Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities

Biotransformation of Sulfonamide Antibiotics in Activated Sludge: The Formation of Pterin-Conjugates Leads to Sustained Risk

(2018) Stefan Achermann et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Analysis of biofilm bacterial communities under different shear stresses using size-fractionated sediment

(2017) Hongwei Fang et al.   Scientific Reports

Activated sludge mass reduction and biodegradability of the endogenous residues by digestion under different aerobic to anaerobic conditions: Comparison and modeling

(2016) C.G. Martínez-García et al.   BIORESOURCE TECHNOLOGY

rRNA Gene Expression of Abundant and Rare Activated-Sludge Microorganisms and Growth Rate Induced Micropollutant Removal

(2016) David C. Vuono et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Scaling laws predict global microbial diversity

(2016) Kenneth J. Locey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

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

(2016) Holger Daims et al.   TRENDS IN MICROBIOLOGY

High-rate activated sludge communities have a distinctly different structure compared to low-rate sludge communities, and are less sensitive towards environmental and operational variables

(2016) Francis A. Meerburg et al.   WATER RESEARCH

Rethinking growth and decay kinetics in activated sludge – towards a new adaptive kinetics approach

(2016) Michael Friedrich et al.   WATER SCIENCE AND TECHNOLOGY

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut

(2016) Henrik M. Roager et al.   Nature Microbiology

High taxonomic variability despite stable functional structure across microbial communities

(2016) Stilianos Louca et al.   Nature Ecology & Evolution

Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest

(2016) Stephanie N Kivlin et al.   PLoS One

Comparison of bacterial communities of conventional and A-stage activated sludge systems

(2016) Alejandro Gonzalez-Martinez et al.   Scientific Reports

Disturbance opens recruitment sites for bacterial colonization in activated sludge

(2015) David C. Vuono et al.   ENVIRONMENTAL MICROBIOLOGY

The activated sludge ecosystem contains a core community of abundant organisms

(2015) Aaron M Saunders et al.   ISME Journal

Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology

(2015) James I. Prosser   NATURE REVIEWS MICROBIOLOGY

Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform

(2015) Lucas Sinclair et al.   PLoS One

Physiological adaptation of growth kinetics in activated sludge

(2015) M. Friedrich et al.   WATER RESEARCH

The effect of different aeration conditions in activated sludge – Side-stream system on sludge production, sludge degradation rates, active biomass and extracellular polymeric substances

(2015) Jonathan Habermacher et al.   WATER RESEARCH

Modeling effects of DO and SRT on activated sludge decay and production

(2015) Guoqiang Liu et al.   WATER RESEARCH

Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time

(2014) Samik Bagchi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability

(2014) David R. Johnson et al.   ENVIRONMENTAL MICROBIOLOGY

Disturbance and temporal partitioning of the activated sludge metacommunity

(2014) David C Vuono et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Uncoupling of microbial community structure and function in decomposing litter across beech forest ecosystems in Central Europe

(2014) Witoon Purahong et al.   Scientific Reports

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

(2013) Anne Chao et al.   ECOLOGICAL MONOGRAPHS

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

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

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

Taxonomic Precision of Different Hypervariable Regions of 16S rRNA Gene and Annotation Methods for Functional Bacterial Groups in Biological Wastewater Treatment

(2013) Feng Guo et al.   PLoS One

A new interpretation of endogenous respiration profiles for the evaluation of the endogenous decay rate of heterotrophic biomass in activated sludge

(2013) M. Friedrich et al.   WATER RESEARCH

Microbial community assembly, theory and rare functions

(2013) Mujalin K. Pholchan et al.   Frontiers in Microbiology

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

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Impact of solid retention time and nitrification capacity on the ability of activated sludge to remove pharmaceuticals

(2012) P. Falås et al.   ENVIRONMENTAL TECHNOLOGY

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

Metagenomic and Metatranscriptomic Analysis of Microbial Community Structure and Gene Expression of Activated Sludge

(2012) Ke Yu et al.   PLoS One

The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors

(2011) Aline Frossard et al.   ISME Journal

454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants

(2011) Tong Zhang et al.   ISME Journal

Bacterial community assembly based on functional genes rather than species

(2011) C. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Diversity of Dominant Bacterial Taxa in Activated Sludge Promotes Functional Resistance following Toxic Shock Loading

(2010) Pascal E. Saikaly et al.   MICROBIAL ECOLOGY

Phylogenetic diversity measures based on Hill numbers

(2010) A. Chao et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Effects of short solids retention time on microbial community in a membrane bioreactor

(2009) Liang Duan et al.   BIORESOURCE TECHNOLOGY

Effect of Sludge Age on the Bacterial Diversity of Bench Scale Sequencing Batch Reactors

(2009) Alper Tunga Akarsubasi et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY