Phylogenetic Analyses of a New Group of Denitrifiers Capable of Anaerobic Growth on Toluene and Description of Azoarcus tolulyticus sp. nov.

Zhou, Jizhong; Fries, M. R.; Chee‐Sanford, Joanne C.; Tiedje, James M.

doi:10.1099/00207713-45-3-500

Cited by 222 publications

(148 citation statements)

References 18 publications

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“…Protocols for DEIRA genomic DNA and total cellular RNA extraction and manipulation were as published (7,11,16,18). Microarray construction was based on the genomic sequence data and annotation provided by the Institute for Genomic Research (Rockville, MD), where a total of 3,187 putative ORFs were assigned to the DEIRA genome (14).…”

Section: Methodsmentioning

confidence: 99%

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

Liu

Zhou

Omelchenko

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

355

414

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Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but the molecular mechanisms underlying this phenotype remain poorly understood. To define the repertoire of DEIRA genes responding to acute irradiation (15 kGy), transcriptome dynamics were examined in cells representing early, middle, and late phases of recovery by using DNA microarrays covering Ϸ94% of its predicted genes. At least at one time point during DEIRA recovery, 832 genes (28% of the genome) were induced and 451 genes (15%) were repressed 2-fold or more. The expression patterns of the majority of the induced genes resemble the previously characterized expression profile of recA after irradiation. DEIRA recA, which is central to genomic restoration after irradiation, is substantially up-regulated on DNA damage (early phase) and down-regulated before the onset of exponential growth (late phase). Many other genes were expressed later in recovery, displaying a growth-related pattern of induction. Genes induced in the early phase of recovery included those involved in DNA replication, repair, and recombination, cell wall metabolism, cellular transport, and many encoding uncharacterized proteins. Collectively, the microarray data suggest that DEIRA cells efficiently coordinate their recovery by a complex network, within which both DNA repair and metabolic functions play critical roles. Components of this network include a predicted distinct ATP-dependent DNA ligase and metabolic pathway switching that could prevent additional genomic damage elicited by metabolism-induced free radicals.T he Gram-positive aerobic bacterium Deinococcus radiodurans R1 (DEIRA) has an extraordinary resistance to ␥-radiation and a wide range of other DNA-damaging conditions, including desiccation and oxidizing agents (1, 2). Ionizing radiation induces DNA double-stranded breaks (DSBs) that are the most lethal form of DNA damage (3). After acute exposures to 10 kGy, early stationary phase (ESP) DEIRA can reassemble its 3.285-Mbp genome, which consists of four haploid genomic copies per cell (4), from hundreds of DNA DSB fragments without lethality or induced mutagenesis (5, 6). Also remarkable is DEIRA's ability to grow at 60 Gy͞h without any discernable effect on its growth rate (7). Because most organisms, generally, can tolerate so few DSBs (8), radiationinduced DSBs and their repair have been difficult to study. In DEIRA, however, there are so many DSBs in fully viable irradiated cells after high-dose irradiation that the steps in DSB repair can be monitored directly in mass culture (5, 9-11). This characteristic has been exploited and used to examine the timing of DNA recombination (5, 10, 12) after high-dose irradiation and has revealed the sequential action of RecA-independent and -dependent pathways during repair (11).Comparative genomic and experimental analyses support the view that DEIRA's extreme radiation resistance phenotype is complex, likely determined collectively by an assortment o...

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Section: Methodsmentioning

confidence: 99%

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

Liu

Zhou

Omelchenko

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

355

414

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“…Genomic DNA was recovered from the isolates as described previously (Zhou et al 1995). SSU rRNA genes were amplified from genomic DNA using modified primers fD1 and rP1 (Weisberg et al 1991, Zhou et al 1995.…”

Section: Methodsmentioning

confidence: 99%

Metal reduction at cold temperatures by Shewanella isolates from various marine environments

Stapleton¹,

Sabree²,

Palumbo³

et al. 2005

Aquat. Microb. Ecol.

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Members of the genus Shewanella capable of reducing metals and forming minerals under cold-temperature conditions were isolated from 3 distinct marine habitats (the coast of Washington State, the Puget Sound, and an iron-rich microbial mat off Hawaii). Cultures of microorganisms were isolated at 8°C on nutrient agar medium prepared in artificial seawater. Isolates in this study could use a wide variety of electron acceptors such as oxygen, nitrate, and metals, and reduce various metals coupled to the oxidation of several organic acids, glucose or hydrogen at temperatures down to 0°C. Akaganeite was reduced to either magnetite or siderite, depending on the test conditions. The geochemical profiles at the sample sites from which these strains were isolated spanned a temperature range of 1.8 to 11°C, and all showed active oxygen and nitrate reduction as well as metal reduction. This confirms previous reports that sediment microorganisms participating in biogeochemical cycles remain active at low temperatures. KEY WORDS: Biogeochemistry · Geomicrobiology · Iron reduction · Cobalt reduction · Magneite Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 38: [81][82][83][84][85][86][87][88][89][90][91] 2005 While their quantitative importance in marine sediments and water columns is not well understood, members of the genus Shewanella are commonly encountered in marine environments (Perry et al. 1993, Thamdrup et al. 2000, Brettar et al. 2002. These isolates have provided useful models for laboratory investigations on metal reduction (Nealson & Saffarini 1994, Kostka & Nealson 1995, food spoilage, barophilic growth (Kato & Nogi 2001) and, more recently, psychrophilic enzymes (Irwin et al. 2001a,b). The present study describes the isolation of members of the genus Shewanella from 3 marine environments. Specifically, strains W3-6-1 and PS-7 were used as models to investigate microbial metal reduction and mineral formation at low temperatures. MATERIALS AND METHODSSite description and sampling. Marine sediment samples were collected from a transect off the coast of Washington State (USA), at 2 locations in Puget Sound (USA) and from an iron-rich microbial mat associated with the Naha Vents on the South Rift of Loihi Seamount near Hawaii. With the exception of the vent sites, sediments were collected by box core sampling. The microbial mat sample was collected during DSRV Pisces V dive number 342 (Emerson & Moyer 2002). Each box core was sub-cored for sectioning using 7.5 and 10 cm cast-acrylic core tubes. Core sectioning took place within approximately 1 h of coring in a glove-box at ~5°C in a N 2 atmosphere. Cores were stored at ~5°C to minimize effects due to warming. Details of sample location, including geographic coordinates, are listed in Table 1.The geochemistry of the sediments was inferred from sediment pore-water distributions. Pore-water was separated from the sediments by centrifugation at 7000 rpm (>10 000 × g) for 20 min; supernatants were filtered thr...

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“…Bacteria were collected by centrifugation and high molecular weight DNA was extracted from the cell pellets using a previously described method (Zhou et al, 1995). The DNA pellets were dissolved in 20 ul of water.…”

Section: Dna Extraction Amplification Labeling and Hybridizationmentioning

confidence: 99%

Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels

Waldron

Nostrand

et al. 2009

Environ. Sci. Technol.

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Phylogenetic Analyses of a New Group of Denitrifiers Capable of Anaerobic Growth on Toluene and Description of Azoarcus tolulyticus sp. nov.

Cited by 222 publications

References 18 publications

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

Metal reduction at cold temperatures by Shewanella isolates from various marine environments

Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels

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