Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis

Heidelberg, John F.; Paulsen, Ian T.; Nelson, Karen E.; Gaidos, Eric; Nelson, William; Read, Timothy D.; Eisen, Jonathan A.; Seshadri, Rekha; Ward, Naomi; Methé, Barbara A.; Clayton, Rebecca A.; Meyer, Terry E.; Tsapin, A. I.; Scott, James; Beanan, Maureen J.; Brinkac, Lauren; Daugherty, Sean C.; DeBoy, Robert T.; Dodson, Robert J.; Durkin, A. Scott; Haft, Daniel H.; Kolonay, James F.; Madupu, Ramana; Peterson, Jeremy; Umayam, Lowell; White, Owen; Wolf, Alex M.; Vamathevan, Jessica; Weidman, Janice; Impraim, Marjorie; Lee, Kathy; Berry, Kristy; Lee, Chris; Mueller, Jacob L.; Khouri, Hoda; Gill, John; Utterback, Terry; McDonald, Lisa; Feldblyum, Tamara; Smith, Hamilton O.; Venter, J. Craig; Nealson, Kenneth H.; Fraser, Claire M.

doi:10.1038/nbt749

Cited by 778 publications

(651 citation statements)

References 43 publications

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“…Because of its metabolic versatility and its ability to reduce metals 7 to less mobile forms, this bacterium has been considered for use in bioremediation of subsurface 8 sites contaminated with metals and, as such, has been studied extensively over the last decade 9 the genome of S. oneidensis MR-1 was recently sequenced (Heidelberg et al 2002). 12 Understanding how environmental conditions (pH, temperature, oxygen) impact its 13 ability to reduce metals is important if S. oneidensis is going to be used to remediate 14 environments contaminated with metals.…”

mentioning

confidence: 99%

Evaluation of the effects of various culture conditions on Cr(VI) reduction by Shewanella oneidensis MR‐1 in a novel high‐throughput mini‐bioreactor

Tang

Laidlaw²,

Gani

et al. 2006

Biotech & Bioengineering

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1The growth and Cr(VI) reduction by Shewanella oneidensis MR-1 was examined using a 2 mini-bioreactor system that independently monitors and controls pH, dissolved oxygen, and 3 temperature for each of its 24, 10-mL reactors. Independent monitoring and control of each 4 reactor in the cassette allows the exploration of a matrix of environmental conditions known to 5 influence S. oneidensis chromium reduction. S. oneidensis MR-1 grew in minimal medium 6 without amino acid or vitamin supplementation under aerobic conditions but required serine and 7 glycine supplementation under anaerobic conditions. Growth was inhibited by dissolved oxygen 8 concentrations >80%. Lactate transformation to acetate was enhanced by low concentration of 9 dissolved oxygen during the logarithmic growth phase. Between 11 and 35°C, the growth rate 10 obeyed the Arrhenius reaction rate-temperature relationship, with a maximum growth rate 11 occurring at 35°C. S. oneidensis MR-1 was able to grow over a wide range of pH (6-9). At 12 neutral pH and temperatures ranging from 30-35°C, S. oneidensis MR-1 reduced 100 µM Cr(VI) 13 to Cr(III) within 20 minutes in the exponential growth phase, and the growth rate was not 14 affected by the addition of chromate; it reduced chromate even faster at temperatures between 35 15 and 39°C. At low temperatures (<25°C), acidic (pH<6.5), or alkaline (pH>8.5) conditions, 100 16 µM Cr(VI) strongly inhibited growth and chromate reduction. The mini-bioreactor system 17 enabled the rapid determination of these parameters reproducibly and easily by performing very 18 few experiments. Besides its use for examining parameters of interest to environmental 19 remediation, the device will also allow one to quickly assess parameters for optimal production 20 of recombinant proteins or secondary metabolites 21

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mentioning

confidence: 99%

Evaluation of the effects of various culture conditions on Cr(VI) reduction by Shewanella oneidensis MR‐1 in a novel high‐throughput mini‐bioreactor

Tang

Laidlaw²,

Gani

et al. 2006

Biotech & Bioengineering

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“…In addition, a number of radionucleotide oxides can be reduced (Myers and Nealson, 1988;Nealson and Scott, 2003;Icopini et al, 2009). Thus, bacteria such as Shewanella significantly impact biogeochemical cycling processes and are of particular interest with regard to bioremediation processes (Heidelberg et al, 2002;Nealson et al, 2002;Lovley et al, 2004;Ward et al, 2004;Hau and Gralnick, 2007). It has been hypothesized that direct interaction of Shewanella cells with, or close proximity to, an appropriate surface facilitates the deposition of electrons (Das and Caccavo, 2000;Gorby et al, 2006;McLean et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Phage-induced lysis enhances biofilm formation in Shewanella oneidensis MR-1

et al. 2010

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Shewanella oneidensis MR-1 is capable of forming highly structured surface-attached communities. By DNase I treatment, we demonstrated that extracellular DNA (eDNA) serves as a structural component in all stages of biofilm formation under static and hydrodynamic conditions. We determined whether eDNA is released through cell lysis mediated by the three prophages LambdaSo, MuSo1 and MuSo2 that are harbored in the genome of S. oneidensis MR-1. Mutant analyses and infection studies revealed that all three prophages may individually lead to cell lysis. However, only LambdaSo and MuSo2 form infectious phage particles. Phage release and cell lysis already occur during early stages of static incubation. A mutant devoid of the prophages was significantly less prone to lysis in pure culture. In addition, the phage-less mutant was severely impaired in biofilm formation through all stages of development, and three-dimensional growth occurred independently of eDNA as a structural component. Thus, we suggest that in S. oneidensis MR-1 prophage-mediated lysis results in the release of crucial biofilm-promoting factors, in particular eDNA.

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“…The chromosome of this bacterium (AE014299; see [36]) included pfa genes (Table 4). However, the marine bacterium P. alcaliphila AL15-21 T and nonmarine yeast produced neither PUFA nor C31:9.…”

Section: Distribution Of C31:9 In Various Microorganisms and Its Possmentioning

confidence: 99%

Possible Biosynthetic Pathways for all cis‐3,6,9,12,15,19,22,25,28‐Hentriacontanonaene in Bacteria

Sugihara

Hori

Nakanowatari

et al. 2009

Lipids

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A very long chain polyunsaturated hydrocarbon, hentriacontanonaene (C31:9), was detected in an eicosapentaenoic acid (EPA)-producing marine bacterium, which was isolated from the mid-latitude seashore of Hokkaido, Japan, and was tentatively identified as mesophilic Shewanella sp. strain osh08 from 16S rRNA gene sequencing. The geometry and position of the double bonds in this compound were determined physicochemically to be all cis at positions 3, 6, 9, 12, 15, 19, 22, 25, and 28. Although C31:9 was detected in all of the seven EPA-or/and docosahexaenoic acid-producing bacteria tested, an EPA-deficient mutant (strain IK-18) of one of these bacteria had no C31:9. Strain IK-18 had defects in the pfaD gene, one of the five pfa genes responsible for the biosynthesis of EPA.Although Escherichia coli DH5 does not produce EPA or DHA inherently, cells transformed with the pfa genes responsible for the biosynthesis of EPA and DHA produced EPA and DHA, respectively, but not C31:9. These results suggest that the Pfa protein complex is involved in the biosynthesis of C31:9 and that pfa genes must not be the only genes responsible for the formation of C31:9. In this report, we determined for the first time the molecular structure of the C31:9 and discuss the possible biosynthetic pathways of this compound. Key words

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Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis

Cited by 778 publications

References 43 publications

Evaluation of the effects of various culture conditions on Cr(VI) reduction by Shewanella oneidensis MR‐1 in a novel high‐throughput mini‐bioreactor

Evaluation of the effects of various culture conditions on Cr(VI) reduction by Shewanella oneidensis MR‐1 in a novel high‐throughput mini‐bioreactor

Phage-induced lysis enhances biofilm formation in Shewanella oneidensis MR-1

Possible Biosynthetic Pathways for all cis‐3,6,9,12,15,19,22,25,28‐Hentriacontanonaene in Bacteria

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