Article
Biology
Robert J. Nichols, Benjamin LaFrance, Naiya R. Phillips, Devon R. Radford, Luke M. Oltrogge, Luis E. Valentin-Alvarado, Amanda J. Bischoff, Eva Nogales, David F. Savage
Summary: Encapsulins are proteinaceous organelle-like compartments in prokaryotes that compartmentalize cargo enzymes. The discovery and characterization of a novel encapsulin in response to sulfate starvation provide insights for understanding the physiological role of these nanocompartments in bacteria.
Article
Microbiology
Stephen K. Dolan, Andre Wijaya, Michael Kohlstedt, Lars Glaeser, Paul Brear, Rafael Silva-Rocha, Christoph Wittmann, Martin Welch
Summary: Pseudomonas aeruginosa is a critical priority pathogen due to its resistance to antibiotics, ubiquity in the environment, and aggressiveness in infections. This study uncovers the pathways and mechanisms used by the pathogen to grow on the abundant substrate propionate. The researchers found that propionate can turn into a potent poison when the organism is unable to metabolize it, preventing bacterial growth. They also discovered the promiscuity of the enzyme 2-methylcitrate synthase, which can compensate for the loss of another essential enzyme in the cell. Understanding these metabolic pathways is crucial for developing targeted interventions against bacterial central metabolism.
Article
Fisheries
Jing Yu, Srinivasan Ramanathan, Liangchuan Chen, Fuyuan Zeng, Xiaoyan Li, Yiyang Zhao, Ling Lin, Sean J. Monaghan, Xiangmin Lin, Huanying Pang
Summary: Antibiotic resistance among aquatic bacterial pathogens, specifically in A. hydrophila, is a growing concern in aquaculture environments. This study conducted a transcriptomic analysis to identify differentially expressed genes between OXY susceptible and resistant strains, revealing down-regulation of sulfur metabolism genes and up-regulation of mannitol metabolism and efflux pump system genes in resistant strains. The findings suggest the involvement of these pathways in OXY resistance evolution in A. hydrophila.
AQUACULTURE REPORTS
(2021)
Article
Microbiology
Bo Wang, Xicheng Wang, Zhuangwei Wang, Kefeng Zhu, Weimin Wu
Summary: This study explored the changes in the rhizosphere microbial community of salt-tolerant and salt-sensitive grapevines under salt stress using metagenomic sequencing. The results showed that salt stress had a greater impact on the rhizosphere microbiota of the salt-tolerant variety, with differentially enriched functions related to cell motility and metabolism. The composition and functions of the rhizosphere microbial community were found to contribute to the enhanced salt tolerance of certain grapevines.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Microbiology
Katie E. Shalvarjian, Dipti D. Nayak
Summary: Methanogenesis is a significant metabolic process carried out by methanogens in the Archaea domain. Although genes involved in methanogenic metabolism have been identified and characterized, the regulation of methane production in response to various signals remains less understood.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Review
Food Science & Technology
Zhenbiao Li, Jing Huang, Lei Wang, Dong Li, Yanpei Chen, Yanqun Xu, Li Li, Hang Xiao, Zisheng Luo
Summary: This article comprehensively reviews the chemical interactions of sulfur dioxide (SO2) with the components of fruit and vegetable products, elaborates on its antimicrobial, anti-browning, and antioxidation mechanisms, discusses its roles in sulfur metabolism, reactive oxygen species (ROS)/redox regulation, resistance induction, and quality maintenance in fruits and vegetables. It also summarizes the application technology of SO2, its safety in human consumption, emphasizes the intrinsic metabolism of SO2 and its consequences for the postharvest physiology and safety of fresh fruits and vegetables. Further research is needed to evaluate the molecular mechanisms of SO2 metabolism in the cells and tissues of fruits and vegetables, and to uncover the interaction mechanisms between SO2 and the components of fruits and vegetables as well as the efficacy and safety of bound SO2. This review has important guiding significance for adjusting an applicable definition of maximum residue limit of SO2 in food.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2023)
Article
Biochemical Research Methods
Zhen Li, Lishan Zhang, Lina Sun, Yuqian Wang, Jiazhen Chen, Huamei Tang, Ling Lin, Xiangmin Lin
Summary: In this study, the regulatory role of SlyA in various physiological functions of A. hydrophila was investigated. The deletion of SlyA affected sulfur and phosphate metabolism, as well as outer membrane permeability. A ChIP-PCR assay demonstrated the direct binding of AhSlyA to promoters of genes related to sulfur metabolism. These findings highlight the importance of SlyA in regulating multiple biological functions in A. hydrophila.
JOURNAL OF PROTEOMICS
(2021)
Review
Biochemistry & Molecular Biology
Hongjun Yu, Gerrit J. Schut, Domink K. Haja, Michael W. W. Adams, Huilin Li
Summary: Modern respiratory complex I, MBH, and MBS likely share a common ancestor and help conserve energy in the Proterozoic era. They may have evolved from an integration of ancestral resistance and pH antiporters and redox-active modules. Recent high-resolution cryo-EM studies have greatly enhanced our understanding of their structures and evolutionary relationships.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Agricultural Engineering
Kaiquan Wang, Mahmood Qaisar, Bilong Chen, Jinghong Xiao, Jing Cai
Summary: The study found that adjusting the hydraulic retention time appropriately can increase the production of sulfide (S-0) and improve the simultaneous removal of sulfide and nitrite. Under different HRT conditions, bacterial community richness and key gene expression will change, affecting the performance of the recirculation system.
BIORESOURCE TECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Tomas Alarcon-Schumacher, Adit Naor, Uri Gophna, Susanne Erdmann
Summary: Viruses play important roles in various environments as ecological, biogeochemical, and evolutionary drivers. Some viruses cause the lysis of their host cells upon infection, while others exhibit chronic infections without cell lysis. The nature and impact of chronic infections in prokaryotic host organisms are not well understood. This study characterizes a novel haloarchaeal virus, HFPV-1, which causes a chronic infection without cell lysis in the model haloarchaeon H. volcanii DS2. The study shows that HFPV-1 and H. volcanii provide a great model system to study virus-host interactions in archaea. HFPV-1 has a wide host range among haloarchaea and may be developed into a genetic tool for studying other inaccessible haloarchaea.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Environmental Sciences
Xiong Li, Di Chen, Ya Yang, Yuanyuan Liu, Landi Luo, Qian Chen, Yongping Yang
Summary: The study identified key genes and pathways involved in the response of turnip landraces to Cd stress through comparative transcriptome analysis.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Review
Biochemistry & Molecular Biology
Xia Deng, Yanyan Li, Chang Guo, Zhicong Zhao, Guoyue Yuan
Summary: Tsukushi (TSK) is a newly identified hepatokine that belongs to the small leucine-rich proteoglycans (SLRPs) family. Initial research focused on its role in various physiological processes, while recent studies have expanded to include cell signaling pathways, proliferation, differentiation, glycolipid metabolism, and energy balance. This article provides a brief overview of TSK's role in physiological and pathological processes.
Article
Microbiology
Christina Johnson, Alexis England, Mason Munro-Ehrlich, Daniel R. Colman, Jennifer L. DuBois, Eric S. Boyd
Summary: Archaeal methanogens, methanotrophs, and alkanotrophs, among the most ancient forms of life, exhibit diverse mechanisms of iron (Fe) and sulfur (S) acquisition, trafficking, deployment, and storage, which have likely evolved in response to differential availability of these elements. Variation in these mechanisms has contributed to the diversification and ecology of these organisms, with some inconsistencies suggesting potential auxotrophy or yet-to-be-discovered pathways for cofactor biosynthesis.
JOURNAL OF BACTERIOLOGY
(2021)
Article
Microbiology
Yu Su, Yuta Michimori, Haruyuki Atomi
Summary: The hyperthermophilic archaeon Thermococcus kodakarensis uses amino acids as a carbon and energy source. Two Class I aminotransferases, TK0548 and TK2268, are responsible for the conversion of specific amino acids. Genetic examination reveals their importance in amino acid metabolism.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Gloria Paya, Vanesa Bautista, Monica Camacho, Julia Esclapez, Maria-Jose Bonete
Summary: This study analyzes 168 Lsm proteins in 109 archaeal species using bioinformatics tools and finds that they are related to RNA metabolism, with different functions depending on their molecular weight.
Article
Microbiology
Diego M. Roldan, Nikos Kyrpides, Tanja Woyke, Nicole Shapiro, William B. Whitman, Stanislava Kralova, Ivo Sedlacek, Hans-Juergen Busse, Rodolfo Javier Menes
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2020)
Article
Geosciences, Multidisciplinary
Yu-Te Lin, William B. Whitman, David C. Coleman, Shih-Hao Jien, Hsueh-Ching Wang, Chih-Yu Chiu
Summary: The study found significant differences in bacterial community composition between coniferous forest and grassland soils at the treeline, with correlations to soil pH, organic C, and C/N. Historical vegetation types also had a significant impact on the abundance of certain bacterial groups.
Article
Microbiology
Diego M. Roldan, Nikos Kyrpides, Tanja Woyke, Nicole Shapiro, William B. Whitman, Stanislava Kralova, Ivo Sedlacek, Hans-Jurgen Busse, Rodolfo Javier Menes
Summary: A novel bacterium strain 9A(T) belonging to the genus Hymenobacter was isolated from an air sample collected at King George Island, maritime Antarctica. The strain is psychrophilic, strictly aerobic, and shows high similarity to Hymenobacter coccineus CCM 8649(T).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Christian Rinke, Maria Chuvochina, Aaron J. Mussig, Pierre-Alain Chaumeil, Adrian A. Davin, David W. Waite, William B. Whitman, Donovan H. Parks, Philip Hugenholtz
Summary: The study proposes a standardized archaeal taxonomy derived from a 122-concatenated-protein phylogeny, resolving polyphyletic groups and normalizing ranks. This taxonomy is based on 2,392 archaeal genomes, identifying 16 archaeal phyla and reclassifying major monophyletic units. Rank normalization corrects for up to 30-fold substitution rate variations and addresses incomplete and uneven archaeal classifications through a genome-based approach.
NATURE MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Tao Wang, Hao Shi, William B. Whitman
Summary: DmdC1 from R. pomeroyi shows high affinity for short-chain acyl-CoAs in addition to its natural substrate MMPA-CoA, and is not affected by potential effectors tested, suggesting minimal adaptations to DMSP metabolism and recent evolution from a short-chain acyl-CoA dehydrogenase involved in fatty acid oxidation.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Taiwo S. Akinyemi, Nana Shao, Zhe Lyu, Ian J. Drake, Yuchen Liu, William B. Whitman
Summary: A library of differentially regulated promoters was designed and characterized based on the pst promoter, enabling significant increases in gene expression when the medium phosphate drops to growth-limiting concentrations. This regulated system decouples growth from heterologous gene expression without requiring an inducer, offering a new approach for microbial cell factories.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
William B. Whitman, Maria Chuvochina, Brian P. Hedlund, Philip Hugenholtz, Konstantinos T. Konstantinidis, Alison E. Murray, Marike Palmer, Donovan H. Parks, Alexander J. Probst, Anna-Louise Reysenbach, Luis M. Rodriguez-R, Ramon Rossello-Mora, Iain Sutcliffe, Stephanus N. Venter
Summary: Genomics has been fully integrated into prokaryotic systematics over the past fifteen years. The SeqCode has been developed to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types, simplifying nomenclature and promoting synergies between different disciplines.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2022)
Article
Microbiology
Martin W. Hahn, Alexandra Pitt, Johanna Schmidt, Ulrike Koll, Jacqueline Wolf, William B. Whitman, Paul L. E. Bodelier, Meina Neumann-Schaal
Summary: This study presents two strains affiliated with the GKS98 cluster. Phylogenetic analysis suggests that these strains are closely related to the family Alcaligenaceae and previously described species Orrella amnicola and Orrella marina. Based on the phylogenomic trees and other characteristics, the authors propose the establishment of new genera Zwartia gen. nov. and Jezberella gen. nov., and the reclassification of Orrella amnicola into the new genus Sheuella gen. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Tao Wang, Qiuyuan Huang, Andrew S. Burns, Mary Ann Moran, William B. Whitman
Summary: Dimethylsulfoniopropionate (DMSP) is an abundant organic compound in marine surface water and a major source of dimethyl sulfide (DMS). Marine bacteria can either mineralize DMSP through demethylation or transform it to DMS. The factors regulating which pathway is utilized are not well understood. In this study, oxidative stress was found to control the switch in DMSP metabolism from demethylation to DMS production in the marine bacterium Ruegeria pomeroyi. These findings provide strong evidence for the role of oxidative stress in regulating DMSP metabolism in the marine environment.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biology
Nana Shao, Yu Fan, Chau-Wen Chou, Shadi Yavari, Robert Williams, I. Jonathan Amster, Stuart M. Brown, Ian J. Drake, Evert C. Duin, William B. Whitman, Yuchen Liu
Summary: This study presents an approach to study methyl-coenzyme M reductases (MCRs) from uncultured archaea by heterologous expression in a culturable methanogen, Methanococcus maripaludis. The results show that promoter, operon structure, and temperature are important factors for MCR production. Structural modeling suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics.
COMMUNICATIONS BIOLOGY
(2022)
Article
Microbiology
Joana Fernandes Couceiro, Tina Keller-Costa, Nikos C. Kyrpides, Tanja Woyke, William B. Whitman, Rodrigo Costa
Summary: In this study, we report the genome sequences of three Aquimarina megaterium strains isolated from the octocoral Euniceila labiata. We uncover their coding potential for versatile carbon metabolism and biosynthesis of natural products belonging to the polyketide, nonribosomal peptide, and terpene compound classes.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Ecology
Brent Nowinski, Xiaoyuan Feng, Christina M. Preston, James M. Birch, Haiwei Luo, William B. Whitman, Mary Ann Moran
Summary: A longitudinal analysis of bacterial genes, genomes, and transcripts during a phytoplankton bloom identified two highly related Rhodobacteraceae species from the uncultured NAC11-7 lineage. Despite having identical 16S rRNA gene sequences, their genomes and transcriptomes revealed species-level divergence. Changes in relative dominance of the species during the bloom confirmed their divergent responses to the same microenvironment. Unique and differentially expressed genes accounted for a small portion of the species' pangenome content, revealing physiological and ecological differences.
Review
Microbiology
Kyle C. C. Costa, William B. B. Whitman
Summary: Methanogenic archaea are the only organisms that produce CH4 as part of their energy-generating metabolism. They are ubiquitous in oxidant-depleted, anoxic environments and play a key role in the degradation of organic matter. This article discusses the importance of model organisms in methanogen research and explores new model systems that will contribute to a better understanding of this unique archaeal metabolism.
JOURNAL OF BACTERIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Wenting Zhang, Derong Ren, Zhihua Li, Lei Yue, William B. Whitman, Xiuzhu Dong, Jie Li
Summary: By integrating multiple data sets of a representative archaeon Methanococcus maripaludis, internal transcription termination sites (ioTTSs) were identified within 38% of operons. Further experiments confirmed the functionality of these ioTTS terminations. Mutations of ioTTSs in ribosomal protein (RP)-RNA polymerase (RNAP) operons not only altered gene expression but also affected cellular processes and growth. This study reveals ioTTS termination as a general and important regulatory mechanism in operon gene expression.
NUCLEIC ACIDS RESEARCH
(2023)