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Article
Open AccessDisentangling the syntrophic electron transfer mechanisms of Candidatus geobacter eutrophica through electrochemical stimulation and machine learning
Interspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in methanogenic environments is still unclear. Our r...
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Article
Open AccessEcology and molecular targets of hypermutation in the global microbiome
Changes in the sequence of an organism’s genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversi...
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Article
Open AccessCatabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses
Current understanding of the carbon cycle in methanogenic environments involves trophic interactions such as interspecies H2 transfer between organotrophs and methanogens. However, many metabolic processes are th...
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Article
Open AccessMachine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes
Microorganisms in activated sludge (AS) play key roles in the wastewater treatment processes. However, their ecological behaviors and differences from microorganisms in other environments have mainly been stud...
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Article
Open AccessQuantifying the contribution of microbial immigration in engineered water systems
Immigration is a process that can influence the assembly of microbial communities in natural and engineered environments. However, it remains challenging to quantitatively evaluate the contribution of this pro...
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Article
Open AccessDiversity and geochemical community assembly processes of the living rare biosphere in a sand-and-gravel aquifer ecosystem in the Midwestern United States
Natural microbial communities consist of a limited number of abundant species and an extraordinarily diverse population of rare species referred to as the rare biosphere. Recent studies have revealed that the ...
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Article
Open AccessCoupling growth kinetics modeling with machine learning reveals microbial immigration impacts and identifies key environmental parameters in a biological wastewater treatment process
Ubiquitous in natural and engineered ecosystems, microbial immigration is one of the mechanisms sha** community assemblage. However, quantifying immigration impact remains challenging especially at individua...
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Article
Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Nat. Biotechnol. 35, 725–731 (2017); published online 8 August 2017; corrected after print 29 November 2017; corrected after print 7 December 2017 In the version of this article initially published, the author...
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Article
Open AccessEffect of divalent ions and a polyphosphate on composition, structure, and stiffness of simulated drinking water biofilms
The biofilm chemical and physical properties in engineered systems play an important role in governing pathogen transmission, fouling facilities, and corroding metal surfaces. Here, we investigated how simulat...
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Article
Open AccessUgly ducklings—the dark side of plastic materials in contact with potable water
Bath toys pose an interesting link between flexible plastic materials, potable water, external microbial and nutrient contamination, and potentially vulnerable end-users. Here, we characterized biofilm communi...
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Article
Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Nat. Biotechnol. 35, 725–731 (2017); published online 8 August 2017; corrected after print 29 November 2017; corrected after print 7 December 2017 In the version of this article initially published, the follow...
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Article
Open AccessDiverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients
Microbial communities drive biogeochemical cycles through networks of metabolite exchange that are structured along energetic gradients. As energy yields become limiting, these networks favor co-metabolic inte...
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Article
Open AccessMinimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Standards for sequencing the microbial 'uncultivated majority', namely bacterial and archaeal single-cell genome sequences, and genome sequences from metagenomic datasets, are proposed.
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Article
Direct treatment of high-strength soft drink wastewater using a down-flow hanging sponge reactor: performance and microbial community dynamics
A stand-alone down-flow hanging sponge (DHS) system with a two-stage configuration was operated for 700 days to treat synthetic soft drink wastewater at 3000 mg/L chemical oxygen demand (COD). Throughout the o...
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Article
Open AccessEvaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity
Anaerobic digestion is a common technology to biologically stabilize wasted solids produced in municipal wastewater treatment. Its efficiency is usually evaluated by calculating the reduction in volatile solid...
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Article
Open AccessXXIV World Allergy Congress 2015
A1 Pirfenidone inhibits TGF-b1-induced extracellular matrix production in nasal polyp-derived fibroblasts
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Article
Global metabolomic responses of Nitrosomonas europaea 19718 to cold stress and altered ammonia feeding patterns
The model ammonia-oxidizing bacterium Nitrosomonas europaea represents one of the environmentally and biotechnologically significant microorganisms. Genome-based studies over the last decade have led to many intr...
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Article
Effects of hydraulic retention time on aerobic granulation and granule growth kinetics at steady state with a fast start-up strategy
A hydraulic retention time (HRT) of 4, 6, and 8 h was employed, respectively, in three reactors to study the effects of HRT on granulation with a newly developed fast granulation strategy, i.e., a strategy by ...
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Reference Work Entry In depth
The Family Dermatophilaceae
The family Dermatophilaceae embraces Gram-positive, high G+C, facultative anaerobic or strictly aerobic chemoorganotrophic bacteria with a wide range of habitats such as animal and human skin, fish guts, and wast...
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Article
Open AccessInsights into the phylogeny and coding potential of microbial dark matter
Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are current...
