Current Biomarker-Based Assessment Underestimates True Denitrification Potential
Current attempts to gauge nitrogen loss from soils rely on the quantitative measurement of nirK and nirS biomarkers. Using Anaeromyobacter dehalogenans as a model, Onley et al. (e01985-17) demonstrated that microbial denitrification occurs in the absence of the key denitrification genes nirK and nirS as long as ferrous iron is present. Since many soils and sediments contain bioavailable iron, their findings indicate that denitrification and associated nitrogen loss to the atmosphere can be comprehensively understood, and potentially managed, only when integrated studies of interlinked biogeochemical cycles are performed.
Changes in Transcriptional Regulation Mediate Sympatric Speciation
Characterizing a natural population of co-evolving, closely related strains provides an opportunity to uncover mechanisms that mediate strain divergence and niche adaptation. Deng et al. (e02015-17) used comparative genomic and transcriptional hybridization to demonstrate that divergence among closely related strains of Shewanella baltica is mediated by both changes in transcriptional regulation of shared genes and gene loss/acquisition, which together contribute to adaptation in different environmental niches. These studies reinforce the importance of considering changes in transcriptional networks in addition to larger changes in gene content and structure when characterizing bacterial genome evolution and niche adaptation.
Novel Whole-Genome Sequencing Method To Study Salmonella Survival In Vivo and Predict Zoonotic Risk
Cattle are a reservoir of Salmonella enterica serovars that can cause human salmonellosis via contaminated beef products. To understand whether all serovars survive equally within cattle and, thus, pose an equal threat to food safety, Vohra et al. (e02262-17) developed a massively parallel whole-genome sequencing method to study serovar survival in vivo. Naturally occurring single nucleotide polymorphisms were used as markers to define the presence and quantity of serovars in tissues of infected calves. The results show that pan-serovar approaches are required to control S. enterica in cattle. This method can reduce animal use in the evaluation of strain phenotypes and control strategies.
Salmonella Detection and Subtyping from Food in a Single, Rapid Workflow
Traditional methods for detection and subtyping of foodborne pathogens are isolate-centric, separate, and time-consuming processes. Hyeon and colleagues (e02340-17) developed a quasimetagenomics approach that substantially shortened culture enrichment through selective capture of Salmonella cells and efficient amplification of genomic DNA. Further acceleration of analysis was achieved by using nanopore real-time sequencing. In one case, Salmonella detection, serotyping, and phylogenetic identification from iceberg lettuce were delivered in a single workflow within 24 hours. This approach has potential in areas where rapid detection and subtyping of foodborne pathogens is important, such as outbreak response and precision tracking and monitoring of the pathogens.
Environmental Microbiota Drives Spontaneous Liquor Fermentation
Spontaneous food fermentation is difficult to control without understanding the effect of the environment on microbial succession and metabolism. Using a microbial source tracking strategy, Wang et al. (e02369-17) found that the environment was the source of many microorganisms important for Chinese liquor fermentation. Changes to the environmental microbiota could drive both microbial succession and metabolic profiles during liquor fermentation. These findings make it feasible to better control spontaneous food fermentation.
- Copyright © 2018 American Society for Microbiology.
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- Current Biomarker-Based Assessment Underestimates True Denitrification Potential
- Changes in Transcriptional Regulation Mediate Sympatric Speciation
- Novel Whole-Genome Sequencing Method To Study Salmonella Survival In Vivo and Predict Zoonotic Risk
- Salmonella Detection and Subtyping from Food in a Single, Rapid Workflow
- Environmental Microbiota Drives Spontaneous Liquor Fermentation
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