The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes

Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers

(2020) Shufeng Liu et al.   ISME Journal

Distribution of comammox and canonical ammonia oxidizing bacteria in tidal flat sediments of the Yangtze River estuary at different depths over four seasons

(2019) Q. Jiang et al.   JOURNAL OF APPLIED MICROBIOLOGY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

(2019) Zhirong Zhao et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Complete ammonia oxidation: an important control on nitrification in engineered ecosystems?

(2018) Christopher E Lawson et al.   CURRENT OPINION IN BIOTECHNOLOGY

Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton

(2018) Emma K. Wear et al.   ENVIRONMENTAL MICROBIOLOGY

Nitrification and the ammonia-oxidizing communities in the central Baltic Sea water column

(2018) Helena Jäntti et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Distribution and environmental assessment of trace elements contamination of water, sediments and flora from Douro River estuary, Portugal

(2018) C. Ribeiro et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Salinity is a key factor driving the nitrogen cycling in the mangrove sediment

(2018) Haitao Wang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes

(2018) Ricardo J. Eloy Alves et al.   Nature Communications

A missing link in the estuarine nitrogen cycle?: Coupled nitrification-denitrification mediated by suspended particulate matter

(2018) Weijing Zhu et al.   Scientific Reports

Distinct distribution patterns of ammonia-oxidizing archaea and bacteria in sediment and water column of the Yellow River estuary

(2018) Mingcong Li et al.   Scientific Reports

“Candidatus Nitrosotenuis aquarius,” an Ammonia-Oxidizing Archaeon from a Freshwater Aquarium Biofilter

(2018) Laura A. Sauder et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Shifts in the Community Dynamics and Activity of Ammonia‐Oxidizing Prokaryotes Along the Yangtze Estuarine Salinity Gradient

(2018) Juan Gao et al.   Journal of Geophysical Research-Biogeosciences

Salinity impact on ammonia oxidizers activity and amoA expression in estuarine sediments

(2017) J.P. Santos et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota

(2017) Wei Qin et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Enhanced nitrogen loss from rivers through coupled nitrification-denitrification caused by suspended sediment

(2017) Xinghui Xia et al.   SCIENCE OF THE TOTAL ENVIRONMENT

The nitrogen cycle: A review of isotope effects and isotope modeling approaches

(2017) Tobias R.A. Denk et al.   SOIL BIOLOGY & BIOCHEMISTRY

Distinct drivers of activity, abundance, diversity and composition of ammonia-oxidizers: evidence from a long-term field experiment

(2017) Junjie Guo et al.   SOIL BIOLOGY & BIOCHEMISTRY

Nanosilver inhibits nitrification and reduces ammonia-oxidising bacterial but not archaealamoAgene abundance in estuarine sediments

(2016) Jessica Beddow et al.   ENVIRONMENTAL MICROBIOLOGY

Coupling of bacterial nitrification with denitrification and anammox supports N removal in intertidal sediments (Arcachon Bay, France)

(2016) Sheryl Oliveira Fernandes et al.   ESTUARINE COASTAL AND SHELF SCIENCE

A meta-analysis of soil salinization effects on nitrogen pools, cycles and fluxes in coastal ecosystems

(2016) Minghua Zhou et al.   GLOBAL CHANGE BIOLOGY

Coupled nitrification-denitrification leads to extensive N loss in subtidal permeable sediments

(2016) Hannah K. Marchant et al.   LIMNOLOGY AND OCEANOGRAPHY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria

(2016) Holger Daims et al.   TRENDS IN MICROBIOLOGY

Nitrification at different salinities: Biofilm community composition and physiological plasticity

(2016) Blanca M. Gonzalez-Silva et al.   WATER RESEARCH

Diversity, abundance and activity of ammonia-oxidizing microorganisms in fine particulate matter

(2016) Jing-Feng Gao et al.   Scientific Reports

Ammonia manipulates the ammonia-oxidizing archaea and bacteria in the coastal sediment-water microcosms

(2015) Yan Zhang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The influence of salinity on the abundance, transcriptional activity, and diversity of AOA and AOB in an estuarine sediment: a microcosm study

(2015) Yan Zhang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Effect of salinity on nitrification efficiency and structure of ammonia-oxidizing bacterial communities in a submerged fixed bed bioreactor

(2015) C. Cortés-Lorenzo et al.   CHEMICAL ENGINEERING JOURNAL

Quantifying the chronic effect of low DO on the nitrification process

(2015) Guoqiang Liu et al.   CHEMOSPHERE

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Complete nitrification by a single microorganism

(2015) Maartje A. H. J. van Kessel et al.   NATURE

Complete nitrification by Nitrospira bacteria

(2015) Holger Daims et al.   NATURE

Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China

(2015) Qiufang Zhang et al.   Frontiers in Microbiology

amoAGene Abundances and Nitrification Potential Rates Suggest that Benthic Ammonia-Oxidizing Bacteria and Not Archaea Dominate N Cycling in the Colne Estuary, United Kingdom

(2014) Jialin Li et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Salinity-dominated change in community structure and ecological function of Archaea from the lower Pearl River to coastal South China Sea

(2014) Wei Xie et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Bacterial Domination Over Archaea in Ammonia Oxidation in a Monsoon-Driven Tropical Estuary

(2014) Vipindas Puthiya Veettil et al.   MICROBIAL ECOLOGY

Temperature Responses of Ammonia-Oxidizing Prokaryotes in Freshwater Sediment Microcosms

(2014) Jin Zeng et al.   PLoS One

Effects of allylthiourea, salinity, and pH on ammonia/ammonium-oxidizing prokaryotes in mangrove sediment incubated in laboratory microcosms

(2013) Yong-Feng Wang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Enrichment and Genome Sequence of the Group I.1a Ammonia-Oxidizing Archaeon “Ca. Nitrosotenuis uzonensis” Representing a Clade Globally Distributed in Thermal Habitats

(2013) Elena V. Lebedeva et al.   PLoS One

Physiology and Diversity of Ammonia-Oxidizing Archaea

(2012) David A. Stahl et al.   Annual Review of Microbiology

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Measuring nitrification in sediments – comparison of two techniques and three15NO measurement methods

(2012) Helena Jäntti et al.   ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES

Genome Sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a Low-Salinity Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary

(2012) A. C. Mosier et al.   JOURNAL OF BACTERIOLOGY

Responses of ammonia-oxidizing archaeal and betaproteobacterial populations to wastewater salinity in a full-scale municipal wastewater treatment plant

(2012) Yi-Ju Wu et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Effect of Elevated Salt Concentrations on the Aerobic Granular Sludge Process: Linking Microbial Activity with Microbial Community Structure

(2011) J. P. Bassin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effect of varying salinity, temperature, ammonia and nitrous acid concentrations on nitrification of saline wastewater in fixed-bed reactors

(2011) U. Sudarno et al.   BIORESOURCE TECHNOLOGY

Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments

(2011) Nicholas J. Bouskill et al.   ENVIRONMENTAL MICROBIOLOGY

Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms

(2011) Daniel T Verhamme et al.   ISME Journal

Diversity, Abundance, and Spatial Distribution of Sediment Ammonia-Oxidizing Betaproteobacteria in Response to Environmental Gradients and Coastal Eutrophication in Jiaozhou Bay, China

(2010) H. Dang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization and quantification of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a nitrogen-removing reactor using T-RFLP and qPCR

(2010) Tao Jin et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The Effects of Varying Salinity on Ammonium Exchange in Estuarine Sediments of the Parker River, Massachusetts

(2010) Nathaniel B. Weston et al.   Estuaries and Coasts

The Effects of Salinity on Nitrogen Losses from an Oligohaline Estuarine Sediment

(2010) Anne E. Giblin et al.   Estuaries and Coasts

Diversity and Abundance of Ammonia-Oxidizing Bacteria and Ammonia-Oxidizing Archaea During Cattle Manure Composting

(2010) Nozomi Yamamoto et al.   MICROBIAL ECOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Spatiotemporal distribution of pharmaceuticals in the Douro River estuary (Portugal)

(2010) Tânia Vieira Madureira et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Influence of river discharge patterns on the hydrodynamics and potential contaminant dispersion in the Douro estuary (Portugal)

(2010) Isabel C. Azevedo et al.   WATER RESEARCH

Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

(2009) Pilar Junier et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Temporal variability in the abundance of ammonia- oxidizing bacteria vs. archaea in sandy sediments of the Douro River estuary, Portugal

(2009) CM Magalhães et al.   AQUATIC MICROBIAL ECOLOGY

Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary

(2008) Annika C. Mosier et al.   ENVIRONMENTAL MICROBIOLOGY

Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary

(2008) Alyson E. Santoro et al.   ENVIRONMENTAL MICROBIOLOGY

Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms

(2008) Maria Tourna et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity and spatio-temporal distribution of ammonia-oxidizing Archaea and Bacteria in sediments of the Westerschelde estuary

(2008) Emel Sahan et al.   FEMS MICROBIOLOGY ECOLOGY