mSystems · 2018 · 19 citations · 72 references
Life SciencesBiochemistryMicrobiologyMetagenomicsMicrobial EcologyWastewater TreatmentBiodegradationBioremediationCholesterol MetabolismSteroid BiosynthesisSteroid MetabolismSterol MetabolismBiological DegradationCholesterol CatabolismMetatranscriptomic AnalysisMicrobial Community ResponsesMicrobial Steroid DegradationRare BiosphereSteroid Catabolic PathwaysWastewater Treatment Plants
Steroids are ubiquitous and abundant natural compounds that display recalcitrance. Biodegradation via sludge communities in wastewater treatment plants is the primary removal process for steroids. To date, compared to studies for aerobic steroid degradation, the knowledge of anaerobic degradation of steroids has been based on only a few model organisms. Due to the increase of anthropogenic impacts, steroid inputs may affect microbial diversity and functioning in ecosystems. Here, we first investigated microbial functional responses to cholesterol, the most abundant steroid in sludge, at the community level. Our metagenomic and metatranscriptomic analyses revealed that the capacities for cholesterol approach, uptake, and degradation are unique traits of certain low-abundance betaproteobacteria, indicating the importance of the rare biosphere in bioremediation. Apparent expression of genes involved in cofactor de novo synthesis and salvage pathways suggests that these micronutrients play important roles for cholesterol degradation in sludge communities.
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Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony Bolger, Marc Lohse, Björn Usadel · Bioinformatics · 2014 · 69.7K citations · Full text
Fast gapped-read alignment with Bowtie 2
Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
Koichiro Tamura, Glen Stecher, Daniel S. Peterson et al. · Molecular Biology and Evolution · 2013 · 47.9K citations · Full text
MUSCLE: multiple sequence alignment with high accuracy and high throughput
R. C. Edgar · Nucleic Acids Research · 2004 · 46.5K citations · Full text