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

Abstract

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...

Nitrite Control over Dissimilatory Nitrate/Nitrite Reduction Pathways in Shewanella loihica Strain PV-4

“…2). This observation also supports that the NO 2 Ϫ concentrations on strain PV-4 may be the reason why the organism initially was identified as a nondenitrifier (38). NO 2 Ϫ toxicity was observed previously in Shewanella oneidensis strain MR-1, and no growth occurred with 4 mM NO 2 Ϫ provided as the electron acceptor (10).…”

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

“…The microorganisms responsible for Fe oxidation on basalts are not entirely clear, although commonly occurring alpha (including Hyphomonas species)-, gamma (including Marinobacter species)-and zetaproteobacteria are potential candidates for mediating this process (134,479). Fe(III)-reducing microorganisms, including Shewanella frigimarina and Shewanella loihica, have been cultivated from basalt enrichments (346) and from seamount sampling (183), and genes involved in iron reduction, mostly cytochromes, have been documented in surveys of environmental DNA from basalts (354). Activities and rates of Fe oxidation or reduction in basalts in the environment are very poorly constrained because appropriate assays are not available.…”

Deferrisoma palaeochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea

“…Within the Bacteria, a variety of Fe(III) reducers have been isolated and described from these globally widespread hydrothermal systems. For example, at deep-sea hydrothermal vents, members of the classes Deltaproteobacteria (Kashefi et al, 2003;Slobodkina et al, 2012b) and Gammaproteobacteria (Gao et al, 2006) of the phylum Proteobacteria, as well as members of the phylum Deferribacteres (species of the genus Deferribacter) have been described (Miroshnichenko et al, 2003;Slobodkina et al, 2009a). In terrestrial hydrothermal vents and springs, members of the phyla Aquificae (Aguiar et al, 2004), Acidobacteria (Losey et al, 2013) and Actinobacteria (Itoh et al, 2011) have been described; however, the majority of the Fe(III)-reducing species in culture belong to the phylum Firmicutes (Slobodkin et al, 1997(Slobodkin et al, , 1999(Slobodkin et al, , 2006Zavarzina et al, 2002;Gorlenko et al, 2004;Sokolova et al, 2004;Haouari et , 2012).…”