Diversity of Bacteria and Archaea in hypersaline sediment from Death Valley National Park, California.

Abstract:

:The objective of this study was to phylogenetically analyze microorganisms from the domains Bacteria and Archaea in hypersaline sediment from Death Valley National Park. Using domain-specific primers, a region of the 16S rRNA gene was amplified using polymerase chain reaction (PCR), and the product was subsequently used to create a clone library. A total of 243 bacterial clones, 99 archaeal clones, and 209 bacterial isolates were examined. The 243 clones from Bacteria were affiliated with the following groups: the Bacilli (59 clones) and Clostridia (1) of the Firmicutes, Bacteroidetes (90), Proteobacteria (27), Cyanobacteria (18), Gemmatimonadetes (41), candidate division OP1 (5), Actinobacteria (1), and the Deinococcus-Thermus division (1). Within the class Bacilli, 46 of 59 clones were tentatively identified as 10 unclassified species. The majority of bacterial isolates (130 of 209) were more closely related to the Bacillus subtilis-B. licheniformis clade than to any other recognized taxon, and an Ecotype Simulation analysis of B. subtilis relatives identified four previously unknown ecotypes. Several new genera were discovered within the Bacteroidetes (4) and the Gemmatimonadetes (2). Of the 99 archaeal clones, 94 were tentatively identified as belonging to 3 new genera within the Halobacteriaceae; other clones represented novel species within each of 4 established genera.

journal_name

Microbiologyopen

journal_title

MicrobiologyOpen

authors

Kim JS,Makama M,Petito J,Park NH,Cohan FM,Dungan RS

doi

10.1002/mbo3.20

subject

Has Abstract

pub_date

2012-06-01 00:00:00

pages

135-48

issue

2

issn

2045-8827

journal_volume

1

pub_type

杂志文章
  • Depletion of acidic phospholipids influences chromosomal replication in Escherichia coli.

    abstract::In Escherichia coli, coordinated activation and deactivation of DnaA allows for proper timing of the initiation of chromosomal synthesis at the origin of replication (oriC) and assures initiation occurs once per cell cycle. In vitro, acidic phospholipids reactivate DnaA, and in vivo depletion of acidic phospholipids, ...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.46

    authors: Fingland N,Flåtten I,Downey CD,Fossum-Raunehaug S,Skarstad K,Crooke E

    更新日期:2012-12-01 00:00:00

  • Revisiting the pink-red pigmented basidiomycete mirror yeast of the phyllosphere.

    abstract::By taking advantage of the ballistoconidium-forming capabilities of members of the genus Sporobolomyces, we recovered ten isolates from deciduous tree leaves collected from Vermont and Washington, USA. Analysis of the small subunit ribosomal RNA gene and the D1/D2 domain of the large subunit ribosomal RNA gene indicat...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.374

    authors: Cobban A,Edgcomb VP,Burgaud G,Repeta D,Leadbetter ER

    更新日期:2016-10-01 00:00:00

  • Virulence behavior of uropathogenic Escherichia coli strains in the host model Caenorhabditis elegans.

    abstract::Urinary tract infections (UTIs) are among the most common bacterial infections in humans. Although a number of bacteria can cause UTIs, most cases are due to infection by uropathogenic Escherichia coli (UPEC). UPEC are a genetically heterogeneous group that exhibit several virulence factors associated with colonizatio...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.756

    authors: Schifano E,Marazzato M,Ammendolia MG,Zanni E,Ricci M,Comanducci A,Goldoni P,Conte MP,Uccelletti D,Longhi C

    更新日期:2019-06-01 00:00:00

  • Temporal transcriptomes of a marine cyanopodovirus and its Synechococcus host during infection.

    abstract::Marine picocyanobacteria belonging to genera Synechococcus and Prochlorococcus are genetically diverged and distributed into distinct biogeographical patterns, and both are infected by genetically closely related cyanopodoviruses. Previous studies have not fully explored whether the two virus-host systems share simila...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.1150

    authors: Huang S,Sun Y,Zhang S,Long L

    更新日期:2020-12-30 00:00:00

  • Deep tillage combined with biofertilizer following soil fumigation improved chrysanthemum growth by regulating the soil microbiome.

    abstract::Sustained monoculture often leads to the inhibition of plant growth, the decrease of the soil microbial diversity, and changes in soil microbial community composition, particularly to the accumulation of soil-borne pathogens. In this study, we conducted field experiments to investigate the practical effects of tilling...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.1045

    authors: Chen H,Zhao S,Zhao J,Zhang K,Jiang J,Guan Z,Chen S,Chen F,Fang W

    更新日期:2020-07-01 00:00:00

  • Investigating cross-contamination by yeast strains from dental solid waste to waste-handling workers by DNA sequencing.

    abstract::Trying to widen the discussion on the risks associated with dental waste, this study proposed to investigate and genetically compare yeast isolates recovered from dental solid waste and waste workers. Three samples were collected from workers' hands, nasal mucosa, and professional clothing (days 0, 30, and 180), and t...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.554

    authors: Vieira CD,Tagliaferri TL,de Carvalho MAR,de Resende-Stoianoff MA,Holanda RA,de Magalhães TFF,Magalhães PP,Dos Santos SG,de Macêdo Farias L

    更新日期:2018-04-01 00:00:00

  • The differential susceptibility of spores from virulent and attenuated Bacillus anthracis strains to aldehyde- and hypochlorite-based disinfectants.

    abstract::This study compared the sensitivity of spores from virulent and attenuated Bacillus anthracis strains in suspension to inactivation by various chemical disinfectants. Spore suspensions from two virulent strains (A0256 and A0372) and two attenuated strains (Sterne and A0141) of B. anthracis were tested against two alde...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.45

    authors: March JK,Cohen MN,Lindsey JM,Millar DA,Lowe CW,Bunnell AJ,O'Neill KL,Schaalje GB,Robison RA

    更新日期:2012-12-01 00:00:00

  • Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species.

    abstract::The intraspecies genomic diversity of the single-strand RNA (+) virus species hepatitis A virus (Hepatovirus), hepatitis C virus (Hepacivirus), and hepatitis E virus (Orthohepevirus) was compared. These viral species all can cause liver inflammation (hepatitis), but share no gene similarity. The codon usage of human h...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.973

    authors: Wassenaar TM,Jun SR,Robeson M,Ussery DW

    更新日期:2020-02-01 00:00:00

  • Effects of cosmetics on the skin microbiome of facial cheeks with different hydration levels.

    abstract::Basic cosmetics was used by volunteers belonging to high (HHG) and low (LHG) hydration groups for 4 weeks, and bacterial communities and biophysical parameters in facial skin were analyzed. Hydration level increases and transepidermal water loss and roughness decreases were observed in both groups after cosmetic use. ...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.557

    authors: Lee HJ,Jeong SE,Lee S,Kim S,Han H,Jeon CO

    更新日期:2018-04-01 00:00:00

  • Autoinducer2 affects trimethoprim-sulfamethoxazole susceptibility in avian pathogenic Escherichia coli dependent on the folate synthesis-associate pathway.

    abstract::Avian pathogenic Escherichia coli (APEC) causes airsacculitis, polyserositis, septicemia, and other mainly extraintestinal diseases in chickens, ducks, geese, pigeons, and other avian species, and is responsible for great economic losses in the avian industry. The autoinducer 2 (AI-2) quorum sensing system is widely p...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.582

    authors: Yu L,Li W,Zhang M,Cui Y,Chen X,Ni J,Yu L,Shang F,Xue T

    更新日期:2018-08-01 00:00:00

  • Mcr colistin resistance gene: a systematic review of current diagnostics and detection methods.

    abstract::Resistance to colistin, mediated by chromosomal mutations and more recently, by plasmid-borne mcr genes, is increasingly being reported in bacterial isolates taken from humans, animals, farms, foods, and the environment. To easily identify and contain this quickly spreading menace, efficient diagnostics that are cheap...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.682

    authors: Osei Sekyere J

    更新日期:2019-04-01 00:00:00

  • A membrane-bound [NiFe]-hydrogenase large subunit precursor whose C-terminal extension is not essential for cofactor incorporation but guarantees optimal maturation.

    abstract::[NiFe]-hydrogenases catalyze the reversible conversion of molecular hydrogen into protons end electrons. This reaction takes place at a NiFe(CN)2 (CO) cofactor located in the large subunit of the bipartite hydrogenase module. The corresponding apo-protein carries usually a C-terminal extension that is cleaved off by a...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.1029

    authors: Hartmann S,Frielingsdorf S,Caserta G,Lenz O

    更新日期:2020-06-01 00:00:00

  • Insights into gene regulation of the halovirus His2 infecting Haloarcula hispanica.

    abstract::Gene expression in Haloarcula hispanica cells infected with the gammapleolipovirus His2 was studied using a custom DNA microarray. Total RNA from cells sampled at 0, 1, 2, 3, and 4.5 hr postinfection was reverse-transcribed into labeled cDNA and hybridized to microarrays, revealing temporal and differential expression...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.1016

    authors: Lee STM,Ding JY,Chiang PW,Dyall-Smith M,Tang SL

    更新日期:2020-05-01 00:00:00

  • The Aeromonas caviae AHA0618 gene modulates cell length and influences swimming and swarming motility.

    abstract::Aeromonas caviae is motile via a polar flagellum in liquid culture, with a lateral flagella system used for swarming on solid surfaces. The polar flagellum also has a role in cellular adherence and biofilm formation. The two subunits of the polar flagellum, FlaA and FlaB, are posttranslationally modified by O-linked g...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.233

    authors: Lowry RC,Parker JL,Kumbhar R,Mesnage S,Shaw JG,Stafford GP

    更新日期:2015-04-01 00:00:00

  • Evaluation of two xenobiotic reductases from Pseudomonas putida for their suitability for magnetic nanoparticle-directed enzyme prodrug therapy as a novel approach to cancer treatment.

    abstract::Directed enzyme prodrug therapy (DEPT) is a cancer chemotherapy strategy in which bacterial enzymes are delivered to a cancer site before prodrug administration, resulting in prodrug activation at the cancer site and more localized treatment. A major limitation to DEPT is the poor effectiveness of the most studied enz...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.1110

    authors: Ball P,Halliwell J,Anderson S,Gwenin V,Gwenin C

    更新日期:2020-10-01 00:00:00

  • A preliminary examination of the bacterial, archaeal, and fungal rhizosphere microbiome in healthy and Phellinus noxius-infected trees.

    abstract::Phellinus noxius is a pathogenic fungus that causes brown root rot disease, resulting in a widespread tree and crop mortality in the tropics and subtropics. Early stages of this disease are largely asymptomatic, hindering early diagnosis and effective treatment. We hypothesized that P. noxius infection would alter the...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.1115

    authors: Tsang KSW,Cheung MK,Lam RYC,Kwan HS

    更新日期:2020-10-01 00:00:00

  • A factor converting viable but nonculturable Vibrio cholerae to a culturable state in eukaryotic cells is a human catalase.

    abstract::In our previous work, we demonstrated that viable but nonculturable (VBNC) Vibrio cholerae O1 and O139 were converted to culturable by coculture with eukaryotic cells. Furthermore, we isolated a factor converting VBNC V. cholerae to culturable (FCVC) from a eukaryotic cell line, HT-29. In this study, we purified FCVC ...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.264

    authors: Senoh M,Hamabata T,Takeda Y

    更新日期:2015-08-01 00:00:00

  • Global transcriptome responses including small RNAs during mixed-species interactions with methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa.

    abstract::Pseudomonas aeruginosa and Staphylococcus aureus mixed-species biofilm infections are more resilient to biocide attacks compared to their single-species counterparts. Therefore, this study used an in vitro model recapitulating bacterial burdens seen in in vivo infections to investigate the interactions of P. aeruginos...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.427

    authors: Miller CL,Van Laar TA,Chen T,Karna SLR,Chen P,You T,Leung KP

    更新日期:2017-06-01 00:00:00

  • Genetic determinants of swimming motility in the squid light-organ symbiont Vibrio fischeri.

    abstract::Bacterial flagellar motility is a complex cellular behavior required for the colonization of the light-emitting organ of the Hawaiian bobtail squid, Euprymna scolopes, by the beneficial bioluminescent symbiont Vibrio fischeri. We characterized the basis of this behavior by performing (i) a forward genetic screen to id...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.96

    authors: Brennan CA,Mandel MJ,Gyllborg MC,Thomasgard KA,Ruby EG

    更新日期:2013-08-01 00:00:00

  • AcuC, a histone deacetylase, contributes to the pathogenicity of Aeromonas hydrophila.

    abstract::The interactions of pathogens and phagocytes are complex. Our study demonstrated that Aeromonas hydrophila B11 can survive in the macrophagocytes of Tilapia mossambica. To explore the regulatory processes of A. hydrophila survival in the macrophagocytes, we used the mini-Tn10 transposon mutagenesis system to build a m...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.468

    authors: Jiang Q,Chen W,Qin Y,Huang L,Xu X,Zhao L,Yan Q

    更新日期:2017-08-01 00:00:00

  • Oscillating behavior of Clostridium difficile Min proteins in Bacillus subtilis.

    abstract::In rod-shaped bacteria, the proper placement of the division septum at the midcell relies, at least partially, on the proteins of the Min system as an inhibitor of cell division. The main principle of Min system function involves the formation of an inhibitor gradient along the cell axis; however, the establishment of...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.337

    authors: Makroczyová J,Jamroškovič J,Krascsenitsová E,Labajová N,Barák I

    更新日期:2016-06-01 00:00:00

  • Meloxicam inhibits biofilm formation and enhances antimicrobial agents efficacy by Pseudomonas aeruginosa.

    abstract::Microbial biofilms are communities of surface-adhered cells enclosed in a matrix of extracellular polymeric substances. Bacterial cells in biofilm are 10~1,000-fold more resistant to antimicrobials than the planktonic cells. Burgeoning antibiotic resistance in Pseudomonas aeruginosa biofilm has necessitated the develo...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.545

    authors: She P,Wang Y,Luo Z,Chen L,Tan R,Wang Y,Wu Y

    更新日期:2018-02-01 00:00:00

  • Posttranslational modification of a vanadium nitrogenase.

    abstract::In microbes that fix nitrogen, nitrogenase catalyzes the conversion of N2 to ammonia in an ATP-demanding reaction. To help conserve energy some bacteria inhibit nitrogenase activity upon exposure to ammonium. The purple nonsulfur phototrophic bacterium Rhodopseudomonas palustris strain CGA009 can synthesize three func...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.265

    authors: Heiniger EK,Harwood CS

    更新日期:2015-08-01 00:00:00

  • CopM is a novel copper-binding protein involved in copper resistance in Synechocystis sp. PCC 6803.

    abstract::Copper resistance system in the cyanobacterium Synechocystis sp. PCC 6803 comprises two operons, copMRS and copBAC, which are expressed in response to copper in the media. copBAC codes for a heavy-metal efflux-resistance nodulation and division (HME-RND) system, while copMRS codes for a protein of unknown function, Co...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.231

    authors: Giner-Lamia J,López-Maury L,Florencio FJ

    更新日期:2015-02-01 00:00:00

  • A putative merR family transcription factor Slr0701 regulates mercury inducible expression of MerA in the cyanobacterium Synechocystis sp. PCC6803.

    abstract::In cyanobacteria, genes conferring mercury resistance are not organized as mer-operon, unlike in other bacterial phyla. Synechocystis contains only a putative MerR regulator, Slr0701, and a mercury reductase, MerA, located aside from each other in the genome. The slr0701-mutant showed reduction in photosynthetic activ...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.838

    authors: Singh DK,Lingaswamy B,Koduru TN,Nagu PP,Jogadhenu PSS

    更新日期:2019-09-01 00:00:00

  • The effect of sulfamonomethoxine treatment on the gut microbiota of Nile tilapia (Oreochromis niloticus).

    abstract::To investigate the possible effects of sulfamonomethoxine (SMM) on Nile tilapia (Oreochromis niloticus), we quantitatively evaluated the microbial shifts in the intestines of Nile tilapia in response to different doses of SMM (200 and 300 mg/kg) using 16S rRNA gene sequencing. At the phylum level, the control group (0...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.1116

    authors: Ming J,Fu Z,Ma Z,Zhou L,Zhang Z,Song C,Yuan X,Wu Q

    更新日期:2020-11-01 00:00:00

  • Immunity protein release from a cell-bound nuclease colicin complex requires global conformational rearrangement.

    abstract::Nuclease colicins bind their target receptor BtuB in the outer membrane of sensitive Escherichia coli cells in the form of a high-affinity complex with their cognate immunity proteins. The release of the immunity protein from the colicin complex is a prerequisite for cell entry of the colicin and occurs via a process ...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.122

    authors: Vankemmelbeke M,Housden NG,James R,Kleanthous C,Penfold CN

    更新日期:2013-10-01 00:00:00

  • Characterizing the bacterial community across the gastrointestinal tract of goats: Composition and potential function.

    abstract::The composition and function of the microbial community in the gastrointestinal tract (GIT) have increasingly captured the attention of nutritionists because these traits affect the nutrient utilization efficiency and health of host animals. Little information has been reported on these aspects of the goat GIT. This s...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.820

    authors: Wang L,Jin L,Xue B,Wang Z,Peng Q

    更新日期:2019-09-01 00:00:00

  • A novel gingipain regulatory gene in Porphyromonas gingivalis mediates host cell detachment and inhibition of wound closure.

    abstract::The black pigmentation-related genes in Porphyromonas gingivalis are primarily involved in regulating gingipain functions. In this study, we identified a pigmentation-related gene, designated as pgn_0361. To characterize the role of pgn_0361 in regulating P. gingivalis-mediated epithelial cell detachment and inhibitio...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.1128

    authors: Liu H,Huang L,Cai Y,Bikker FJ,Wei X,Mei Deng D

    更新日期:2020-12-01 00:00:00

  • Detection of methicillin-resistant Staphylococcus aureus persistence in osteoblasts using imaging flow cytometry.

    abstract::Methicillin-resistant S. aureus has been reported as the main pathogen involved in chronic infections, osteomyelitis, and prosthetic joint infections. The host/pathogen interaction is dynamic and requires several changes to promote bacterial survival. Here, we focused on the internalization and persistence behavior of...

    journal_title:MicrobiologyOpen

    pub_type: 杂志文章

    doi:10.1002/mbo3.1017

    authors: Bongiorno D,Musso N,Lazzaro LM,Mongelli G,Stefani S,Campanile F

    更新日期:2020-05-01 00:00:00