Shewanella amazonensis sp. nov., a novel metal-reducing facultative anaerobe from Amazonian shelf muds

Venkateswaran, Kasthuri; Dollhopf, Michael E.; Aller, Robert C.; Stackebrandt, Erko; Nealson, Kenneth H.

doi:10.1099/00207713-48-3-965

Cited by 119 publications

(86 citation statements)

References 29 publications

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“…Among these, a number of genes were shared by NC and NS samples (Supplementary Table S3), including the C-fixing pcc gene derived from Deinococcus geothermalis, a radiation-resistant and slightly thermophilic species with an optimum growth temperature at 45-50 1C (Ferreira et al, 1997). Starchdegradation amyA genes derived from Shewanella amazonensis with an optimum growth temperature range around 35 1C (Venkateswaran et al, 1998) and chitin-degradation endochitinase genes derived from Bacillus thuringiensis were also shared. P and S cycle genes.…”

Section: Resultsmentioning

confidence: 99%

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

et al. 2014

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Despite microbes’ key roles in driving biogeochemical cycles, the mechanism of microbe-mediated feedbacks to global changes remains elusive. Recently, soil transplant has been successfully established as a proxy to simulate climate changes, as the current trend of global warming coherently causes range shifts toward higher latitudes. Four years after southward soil transplant over large transects in China, we found that microbial functional diversity was increased, in addition to concurrent changes in microbial biomass, soil nutrient content and functional processes involved in the nitrogen cycle. However, soil transplant effects could be overridden by maize cropping, which was attributed to a negative interaction. Strikingly, abundances of nitrogen and carbon cycle genes were increased by these field experiments simulating global change, coinciding with higher soil nitrification potential and carbon dioxide (CO2) efflux. Further investigation revealed strong correlations between carbon cycle genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycle genes and nitrification. These findings suggest that changes of soil carbon and nitrogen cycles by soil transplant and cropping were predictable by measuring microbial functional potentials, contributing to a better mechanistic understanding of these soil functional processes and suggesting a potential to incorporate microbial communities in greenhouse gas emission modeling.

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Section: Resultsmentioning

confidence: 99%

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

et al. 2014

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“…In a similar study with Black Sea sediment clone libraries from the highest dilution of the acetateoxidizing manganese reducers revealed 16S rRNA gene sequences related to Arcobacter and Pelobacter within the Desulfuromonadales and additional, after subcultivation on lactate, to Shewanella , which were related to the sequences of this study (90 to 497% sequences identity to the respective sequences) ( Figure 5). Shewanella and members of the Desulfuromonadales are two groups with the ability to reduce iron and manganese, which are recovered frequently through cultivation for example, with iron oxides as electron acceptor or acetate as electron donor (Caccavo et al, 1992;Venkateswaran et al, 1998;Snoeyenbos-West et al, 2000;Holmes et al, 2002;Vandieken et al, 2006a). S. putrefaciens is one of the few strains isolated directly by manganese oxide reduction (Myers and Nealson, 1988;Nealson et al, 1991).…”

Section: Resultsmentioning

confidence: 99%

Three manganese oxide-rich marine sediments harbor similar communities of acetate-oxidizing manganese-reducing bacteria

et al. 2012

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Dissimilatory manganese reduction dominates anaerobic carbon oxidation in marine sediments with high manganese oxide concentrations, but the microorganisms responsible for this process are largely unknown. In this study, the acetate-utilizing manganese-reducing microbiota in geographically well-separated, manganese oxide-rich sediments from Gullmar Fjord (Sweden), Skagerrak (Norway) and Ulleung Basin (Korea) were analyzed by 16S rRNA-stable isotope probing (SIP). Manganese reduction was the prevailing terminal electron-accepting process in anoxic incubations of surface sediments, and even the addition of acetate stimulated neither iron nor sulfate reduction. The three geographically distinct sediments harbored surprisingly similar communities of acetateutilizing manganese-reducing bacteria: 16S rRNA of members of the genera Colwellia and Arcobacter and of novel genera within the Oceanospirillaceae and Alteromonadales were detected in heavy RNA-SIP fractions from these three sediments. Most probable number (MPN) analysis yielded up to 10 6 acetate-utilizing manganese-reducing cells cm À 3 in Gullmar Fjord sediment. A 16S rRNA gene clone library that was established from the highest MPN dilutions was dominated by sequences of Colwellia and Arcobacter species and members of the Oceanospirillaceae, supporting the obtained RNA-SIP results. In conclusion, these findings strongly suggest that (i) acetatedependent manganese reduction in manganese oxide-rich sediments is catalyzed by members of taxa (Arcobacter, Colwellia and Oceanospirillaceae) previously not known to possess this physiological function, (ii) similar acetate-utilizing manganese reducers thrive in geographically distinct regions and (iii) the identified manganese reducers differ greatly from the extensively explored iron reducers in marine sediments.

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“…While many Shewanella strains remain uncharacterized, there are 32 recognized Shewanella species: the latter were isolated from a variety of sources, primarily aquatic environments and sediments (Bowman et al, 1997;Bozal et al, 2002;Brettar et al, 2002;Coyne et al, 1989;Ivanova et al, 2001 Ivanova et al, , 2003a Ivanova et al, , b, 2004aLeonardo et al, 1999;Makemson et al, 1997;Nogi et al, 1998;Nozue et al, 1992;Satomi et al, 2003Satomi et al, , 2006Skerratt et al, 2002; Toffin et al, 2004;Venkateswaran et al, 1998Venkateswaran et al, , 1999Xu et al, 2005; Yoon et al, 2004a, b;Zhao et al, 2005Zhao et al, , 2006Ziemke et al, 1998). The bacteria of this genus have attracted great attention because of their diverse respiratory capacities, illustrated by their ability to utilize a wide range of terminal electron acceptors, including oxygen, nitrate, metals and sulfur compounds (Kostka et al, 1996;Myers & Nealson, 1988;Venkateswaran et al, 1999; http://www.…”

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confidence: 99%

Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean

Gao

Obraztova

Stewart

et al. 2006

International Journal of Systematic and Evolutionary Microbiology

109

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A novel marine bacterial strain, PV-4 T , isolated from a microbial mat located at a hydrothermal vent of Loihi Seamount in the Pacific Ocean, has been characterized. This micro-organism is orangey in colour, Gram-negative, polarly flagellated, facultatively anaerobic and psychrotolerant (temperature range, 0-42 6C). No growth was observed with nitrate, nitrite, DMSO or thiosulfate as the electron acceptor and lactate as the electron donor. The major fatty acid detected in strain PV-4 T was iso-C 15 : 0 . Strain PV-4 T had ubiquinones consisting mainly of Q-7 and Q-8, and possessed menaquinone MK-7. The DNA G+C content of the strain was 53?8 mol% and the genome size was about 4?5 Mbp. Phylogenetic analyses based on 16S rRNA gene sequences placed PV-4 T within the genus Shewanella. PV-4 T exhibited 16S rRNA gene sequence similarity levels of 99?6 and 97?5 %, respectively, with respect to the type strains of Shewanella aquimarina and Shewanella marisflavi. DNA from strain PV-4 T showed low mean levels of relatedness to the DNAs of S. aquimarina (50?5 %) and S. marisflavi (8?5 %). On the basis of phylogenetic and phenotypic characteristics, the bacterium was classified in the genus Shewanella within a distinct novel species, for which the name Shewanella loihica sp. nov. is proposed. The type strain is PV-4 T (=ATCC BAA-1088 T =DSM 17748 T ).The genus Shewanella consists of rod-shaped, Gramnegative, facultatively anaerobic, readily cultivated gammaproteobacteria (Gauthier et al., 1995;MacDonell & Colwell, 1985;Venkateswaran et al., 1999). While many Shewanella strains remain uncharacterized, there are 32 recognized Shewanella species: the latter were isolated from a variety of sources, primarily aquatic environments and sediments (Bowman et al., 1997;Bozal et al., 2002;Brettar et al., 2002;Coyne et al., 1989;Ivanova et al., 2001 Ivanova et al., , 2003a Ivanova et al., , b, 2004aLeonardo et al., 1999;Makemson et al., 1997;Nogi et al., 1998;Nozue et al., 1992;Satomi et al., 2003Satomi et al., , 2006Skerratt et al., 2002; Toffin et al., 2004;Venkateswaran et al., 1998Venkateswaran et al., , 1999Xu et al., 2005; Yoon et al., 2004a, b;Zhao et al., 2005Zhao et al., , 2006Ziemke et al., 1998). The bacteria of this genus have attracted great attention because of their diverse respiratory capacities, illustrated by their ability to utilize a wide range of terminal electron acceptors, including oxygen, nitrate, metals and sulfur compounds (Kostka et al., 1996;Myers & Nealson, 1988;Venkateswaran et al., 1999; http://www. shewanella.org). Some Shewanella strains are also able to degrade pollutants such as chlorinated solvents (Petrovskis et al., 1994), petroleum (Semple & Westlake, 1987) and RDX (1,3,5-trinitroperhydro-1,3,5-triazine) (Zhao et al., 2004), some can produce polyunsaturated fatty acids (Bowman et al., 1997;Russell & Nichols, 1999;Satomi et al., 2003) and some are able to grow under extreme conditions (Bozal et al., 2002;Kato et al., 1998;Nogi et al., 1998;Stapleton et al., 2005).In a previous study, several She...

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Shewanella amazonensis sp. nov., a novel metal-reducing facultative anaerobe from Amazonian shelf muds

Cited by 119 publications

References 29 publications

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

Three manganese oxide-rich marine sediments harbor similar communities of acetate-oxidizing manganese-reducing bacteria

Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean

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