Metabarcoding under Brine: Microbial Ecology of Five Hypersaline Lakes at Rottnest Island (WA, Australia)

eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity

(2021) Mahsa Mousavi‐Derazmahalleh et al.   Molecular Ecology Resources

Rainfall as a trigger of ecological cascade effects in an Australian groundwater ecosystem

(2021) Mattia Saccò et al.   Scientific Reports

Enhanced anaerobic digestion of waste-activated sludge via bioaugmentation strategy—Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) analysis through hydrolytic enzymes and possible linkage to system performance

(2021) Roent Dune A. Cayetano et al.   BIORESOURCE TECHNOLOGY

Comprehensive gene and pathway analysis of cervical cancer progression

(2020) Yuexiong Yi et al.   Oncology Letters

Spherulitic microbialites from modern hypersaline lakes, Rottnest Island, Western Australia

(2020) Karl Bischoff et al.   Geobiology

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

Diversity of halophilic and halotolerant bacteria in the largest seasonal hypersaline lake (Aran-Bidgol-Iran)

(2020) Maryam Didari et al.   Journal of Environmental Health Science and Engineering

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences

(2020) Franziska Wemheuer et al.   Environmental Microbiome

Tracking down carbon inputs underground from an arid zone Australian calcrete

(2020) Mattia Saccò et al.   PLoS One

Changes in soil microbial communities in post mine ecological restoration: Implications for monitoring using high throughput DNA sequencing

(2020) M. van der Heyde et al.   SCIENCE OF THE TOTAL ENVIRONMENT

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Comparative metagenomics of microbial mats from hypersaline lakes at Rottnest Island (WA, Australia), advancing our understanding of the effect of mat community and functional genes on microbialite accretion

(2019) Juliana Mendes Monteiro et al.   LIMNOLOGY AND OCEANOGRAPHY

Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water

(2019) Luke E. Holman et al.   Scientific Reports

Seasonal and diurnal evaporation from a deep hypersaline lake: The Dead Sea as a case study

(2018) I. Hamdani et al.   JOURNAL OF HYDROLOGY

Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles

(2018) François Keck et al.   Molecular Ecology Resources

Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns

(2018) Clara López-Hermoso et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

(2018) Stefan Janssen et al.   mSystems

Co-existence of Methanogenesis and Sulfate Reduction with Common Substrates in Sulfate-Rich Estuarine Sediments

(2017) Michal Sela-Adler et al.   Frontiers in Microbiology

Zooplankton Community Profiling in a Eutrophic Freshwater Ecosystem-Lake Tai Basin by DNA Metabarcoding

(2017) Jianghua Yang et al.   Scientific Reports

A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae fam nov.

(2016) Radhey S. Gupta et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems

(2016) Darren M. Evans et al.   FUNCTIONAL ECOLOGY

Island groundwater resources, impacts of abstraction and a drying climate: Rottnest Island, Western Australia

(2016) Eliza Bryan et al.   JOURNAL OF HYDROLOGY

Estimating the volume and age of water stored in global lakes using a geo-statistical approach

(2016) Mathis Loïc Messager et al.   Nature Communications

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes

(2016) Shoko Iwai et al.   PLoS One

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov.

(2014) R. S. Gupta et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Protease Inhibitors from Marine Actinobacteria as a Potential Source for Antimalarial Compound

(2014) L. Karthik et al.   PLoS One

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Recent studies in microbial degradation of petroleum hydrocarbons in hypersaline environments

(2014) Babu Z. Fathepure   Frontiers in Microbiology

Unexplored hypersaline habitats are sources of novel actinomycetes

(2014) Polpass Arul Jose et al.   Frontiers in Microbiology

Life in the salinity gradient: Discovering mechanisms behind a new biodiversity pattern

(2013) Irena Telesh et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community

(2013) Sheila Podell et al.   ISME Journal

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

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

Actinomycetes Diversity among rRNA Gene Clones and Cellular Isolates from Sambhar Salt Lake, India

(2013) A. K. Yadav et al.   TheScientificWorldJOURNAL

Substrate Limitation for Methanogenesis in Hypersaline Environments

(2012) Cheryl A. Kelley et al.   ASTROBIOLOGY

Identification and characterization of Francisella species from natural warm springs in Utah, USA

(2012) C.A. Whitehouse et al.   LETTERS IN APPLIED MICROBIOLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Hygroscopic Salts and the Potential for Life on Mars

(2010) Alfonso F. Davila et al.   ASTROBIOLOGY

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

Bacterial phenylalanine and phenylacetate catabolic pathway revealed

(2010) R. Teufel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

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

Working toward the Future: Insights into Francisella tularensis Pathogenesis and Vaccine Development

(2009) R. D. Pechous et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Heterotrophic denitrification at extremely high salt and pH by haloalkaliphilic Gammaproteobacteria from hypersaline soda lakes

(2008) A. A. Shapovalova et al.   EXTREMOPHILES