Comparative genomic analysis of 455 Lactiplantibacillus plantarum isolates: Habitat-specific genomes shaped by frequent recombination

Food Microbiology, Journal Year: 2022, Volume and Issue: 104, P. 103989 - 103989

Published: Jan. 16, 2022

Language: Английский

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Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations

Applied and Environmental Microbiology, Journal Year: 2023, Volume and Issue: 89(3)

Published: March 13, 2023

Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate the nitrifying guild sediments an acid mine lake (AML). The water was characterized by acidic pH below 5 a high ammonium concentration 175 mg-N/liter, which rare on earth. Nitrification active maximum nitrate production potential 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined AML sediments, comammox Nitrospira AOA

Language: Английский

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Critical steps in an environmental metaproteomics workflow

Environmental Microbiology, Journal Year: 2024, Volume and Issue: 26(5)

Published: May 1, 2024

Abstract Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As still maturing, it lacks consistent workflows, making challenging for non‐expert researchers to navigate. This review aims introduce workflow environmental metaproteomics. It outlines standard practices sample collection, processing, analysis, offers strategies overcome unique challenges presented by common matrices such as soil, freshwater, marine environments, biofilms, sludge, symbionts. The also highlights bottlenecks in data analysis are specific samples suggestions obtain high‐quality datasets. includes recent benchmarking studies descriptions software packages specifically built analysis. article written without assuming reader's familiarity with single‐organism proteomic accessible those new proteomics or mass spectrometry general. primer improve accessibility this exciting technology empower tackle ambitious research questions. While primarily resource field, should be useful established looking streamline troubleshoot their experiments.

Language: Английский

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Critical analysis of polycyclic tetramate macrolactam biosynthetic gene cluster phylogeny and functional diversity

Applied and Environmental Microbiology, Journal Year: 2024, Volume and Issue: 90(6)

Published: May 21, 2024

ABSTRACT Polycyclic tetramate macrolactams (PTMs) are bioactive natural products commonly associated with certain actinobacterial and proteobacterial lineages. These molecules have been the subject of numerous structure-activity investigations since 1970s. New members continue to be pursued in wild engineered bacterial strains, advances PTM biosynthesis suggest their outwardly simplistic biosynthetic gene clusters (BGCs) belie unexpected product complexity. To address origins this complexity understand its influence on discovery, we engaged a combination bioinformatics systematically classify BGCs PTM-targeted metabolomics compare select BGC types. By comparing groups producers mutants, exposed knowledge gaps that complicate bioinformatics-driven predictions. In sum, provide new insights into evolution while accounting for PTMs discovered thus far. The combined computational metabologenomic findings presented here should prove useful guiding future discovery. IMPORTANCE macrolactam (PTM) pathways frequently found within genomes biotechnologically important bacteria, including Streptomyces Lysobacter spp . Their molecular typically bioactive, having substantial agricultural therapeutic interest. Leveraging genomics discovery related is desirable, but drawing accurate structural predictions from alone remains challenging. This difficulty stems previously underappreciated remaining gaps, compounded by stream yet-uncharacterized loci gleaned recently sequenced genomes. We following study create framework cataloging historic clusters, identifying cluster variations, tracing evolutionary paths these molecules. Our data chemistry discoverable nature. However, our metabolomic mutational analyses emphasize practical limitations genomics-based exposing hidden

Language: Английский

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Weak magnetic field promotes denitrification by stimulating ferromagnetic ion-containing metalloprotein expression

Water Research, Journal Year: 2024, Volume and Issue: 262, P. 122116 - 122116

Published: July 17, 2024

Language: Английский

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