Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia.

Abstract:

:Dehalococcoidia (Dia) class microorganisms are frequently found in various pristine and contaminated environments. Metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) studies have substantially improved the understanding of Dia microbial ecology and evolution; however, an updated thorough investigation on the genomic and evolutionary characteristics of Dia microorganisms distributed in geographically distinct environments has not been implemented. In this study, we analyzed available genomic data to unravel Dia evolutionary and metabolic traits. Based on the phylogeny of 16S rRNA genes retrieved from sixty-seven genomes, Dia microorganisms can be categorized into three groups, the terrestrial cluster that contains all Dehalococcoides and Dehalogenimonas strains, the marine cluster I, and the marine cluster II. These results reveal that a higher ratio of horizontally transferred genetic materials was found in the Dia marine clusters compared to that of the Dia terrestrial cluster. Pangenome analysis further suggests that Dia microorganisms have evolved cluster-specific enzymes (e.g., dehalogenase in terrestrial Dia, sulfite reductase in marine Dia) and biosynthesis capabilities (e.g., siroheme biosynthesis in marine Dia). Marine Dia microorganisms are likely adapted to versatile metabolisms for energy conservation besides organohalide respiration. The genomic differences between marine and terrestrial Dia may suggest distinct functions and roles in element cycling (e.g., carbon, sulfur, chlorine), which require interdisciplinary approaches to unravel the physiology and evolution of Dia in various environments.

journal_name

Front Microbiol

authors

Yang Y,Zhang Y,Cápiro NL,Yan J

doi

10.3389/fmicb.2020.546063

subject

Has Abstract

pub_date

2020-09-08 00:00:00

pages

546063

issn

1664-302X

journal_volume

11

pub_type

杂志文章
  • Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria.

    abstract::Biological nitrogen fixation plays a crucial role in the nitrogen cycle. An ability to fix atmospheric nitrogen, reducing it to ammonium, was described for multiple species of Bacteria and Archaea. The transcriptional regulatory network for nitrogen fixation was extensively studied in several representatives of the cl...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01343

    authors: Tsoy OV,Ravcheev DA,Čuklina J,Gelfand MS

    更新日期:2016-08-26 00:00:00

  • Saccharomyces cerevisiae CNCM I-3856 as a New Therapeutic Agent Against Oropharyngeal Candidiasis.

    abstract::Oropharyngeal candidiasis is a common opportunistic mucosal infection of the oral cavity, mainly caused by an overgrowth of Candida albicans. This infection can inhibit nutritional intakes and strongly affect quality of life. To date, standard therapeutic strategies involving the administration of antifungal drugs can...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.01469

    authors: Roselletti E,Sabbatini S,Ballet N,Perito S,Pericolini E,Blasi E,Mosci P,Cayzeele Decherf A,Monari C,Vecchiarelli A

    更新日期:2019-07-11 00:00:00

  • In Kluyveromyces lactis a Pair of Paralogous Isozymes Catalyze the First Committed Step of Leucine Biosynthesis in Either the Mitochondria or the Cytosol.

    abstract::Divergence of paralogous pairs, resulting from gene duplication, plays an important role in the evolution of specialized or novel gene functions. Analysis of selected duplicated pairs has elucidated some of the mechanisms underlying the functional diversification of Saccharomyces cerevisiae (S. cerevisiae) paralogous ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01843

    authors: Aguirre-López B,Escalera-Fanjul X,Hersch-González J,Rojas-Ortega E,El-Hafidi M,Lezama M,González J,Bianchi MM,López G,Márquez D,Scazzocchio C,Riego-Ruiz L,González A

    更新日期:2020-08-04 00:00:00

  • Novel Widespread Marine Oomycetes Parasitising Diatoms, Including the Toxic Genus Pseudo-nitzschia: Genetic, Morphological, and Ecological Characterisation.

    abstract::Parasites are key drivers of phytoplankton bloom dynamics and related aquatic ecosystem processes. Yet, the dearth of morphological and molecular information hinders the assessment of their diversity and ecological role. Using single-cell techniques, we characterise morphologically and molecularly, intracellular paras...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.02918

    authors: Garvetto A,Nézan E,Badis Y,Bilien G,Arce P,Bresnan E,Gachon CMM,Siano R

    更新日期:2018-12-03 00:00:00

  • Heparin-Binding Hemagglutinin Adhesin (HBHA) Is Involved in Intracytosolic Lipid Inclusions Formation in Mycobacteria.

    abstract::The heparin-binding hemagglutinin adhesin (HBHA) is an important virulence factor of Mycobacterium tuberculosis. It is a surface-displayed protein that serves as an adhesin for non-phagocytic cells and is involved in extra-pulmonary dissemination of the tubercle bacillus. It is also an important latency antigen useful...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.02258

    authors: Raze D,Verwaerde C,Deloison G,Werkmeister E,Coupin B,Loyens M,Brodin P,Rouanet C,Locht C

    更新日期:2018-09-24 00:00:00

  • Characterization of the surfaceome of the metal-reducing bacterium Desulfotomaculum reducens.

    abstract::Desulfotomaculum reducens strain MI-1 is a Gram-positive, sulfate-reducing bacterium also capable of reducing Fe(III). Metal reduction in Gram-positive bacteria is poorly understood. Here, we investigated Fe(III) reduction with lactate, a non-fermentable substrate, as the electron donor. Lactate consumption is concomi...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2014.00432

    authors: Dalla Vecchia E,Shao PP,Suvorova E,Chiappe D,Hamelin R,Bernier-Latmani R

    更新日期:2014-08-19 00:00:00

  • Functional Biology and Molecular Mechanisms of Host-Pathogen Interactions for Aflatoxin Contamination in Groundnut (Arachis hypogaea L.) and Maize (Zea mays L.).

    abstract::Aflatoxins are secondary metabolites produced by soilborne saprophytic fungus Aspergillus flavus and closely related species that infect several agricultural commodities including groundnut and maize. The consumption of contaminated commodities adversely affects the health of humans and livestock. Aflatoxin contaminat...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2020.00227

    authors: Soni P,Gangurde SS,Ortega-Beltran A,Kumar R,Parmar S,Sudini HK,Lei Y,Ni X,Huai D,Fountain JC,Njoroge S,Mahuku G,Radhakrishnan T,Zhuang W,Guo B,Liao B,Singam P,Pandey MK,Bandyopadhyay R,Varshney RK

    更新日期:2020-03-03 00:00:00

  • Shifts in methanogenic community composition and methane fluxes along the degradation of discontinuous permafrost.

    abstract::The response of methanogens to thawing permafrost is an important factor for the global greenhouse gas budget. We tracked methanogenic community structure, activity, and abundance along the degradation of sub-Arctic palsa peatland permafrost. We observed the development of pronounced methane production, release, and a...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.00356

    authors: Liebner S,Ganzert L,Kiss A,Yang S,Wagner D,Svenning MM

    更新日期:2015-05-12 00:00:00

  • Bacterial Community Composition in the Sea Surface Microlayer Off the Peruvian Coast.

    abstract::The sea surface microlayer (SML) is located at the air-sea interface, with microorganisms and organic matter in the SML influencing air-sea exchange processes. Yet understanding of the SML bacterial (bacterioneuston) community composition and assembly remains limited. Availability of organic matter, UV radiation and w...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.02699

    authors: Zäncker B,Cunliffe M,Engel A

    更新日期:2018-11-15 00:00:00

  • Sequelae of Fetal Infection in a Non-human Primate Model of Listeriosis.

    abstract::Listeria monocytogenes (Lm) is a common environmental bacterium that thrives on vegetation and soil matter, but can infect humans if contaminated food products are ingested, resulting in severe disease in immunosuppressed populations, including pregnant women and newborns. To better understand how the unique immunolog...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.02021

    authors: Wolfe B,Kerr AR,Mejia A,Simmons HA,Czuprynski CJ,Golos TG

    更新日期:2019-09-11 00:00:00

  • Negative Plant-Soil Feedback Driven by Re-assemblage of the Rhizosphere Microbiome With the Growth of Panax notoginseng.

    abstract::There is a concerted understanding of the accumulation of soil pathogens as the major driving factor of negative plant-soil feedback (NPSF). However, our knowledge of the connection between plant growth, pathogen build-up and soil microbiome assemblage is limited. In this study, significant negative feedback between t...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.01597

    authors: Luo L,Guo C,Wang L,Zhang J,Deng L,Luo K,Huang H,Liu Y,Mei X,Zhu S,Yang M

    更新日期:2019-07-26 00:00:00

  • Keystone Microbiomes Revealed by 14 Years of Field Restoration of the Degraded Agricultural Soil Under Distinct Vegetation Scenarios.

    abstract::Agricultural intensification accelerates the degradation of cropland, and restoration has been managed by changing its vegetation. However, the keystone microbiome that drives the decomposition of plant-associated organic matter in the restoration is poorly understood. In this study, we established a 14-year field res...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01915

    authors: Zhang Z,Han X,Yan J,Zou W,Wang E,Lu X,Chen X

    更新日期:2020-08-18 00:00:00

  • Yeast Biodiversity from DOQ Priorat Uninoculated Fermentations.

    abstract::Climate, soil, and grape varieties are the primary characteristics of terroir and lead to the definition of various appellations of origin. However, the microbiota associated with grapes are also affected by these conditions and can leave a footprint in a wine that will be part of the characteristics of terroir. Thus,...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.00930

    authors: Padilla B,García-Fernández D,González B,Izidoro I,Esteve-Zarzoso B,Beltran G,Mas A

    更新日期:2016-06-15 00:00:00

  • Bacterial Communities: Interactions to Scale.

    abstract::In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between di...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2016.01234

    authors: Stubbendieck RM,Vargas-Bautista C,Straight PD

    更新日期:2016-08-08 00:00:00

  • Chitosan, a Biopolymer With Triple Action on Postharvest Decay of Fruit and Vegetables: Eliciting, Antimicrobial and Film-Forming Properties.

    abstract::Chitosan is a natural biopolymer from crab shells that is known for its biocompatibility, biodegradability, and bioactivity. In human medicine, chitosan is used as a stabilizer for active ingredients in tablets, and is popular in slimming diets. Due to its low toxicity, it was the first basic substance approved by the...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2018.02745

    authors: Romanazzi G,Feliziani E,Sivakumar D

    更新日期:2018-12-04 00:00:00

  • Streptococcus canis Are a Single Population Infecting Multiple Animal Hosts Despite the Diversity of the Universally Present M-Like Protein SCM.

    abstract::Streptococcus canis is an animal pathogen which occasionally causes infections in humans. The S. canis M-like protein (SCM) encoded by the scm gene, is its best characterized virulence factor but previous studies suggested it could be absent in a substantial fraction of isolates. We studied the distribution and variab...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.00631

    authors: Pinho MD,Foster G,Pomba C,Machado MP,Baily JL,Kuiken T,Melo-Cristino J,Ramirez M,Portuguese Group for the Study of Streptococcal Infections.

    更新日期:2019-03-29 00:00:00

  • Relapse Versus Reinfection of Recurrent Tuberculosis Patients in a National Tuberculosis Specialized Hospital in Beijing, China.

    abstract::Tuberculosis (TB) recurrence can result from either relapse of an original infection or exogenous reinfection with a new strain of Mycobacterium tuberculosis (MTB). The aim of this study was to assess the roles of relapse and reinfection among recurrent TB cases characterized by a high prevalence rate of drug-resistan...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.01858

    authors: Zong Z,Huo F,Shi J,Jing W,Ma Y,Liang Q,Jiang G,Dai G,Huang H,Pang Y

    更新日期:2018-08-14 00:00:00

  • A Novel Bacteriophage Lysin-Human Defensin Fusion Protein Is Effective in Treatment of Clostridioides difficile Infection in Mice.

    abstract::Clostridioides difficile is the leading cause of worldwide antibiotics-associated diarrhea. In this study, we report the construction and evaluation of a novel bacteriophage lysin-human defensin fusion protein targeting C. difficile. The fusion protein, designated LHD, is composed of two parts connected by a 3-repeati...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.03234

    authors: Peng Z,Wang S,Gide M,Zhu D,Lamabadu Warnakulasuriya Patabendige HM,Li C,Cai J,Sun X

    更新日期:2019-01-11 00:00:00

  • Different Transcriptional Responses from Slow and Fast Growth Rate Strains of Listeria monocytogenes Adapted to Low Temperature.

    abstract::Listeria monocytogenes has become one of the principal foodborne pathogens worldwide. The capacity of this bacterium to grow at low temperatures has opened an interesting field of study in terms of the identification and classification of new strains of L. monocytogenes with different growth capacities at low temperat...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.00229

    authors: Cordero N,Maza F,Navea-Perez H,Aravena A,Marquez-Fontt B,Navarrete P,Figueroa G,González M,Latorre M,Reyes-Jara A

    更新日期:2016-03-01 00:00:00

  • Parasites in algae mass culture.

    abstract::Parasites are now known to be ubiquitous across biological systems and can play an important role in modulating algal populations. However, there is a lack of extensive information on their role in artificial ecosystems such as algal production ponds and photobioreactors. Parasites have been implicated in the demise o...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2014.00278

    authors: Carney LT,Lane TW

    更新日期:2014-06-06 00:00:00

  • A PAS domain-containing regulator controls flagella-flagella interactions in Campylobacter jejuni.

    abstract::The bipolar flagella of the foodborne bacterial pathogen Campylobacter jejuni confer motility, which is essential for virulence. The flagella of C. jejuni are post-translationally modified, but how this process is controlled is not well understood. In this work, we have identified a novel PAS-domain containing regulat...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.00770

    authors: Reuter M,Periago PM,Mulholland F,Brown HL,van Vliet AH

    更新日期:2015-07-30 00:00:00

  • Environmental and Host Effects on Skin Bacterial Community Composition in Panamanian Frogs.

    abstract::Research on the amphibian skin microbiota has focused on identifying bacterial taxa that deter a pathogenic chytrid fungus, and on describing patterns of microbiota variation. However, it remains unclear how environmental variation affects amphibian skin bacterial communities, and whether the overall functional divers...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.00298

    authors: Varela BJ,Lesbarrères D,Ibáñez R,Green DM

    更新日期:2018-02-22 00:00:00

  • Analysis of Two Complementary Single-Gene Deletion Mutant Libraries of Salmonella Typhimurium in Intraperitoneal Infection of BALB/c Mice.

    abstract::Two pools of individual single gene deletion (SGD) mutants of S. Typhimurium 14028s encompassing deletions of 3,923 annotated non-essential ORFs and sRNAs were screened by intraperitoneal (IP) injection in BALB/c mice followed by recovery from spleen and liver 2 days post infection. The relative abundance of each muta...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.01455

    authors: Silva-Valenzuela CA,Molina-Quiroz RC,Desai P,Valenzuela C,Porwollik S,Zhao M,Hoffman RM,Andrews-Polymenis H,Contreras I,Santiviago CA,McClelland M

    更新日期:2016-01-05 00:00:00

  • Biofilm Formation by Pseudallescheria/Scedosporium Species: A Comparative Study.

    abstract::Pseudallescheria/Scedosporium species are medically important fungi that are present in soil and human impacted areas and capable of causing a wide spectrum of diseases in humans. Although little is known about their pathogenesis, their growth process and infection routes are very similar to those of Aspergillus speci...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.01568

    authors: Rollin-Pinheiro R,de Meirelles JV,Vila TVM,Fonseca BB,Alves V,Frases S,Rozental S,Barreto-Bergter E

    更新日期:2017-08-18 00:00:00

  • A ten-year search for synchronous cells: obstacles, solutions, and practical applications.

    abstract::My effort to use synchronously dividing cultures to examine the Escherichia coli cell cycle involved a 10-year struggle with failure after failure punctuated by a few gratifying successes, especially at the end. In this essay, I recount my personal journey in this obsessive experimental pursuit. That narrative is foll...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2015.00238

    authors: Helmstetter CE

    更新日期:2015-03-25 00:00:00

  • Effect of Bifidobacterium breve in Combination With Different Antibiotics on Clostridium difficile.

    abstract::While combinations of probiotics with antibiotics have exhibited beneficial and adverse effects in the treatment of Clostridium difficile infection (CDI), no substantive explanation has been provided for these effects. In this study, C. difficile ATCC 9689 (CD) was treated with Bifidobacterium breve (YH68) in combinat...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.02953

    authors: Yang J,Yang H

    更新日期:2018-12-04 00:00:00

  • Prevalence, Molecular Characterization, and Antibiotic Susceptibility of Cronobacter sakazakii Isolates from Powdered Infant Formula Collected from Chinese Retail Markets.

    abstract::Cronobacter sakazakii is an opportunistic pathogen that causes severe infections in neonates and infants through contaminated powdered infant formula (PIF). Therefore, the aim of this study was a large-scale study on determine the prevalence, molecular characterization and antibiotic susceptibility of C. sakazakii iso...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.02026

    authors: Fei P,Jiang Y,Jiang Y,Yuan X,Yang T,Chen J,Wang Z,Kang H,Forsythe SJ

    更新日期:2017-10-17 00:00:00

  • Mixed Phenolic Acids Mediated Proliferation of Pathogens Talaromyces helicus and Kosakonia sacchari in Continuously Monocultured Radix pseudostellariae Rhizosphere Soil.

    abstract::Radix pseudostellariae L. is a common and popular Chinese medication. However, continuous monoculture has increased its susceptibility to severe diseases. We identified two pathogenic microorganisms, Talaromyces helicus M. (KU355274) and Kosakonia sacchari W. (KU324465), and their antagonistic bacterium, Bacillus pumi...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.00335

    authors: Wu H,Wu L,Wang J,Zhu Q,Lin S,Xu J,Zheng C,Chen J,Qin X,Fang C,Zhang Z,Azeem S,Lin W

    更新日期:2016-03-17 00:00:00

  • The Rhizosphere Microbiome of Mikania micrantha Provides Insight Into Adaptation and Invasion.

    abstract::Mikania micrantha is a noxious invasive plant causing enormous economic losses and ecological damage. Soil microbiome plays an important role in the invasion process of M. micrantha, while little is known about its rhizosphere microbiome composition and function. In this study, we identified the distinct rhizosphere m...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01462

    authors: Yin L,Liu B,Wang H,Zhang Y,Wang S,Jiang F,Ren Y,Liu H,Liu C,Wan F,Wang H,Qian W,Fan W

    更新日期:2020-07-07 00:00:00

  • Therapeutic Potential of a Scorpion Venom-Derived Antimicrobial Peptide and Its Homologs Against Antibiotic-Resistant Gram-Positive Bacteria.

    abstract::The alarming rise in the prevalence of antibiotic resistance among pathogenic bacteria poses a unique challenge for the development of effective therapeutic agents. Antimicrobial peptides (AMPs) have attracted a great deal of attention as a possible solution to the increasing problem of antibiotic-resistant bacteria. ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.01159

    authors: Liu G,Yang F,Li F,Li Z,Lang Y,Shen B,Wu Y,Li W,Harrison PL,Strong PN,Xie Y,Miller K,Cao Z

    更新日期:2018-05-29 00:00:00