SGM Journals
Proteobacteria

Shewanella sediminis sp. nov., a novel Na+-requiring and hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading bacterium from marine sediment

Jian-Shen Zhao, Dominic Manno, Chantale Beaulieu, Louise Paquet, Jalal Hawari

  • Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Quebec, Canada H4P 2R2
  • Correspondence
    Jalal Hawari
    jalal.hawari{at}cnrc-nrc.gc.ca

    • International Journal of Systematic and Evolutionary Microbiology 2005; 55(4):1511–1520 · https://doi.org/10.1099/ijs.0.63604-0

    View at publisher PubMed

    Abstract

    Previously, a psychrophilic rod-shaped marine bacterium (strain HAW-EB3T) isolated from Halifax Harbour sediment was noted for its ability to degrade hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). In the present study phenotypic, chemotaxonomic and genotypic characterization showed that strain HAW-EB3T represents a novel species of Shewanella. Strain HAW-EB3T contained lysine decarboxylase, which is absent in other known Shewanella species, and distinguished itself from most other species of Shewanella by the presence of arginine dehydrolase, ornithine decarboxylase and chitinase, and by its ability to oxidize and ferment N-acetyl-d-glucosamine. Strain HAW-EB3T grew on several carbon sources (N-acetyl-d-glucosamine, Tween 40, Tween 80, acetate, succinate, butyrate and serine) and showed distinctive fatty acid and quinone compositions. Both phenotypic and 16S rRNA gene phylogenetic cluster analyses demonstrated that HAW-EB3T belongs to the Na+-requiring group of Shewanella species. The HAW-EB3T 16S rRNA gene sequence displayed ⩽97·4 % similarity to all known Shewanella species and was most similar to those of two bioluminescent species, Shewanella hanedai and Shewanella woodyi. However, gyrB of strain HAW-EB3T was significantly different from those of other Shewanella species, with similarities less than 85 %. DNA-DNA hybridization showed that its genomic DNA was less than 25 % related to that of S. hanedai or S. woodyi. Therefore we propose Shewanella sediminis sp. nov., with HAW-EB3T (=NCIMB 14036T=DSM 17055T) as the type strain.

    • The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence and the gyrB gene sequence of strain HAW-EB3T are AY579750 and AY842130, respectively.

    • A table of the quinone compositions of strain HAW-EB3T and other species of Shewanella is available as supplementary material in IJSEM Online.

    In a previous study several Shewanella strains capable of degrading hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) were isolated from an unexploded-ordnance-dumping site (Emerald Basin, 215 m deep), 50 nautical miles from Halifax Harbour (Nova Scotia, Canada), Atlantic Ocean (Zhao et al., 2004a, b). In order to understand RDX metabolism and thus in situ biodegradation (natural attenuation) of the cyclic nitramine explosives at the Halifax site, phenotypic and genetic characterization of the isolates is necessary.

    Shewanella genus was proposed by MacDonell & Colwell (1985) for two bacteria previously classified as Alteromonas putrefaciens (Long & Hammer, 1941; Lee et al., 1977) and Alteromonas hanedai (Jensen et al., 1980), and one deep-sea barophilic isolate (Deming et al., 1984). Shewanella were defined as rod-shaped, Gram-negative, oxidase-positive, motile and chemo-organotrophic aquatic bacteria with 44–47 mol% G+C (MacDonell & Colwell, 1985). Since then many new species have been found, mostly from sea water, sediment and marine organisms, and currently there are 28 recognized Shewanella species (Shewanellaceae, ‘Alteromonadales’, class ‘Gammaproteobacteria’) at the time of writing this article (Bozal et al., 2002; Coyne et al., 1989; Bowman et al., 1997; Makemson et al., 1997; Nogi et al., 1998; Leonardo et al., 1999; Brettar et al., 2002; Ivanova et al., 2001, 2003a, b, 2004a, b, c; Skerratt et al., 2002; Satomi et al., 2003; Simidu et al., 1990; Toffin et al., 2004; Venkateswaran et al., 1998b; Yoon et al., 2004a, b; Ziemke et al., 1998).

    Some strains of Shewanella are known for polyunsaturated fatty acid production (Russell & Nichols, 1999; Bowman et al., 1997; Satomi et al., 2003), metal reduction (Myers & Nealson, 1988; Kostka et al., 1996), growth at low temperature (Deming et al., 1984; Jensen et al., 1980; Bozal et al., 2002) and high pressure (Nogi et al., 1998; Deming et al., 1984; Kato et al., 1998), or for the degradation of pollutants such as RDX (Zhao et al., 2004b), petroleum (Semple & Westlake, 1987) and chlorinated solvents (Petrovskis et al., 1994). The objective of the present study is to extensively characterize the RDX-degrading isolate, Shewanella sp. HAW-EB3T, and compare it with the properties of known Shewanella species. We found that strain HAW-EB3T represents a novel species of Shewanella, designated Shewanella sediminis sp. nov.

    Scanning (Hitachi S3000N) or negatively stained transmission (Hitachi H7500) electron micrographs of strain HAW-EB3T cells were prepared according to previously described protocols (Beveridge et al., 1994; Bozal et al., 2002).

    NaCl tolerance was tested on pre-cooled Brewer's anaerobic agar (Becton Dickson; the reagent contained 0·5 % NaCl) that contained 0·5, 1·5, 2·0, 2·5, 3·0, 4·0, 6·0 or 8·0 % NaCl, followed by aerobic incubation at 10 °C for 5 days. Bacterial growth was estimated using the following equation: biomass=π×(D/2)2×c.f.u., where D represents mean diameter of colonies and one unit was equal to 50 μm. A Na+-free agar that contained 0·3 % bacto beef extract and 0·5 % bacto peptone was used to test growth in the absence of Na+.

    Standard protocols were employed to test Gram reaction, catalase and oxidase activities, spore formation and acid production from various sugars (in Leifson Modified O-F medium) (Smibert & Krieg, 1994). Enzymic hydrolyses of various substrates including casein (skimmed milk, 50 %), gelatin (1 %), Tween 20, -40 and -80 (1 %), olive oil (1 %), lecithin (5 % egg yolk), pure chitin (0·3 %), alginate (1 %) and starch (1 %) were conducted using marine broth 2216 (Becton Dickinson) as a basal medium as described by Bowman (2001). Production of H2S from thiosulfate was tested in marine agar 2216 (Becton Dickinson) supplemented with NaS2O3 (1 %). DNase was determined using BBL DNA test agar (Becton Dickinson) supplemented with sea salts (4 %). API Rapid 20E and ID32A (BioMérieux) test kits were used to detect additional enzymic activites as listed in the species description. GN2 microplates (Biolog) were used for metabolism of sugars, organic acids, amino acids, peptides and nucleosides (Table 1⇓). Cells of 0·9 OD600, higher than the 0·3 OD600 instructed by the manufacturer, were used for GN2 tests because no oxidation of substrates was found at 0·3 OD600. Aerobic utilization of substrates (0·1 %) as sole carbon and energy sources by washed cells of strain HAW-EB3T was evaluated in 24-well cell culture clusters containing NH4Cl (0·1 %) to serve as a nitrogen source in basic marine salts medium at pH 7·0 for 2, 4, 6 and 8 weeks. The basic marine salt medium was supplemented with a trace metal solution as described previously (Zhao et al., 2003). The substrates that caused more than 15 % increases in OD600 (initial OD600, 0·1) were recorded as positive because the variation at the low OD600 measurement was 5–10 %; those exhibiting a change less than 15 % in OD600 were considered uncertain or negative. Reduction of electron acceptors was conducted on Brewer's anaerobic agar supplemented with 2 % NaCl and one of the substrates MnO2 (40 mM), ferric citrate (40 mM), amorphous iron oxide (FeOOH, 40 mM), trimethylamine N-oxide (TMAO) (5mM), nitrate (5 mM), nitrite (5 mM) or elemental sulfur (40 mM, stock solution prepared as described by Moser & Nealson, 1996), followed by incubation in anaerobic jars for 30 days. Clear zones around colonies were used to indicate Fe(III), Mn(IV) and sulfur reduction (Myers & Nealson, 1988). The enhanced growth of HAW-EB3T in the presence of TMAO, nitrate and nitrite was used as an indicator for dissimilatory reduction. All of the above physiological properties were tested at 10 °C unless noted otherwise. All of the phenotypic tests were run in triplicate.

    Table 1.

    Characterization of HAW-EB3T and related species of Shewanella

    +, Positive; −, negative; NAG, N-acetylglucosamine; G, glucose; C, chitin; nd, no data. Data sources: Bowman et al. (1997); Deming et al. (1984); Jensen et al. (1980); Kato et al. (1998); MacDonell & Colwell (1985); Makemson et al. (1997); Nogi et al. (1998); Venkateswaran et al. (1999); this study.

    Strain HAW-EB3T, a Gram-negative bacterium, grew well aerobically in marine broth or agar 2216 (Becton Dickinson) or Brewer's anaerobic agar supplemented with either sea salts (Sigma, 4 %) or 2 % NaCl at 10 °C. The biomass of strain HAW-EB3T exhibited a slightly orangish or pinkish colour, typical of species of Shewanella (Venkateswaran et al., 1999). Strain HAW-EB3T also grew anaerobically on marine agar 2216 and Brewer's anaerobic agar supplemented with 2 % NaCl. Scanning electron micrographs showed that strain HAW-EB3T was a rod-shaped bacterium (0·5–1 μm in diameter and 1·5–2·0 μm in length) (Fig. 1⇓a). Negatively stained transmission electron micrographs showed the presence of a single polar flagellum (Fig. 1b⇓), consistent with species of Shewanella (MacDonell & Colwell, 1985).

    Figure image not available in archive
    Fig. 1.

    Micrographs of strain HAW-EB3T: (a) scanning electron micrograph of cells; (b) transmission electron micrograph of a negatively stained cell showing a single polar flagellum.

    The physiological and biochemical properties of strain HAW-EB3T are presented in the species description below. Generally, physiological and biochemical properties of strain HAW-EB3T were consistent with Shewanella species, most of which are positive for catalase, oxidase, lipase and growth on glucose and/or N-acetyl-d-glucosamine, certain short chain fatty acids and amino acids at temperatures mostly ranging from 4–30 °C and in the presence of 1–4 % (w/w) NaCl (Bozal et al., 2002; Brettar et al., 2002; Ivanova et al., 2001, 2003a, b, 2004a, b; Leonardo et al., 1999; Rossello-Mora et al., 1994; Satomi et al., 2003; Skerratt et al., 2002; Toffin et al., 2004; Venkateswaran et al., 1999; Vogel et al., 1997; Yoon et al., 2004a, b; Zhao et al., 2004b; Ziemke et al., 1998). Strain HAW-EB3T was a psychrophilic bacterium, growing at 4–25 °C with 10 °C as an optimum and no growth observed at 30 °C (Zhao et al., 2004b). In the case of salinity tolerance, strain HAW-EB3T was a Na+-requiring and moderately halophilic bacterium, growing at 1–4 % (w/w) NaCl with an optimum of 2 %. Like all species of Shewanella, strain HAW-EB3T reduced nitrate and TMAO under anaerobic conditions. In the case of acid substrate profiles, strain HAW-EB3T utilized acetate, pyruvate, butyrate and valerate, similar to several Shewanella species including Shewanella hanedai, Shewanella gelidimarina, Shewanella algae (Simidu et al., 1990) and Shewanella frigidimarina.

    Most Shewanella species are reported to utilize glucose and/or N-acetyl-d-glucosamine, fructose, sucrose or galactose as aerobic substrate(s). In comparison to known Shewanella species regarding utilization of sugars, strain HAW-EB3T only utilized N-acetyl-d-glucosamine among the seven sugars tested (glucose, galactose, lactose, fructose, sucrose, mannose and N-acetyl-d-glucosamine), similar to S. gelidimarina (Bowman et al., 1997). More than half (16 species) of all known Shewanella species (28 species in total) including strain HAW-EB3T are fermentative. In the case of strain HAW-EB3T, N-acetyl-d-glucosamine was fermented, as observed for S. gelidimarina. Most other fermentative species (Shewanella benthica, S. hanedai, S. frigidimarina, Shewanella livingstonensis, Shewanella violacea, Shewanella affinis, Shewanella felis, Shewanella japonica, Shewanella pacifica and Shewanella waksmanii) fermented glucose, a few (Shewanella marinintestina, Shewanella schlegeliana and Shewanella sairae) fermented ribose.

    In contrast to reports that most species of Shewanella are negative for chitinase, strain HAW-EB3T produced this enzyme, similar to S. hanedai and S. gelidimarina. More importantly, strain HAW-EB3T contained lysine decarboxylase, which is absent in all reported species of Shewanella. Strain HAW-EB3T also exhibited activities of arginine dehydrolase and ornithine decarboxylase, which are only found in a few species (Venkateswaran et al., 1999; Ivanova et al., 2004a, b; Bozal et al., 2002). Strain HAW-EB3T also did not exhibit gelatinase activity as found in most Shewanella species.

    Thirty-two characteristics of strain HAW-EB3T and 28 other known species of Shewanella were used for further phenotypic cluster analyses using methods described by Eisen et al. (1998) (Cluster and Maple Tree View software, version 2.11; Pearson correlation similarity, uncentred, agglomerative hierarchical clustering, complete linkage). The 32 characteristics were: fermentation; growth factor requirement; growth in the presence of 0 %, 1 %, 2 %, 4 %, 6 %, 8 % and 10 % (w/v) NaCl; reduction of Fe(III) or TMAO; H2S formation; growth at 4, 21, 30, 35, 37 and 42 °C; lipase; gelatinase; chitinase; alginase; amylase; utilization of glucose, fructose, sucrose, N-acetyl-d-glucosamine and citrate; alginine dehydrolase; ornithine decarboxylase and lysine decarboxylase. Data matrix values were prepared as follows: 4, positive; 2, weakly positive; 1, dependent or varying data; −2, negative; −, missing data. All species of Shewanella separated into two clusters (Fig. 2⇓). The first cluster (I) was composed of Na+-requiring and psychrophilic species, including strain HAW-EB3T, two barophilic species (S. benthica and S. violacea), two bioluminescent species (Shewanella woodyi and S. hanedai), three marine intestinal inhabitants (S. marinintestina, S. schlegeliana and S. sairae) and one iron-reducer (S. gelidimarina). The second cluster (II) contained mainly non-Na+-requiring and 6 % NaCl-tolerant species with several exceptions (see legend to Fig. 2⇓). The cluster analysis indicated that HAW-EB3T appeared most similar to S. gelidimarina and S. woodyi of cluster I (Fig. 2⇓). However, strain HAW-EB3T was significantly different from S. gelidimarina and S. woodyi and other related species of Shewanella in many phenotypic characteristics as listed in Table 1⇑.

    Figure image not available in archive
    Fig. 2.

    Phenotypic cluster analysis of Shewanella species. Cluster I: all species are Na+-requiring psychrophiles and do not grow at 35 °C. Cluster II: most species do not require Na+ for growth (except S. pacifica, Shewanella gaetbuli, Shewanella aquimarina and Shewanella olleyana), tolerate 6 % NaCl (except S. japonica, Shewanella oneidensis and Shewanella amazonensis) and grow at 35 °C (except S. pacifica, S. felis, Shewanella denitrificans, S. affinis, S. livingstonensis and S. frigidimarina). All Shewanella species grow at 4 °C except Shewanella colwelliana of cluster I, and S. affinis, S. aquimarina, S. algae and S. amazonensis of cluster II. The phenotypic properties (see text for details) used for cluster analysis of known species of Shewanella are from the following references: Bowman et al. (1997); Bozal et al. (2002); Brettar et al. (2002); Deming et al. (1984); Ivanova et al. (2001, 2003a, b, 2004a, b); Jensen et al. (1980); Lee et al. (1977); Leonardo et al. (1999); MacDonell & Colwell (1985); Makemson et al. (1997); Myers & Nealson (1988); Nogi et al. (1998); Nozue et al. (1992); Rossello-Mora et al. (1994); Satomi et al. (2003); Simidu et al. (1990); Skerratt et al. (2002); Toffin et al. (2004); Venkateswaran et al. (1998b, 1999); Vogel et al. (1997); Weiner et al. (1985, 1988); Yoon et al. (2004a, b); Zhao et al. (2004b); Ziemke et al. (1998). The phenotypic properties of strain HAW-EB3T are from the present study.

    Using a protocol described previously by Bowman (2001) and Fay & Richli (1991), cellular fatty acids were extracted from cells (pre-grown in marine broth 2216 at 10 °C for 5 days) and analysed from their methyl esters or 2-alkenyl-4,4-dimethyloxazoline-derivatives on a GC-MS system composed of a HP5-MS capillary column (50 m) and a MS detector (6890 MSD 5973, Agilent Technologies). A standard mixture of bacterial fatty acid methyl esters (CP Mix; Matreya) was used as a reference. Fatty acids found in HAW-EB3T were similar to those of Shewanella species in cluster I (Fig. 2⇑; Table 2⇓; Russell & Nichols, 1999). Like S. gelidimarina, S. benthica and S. hanedai (Bowman et al., 1997; Satomi et al., 2003; Brettar et al., 2002), strain HAW-EB3T produced unsaturated palmitoleic acid C16 : 1ω7 (33 %) and saturated palmitoleic acid C16 : 0 (17 %) as major acids. HAW-EB3T also produced eicosapentaenoic acid (C20 : 5ω3) as found in most species of Shewanella in cluster I (Fig. 2⇑).

    Table 2.

    Fatty acid compositions of Shewanella species

    Each fatty acid methyl ester of strain HAW-EB3T was quantified based on the peak area of its total ion chromatogram MS spectra scanned between 45 and 500 Da relative to those of all fatty acid methyl esters found.

    In the present study we analysed the quinone compositions of strain HAW-EB3T and two related Shewanella species for comparison: S. woodyi ATCC 51908T (grown in marine broth 2216 at 21 °C; Makemson et al., 1997) and S. hanedai ATCC 33224T (grown in Photobacterium broth at 10 °C; Jensen et al., 1980) purchased from the American Type Culture Collection. Briefly, quinones extracted using the method described by Collins (1985), were identified by their UV spectra (Collins, 1994) of chromatographic peaks obtained on a Waters HPLC-UV system (Discovery C18 column, 25 cm×4·6 mm×5 μm, Supelco; 70 % methanol/30 % acetonitrile at rate of 1·5 ml min−1; 40 °C; 2996 photodiode array UV detector) and by their mass spectra (Nishijima et al., 1997; Akagawa-Matsushita et al., 1992) obtained on a LC/UV-MS system (Platform LC fronted with Agilent 1100 Micromass). Menaquinone (MK)-4 (6H) (vitamin K1), MK-4 (vitamin K2), ubiquinone (Q)-6 and -10 (Aldrich) were used as standards. Strain HAW-EB3T produced (A273, relative to the sum of total quinones) Q-7 (33·7 %), Q-8 (13·5 %), MK-7 (48·6 %) and methylmenaquinone (MMK)-7 (4·2 %), consistent with quinone profiles previously reported for Shewanella species (Akagawa-Matsushita et al., 1992; Venkateswaran et al., 1999; Bozal et al., 2002) and those of S. woodyi (Q-7, 53·3 %; Q-8, 34·5 %; MK-7, 9·2 %; MMK-7, 2·9 %) and S. hanedai (Q-7, 11 %; Q-8, 24 %; MK-7, 56 %; MMK-7, 9 %) obtained in the present study (Supplementary Table, available in IJSEM Online).

    DNA extraction, amplification and sequencing were conducted according to standard molecular biology methods (Sambrook & Russell, 2001). The universal primers described previously by Yoon et al. (1998) were used for amplification of the 16S rRNA gene. The 16S rRNA gene (1288 bases) sequence was compared to published sequences using blast. The gene sequences of the isolate and those of closely related species were aligned using clustal_x (1.81). The neighbour-joining method (in the mega2 package; Kumar et al., 2001), based on the pair-wise nucleotide distance of the Kimura two-parameter, was used to build the phylogenetic tree. The number of bootstrap repetitions was 4000.

    Phylogenetic analysis of the 16S rRNA gene sequences of strain HAW-EB3T and known species of Shewanella clearly showed that strain HAW-EB3T belonged to the Shewanella genus (Fig. 3⇓). The 16S rRNA gene sequence cluster analysis separated all species of Shewanella into two clusters (I′ and II′; Fig. 3⇓) similar to those obtained by phenotypic analysis (Fig. 2⇑). Cluster I′ contained mainly Na+-requiring species (13 out of 16) whereas cluster II′ contained mainly non-Na+-requiring species (10 out of 13). The isolate HAW-EB3T 16S rRNA gene sequence displayed ⩽97·4 % similarity to those of the known Shewanella species and was found to best match those in cluster I′.

    Figure image not available in archive
    Fig. 3.

    Phylogenetic tree of 16S rRNA gene of type strains of Shewanella species and strain HAW-EB3T. The phylogenetic tree was generated based on the pair-wise nucleotide distance of the Kimura two-parameter using the neighbour-joining method (pair-wise deletion) included in the mega2 software package (Kumar et al., 2001). The bar indicates the difference of 1 nucleotide per 100. The numbers beside the nodes are the statistical bootstrap values (values lower than 50 are not shown).

    According to 16S rRNA gene sequence, two bioluminescent marine bacteria S. hanedai and S. woodyi of cluster I′ were phylogenetically most related to strain HAW-EB3T, with similarities of 96·4 % and 97·4 %, respectively. As reported by Stackebrandt & Goebel (1994), strains sharing less than 97·5 % 16S rRNA gene similarity are unlikely to belong to the same species. Therefore strain HAW-EB3T was not likely to be a strain belonging to S. hanedai or S. woodyi, but rather possibly represented a new species.

    The sequence of gyrB (coding the β-unit of DNA topoisomerase II) has been used to differentiate species similar in their 16S rRNA genes sequences (Fox et al., 1992; Stackebrandt & Goebel, 1994). To further differentiate strain HAW-EB3T from related Shewanella species, we also sequenced gyrB (1007 bases) of strain HAW-EB3T using previously described universal primers (Yamamoto & Harayama, 1995; Venkateswaran et al., 1998a), and compared its sequence with those of other Shewanella species (Fig. 4⇓). The gyrB sequence similarity between HAW-EB3T and other species of Shewanella (S. hanedai, 82·7 %; S. woodyi, 85·4 %; S. gelidimarina, 79·6 %; S. benthica, 82·6 %) (Fig. 4⇓) was found to be lower than the 90 % species cut-off value proposed by Venkateswaran et al. (1999) for Shewanella. We also found that the similarity of gyrB between species of Shewanella ranged from 60 % to 90 %, with the exception of S. marinintestina and S. sairae, which were 92·2 % similar (Fig. 4⇓). The sequence data on gyrB further supported that HAW-EB3T represented a new species of Shewanella.

    Figure image not available in archive
    Fig. 4.

    Phylogenetic tree of gyrB of Shewanella species and strain HAW-EB3T. The phylogenetic tree was generated based on pair-wise nucleotide distance of Kimura two-parameter using the neighbour-joining method (pair-wise deletion) included in mega2 software package. The bar indicates the difference of 5 nucleotides per 100. The numbers beside the nodes are the statistical bootstrap values (values lower than 50 are not shown).

    Marmur's procedure (Johnson, 1994) was used to prepare and purify genomic DNA (1–5 mg) for DNA–DNA hybridization and G+C content measurement. DNA–DNA hybridization was determined based on the spectrophotometric measurement of renaturation rates as described by Johnson (1985b) and Bowman et al. (1998). As defined by Wayne et al. (1987), a species only includes those strains with approximately 70 % or greater genomic DNA–DNA relatedness. In the present study we found that the genomic DNA of strain HAW-EB3T was less than 70 % related to that of S. hanedai (with 25 % DNA relatedness) and S. woodyi (with 17·8 % DNA relatedness) (n=5), confirming that it represents a new species of Shewanella. The genetic finding was also consistent with the significant phenotypic difference between strain HAW-EB3T and the two known bioluminescent species, S. hanedai and S. woodyi (Table 1⇑).

    According to the UV absorbance (A269/A280) at pH 3·0 and the thermal melting profile (Tm) of genomic DNA as described by Johnson (1985a), the G+C content of HAW-EB3T was found to be 45 mol%, consistent with the reported values for other species of Shewanella (39–53 %) (Table 1⇑).

    Based on the previous discussions of phenotypic, chemotaxonomic (fatty acid and quinone compositions) and genetic data (Gillis et al., 2001), we propose that HAW-EB3T represents a new species of Shewanella, designated Shewanella sediminis sp. nov.

    Description of Shewanella sediminis sp. nov.

    Shewanella sediminis (se.di.mi′nis. L. gen. n. sediminis of sediment, the source of the type strain).

    Gram-negative, motile, non-spore-forming rods with mean length of 1·7 μm and mean diameter of 0·7 μm. Single flagellum is found at polar position. Biomass is slightly pinkish and non-bioluminescent. Growth at temperatures ranging from 4 to 25 °C, with 10 °C as optimum. No growth at 30 °C. Na+ is required for growth. Growth at 1–4 % NaCl, with 2 % NaCl as optimum, but no growth at 5 % NaCl. Anaerobic growth on Brewer's anaerobic agar supplemented with 2 % NaCl. TMAO, MnO2, nitrate, nitrite, thiosulfate and RDX are reduced. Negative for reduction of Fe(III) and elemental sulfur. Casein, chitin and DNA are hydrolysed, but not gelatin, alginate, starch and agar. Positive for catalase, oxidase, nitroreductase, arginine dehydrolase, ornithine decarboxylase, lysine decarboxylase, N-acetyl-β-d-glucosaminidase, β-galactosidase, β-galactosidase-6-phosphate, alkaline phosphatase, proline arylamidase, leucine glycine arylamidase, alanine arylamidase, and glutamyl glutamic acid arylamidase. Weakly positive for urease. Negative for β-glucosidase and p-nitrophenylalanine deaminase by API rapid test, and for α-galactosidase, α-glucosidase, β-glucosidase, α-arabinosidase, β-glucuronidase, mannose and raffinose fermentation, indole production, argine arylamidase, phenyl arylamidase, leucine arylamidase, pyroglutamic acid arylamidase, tyrosine arylamidase and glycine arylamidase by Rapid ID32 A test. H2S is produced from thiosulfate. By Biolog GN2 microplate test, positive for utilization of N-acetyl-d-glucosamine, acetate, methyl pyruvate, propionate, dl-lactate, l-alanine, l-aspartate, glycyl-l-aspartic acid, glycine-l-glutamic acid, l-alanine-glycine, inosine, uridine and thymidine; weakly positive for Tween 80, β-hydroxy butyrate, l-leucine and l-proline; negative for α-cyclodextrin, dextrin, glycogen, adonitol, l-arabinose, d-arabitol, i-erythritol, d-fucose, m-inositol, lactulose, d-melibiose, methyl β-d-glucoside, d-raffinose, l-rhamnose, d-trehalose, turanose, xylitol, succinic acid mono methyl ester, cis-aconitic acid, formic acid, d-galactonic acid lactone, d-galacturonic acid, d-glucosaminic acid, d-glucuronic acid, α- or γ-hydroxybutyric acid, p-hydroxy phenylacetic acid, itaconic acid, α-keto glutaric acid, α-ketovaleric acid, quinic acid, d-saccharic acid, sebacic acid, bromosuccinic acid, succinamic acid, glucuronamide, l-alaninamide, d-alanine, hydroxy-l-proline, l-ornithine, l-pyroglutamic acid, d-serine, dl-carnitine, γ-aminobutyric acid, urocanic acid, phenylethylamine, 2-aminoethanol, 2,3-butanediol, dl-α-glycerolphosphate, α-d-glucose 1-phosphate and d-glucose 6-phosphate. N-acetyl-d-glucosamine is oxidized and fermented to acid. Galactose, lactose, fructose, sucrose, mannose and glucose are not oxidized or fermented to acids. N-Acetyl-d-glucosamine, Tween 40, Tween 80, acetate, succinate, butyrate, valerate, pyruvate, serine, proline, peptone and yeast extract are sole carbon and energy sources. Tween 20, malate, propionate and glutamic acid are weak carbon sources. Galactose, lactose, fructose, sucrose, mannose, glucose, citrate, lactate, formate, phenol, glycine, leucine and threonine are not utilized. Fatty acids C12 : 0 3-OH (7 %), C13 : 0 3-OH (8 %), C14 : 0 (4 %), Ci15 : 0 (8 %), C16 : 0 (17 %), C16 : 1ω7 (33 %), C18 : 0 (2 %), C18 : 1ω7 (7 %) and C20 : 5ω3 (3 %) are produced. Quinone composition is Q-7 (33 %), Q-8 (13 %), MK-7 (49 %) and MMK-7 (4 %). The G+C content is 45 mol%.

    The type strain, HAW-EB3T (=NCIMB 14036T=DSM 17055T), was isolated from a site 215 m deep and 50 nautical miles from Halifax Harbour, in the Atlantic Ocean.

    Acknowledgments

    Financial support from the USA Navy Office of Naval Research (ONR) (Award N000140310269) is gratefully acknowledged. The authors would like to thank Sonia Thiboutot, Guy Ampleman and D. Faucher (Defense Research and Development Canada, Valcartier, Quebec, Canada) and K. Penny (Canadian Navy) for sampling sediment. Dr Edwin Wang is acknowledged for discussion of phenotypic cluster analyses. Mass spectral analysis of bacterial quinones was conducted by Annamaria Halasz. TEM and SEM electron micrographs were prepared by C. Leggiadro and D. O'Neil of the Institute of Marine Biosciences, National Research Council, Halifax, Nova Scotia, Canada. The authors would also like to thank Dr Jean Euzéby (École Nationale Vétérinaire, France) and Professor Jiri Tucker (McGill University, Canada) for advice on Latin nominations.

    References

    1. Akagawa-Matsushita, M., Itoh, T., Katayama, Y., Kuraishi, H. & Yamasato, K. (1992). Isoprenoid quinone composition of some marine Alteromonas, Marinomonas, Deleya, Pseudomonas and Shewanella species. J Gen Microbiol 138, 2275–2281.
    2. Beveridge, T. J., Popkin, T. J. & Cole, R. M. (1994). Electron microscopy. In Methods for General and Molecular Bacteriology, pp. 42–71. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
    3. Bowman, J. P. (2001). Methods for psychrophilic bacteria. In Methods in Microbiology, vol. 30, pp. 591–615. Edited by J. H. Paul. London: Academic Press.
    4. Bowman, J. P., McCammon, S. A., Nichols, D. S., Skerratt, J. H., Rea, S. M., Nichols, P. D. & McMeekin, T. A. (1997). Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov., novel Antarctic species with the ability to produce eicosapentaenoic acid (20 : 5ω3) and grow anaerobically by dissimilatory Fe(III) reduction. Int J Syst Bacteriol 47, 1040–1047.
    5. Bowman, J. P., McCammon, S. A., Lewis, T., Skerratt, J. H., Nichols, D. S. & McMeekin, T. A. (1998). Psychroflexus torquis gen. nov., sp. nov., a psychrophilic species from Antarctic sea ice, and reclassification of Flavobacterium gondwanense (Dobson et al. 1993) as Psychroflexus gondwanense gen. nov., comb. nov. Microbiology 144, 1601–1609.
    6. Bozal, N., Montes, M. J., Tudela, E., Jimenez, F. & Guinea, J. (2002). Shewanella frigidimarina and Shewanella livingstonensis sp. nov. isolated from Antarctic coastal areas. Int J Syst Evol Microbiol 52, 195–205.
    7. Brettar, I., Christen, R. & Hofle, M. G. (2002). Shewanella denitrificans sp. nov., a vigorously denitrifying bacterium isolated from the oxic-anoxic interface of the Gotland Deep in the central Baltic Sea. Int J Syst Evol Microbiol 52, 2211–2217.
    8. Collins, M. D. (1985). Analysis of isoprenoid quinones. Methods Microbiol 18, 325–366.
    9. Collins, M. D. (1994). Isoprenoid quinones. In Chemical Methods in Prokaryotic Systematics, pp. 265–309. Edited by M. Goodfellow & A. G. O'Donnell. Chichester: Wiley and Sons.
    10. Coyne, V. E., Pillidge, C. J., Sledjeski, D. D., Hori, H., Ortiz-Conde, B. A., Muir, D. G., Weiner, R. M. & Colwell, R. R. (1989). Reclassification of Alteromonas colwelliana to the genus Shewanella by DNA-DNA hybridization, serology and 5S ribosomal RNA sequence data. Syst Appl Microbiol 12, 275–279.
    11. Deming, J. W., Hada, H., Colwell, R. R., Luehrsen, K. R. & Fox, G. E. (1984). The ribonucleotide sequence of 5S rRNA from two strain of deep-sea barophilic bacteria. J Gen Microbiol 130, 1911–1920.
    12. Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95, 14863–14868.
    13. Fay, L. & Richli, U. (1991). Location of double bonds in polyunsaturated fatty acids by gas chromatography-mass spectrometry after 4,4-dimethyloxazoline derivatization. J Chromatogr 541, 89–98.
    14. Fox, G. E., Wisotzkey, J. D. & Jurtshuk, P., Jr (1992). How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42, 166–170.
    15. Gillis, M., Vandamme, P., De Vos, P., Swings, J. & Kersters, K. (2001). Polyphasic taxonomy. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, pp. 43–48. Edited by D. R. Boone & R. W. Castenholz. New York: Springer.
    16. Ivanova, E. P., Sawabe, T., Gorshkova, N. M., Svetashev, V. I., Mikhailov, V. V., Nicolau, D. V. & Christen, R. (2001). Shewanella japonica sp. nov. Int J Syst Evol Microbiol 51, 1027–1033.
    17. Ivanova, E. P., Nedashkovskaya, O. I., Zhukova, N. V., Nicolau, D. V., Christen, R. & Mikhailov, V. V. (2003a). Shewanella waksmanii sp. nov., isolated from a sipuncula (Phascolosoma japonicum). Int J Syst Evol Microbiol 53, 1471–1477.
    18. Ivanova, P. E., Sawabe, T., Hayashi, K., Gorshkova, N. M., Zhukova, N. V., Nedashkovskaya, N. V., Mikhailov, O. I., Nicolau, V. V. & Christen, R. (2003b). Shewanella fidelis sp. nov., isolated from sediments and sea water. Int J Syst Evol Microbiol 53, 577–582.
    19. Ivanova, E. P., Nedashkovskaya, O. I., Sawabe, T., Zhukova, N. V., Frolova, G. M., Nicolau, D. V., Mikhailov, V. V. & Bowman, J. P. (2004a). Shewanella affinis sp. nov., isolated from marine invertebrates. Int J Syst Evol Microbiol 54, 1089–1093.
    20. Ivanova, E. P., Gorshkova, N. M., Bowman, J. P., Lysenko, A. M., Zhukova, N. V., Sergeev, A. F., Mikhailov, V. V. & Nicolau, D. V. (2004b). Shewanella pacifica sp. nov., a polyunsaturated fatty acid-producing bacterium isolated from sea water. Int J Syst Evol Microbiol 54, 1083–1087.
    21. Ivanova, E. P., Flavier, S. & Christen, R. (2004c). Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov. Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int J Syst Evol Microbiol 54, 1773–1788.
    22. Jensen, M. J., Tebo, B. M., Baumann, P., Mandel, M. & Nealson, K. H. (1980). Characterization of Alteromonas hanedai (sp. nov.), a non-fermentative luminous species of marine origin. Curr Microbiol 3, 311–315.
    23. Johnson, J. L. (1985a). Determination of DNA base composition. Methods Microbiol 18, 23–24.
    24. Johnson, J. L. (1985b). DNA reassociation and RNA hybridisation of bacterial nucleic acids. Methods Microbiol 18, 33–74.
    25. Johnson, J. L. (1994). Similarity analysis of DNAs. In Methods for General and Molecular Bacteriology, pp. 655–682. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
    26. Kato, C., Li, L., Nogi, Y., Nakamura, Y., Tamaoka, J. & Horikoshi, K. (1998). Extremely barophilic bacteria isolated from the Mariana Trench, Challenger Deep, at a depth of 11,000 meters. Appl Environ Microbiol 64, 1510–1513.
    27. Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. (2001). mega2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245.
    28. Lee, J. V., Gibson, D. M. & Shewan, J. M. (1977). A numerical taxonomic study of some pseudomonas-like marine bacteria. J Gen Microbiol 98, 439–451.
    29. Leonardo, M. R., Moser, D. P., Barbieri, E., Brantner, C. A., MacGregor, B. J., Paster, B. J., Stackebrandt, E. & Nealson, K. H. (1999). Shewanella pealeana sp. nov., a member of the microbial community associated with the accessory nidamental gland of the squid Loligo pealei. Int J Syst Bacteriol 49, 1341–1351.
    30. Long, H. F. & Hammer, B. W. (1941). Classification of organisms important in dairy products. III. Pseudomonas putrefaciens. Iowa Agric Exp Stn Res Bull 285, 176–195.
    31. MacDonell, M. T. & Colwell, R. R. (1985). Phylogeny of the Vibrionaceae, and recommendation for two new genera, Listonella and Shewanella. Syst Appl Microbiol 6, 171–182.
    32. Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F. (1997). Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034–1039.
    33. Moser, D. P. & Nealson, K. H. (1996). Growth of the facultative anaerobic Shewanella putrefaciens by elemental sulfur reduction. Appl Environ Microbiol 62, 2100–2105.
    34. Myers, C. R. & Nealson, K. H. (1988). Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240, 1319–1321.
    35. Nishijima, M., Araki-Sakai, M. & Sano, H. (1997). Identification of isoprenoid quinones by frit-FAB liquid chromatography-mass spectrometry for the chemotaxonomy of microorganisms. J Microbiol Methods 28, 113–122.
    36. Nogi, Y., Kato, C. & Horikoshi, K. (1998). Taxonomic studies of deep-sea barophilic Shewanella strains and description of Shewanella violacea sp. nov. Arch Microbiol 170, 331–338.
    37. Nozue, H., Hayashi, T., Hashimoto, Y., Ezaki, T., Hamasaki, K., Ohwada, K. & Terawaki, Y. (1992). Isolation and characterization of Shewanella alga from human clinical specimens and emendation of the description of S. alga Simidu et al., 1990, 335. Int J Syst Bacteriol 42, 628–634.
    38. Petrovskis, E. A., Vogel, T. M. & Adriaens, P. (1994). Effects of electron acceptors and donors on transformation of tetrachloromethane by Shewanella putrefaciens MR-1. FEMS Microbiol Lett 121, 357–364.
    39. Rossello-Mora, R. A., Caccavo, J. R. F., Osterlehner, K. & 7 other authors (1994). Isolation and taxonomic characterization of a halotolerant, facultatively iron-reducing bacterium. Syst Appl Microbiol 17, 569–573.
    40. Russell, N. J. & Nichols, D. S. (1999). Polyunsaturated fatty acids in marine bacteria – a dogma rewritten. Microbiology 145, 767–779.
    41. Sambrook, J. & Russell, D. W. (2001). Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
    42. Satomi, M., Oikawa, H. & Yano, Y. (2003). Shewanella marinintestina sp. nov., Shewanella schlegeliana sp. nov. and Shewanella sairae sp. nov., novel eicosapentaenoic-acid-producing marine bacteria isolated from sea-animal intestines. Int J Syst Evol Microbiol 53, 491–499.
    43. Semple, K. M. & Westlake, D. W. S. (1987). Characterization of iron reducing Alteromonas putrefaciens strains from oil field fluids. Can J Microbiol 35, 925–931.
    44. Simidu, U., Kita-Tsukamoto, K., Yasumoto, T. & Yotsu, M. (1990). Taxonomy of four marine bacterial strains that produce tetrodotoxin. Int J Syst Bacteriol 40, 331–336.
    45. Skerratt, J. H., Bowman, J. P. & Nichols, P. D. (2002). Shewanella olleyana sp. nov., a marine species isolated from a temperate estuary which produces high levels of polyunsaturated fatty acids. Int J Syst Evol Microbiol 52, 2101–2106.
    46. Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
    47. Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846–849.
    48. Toffin, L., Bidault, A., Pignet, P., Tindall, B. J., Slobodkin, A., Kato, C. & Prieur, D. (2004). Shewanella profunda sp. nov., isolated from deep marine sediment of the Nankai Trough. Int J Syst Evol Microbiol 54, 1943–1949.
    49. Venkateswaran, K., Dohmoto, N. & Harayama, S. (1998a). Cloning and nucleotide sequence of the gyrB gene of Vibrio parahaemolyticus and its application in detection of this pathogen in shrimp. Appl Environ Microbiol 64, 681–687.
    50. Venkateswaran, K., Dollhopf, M. E., Aller, R., Stackebrandt, E. & Nealson, K. H. (1998b). Shewanella amazonensis sp. nov., a novel metal-reducing facultative anaerobe from Amazonian shelf muds. Int J Syst Bacteriol 48, 965–972.
    51. Venkateswaran, K., Moser, D. P., Dollhopf, M. E. & 10 other authors (1999). Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 49, 705–724.
    52. Vogel, B. F., Jørgensen, K., Christensen, H., Olsen, J. E. & Gram, L. (1997). Differentiation of Shewanella putrefaciens and Shewanella alga on the basis of whole-cell protein profiles, ribotyping, phenotypic characterization, and 16S rRNA gene sequence analysis. Appl Environ Microbiol 63, 2189–2199.
    53. Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.
    54. Weiner, R. M., Segall, A. M. & Colwell, R. R. (1985). Characterization of a marine bacterium associated with Crassostrea virginica (the Eastern Oyster). Appl Environ Microbiol 49, 83–90.
    55. Weiner, R. M., Coyne, V. E., Brayton, P., West, P. & Raiken, S. F. (1988). Alteromonas colwelliana sp. nov., an isolate from oyster habitats. Int J Syst Bacteriol 38, 240–244.
    56. Yamamoto, S. & Harayama, S. (1995). PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61, 1104–1109.
    57. Yoon, J. H., Lee, S. T. & Park, Y. H. (1998). Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int J Syst Bacteriol 48, 187–194.
    58. Yoon, J.-H., Kang, K.-H., Oh, T.-K. & Park, Y.-H. (2004a). Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea. Int J Syst Evol Microbiol 54, 487–491.
    59. Yoon, J. H., Yeo, S. H., Kim, I. G. & Oh, T. K. (2004b). Shewanella marisflavi sp. nov. and Shewanella aquimarina sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 54, 2347–2352.
    60. Zhao, J.-S., Paquet, L., Halasz, A. & Hawari, J. (2003). Metabolism of hexahydro-1,3,5-trinitro-1,3,5-triazine through initial reduction to hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine followed by denitration in Clostridium bifermentans HAW-1. Appl Microbiol Biotechnol 63, 187–193.
    61. Zhao, J.-S., Greer, C. W., Thiboutot, S., Ampleman, G. & Hawari, J. (2004a). Biodegradation of nitramine explosives hexahydro-1,3,5-trinitro-1,3,5-triazine and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine in cold marine sediment under anaerobic and oligotrophic conditions. Can J Microbiol 50, 91–96.
    62. Zhao, J.-S., Spain, J., Thiboutot, S., Ampleman, G., Greer, C. & Hawari, J. (2004b). Phylogeny of cyclic nitramine-degrading psychrophilic bacteria in marine sediment and their potential role in the natural attenuation of explosives. FEMS Microbiol Ecol 49, 349–357.
    63. Ziemke, F., Hofle, M. G., Lalucat, J. & Rossello-Mora, R. (1998). Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 48, 179–186.