Methylosulfonomonas methylovora gen. nov., sp. nov., and Marinosulfonomonas methylotropha gen. nov., sp. nov.: novel methylotrophs able to grow on methanesulfonic acid

Two novel genera of restricted facultative methylotrophs are described; both Methylosulfonomonas and Marinosulfonomonas are unique in being able to grow on methanesulfonic acid as their sole source of carbon and energy. Five identical strains of Methylosulfonomonas were isolated from diverse soil samples in England and were shown to differ in their morphology, physiology, DNA base composition, molecular genetics, and 16S rDNA sequences from the two marine strains of Marinosulfonomonas, which were isolated from British coastal waters. The marine strains were almost indistinguishable from each other and are considered to be strains of one species. Type species of each genus have been identified and named Methylosulfonomonas methylovora (strain M2) and Marinosulfonomonas methylotropha (strain PSCH4). Phylogenetic analysis using 16S rDNA sequencing places both genera in the α-Proteobacteria. Methylosulfonomonas is a discrete lineage within the α-2 subgroup and is not related closely to any other known bacterial genus. The Marinosulfonomonas strains form a monophyletic cluster in the α-3 subgroup of the Proteobacteria with Roseobacter spp. and some other partially characterized marine bacteria, but they are distinct from these at the genus level. This work shows that the isolation of bacteria with a unique biochemical character, the ability to grow on methanesulfonic acid as energy and carbon substrate, has resulted in the identification of two novel genera of methylotrophs that are unrelated to any other extant methylotroph genera. Received: 19 July 1996 / Accepted: 7 October 1996     

Methanohalophilus zhilinae sp. nov., an alkaliphilic, halophilic, methylotrophic methanogen

Methanohalophilus zhilinae, a new alkaliphilic, halophilic, methylotrophic species of methanogenic bacteria, is described. Strain WeN5T (T = type strain) from Bosa Lake of the Wadi el Natrun in Egypt was designated the type strain and was further characterized. This strain was nonmotile, able to catabolize dimethylsulfide, and able to grow in medium with a methyl group-containing substrate (such as methanol or trimethylamine) as the sole organic compound added. Sulfide (21 mM) inhibited cultures growing on trimethylamine. The antibiotic susceptibility pattern of strain WeN5T was typical of the pattern for archaeobacteria, and the guanine-plus-cytosine content of the deoxyribonucleic acid was 38 mol%. Characterization of the 16S ribosomal ribonucleic acid sequence indicated that strain WeN5T is phylogenetically distinct from members of previously described genera other than Methanohalophilus and supported the partition of halophilic methanogens into their own genus.     

Chlorobaculum macestae sp. nov., a new green sulfur bacterium

The investigated green sulfur bacterium, strain M, was isolated from a sulfidic spring on the Black Sea Coast of the Caucasus. The cells of strain M are straight or curved rods 0.6-0.9 x 1.8-4.2 microm in size. According to the cell wall structure, the bacteria are gram-negative. Chlorosomes are located along the cell periphery. Strain M is an obligate anaerobe capable of photoautotrophic growth on sulfide, thiosulfate, and H2. It utilizes ammonium, urea, casein hydrolysate, and N2 as nitrogen sources and sulfide, thiosulfate, and elemental sulfur as sulfur sources. Bacteriochlorophyll c and the carotenoid chlorobactene are the main pigments. The optimal growth temperature is 25-28 degrees C; the optimal pH is 6.8. The strain does not require NaCl. Vitamin B12 stimulates growth. The content of the G+C base pairs in the DNA of strain M is 58.3 mol %. In the phylogenetic tree constructed on the basis of analysis of nucleotide sequences of 16S rRNA genes, strain M forms a separate branch, which occupies an intermediate position between the phylogenetic cluster containing representatives of the genus Chlorobaculum (94.9-96.8%) and the cluster containing species of the genus Chlorobium (94.1-96.5%). According to the results of analysis of the amino acid sequence corresponding to the fmo gene, strain M represents a branch which, unlike that in the "ribosomal" tree, falls into the cluster of the genus Chlorobaculum (95.8-97.2%). Phylogenetic analysis of the amino acid sequence corresponding to the nifH gene placed species of the genera Chlorobaculum and Chlorobium into a single cluster, whereas strain M formed a separate branch. The results obtained allow us to describe strain M as a new species of the genus Chlorobaculum. Chlorobaculum macestae sp. nov.     

Oxalobacter formigenes gen. nov., sp. nov.: oxalate-degrading anaerobes that inhabit the gastrointestinal tract

This report describes a new group of anaerobic bacteria that degrade oxalic acid. The new genus and species, Oxalobacter formigenes, are inhabitants of the rumen and also of the large bowel of man and other animals where their actions in destruction of oxalic acid may be of considerable importance to the host. Isolates from the rumen of a sheep, the cecum of a pig, and from human feces were all similar Gram-negative, obligately anaerobic rods, but differences between isolates in cellular fatty acid composition and in serologic reaction were noted. Measurements made with type strain OxB indicated that 1 mol of protons was consumed per mol of oxalate degraded to produce approximately 1 mol of CO₂ and 0.9 mol of formate. Substances that replaced oxalate as a growth substrate were not found.     

Natrarchaeobius chitinivorans gen. nov., sp. nov., and Natrarchaeobius halalkaliphilus sp. nov., alkaliphilic,chitin-utilizing haloarchaea from hypersaline alkaline lakes

Two groups of alkaliphilic haloarchaea from hypersaline alkaline lakes in Central Asia, Egypt and North America were enriched and isolated in pure culture using chitin as growth substrate. These cultures, termed AArcht, were divided into two groups: group 1 which includes eleven isolates from highly alkaline soda lakes and group 2 which contains a single isolate obtained from the alkaline hypersaline Searles Lake. The colonies of chitin-utilizing natronoarchaea were red-pigmented and surrounded by large zones of chitin hydrolysis. The free cells of both groups were mostly flat nonmotile rods, while the cells that attached to chitin or formed colonies on chitin plates were mostly coccoid. The isolates are obligate aerobic saccharolytic archaea utilizing chitin and chitosane (less actively) as the only sugar polymers as well as a few hexoses as their carbon and energy source. Both groups are extremely halophilic, growing optimally at 3.5–4 M total Na⁺, but they differ in their pH profiles: the main group 1 isolates are obligately alkaliphilic, while the single group 2 strain (AArcht-Sl^T) is alkalitolerant. The core archaeal lipids in both groups are dominated by C₂₀–C₂₀ and C₂₀–C₂₅ dialkyl glycerol ethers (DGE) in approximately equal proportion. Phylogenetic analysis indicated that the isolates form an independent genus-level lineage within the family Natrialbaceae with 3 species-level subgroups. The available genomes of the closest cultured relatives of the AArcht strains, belonging to the genera Natrialba and Halopiger, do not encode any chitinase-related genes. On the basis of their unique phenotypic properties and distinct phylogeny, we suggest that the obligate alkaliphilic AArcht isolates (group 1) with an identical phenotype are classified into a new genus and species Natrarchaeobius chitinivorans gen. nov., sp. nov., with strain AArcht4^T as the type strain (JCM 32476^T = UNIQEM U966^T), while the facultatively alkaliphilic strain AArcht-Sl^T (group 2) — as a new species Natrarchaeobius halalkaliphilus sp. nov. (JCM 32477^T = UNIQEM U969^T).     

Aquabacter spiritensis,gen. nov., sp. nov. an aerobic,gas-vacuolate aquatic bacterium

A gram-negative, rod-shaped, gas-vacuolate, aerobic, heterotrophic bacterium was isolated from Spirit Lake, Washington. It was further characterized by phase-contrast and electron microscopy and phenotypic tests. The isolate does not utilize carbohydrates. Deoxyribonucleic acid-ribosomal ribonucleic acid (rRNA) hybridizations showed that this bacterium is a member of rRNA superfamily IV where it occupies a separate position on the Azorhizobium caulinodans rRNA sub-branch which, is part of an rRNA cluster containing also the Beijerinckia, the Bradyrhizobium japonicum and the Rhodopseudomonas palustris sub-branches. Its relationship to other gas-vacuolated genera within rRNA superfamily IV is discussed. A new genus Aquabacter with one species Aquabacter spiritensis is proposed. The type strain is strain SPL-1 (=ATCC 43981=LMG 8611).     

Fermentation of trihydroxybenzenes by Pelobacter acidigallici gen. nov. sp. nov., a new strictly anaerobic,non-sporeforming bacterium

Five strains of rod-shaped, Gram-negative, non-sporing, strictly anaerobic bacteria were isolated from limnic and marine mud samples with gallic acid or phloroglucinol as sole substrate. All strains grew in defined mineral media without any growth factors; marine isolates required salt concentrations higher than 1% for growth, two freshwater strains only thrived in freshwater medium. Gallic acid, pyrogallol, 2,4,6-trihydroxybenzoic acid, and phloroglucinol were the only substrates utilized and were fermented stoichiometrically to 3 mol acetate (and 1 mol CO₂) per mol with a growth yield of 10g cell dry weight per mol of substrate. Neither sulfate, sulfur, nor nitrate were reduced. The DNA base ratio was 51.8% guanine plus cytosine. A marine isolate, Ma Gal 2, is described as type strain of a new genus and species, Pelobacter acidigallici gen. nov. sp. nov., in the family Bacteroidaceae. In coculture with Acetobacterium woodii, the new isolates converted also syringic acid completely to acetate. Cocultures with Methanosarcina barkeri converted the respective substrates completely to methane and carbon dioxide.     

Thermodesulfobacterium hveragerdense sp. nov., and Thermodesulfovibrio islandicus sp. nov., two thermophilic sulfate reducing bacteria isolated from a Icelandic hot spring

Two thermophilic non-sporeforming sulfate-reducing bacteria (SRB) were isolated from microbial mats collected from an Icelandic hot spring. Strain JSP was a gram negative rod, with an average cell size of 2.8 x 0.5 microm. No flagella were found. Growth occurred between 55 and 74 degrees C with an optimum between 70 and 74 degrees C at pH 7.0. The G+C content was 40 mol%. Strain R1Ha3 was a gram negative vibrio-shaped rod with an average cell size of 1.7 x 0.4 microm. Motility was observed mediated by one polar flagellum. The growth optimum at pH 7.0 was 65 degrees C, and growth occurred between 45 and 70 degrees C. The G+C content was 38 mol%. In the presence of sulfate, both strains used lactate, pyruvate and H2 as electron donors. In addition, strain R1Ha3 used formate. Pyruvate was the only substrate supporting fermentative growth of both strains. Growth occurred with sulfate as well as thiosulfate as electron acceptors. Furthermore, strain R1Ha3 reduced nitrate and strain JSP reduced sulfite. Neither of the strains were able to oxidize lactate completely to CO2 and neither of the strains contained desulfoviridin. 16S rDNA sequencing placed strain JSP in the genus Thermodesulfobacterium and strain R1Ha3 in the genus Thermodesulfovibrio. Based on the DNA-DNA hybridization studies and differences in morphology and physiology to their closest relatives the two new isolates were considered as new species. Strain JSP is named Thermodesulfobacterium hveragerdense and strain R1Ha3 Thermodesulfovibrio islandicus.     

Malonomonas rubra gen. nov. sp. nov., a microaerotolerant anaerobic bacterium growing by decarboxylation of malonate

From anoxic marine sediment samples, new anaerobic, microaerotolerant, Gram-negative, non-sporeforming bacteria were isolated which grew in mineral medium with malonate as sole source of carbon and energy. Cells were motile thin rods, often forming large aggregates. Malonate was decarboxylated to acetate with concomitant growth yields of 1.9–2.1 g dry cell matter per mol malonate degraded. Fumarate and malate were fermented to succinate and CO₂. No other substrates were used. No inorganic electron acceptors were reduced. At least 150 mM NaCl was required for growth with either substrate. High amounts of a periplasmic cytochrome c were detected, as well as small amounts of a membrane-bound cytochrome b. All enzymes of the citric acid cycle were found to be present. The DNA base ratio was 48.3 mol% guanine plus cytosine. Since this new bacterium cannot be affiliated with any of the known genera and species, a new genus and species, Malonomonas rubra is proposed.     

Granulosicoccaceae fam. nov., to include Granulosicoccus antarcticus gen. nov., sp. nov., a non-phototrophic, obligately aerobic chemoheterotroph in the order Chromatiales, isolated from Antarctic seawater

A Gram-negative, motile by tuft flagella, obligately aerobic chemoorganoheterotrophic, sphere-form bacterium, designated IMCC3135(T), was isolated from the Antarctic surface seawater of King George Island, West Antarctica. The strain was mesophilic, neutrophilic, and requiring NaCl for growth, but neither halophilic nor halotolerant. The 16S rRNA gene sequence analysis indicated that the strain was most closely related to genera of the order Chromatiales in the class Gammaproteobacteria. The most closely related genera showed less than 90% 16S rRNA gene sequence similarity and included Thioalkalispira (89.9%), Thioalkalivibrio (88.0%-89.5%), Ectothiorhodospira (87.9%-89.3%), Chromatium (88.3%-88.9%), and Lamprocystis (87.7%-88.9%), which represent three different families of the order Chromatiales. Phylogenetic analyses showed that this Antarctic strain represented a distinct phylogenetic lineage in the order Chromatiales and could not be assigned to any of the defined families in the order. Phenotypic characteristics, including primarily non-phototrophic, non-alkaliphilic, non-halophilic, and obligately aerobic chemoheterotrophic properties, differentiated the strain from other related genera. The very low sequence similarities (<90%) and distant relationships between the strain and members of the order suggested that the strain merited classification as a novel genus within a novel family in the order Chromatiales. On the basis of these taxonomic traits, a novel genus and species is proposed, Granulosicoccus antarcticus gen. nov., sp. nov., in a new family Granulosicoccaceae fam. nov. Strain IMCC3135(T) (=KCCM 42676(T)=NBRC 102684(T)) is the type strain of Granulosicoccus antarcticus.     

Selenihalanaerobacter shriftii gen. nov., sp. nov., a halophilic anaerobe from Dead Sea sediments that respires selenate

We isolated an obligately anaerobic halophilic bacterium from the Dead Sea that grew by respiration of selenate. The isolate, designated strain DSSe-1, was a gram-negative, non-motile rod. It oxidized glycerol or glucose to acetate + CO2 with concomitant reduction of selenate to selenite plus elemental selenium. Other electron acceptors that supported anaerobic growth on glycerol were nitrate and trimethylamine-N-oxide; nitrite, arsenate, fumarate, dimethylsulfoxide, thiosulfate, elemental sulfur, sulfite or sulfate could not serve as electron acceptors. Growth on glycerol in the presence of nitrate occurred over a salinity range from 100 to 240 g/l, with an optimum at 210 g/l. Analysis of the 16S rRNA gene sequence suggests that strain DSSe-1 belongs to the order Halanaerobiales, an order of halophilic anaerobes with a fermentative or homoacetogenic metabolism, in which anaerobic respiratory metabolism has never been documented. The highest 16S rRNA sequence similarity (90%) was found with Acetohalobium arabaticum (X89077). On the basis of physiological properties as well as the relatively low homology of 16S rRNA from strain DSSe-1 with known genera, classification in a new genus within the order Halanaerobiales, family Halobacteroidaceae is warranted. We propose the name Selenihalanaerobacter shriftii. Type strain is strain DSSe-1 (ATCC accession number BAA-73).     

Lihuaxuella thermophila gen. nov., sp. nov., isolated from a geothermal soil sample in Tengchong, Yunnan, south-west China

A novel filamentous bacterium, designated YIM 77831^T, was isolated from a geothermal soil sample collected at Rehai National Park, Tengchong, Yunnan province, south-west China. Growth occurred from 28 to 65 °C (optimum 50 °C), pH 6.0–8.0 (optimum pH 7.0). The strain formed branched substrate mycelia, endospores were produced on the substrate mycelium and aerial mycelium was not produced on any of the growth media tested. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YIM 77831^T was affiliated with the family Thermoactinomycetaceae. The stain YIM 77831^T contained meso-diaminopimelic acid in the cell wall. Whole-cell hydrolysates contained glucose, galactose, mannose, ribose and rhamnose. The polar lipids were phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid and four unknown phospholipids. The only menaquinone was MK-7. Major fatty acids were iso-C_15:0, anteiso-C_15:0 and anteiso-C_17:0. The G+C content was 55.6 mol%. On the basis of the morphological and chemotaxonomic characteristics as well as genotypic data, strain YIM 77831^T represents a novel genus and species, Lihuaxuella thermophila gen. nov., sp. nov., in the family Thermoactinomycetaceae. The type strain is YIM 77831^T (CCTCC AA 2011024^T = JCM 18059^T).     

Three new species of the genus Peptostreptococcus isolated from humans: Peptostreptococcus vaginalis sp. nov., Peptostreptococcus lacrimalis sp. nov., and Peptostreptococcus lactolyticus sp. nov.

We describe three new species of the genus Peptostreptococcus which were isolated from human specimens and were tentatively identified as Peptostreptococcus prevotii. These three organisms were not homologous with previously described type strains of the genus Peptostreptococcus. A total of 12 strains that were identified biochemically as P. prevotii were divided into five independent DNA similarity groups; 10 of these strains were divided into three similarity groups which exhibited significant phenotypic differences from previously described species. Therefore, we propose the following new species: Peptostreptococcus vaginalis for group 1 strains, Peptostreptococcus lacrimalis for group 2 strains, and Peptostreptococcus lactolyticus for group 3 strains. The type strain of P. vaginalis is strain GIFU 12669 (= JCM 8138), the type strain of P. lacrimalis is strain GIFU 7667 (= JCM 8139), and the type strain of P. lactolyticus is strain GIFU 8586 (= JCM 8140).     

Rhodovarius lipocyclicus gen. nov. sp. nov., a new genus of the alpha-1 subclass of the Proteobacteria

A bacterial strain (CCUG 44693T) was recovered during an industrial hygiene control. Phylogenetic analyses using the 16S rRNA gene sequence of the isolate indicated that it represents a new lineage in the alpha-1 subclass of the Proteobacteria, with the highest sequence similarity of 93.3% to the type strain of Muricoccus roseus. In the polyamine pattern spermidine was the predominant compound. The polar lipid profile consisted of the major lipids phosphatidyl ethanolamine, phosphatidyl dimethylethanolamine, phosphatidyl glycerol, phosphatidyl cholin and an unknown amino lipid. The major respiratory quinone was a ubiquinone Q-10 and the major whole cell fatty acids were 19:0 cyclo omega8c and 18:1 omega7c. The isolate also contained 18:1 2-OH and other fatty acids typical for members of the alpha-1 subclass of the Proteobacteria in addition to 10:0 2-OH in low amounts, not detected in members of closely related genera. The strain grew heterotrophically and strictly aerobically and formed red-colored colonies on tryptone soy agar. Bacteriochlorophyll a could not be detected by direct spectrophotometric analyses of aerobically grown cells. On the basis of the phylogenetic analyses, chemotaxonomic and biochemical characteristics, we propose that strain CCUG 44693T (CIP 108310T) represents a new genus of the alpha-1 subclass of the Proteobacteria for which we propose the name Rhodovarius lipocyclicus gen. nov. sp. nov.     

Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium

Five strains were isolated which form a physiologically and phylogenetically coherent group of chlororespiring microorganisms and represent the first taxon in the Myxobacteria capable of anaerobic growth. The strains were enriched and isolated from various soils and sediments based on their ability to grow using acetate as an electron donor and 2-chlorophenol (2-CPh) as an electron acceptor. They are slender gram-negative rods with a bright red pigmentation that exhibit gliding motility and form spore-like structures. These unique chlororespiring myxobacteria also grow with 2,6-dichlorophenol, 2,5-dichlorophenol, 2-bromophenol, nitrate, fumarate, and oxygen as terminal electron acceptors, with optimal growth occurring at low concentrations (<1 mM) of electron acceptor. 2-CPh is reduced by all strains as an electron acceptor in preference to nitrate, which is reduced to ammonium. Acetate, H(2), succinate, pyruvate, formate, and lactate were used as electron donors. None of the strains grew by fermentation. The 16S ribosomal DNA (rDNA) sequences of the five strains form a coherent cluster deeply branching within the family Myxococcaceae within the class Myxobacteria and are mostly closely associated with the Myxococcus subgroup. With the exception of anaerobic growth and lack of a characteristic fruiting body, these strains closely resemble previously characterized myxobacteria and therefore should be considered part of the Myxococcus subgroup. The anaerobic growth and 9.0% difference in 16S rDNA sequence from those of other myxobacterial genera are sufficient to place these strains in a new genus and species designated Anaeromyxobacter dehalogenans. The type strain is 2CP-1 (ATCC BAA-258).     

Clostridium grantii sp. nov., a new obligately anaerobic,alginolytic bacterium isolated from mullet gut

A gram-positive, motile, rod-shaped, strictly anaerobic, sporulating bacterium was isolated from an enrichment initiated with mullet gut contents. The organism grew optimally at 30°C and pH6.5, and at a salinity of 1–10³. Out of a variety of polysaccharides tested as growth substrates, only alginate supported growth in either semidefined or complex culture medium. The organism also grew on a variety of mono- and disaccharides. Moles product per 100mol of alginate monomer degraded were: acetate, 186; ethanol, 19; formate, 54; and CO₂, 0.19. Moles product per 100mol of hexose in cellobiose or glucose degraded were: acetate, 135; ethanol,61; formate, 63: and CO₂, 61. Hydrogen was not detectable during the incubations (detection limit, <10^-5atm) and propionate, butyrate, lactate, or succinate were not produced as fermentation end products (<2 mol per 100 mol of monomer). The G+C content of DNA from the bacterium was 30.2±0.3 mol%, and the cell walls contained the peptidoglycan component meso-diaminopimelic acid. A phylogenetic analysis of the 16S rDNA sequence indicated that the organism grouped closely with members of the RNA-DNA homology group 1 of the genus Clostridium. However, it differed from other species of the genus with regard to morphology, growth temperature optimum, substrate range, and fermentation pattern and is therefore designated as a new species of Clostridium; the type strain is A-1 (DSM 8605).     

Description of the novel perchlorate-reducing bacteria Dechlorobacter hydrogenophilus gen. nov., sp. nov. and Propionivibrio militaris, sp. nov.

Novel dissimilatory perchlorate-reducing bacteria (DPRB) were isolated from enrichments conducted under conditions different from those of all previously described DPRB. Strain LT-1^T was enriched using medium buffered at pH 6.6 with 2-(N-morpholino)ethanesulfonic acid (MES) and had only 95% 16S rRNA gene identity with its closest relative, Azonexus caeni. Strain MP^T was enriched in the cathodic chamber of a perchlorate-reducing bioelectrical reactor (BER) and together with an additional strain, CR (99% 16S rRNA gene identity), had 97% 16S rRNA gene identity with Propionivibrio limicola. The use of perchlorate and other electron acceptors distinguished strains MP^T and CR from P. limicola physiologically. Strain LT-1^T had differences in electron donor utilization and optimum growth temperatures from A. caeni. Strains LT-1^T and MP^T are the first DPRB to be described in the Betaproteobacteria outside of the Dechloromonas and Azospira genera. On the basis of phylogenetic and physiological features, strain LT-1^T represents a novel genus in the Rhodocyclaceae; strain MP^T represents a novel species within the genus Propionivibrio. The names Dechlorobacter hydrogenophilus gen. nov., sp. nov and Propionivibrio militaris sp. nov. are proposed.