Kalvelage et al.   PLoS One

Simultaneous Heterotrophic Nitrification and Aerobic Denitrification by the Marine Origin Bacterium Pseudomonas sp. ADN-42

(2014) Ruofei Jin et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Climate change and dead zones

(2014) Andrew H. Altieri et al.   GLOBAL CHANGE BIOLOGY

The effects of a microcystin-producing and lacking strain of Microcystis on the survival of a widespread tropical copepod (Notodiaptomus iheringi)

(2014) Kemal Ali Ger et al.   HYDROBIOLOGIA

Vertical distribution of diazotrophic bacterial community associated with temperature and oxygen gradients in a subtropical reservoir

(2014) Zheng Yu et al.   HYDROBIOLOGIA

Survey on diversity of marine/saline anaerobic Heterolobosea (Excavata: Discoba) with description of seven new species

(2014) T. Panek et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Beyond hypoxia: Occurrence and characteristics of black blooms due to the decomposition of the submerged plant Potamogeton crispus in a shallow lake

(2014) Qiushi Shen et al.   JOURNAL OF ENVIRONMENTAL SCIENCES

Denitrifier Community in the Oxygen Minimum Zone of a Subtropical Deep Reservoir

(2014) Zheng Yu et al.   PLoS One

Optical characterization of black water blooms in eutrophic waters

(2014) Hongtao Duan et al.   SCIENCE OF THE TOTAL ENVIRONMENT

The responses of the taxa composition of particle-attached bacterial community to the decomposition of Microcystis blooms

(2014) Keqiang Shao et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Effects of water stratification and mixing on microbial community structure in a subtropical deep reservoir

(2014) Zheng Yu et al.   Scientific Reports

Benthic protists and fungi of Mediterranean deep hypsersaline anoxic basin redoxcline sediments

(2014) Joan M. Bernhard et al.   Frontiers in Microbiology

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

(2014) Jai Ram Rideout et al.   PeerJ

Feedback Mechanisms Between Cyanobacterial Blooms, Transient Hypoxia, and Benthic Phosphorus Regeneration in Shallow Coastal Environments

(2013) Mindaugas Zilius et al.   Estuaries and Coasts

Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches

(2013) Bernd Wemheuer et al.   FEMS MICROBIOLOGY ECOLOGY

Effects of sludge dredging on the prevention and control of algae-caused black bloom in Taihu Lake, China

(2013) Wei He et al.   JOURNAL OF ENVIRONMENTAL SCIENCES

Water Stratification Affects the Microeukaryotic Community in a Subtropical Deep Reservoir

(2013) Zheng Yu et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

Genomic, Proteomic, and Biochemical Analyses of Oleaginous Mucor circinelloides: Evaluating Its Capability in Utilizing Cellulolytic Substrates for Lipid Production

(2013) Hui Wei et al.   PLoS One

Microorganisms and typical organic matter responsible for lacustrine “black bloom”

(2013) Ziyan Feng et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Factors affecting the development and dynamics of hypoxia in a large shallow stratified lake: Hourly to seasonal patterns

(2013) Damien Bouffard et al.   WATER RESOURCES RESEARCH

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

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Effect of oxygen minimum zone formation on communities of marine protists

(2012) William Orsi et al.   ISME Journal

Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1

(2012) Sari Peura et al.   ISME Journal

Comparing the Hyper-Variable V4 and V9 Regions of the Small Subunit rDNA for Assessment of Ciliate Environmental Diversity

(2012) Micah Dunthorn et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages

(2012) R. K. Colwell et al.   Journal of Plant Ecology

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou 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

Testing the Limits of 454 Pyrotag Sequencing: Reproducibility, Quantitative Assessment and Comparison to T-RFLP Fingerprinting of Aquifer Microbes

(2012) Giovanni Pilloni et al.   PLoS One

Microbial oceanography of anoxic oxygen minimum zones

(2012) O. Ulloa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prevalence of partnerships between bacteria and ciliates in oxygen-depleted marine water columns

(2012) William Orsi et al.   Frontiers in Microbiology

Marine Fungi: Their Ecology and Molecular Diversity

(2011) Thomas A. Richards et al.   Annual Review of Marine Science

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Hypoxia by degrees: Establishing definitions for a changing ocean

(2011) A.F. Hofmann et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Microbial metatranscriptomics in a permanent marine oxygen minimum zone

(2011) Frank J. Stewart et al.   ENVIRONMENTAL MICROBIOLOGY

Characterization of the bacterial community composition in a hypoxic zone induced by Microcystis blooms in Lake Taihu, China

(2011) Huabing Li et al.   FEMS MICROBIOLOGY ECOLOGY

Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California

(2011) J Michael Beman et al.   ISME Journal

Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing

(2011) Jan Pawlowski et al.   PLoS One

Evaluation and application of a three-dimensional water quality model in a shallow lake with complex morphometry

(2010) Shahram Missaghi et al.   ECOLOGICAL MODELLING

Microbial eukaryotic community in response to Microcystis spp. bloom, as assessed by an enclosure experiment in Lake Taihu, China

(2010) Meijun Chen et al.   FEMS MICROBIOLOGY ECOLOGY

Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA

(2010) Jon Bråte et al.   ISME Journal

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

A Drinking Water Crisis in Lake Taihu, China: Linkage to Climatic Variability and Lake Management

(2009) Boqiang Qin et al.   ENVIRONMENTAL MANAGEMENT

Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia

(2009) Elena Zaikova et al.   ENVIRONMENTAL MICROBIOLOGY

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Fungal diversity in oxygen-depleted regions of  the Arabian Sea revealed by targeted environmental sequencing combined with cultivation

(2009) Cathrine S. Jebaraj et al.   FEMS MICROBIOLOGY ECOLOGY

Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge

(2009) Delphine Rivière et al.   ISME Journal

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Eutrophication science: where do we go from here?

(2009) Val H. Smith et al.   TRENDS IN ECOLOGY & EVOLUTION

Diversity and activity of aquatic fungi under low oxygen conditions

(2008) A. O. MEDEIROS et al.   FRESHWATER BIOLOGY

Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

(2008) Anders F. Andersson et al.   PLoS One

Impacts of Atmospheric Anthropogenic Nitrogen on the Open Ocean

(2008) R. A. Duce et al.   SCIENCE

Spreading Dead Zones and Consequences for Marine Ecosystems

(2008) R. J. Diaz et al.   SCIENCE