Article
Engineering, Environmental
Lei Xue, David J. Kieber
Summary: Research has identified a new source of acrylate in seawater as a product of the photolysis of dissolved organic matter (DOM). Photochemical production rates are positively correlated with seawater absorption coefficient and are mainly initiated by UV radiation, with UV-B and UV-A contributing to the total production.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Oceanography
Juan Yu, Su Wang, Jing-Guang Lai, Ji-Yuan Tian, Hao-Quan Zhang, Gui-Peng Yang, Rong Chen
Summary: This study investigated the spatial distributions of DMS, DMSP, DLA, and the abundances of bacteria, DMSP-consuming bacteria, and dimethyl sulfoxide-consuming bacteria in the surface seawater of the Bohai Sea and Yellow Sea during autumn 2020. The results showed that the distributions of DMS and dissolved DMSP were significantly correlated with DLA. Grazing by microzooplankton promoted the conversion of DMSP to DMS, and mesozooplankton copepod grazing stimulated DMS production.
JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS
(2023)
Article
Multidisciplinary Sciences
Ming Peng, Chun-Yang Li, Xiu-Lan Chen, Beth T. Williams, Kang Li, Ya-Nan Gao, Peng Wang, Ning Wang, Chao Gao, Shan Zhang, Marie C. Schoelmerich, Jillian F. Banfield, J. Benjamin Miller, Nick E. Le Brun, Jonathan D. Todd, Yu-Zhong Zhang
Summary: This study characterizes the structure and mechanism of the DMSP synthesis enzyme MmtN and identifies functional MmtN enzymes in various organisms. The study provides important insights into SMM and/or DMSP production and proposes additional roles for these compounds.
NATURE COMMUNICATIONS
(2022)
Article
Oceanography
Juan Yu, Sheng-Hui Zhang, Ji-Yuan Tian, Zheng-Yu Zhang, Li-Jun Zhao, Rui Xu, Gui-Peng Yang, Jing-Guang Lai, Xue-Dan Wang
Summary: The fate of DMSP, the precursor of the important gas DMS, is influenced by marine community structure. DMSP degradation by DCB is a significant factor in DMSPd sink. The spatial distribution of DCB abundance is affected by regional hydrography and upwelling.
JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS
(2021)
Article
Biology
Noa Barak-Gavish, Bareket Dassa, Constanze Kuhlisch, Inbal Nussbaum, Alexander Brandis, Gili Rosenberg, Roi Avraham, Assaf Vardi
Summary: Unicellular algae, known as phytoplankton, have significant impacts on the marine environment by serving as the foundation of marine food webs and playing key roles in biogeochemical cycling. The interactions between phytoplankton and heterotrophic bacteria affect the fitness of both partners. The molecular mechanisms underlying these interactions, particularly metabolic exchanges, are not well understood.
Article
Environmental Sciences
Kitack Lee, Jun-Seok Kim, Ki-Tae Park, Min-Ji Park, Eunho Jang, Kristinn Gudmundsson, Solveig R. Olafsdottir, Jon Olafsson, Young Jun Yoon, Bang -Yong Lee, Sae Yun Kwon, Jonghun Kam
Summary: In two spring blooms in the Icelandic Sea, the concentrations of chlorophyll-a and DMSP, as well as the DMSP lyase activity, were measured. The distribution of ocean parameters related to biology showed associations, but the statistical significance of the association varied between different ocean domains and years. The dominance of DMSP-rich phytoplankton indicated that variations in these organisms were likely a main factor influencing the statistical significance. The study also demonstrated the consistency between DMS production capacity and in situ ocean S data.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Limnology
Qian-Yao Ma, Hong-Hai Zhang, Feng Xu, Gui-Peng Yang
Summary: Biogenic dimethylated sulfur compounds, including DMS, DMSP, and dimethylsulfoxide, have important roles in the physiological metabolism processes of marine algae, climate regulation, and global sulfur cycles. However, the contribution of each transformation pathway and the factors that control them are still uncertain. This study measured the major transformation pathways and fluxes of DMS in the East China Continental Sea simultaneously, revealing rapid turnover times and the significant contributions of bacterial consumption and microbial consumption. The study also identified the sediment-seawater interface as a small source of DMS. Overall, the study provides a comprehensive understanding of the organosulfur cycle in continental shelf seas.
LIMNOLOGY AND OCEANOGRAPHY
(2022)
Article
Meteorology & Atmospheric Sciences
Jia-Wei Shen, Liang Zhao, Hao Wei
Summary: Understanding the response of oceanic dimethyl sulfide flux (F-DMS) to multi-pressures is crucial for the regional aerosol budget. Results from 4-group experiments show that the F-DMS in the Yellow and East China seas will increase under different climate change scenarios, and the peak in the 2050s will occur earlier than in the 1980s. Climate change will have a greater impact on F-DMS in the future, particularly due to changes in wind patterns.
JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES
(2023)
Article
Limnology
Brandon J. J. McNabb, Philippe D. D. Tortell
Summary: We developed two machine learning models to accurately map the Southern Ocean distribution of dimethyl sulfide (DMS), a climate-active gas. The models outperformed traditional statistical techniques and existing climatologies, providing more accurate and unbiased predictions. The models revealed that wind-driven mixing is the main control on DMS distributions, and identified factors like mixed layer depth and sea-ice cover as important drivers of DMS seasonality. Additionally, our work estimated the Southern Ocean sea-air DMS flux and highlighted the region's significance in the marine sulfur cycle.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
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
Microbiology
Zhao-Jie Teng, Peng Wang, Xiu-Lan Chen, Richard Guillonneau, Chun-Yang Li, Song-Bao Zou, Jun Gong, Kai-Wen Xu, Lin Han, Chao Wang, David J. Scanlan, Yin Chen, Yu-Zhong Zhang
Summary: The marine bacterium Puniceibacterium antarcticum SM1211 can produce acrylate from dimethylsulfoniopropionate (DMSP) cleavage by the DMSP lyase, DddL, which protects against grazing by a ciliate predator, influencing community structure.
NATURE MICROBIOLOGY
(2021)
Article
Environmental Sciences
Stephanie G. G. Gardner, Matthew R. R. Nitschke, James O'Brien, Cherie A. A. Motti, Justin R. R. Seymour, Peter J. J. Ralph, Katherina Petrou, Jean-Baptiste Raina
Summary: Thermal stress increases DMSP concentrations in coral mucus and leads to a higher abundance of the cleavage pathway in coral-associated bacteria.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Environmental Sciences
Fulin Sun, Youshao Wang, Zhaoyu Jiang, Cuici Sun, Yutu Wang, Meilin Wu
Summary: This study explored the abundance and diversity of Roseobacter group DMSP degradation genes in the South China Sea. The results showed a higher abundance of dmdA and dddP genes in surface water above 75 m, and demethylation was the main degradation pathway. High-throughput sequencing analysis revealed a significant layering structure in the distribution of the dmdA gene and high taxonomic diversity in near-surface waters. Different sites and water depths influenced the specificity of dmdA genes in the Roseobacter group. The South China Sea harbors a high diversity of DMSP-degrading bacteria.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Giovanna Pesante, Edith Forestier, Swen Langer, Andrew Danby, John Angus, Mark Gronnow, Joseph P. Bennett, Tony R. Larson, Thierry Tonon
Summary: An analytical method was developed to simultaneously measure acrylic acid (AA), dimethylsulfoniopropionate (DMSP), and related intermediates in Ulva macroalgae. Different treatments were applied to process the compounds, and the amount of AA was quantified. The results showed that enzyme treatments did not yield higher amounts of AA compared to chemical or physical extractions, which is promising for industrial applications. Additionally, the biochemical characteristics of two candidate enzymes UM021_MBP and UM030_Halo7 from Ulva mutabilis were investigated, providing insights into AA biosynthesis in Ulva and its potential extraction in biorefineries.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2023)
Article
Biotechnology & Applied Microbiology
Qun Lin, Linxin Shang, Xiaoli Wang, Zhong Hu, Hong Du, Hui Wang
Summary: This study investigated the capacity of seven dinoflagellates to synthesize DMSP and their impact on the associated bacterial community composition. Results showed that DMSP levels significantly influenced the abundance and composition of bacterial community in the phycosphere of dinoflagellates. Additionally, genomic analysis indicated the presence of Roseobacter-clade bacteria capable of degrading DMSP through cleavage pathway.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2021)
Article
Microbiology
Zefeng Zhang, Fang Qin, Feng Chen, Xiao Chu, Haiwei Luo, Rui Zhang, Sen Du, Zhen Tian, Yanlin Zhao
Summary: The study isolated and genomically characterized 10 new pelagiphages, expanding our understanding of these viruses and revealing their global distribution in the ocean, their impacts on marine ecosystems, and their infection strategies. The availability of newly isolated pelagiphages and their genome sequences will allow researchers to further explore their infectivities and ecological strategies.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Ecology
Xiao Chu, Siyao Li, Sishuo Wang, Danli Luo, Haiwei Luo
Summary: The study found that pseudogenization plays a significant role in shaping genome content and driving ecological diversification of marine roseobacters. Through characterization of pseudogenes in newly sequenced marine bacterial isolates, it was revealed that pseudogenes play an important role in the accessory genomes of bacteria, with many pseudogenization events correlated with ancestral niche shifts.
Article
Ecology
Jiahao Gu, Xiaojun Wang, Xiaopan Ma, Ying Sun, Xiang Xiao, Haiwei Luo
Summary: A study found that a particular species of Thermococcus has a mutation rate much higher than other free-living prokaryotes, which is not selectively favored but driven by random genetic drift. Additionally, genome size is negatively correlated with mutation rate and positively correlated with effective population size.
Article
Microbiology
Bin-Bin Xie, Jin-Cheng Rong, Bai-Lu Tang, Sishuo Wang, Guiming Liu, Qi-Long Qin, Xi-Ying Zhang, Weipeng Zhang, Qunxin She, Yin Chen, Fuchuan Li, Shengying Li, Xiu-Lan Chen, Haiwei Luo, Yu-Zhong Zhang
Summary: Chromosome replication is essential for cell division, with bidirectional replication being the rule for bacterial chromosomes. In Pseudoalteromonas, chromids can replicate either unidirectionally or bidirectionally, indicating a single evolutionary transition from unidirectionality to bidirectionality. This study sheds light on the physiological aspects of chromosome replication and the early evolutionary history of bacterial chromosomes.
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
Microbiology
Xingqin Lin, Jesse McNichol, Xiao Chu, Yang Qian, Haiwei Luo
Summary: This study reveals that marine intertidal sediments serve as important habitats for denitrifying bacteria, with different ecotypes showing distinct denitrification abilities and growth patterns under varying oxygen concentrations and carbon sources. The evidence suggests the presence of cryptic niches in coastal intertidal sediments that support divergent evolution of denitrifying bacteria.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Ecology
Zhuoyu Chen, Xiaojun Wang, Yu Song, Qinglu Zeng, Yao Zhang, Haiwei Luo
Summary: The authors found that the effective population size of Prochlorococcus is smaller than that of many free-living bacteria, indicating the important role of drift in their evolution. Despite sharing characteristics with endosymbiotic bacteria, Prochlorococcus have a different evolutionary mechanism, where genetic drift plays a key role.
NATURE ECOLOGY & EVOLUTION
(2022)
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)