Diversity of Pelagic and Benthic Bacterial Assemblages in the Western Pacific Ocean.

Abstract:

:Despite numerous studies on marine prokaryotes, the vertical distribution patterns of bacterial community, either on the taxonomic composition or the functional structure, remains relatively unexplored. Using HiSeq-derived 16S rRNA data, the depth-related distribution patterns of taxonomic diversity and functional structure predicted from diversity data in the water column and sediments of the Western Pacific Ocean were explored. The OTU richness declined along the water column after peaking between 100 to 200 m deep. Relative abundance of Cyanobacteria and SAR11 decreased significantly with depth, while Actinobacteria and Gammaproteobacteria increased. This clearly mirrors the vertical distribution pattern of the predicted functional composition with the shift between phototrophic to chemoheterotrophic groups from the surface to the deeper layers. In terms of community composition and functional structure, the epipelagic zone differed from other deeper ones (i.e., meso-, bathy-, and abyssopelagic zones) where no obvious differences were detected. For the epipelagic zone, temperature, dissolved oxygen, and salinity were recognized as the crucial factors shaping both community composition and the functional structure of bacteria. Compared with water samples, benthic sediment samples harbored unexpectedly higher read abundance of Proteobacteria, presenting distinguishable taxonomic and functional compositions. This study provides novel knowledge on the vertical distribution of bacterial taxonomic and functional compositions in the western Pacific.

journal_name

Front Microbiol

authors

Wang M,Ma Y,Feng C,Cai L,Li W

doi

10.3389/fmicb.2020.01730

subject

Has Abstract

pub_date

2020-09-10 00:00:00

pages

1730

issn

1664-302X

journal_volume

11

pub_type

杂志文章
  • iTRAQ Proteomic Analysis Reveals That Metabolic Pathways Involving Energy Metabolism Are Affected by Tea Tree Oil in Botrytis cinerea.

    abstract::Tea tree oil (TTO) is a volatile essential oil obtained from the leaves of the Australian tree Melaleuca alternifolia by vapor distillation. Previously, we demonstrated that TTO has a strong inhibitory effect on Botrytis cinerea. This study investigates the underlying antifungal mechanisms at the molecular level. A pr...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.01989

    authors: Xu J,Shao X,Wei Y,Xu F,Wang H

    更新日期:2017-10-12 00:00:00

  • Enzymatic modifications of exopolysaccharides enhance bacterial persistence.

    abstract::Biofilms are surface-attached communities of bacterial cells embedded in a self-produced matrix that are found ubiquitously in nature. The biofilm matrix is composed of various extracellular polymeric substances, which confer advantages to the encapsulated bacteria by protecting them from eradication. The matrix compo...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2015.00471

    authors: Whitfield GB,Marmont LS,Howell PL

    更新日期:2015-05-15 00:00:00

  • Driving HIV-1 into a Vulnerable Corner by Taking Advantage of Viral Adaptation and Evolution.

    abstract::Anti-retroviral therapy (ART) is crucial for controlling human immunodeficiency virus type-1 (HIV-1) infection. Recently, progress in identifying and characterizing highly potent broadly neutralizing antibodies has provided valuable templates for HIV-1 therapy and vaccine design. Nevertheless, HIV-1, like many RNA vir...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2017.00390

    authors: Harada S,Yoshimura K

    更新日期:2017-03-16 00:00:00

  • Anilinopyrimidine Resistance in Botrytis cinerea Is Linked to Mitochondrial Function.

    abstract::Crop protection anilinopyrimidine (AP) fungicides were introduced more than 20 years ago for the control of a range of diseases caused by ascomycete plant pathogens, and in particular for the control of gray mold caused by Botrytis cinerea. Although early mode of action studies suggested an inhibition of methionine bi...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.02361

    authors: Mosbach A,Edel D,Farmer AD,Widdison S,Barchietto T,Dietrich RA,Corran A,Scalliet G

    更新日期:2017-11-30 00:00:00

  • Invasion of Nostocales (cyanobacteria) to Subtropical and Temperate Freshwater Lakes - Physiological, Regional, and Global Driving Forces.

    abstract::Similar to the increased number of studies on invasive plants and animals in terrestrial and aquatic ecosystems, many reports were recently published on the invasion of Nostocales (cyanobacteria) to freshwater environments worldwide. Invasion and proliferation of Nostocales in new habitats have the potential to signif...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2012.00086

    authors: Sukenik A,Hadas O,Kaplan A,Quesada A

    更新日期:2012-03-09 00:00:00

  • Occurrence of Hepatitis E Virus in Pigs and Pork Cuts and Organs at the Time of Slaughter, Spain, 2017.

    abstract::Zoonotic hepatitis E, mainly caused by hepatitis E virus (HEV) genotype (gt) 3, is a foodborne disease that has emerged in Europe in recent decades. The main animal reservoir for genotype 3 is domestic pigs. Pig liver and liver derivates are considered the major risk products, and studies focused on the presence of HE...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.02990

    authors: García N,Hernández M,Gutierrez-Boada M,Valero A,Navarro A,Muñoz-Chimeno M,Fernández-Manzano A,Escobar FM,Martínez I,Bárcena C,González S,Avellón A,Eiros JM,Fongaro G,Domínguez L,Goyache J,Rodríguez-Lázaro D

    更新日期:2020-01-28 00:00:00

  • The Lactococcus lactis Pan-Plasmidome.

    abstract::Plasmids are autonomous, self-replicating, extrachromosomal genetic elements that are typically not essential for growth of their host. They may encode metabolic capabilities, which promote the maintenance of these genetic elements, and may allow adaption to specific ecological niches and consequently enhance survival...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.00707

    authors: Kelleher P,Mahony J,Bottacini F,Lugli GA,Ventura M,van Sinderen D

    更新日期:2019-04-04 00:00:00

  • Evidence That Microorganisms at the Animal-Water Interface Drive Sea Star Wasting Disease.

    abstract::Sea star wasting (SSW) disease describes a condition affecting asteroids that resulted in significant Northeastern Pacific population decline following a mass mortality event in 2013. The etiology of SSW is unresolved. We hypothesized that SSW is a sequela of microbial organic matter remineralization near respiratory ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.610009

    authors: Aquino CA,Besemer RM,DeRito CM,Kocian J,Porter IR,Raimondi PT,Rede JE,Schiebelhut LM,Sparks JP,Wares JP,Hewson I

    更新日期:2021-01-06 00:00:00

  • Dissemination of Linezolid Resistance Through Sex Pheromone Plasmid Transfer in Enterococcus faecalis.

    abstract::Despite recent recognition of the ATP-binding cassette protein OptrA as an important mediator of linezolid resistance in Enterococcus faecalis worldwide, the mechanisms of optrA gene acquisition and transfer remain poorly understood. In this study, we performed comprehensive molecular and phenotypic profiling of 44 op...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01185

    authors: Zou J,Tang Z,Yan J,Liu H,Chen Y,Zhang D,Zhao J,Tang Y,Zhang J,Xia Y

    更新日期:2020-06-04 00:00:00

  • Development of a Sterne-Based Complement Fixation Test to Monitor the Humoral Response Induced by Anthrax Vaccines.

    abstract::Anthrax is a zoonotic disease caused by Bacillus anthracis spore-forming bacterium. Since it is primarily a disease of animals, the control in animals, and humans depend on the prevention in livestock, principally cattle, sheep, and goats. Most veterinary vaccines utilize the toxigenic, uncapsulated (pXO1+/pXO2-) B. a...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.00019

    authors: Adone R,Sali M,Francia M,Iatarola M,Donatiello A,Fasanella A

    更新日期:2016-01-28 00:00:00

  • High-Throughput Sequencing-Based Identification of Arabidopsis miRNAs Induced by Phytophthora capsici Infection.

    abstract::MicroRNAs (miRNAs) are a group of small non-coding endogenous RNAs. In plants, miRNAs play vital functions in regulating growth, development, and stress response. However, the role of miRNAs in Arabidopsis-Phytophthora capsici (P. capsici) model pathosystem is poorly understood. Here, we used a high-throughput sequenc...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01094

    authors: Zhu X,He S,Fang D,Guo L,Zhou X,Guo Y,Gao L,Qiao Y

    更新日期:2020-06-23 00:00:00

  • Sterol Synthesis in Diverse Bacteria.

    abstract::Sterols are essential components of eukaryotic cells whose biosynthesis and function has been studied extensively. Sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and en...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.00990

    authors: Wei JH,Yin X,Welander PV

    更新日期:2016-06-24 00:00:00

  • A Bivalent Human Adenovirus Type 5 Vaccine Expressing the Rabies Virus Glycoprotein and Canine Distemper Virus Hemagglutinin Protein Confers Protective Immunity in Mice and Foxes.

    abstract::The development of a safe and efficient multivalent vaccine has great prospects for application. Both rabies virus (RABV) and canine distemper virus (CDV) are highly infectious antigens, causing lethal diseases in domestic dogs and other carnivores worldwide. In this study, a replication-deficient human adenovirus 5 (...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01070

    authors: Yan L,Zhao Z,Xue X,Zheng W,Xu T,Liu L,Tian L,Wang X,He H,Zheng X

    更新日期:2020-06-16 00:00:00

  • Variation in the nuclear effects of infection by different human rhinovirus serotypes.

    abstract::Human rhinovirus (HRV) is a positive sense RNA virus, which, despite replicating in the cytoplasm, has a significant impact on nuclear transport and nuclear localization of host proteins. A number of studies have identified differences between HRV serotypes, with respect to host response, protease activity and replica...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.00875

    authors: Walker EJ,Jensen LM,Croft S,Ghildyal R

    更新日期:2015-08-24 00:00:00

  • Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity.

    abstract::Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, has emerged as a global pandemic worldwide. In this study, we used ARTIC primers-based amplicon sequencing to profile 225 SARS-CoV-2 genomes from India. Phylogenetic analysis of 202 high-quality assem...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.594928

    authors: Raghav S,Ghosh A,Turuk J,Kumar S,Jha A,Madhulika S,Priyadarshini M,Biswas VK,Shyamli PS,Singh B,Singh N,Singh D,Datey A,Avula K,Smita S,Sabat J,Bhattacharya D,Kshatri JS,Vasudevan D,Suryawanshi A,Dash R,Senapati

    更新日期:2020-11-23 00:00:00

  • ClubSub-P: Cluster-Based Subcellular Localization Prediction for Gram-Negative Bacteria and Archaea.

    abstract::The subcellular localization (SCL) of proteins provides important clues to their function in a cell. In our efforts to predict useful vaccine targets against Gram-negative bacteria, we noticed that misannotated start codons frequently lead to wrongly assigned SCLs. This and other problems in SCL prediction, such as th...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2011.00218

    authors: Paramasivam N,Linke D

    更新日期:2011-11-08 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

  • Biophysical Characterization of Membrane Phase Transition Profiles for the Discrimination of Outer Membrane Vesicles (OMVs) From Escherichia coli Grown at Different Temperatures.

    abstract::Dynamic Light Scattering (DLS), Small Angle X-ray Scattering (SAXS) and Transmission Electron Microscopy (TEM) are physical techniques widely employed to characterize the morphology and the structure of vesicles such as liposomes or human extracellular vesicles (exosomes). Bacterial extracellular vesicles are similar ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.00290

    authors: Sarra A,Celluzzi A,Bruno SP,Ricci C,Sennato S,Ortore MG,Casciardi S,Del Chierico F,Postorino P,Bordi F,Masotti A

    更新日期:2020-02-27 00:00:00

  • Pig Farmers' Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes.

    abstract::Airborne bacterial communities are subject to conditions ill-suited to microbial activity and growth. In spite of this, air is an important transfer medium for bacteria, with the bacteria in indoor air having potentially major consequences for the health of a building's occupants. A major example is the decreased dive...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.00870

    authors: Vestergaard DV,Holst GJ,Basinas I,Elholm G,Schlünssen V,Linneberg A,Šantl-Temkiv T,Finster K,Sigsgaard T,Marshall IPG

    更新日期:2018-05-01 00:00:00

  • Clever Cooperation: Interactions Between EspF and Host Proteins.

    abstract::EspF is a central effector protein of enterohemorrhagic Escherichia coli (EHEC), enteropathogenic E. coli (EPEC), and Citrobacter rodentium (CR) that is secreted through the type III secretion system to host cells. The interaction between EspF and host proteins plays an important role in bacterial pathogenesis. EspF p...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2018.02831

    authors: Hua Y,Yan K,Wan C

    更新日期:2018-11-22 00:00:00

  • Lipoprotein SPD_1609 of Streptococcus pneumoniae Promotes Adherence and Invasion to Epithelial Cells Contributing to Bacterial Virulence.

    abstract::In most bacteria, iron plays a vital role in pathogenesis processes. To support survival and infection, Streptococcus pneumoniae has evolved three ABC transporters, PiaABC, PiuABC, and PitABC. Moreover, indirect evidence supports that operon 804 may be a novel ABC transporter in S. pneumoniae. We have recently describ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.01769

    authors: Yang XY,Li N,Xu JY,Sun X,He QY

    更新日期:2019-07-30 00:00:00

  • Progress in Ameliorating Beneficial Characteristics of Microbial Cellulases by Genetic Engineering Approaches for Cellulose Saccharification.

    abstract::Lignocellulosic biomass is a renewable and sustainable energy source. Cellulases are the enzymes that cleave β-1, 4-glycosidic linkages in cellulose to liberate sugars that can be fermented to ethanol, butanol, and other products. Low enzyme activity and yield, and thermostability are, however, some of the limitations...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2020.01387

    authors: Dadwal A,Sharma S,Satyanarayana T

    更新日期:2020-06-24 00:00:00

  • Genetic Adaptation of a Mevalonate Pathway Deficient Mutant in Staphylococcus aureus.

    abstract::In this study we addressed the question how a mevalonate (MVA)-auxotrophic Staphylococcus aureusΔmvaS mutant can revert to prototrophy. This mutant couldn't grow in the absence of MVA. However, after a long lag-phase of 4-6 days the mutant adapted from auxotrophic to prototrophic phenotype. During that time, it acquir...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.01539

    authors: Reichert S,Ebner P,Bonetti EJ,Luqman A,Nega M,Schrenzel J,Spröer C,Bunk B,Overmann J,Sass P,François P,Götz F

    更新日期:2018-07-12 00:00:00

  • Technological Microbiology: Development and Applications.

    abstract::Over thousands of years, modernization could be predicted for the use of microorganisms in the production of foods and beverages. However, the current accelerated pace of new food production is due to the rapid incorporation of biotechnological techniques that allow the rapid identification of new molecules and microo...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2017.00827

    authors: Vitorino LC,Bessa LA

    更新日期:2017-05-10 00:00:00

  • Prevalence and Molecular Epidemiology of Human T-Lymphotropic Virus (HTLV) Infection in People Living With HIV/AIDS in the Pará State, Amazon Region of Brazil.

    abstract::The human T-lymphotropic virus (HTLV) is part of the group of retroviruses that share similar routes of transmission to the human immunodeficiency virus (HIV). Coinfection of these viruses can affect the clinical course of both infections, and reports have shown a quicker progression to AIDS and the development of HIV...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.572381

    authors: Alencar SP,Souza MC,Fonseca RRS,Menezes CR,Azevedo VN,Ribeiro ALR,Lima SS,Laurentino RV,Barbosa MDAAP,Freitas FB,Oliveira-Filho AB,Machado LFA

    更新日期:2020-10-22 00:00:00

  • Inactivation of Salmonella spp. and Listeria spp. by Palmitic, Stearic, and Oleic Acid Sophorolipids and Thiamine Dilauryl Sulfate.

    abstract::Food contaminated with human pathogens, such as Salmonella spp. and Listeria monocytogenes, frequently causes outbreaks of foodborne illness. Consumer concern over the use of synthesized antimicrobials to enhance microbial food safety has led to a search of natural alternatives. The objectives of this study were to ev...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.02076

    authors: Zhang X,Ashby R,Solaiman DK,Uknalis J,Fan X

    更新日期:2016-12-22 00:00:00

  • Gut Microbial Dysbiosis and Plasma Metabolic Profile in Individuals With Vitiligo.

    abstract::Autoimmune diseases are increasingly linked to aberrant gut microbiome and relevant metabolites. However, the association between vitiligo and the gut microbiome remains to be elucidated. Thus, we conducted a case-control study through 16S rRNA sequencing and serum untargeted-metabolomic profiling based on 30 vitiligo...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.592248

    authors: Ni Q,Ye Z,Wang Y,Chen J,Zhang W,Ma C,Li K,Liu Y,Liu L,Han Z,Gao T,Jian Z,Li S,Li C

    更新日期:2020-12-14 00:00:00

  • Genome-enabled studies of anaerobic, nitrate-dependent iron oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans.

    abstract::Thiobacillus denitrificans is a chemolithoautotrophic bacterium capable of anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, both of which can strongly influence the long-term efficacy of in situ reductive immobilization of uranium in contaminated aquifers. We previously identified two c-type cytochromes involv...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2013.00249

    authors: Beller HR,Zhou P,Legler TC,Chakicherla A,Kane S,Letain TE,A O'Day P

    更新日期:2013-08-27 00:00:00

  • Plasmid Transfer in the Ocean - A Case Study from the Roseobacter Group.

    abstract::Plasmid mediated horizontal gene transfer (HGT) has been speculated to be one of the prime mechanisms for the adaptation of roseobacters (Rhodobacteraceae) to their ecological niches in the marine habitat. Their plasmids contain ecologically crucial functional modules of up to ∼40-kb in size, e.g., for aerobic anoxyge...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.01350

    authors: Petersen J,Wagner-Döbler I

    更新日期:2017-07-18 00:00:00

  • Characterization of Chemosynthetic Microbial Mats Associated with Intertidal Hydrothermal Sulfur Vents in White Point, San Pedro, CA, USA.

    abstract::The shallow-sea hydrothermal vents at White Point (WP) in Palos Verdes on the southern California coast support microbial mats and provide easily accessed settings in which to study chemolithoautotrophic sulfur cycling. Previous studies have cultured sulfur-oxidizing bacteria from the WP mats; however, almost nothing ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01163

    authors: Miranda PJ,McLain NK,Hatzenpichler R,Orphan VJ,Dillon JG

    更新日期:2016-07-27 00:00:00