Ectothiorhodosinus mongolicum gen. nov., sp. nov.,--a new purple sulfur bacterium from soda lake in Mongolia

A new purple sulfur bacterium (strain M9) was isolated from the steppe soda Lake Dzun Uldziin Nur (pH 9.4; mineralization, 3.3%) situated in southeastern Mongolia. Individual cells appear as vibrios 0.3-0.5 x 0.7-1 micron in size. The dividing cells often do not separate from each other, forming an almost closed ring. The internal photosynthetic membranes are represented by concentric lamellae lining the cell wall. Photosynthetic pigments are bacteriochlorophyll a and carotenoids of the spirilloxanthin series. The main carotenoid (> 96%) is spirilloxanthin. Two typical light-harvesting complexes (LH1 and LH2) are present in the membranes in a 1:1 ratio. The bacterium is an anaerobe and facultative photoorganoheterotroph. Photolithoautotrophic growth on sulfide is scarce. Thiosulfate is utilized as an electron donor only in the presence of organic matter. Globules of elemental sulfur are formed as an intermediary product of sulfide and thiosulfate oxidation and are deposited outside the cells. The end product of oxidation is sulfate. In the presence of sulfide and carbonates, acetate, lactate, malate, pyruvate, propionate, succinate, and fumarate are used as the additional sources of carbon in anoxygenic photosynthesis. Vitamin are not required. The bacterium is an alkaliphile the pH optimum is at 8.3-9.1, the pH range is 7.6-10.1. The optimum NaCl concentration in the medium is 1 to 7%; the range is 0.5 to 0.9%. The optimum carbonate content in the medium is 2%; the range is 1 to 10%. The best growth occurs at 30-35 degrees C. The DNA G + C content is 57.5 mol%. According to the results of analysis of the 16S rRNA gene sequences, the new isolate M9 belongs to the phylogenetic cluster containing representatives of the family Ectothiorhodospiraceae within the class "Gammaproteobacteria." In this class, the new isolate forms a new branch, which occupies an intermediate position between the representatives of the genera Ectothiorhodospira and Thiorhodospira. Based on the phenotypic and genetic characteristics, the new purple sulfurbacterium was assigned to a new species of a new genus of the family Ectothiorhodospiraceae, Ectothiorhodosinus mongolicum gen. nov., sp. nov.     

Desulfosporomusa polytropa gen. nov., sp. nov., a novel sulfate-reducing bacterium from sediments of an oligotrophic lake

Five strains of sulfate-reducing bacteria were isolated from the highest positive dilutions of a most probable number (MPN) series supplemented with lactate and inoculated with sediments from the oligotrophic Lake Stechlin. The isolates were endospore-forming and were motile by means of laterally inserted flagella. They stained Gram-negative and contained b-type cytochromes. CO difference spectra indicated the presence of P582 as a sulfite reductase. Phylogenetic analyses of the 16S rDNA sequences revealed that the isolates were very closely affiliated with the genus Sporomusa. However, sulfate and amorphous Fe(OH)₃, but not sulfite, elemental sulfur, MnO₂, or nitrate were used as terminal electron acceptors. Homoacetogenic growth was found with H₂/CO₂ gas mixture, formate, methanol, ethanol, and methoxylated aromatic compounds. The strains grew autotrophically with H₂ plus CO₂ in the presence or absence of sulfate. Formate, butyrate, several alcohols, organic acids, carbohydrates, some amino acids, choline, and betaine were also utilized as substrates. The growth yield with lactate and sulfate as substrate was 7.0 g dry mass/mol lactate and thus two times higher than in sulfate-free fermenting cultures. All isolates were able to grow in a temperature range of 4–37°C. Physiologically and by the presence of a Gram-negative cell wall, the new isolates resemble known Desulfosporosinus species. However, phylogenetically they are affiliated with the Gram-negative genus Sporomusa belonging to the Selenomonas subgroup of the Firmicutes. Therefore, the new isolates reveal a new phylogenetic lineage of sulfate-reducing bacteria. A new genus and species, Desulfosporomusa polytropa gen. nov., sp. nov. is proposed.Dedicated to Prof. H. G. Schlegel on the occasion of his 80th birthday.     

Geoalkalibacter ferrihydriticus gen. nov., sp. nov., the first alkaliphilic representative of the family Geobacteraceae, isolated from a soda lake

Investigation of iron reduction in bottom sediments of alkaline soda lakes resulted in the isolation of a new obligately anaerobic iron-reducing bacterium, strain Z-0531, from Lake Khadyn (Tuva Republic, Russia) sediment samples. The cells of strain Z-0531 are short (1.0-1.5 by 0.3-0.5 microm), motile, non-spore-forming, gram-negative rods. The isolate is an obligate alkaliphile, developing in the pH range of 7.8-10.0, with an optimum at pH 8.6. It does not require NaCl but grows at NaCl concentrations of 0-50 g/1l. It can oxidize acetate with such electron acceptors as amorphous Fe(llI) hydroxide (AFH), EDTA-Fe(III), anthraquinone-2,6-disulfonate (quinone), Mn(IV), and S(0). On media with EDTA-Fe(III), the isolate can oxidize, apart from acetate, ethanol, pyruvate, oxalate, arginine, tartrate, lactate, propionate, and serine. H2 is not utilized. The reduced products formed during growth with AFH are siderite or magnetite, depending on the growth conditions. The isolate is incapable of fermenting sugars, peptides, and amino acids. Yeast extract or vitamins are required as growth factors. The organism is capable of dinitrogen fixation and harbors the nifH gene. The DNA G+C content is 55.3 mol %. 16S rRNA analysis places strain Z-0531 into the family Geobacteraceae. Its closest relative (93% similarity) is Desulfuromonas palmitatis. Based on phenotypic distinctions and phylogenetic position, it is proposed that strain Z-0531 be assigned to the new genus and species Geoalkalibacter ferrihydriticus gen. nov., sp. nov.     

Alkaliflexus imshenetskii gen. nov. sp. nov., a new alkaliphilic gliding carbohydrate-fermenting bacterium with propionate formation from a soda lake

Anaerobic saccharolytic bacteria thriving at high pH values were studied in a cellulose-degrading enrichment culture originating from the alkaline lake, Verkhneye Beloye (Central Asia). In situ hybridization of the enrichment culture with 16S rRNA-targeted probes revealed that abundant, long, thin, rod-shaped cells were related to Cytophaga. Bacteria of this type were isolated with cellobiose and five isolates were characterized. Isolates were thin, flexible, gliding rods. They formed a spherical cyst-like structure at one cell end during the late growth phase. The pH range for growth was 7.5–10.2, with an optimum around pH 8.5. Cultures produced a pinkish pigment tentatively identified as a carotenoid. Isolates did not degrade cellulose, indicating that they utilized soluble products formed by so far uncultured hydrolytic cellulose degraders. Besides cellobiose, the isolates utilized other carbohydrates, including xylose, maltose, xylan, starch, and pectin. The main organic fermentation products were propionate, acetate, and succinate. Oxygen, which was not used as electron acceptor, impaired growth. A representative isolate, strain Z-7010, with Marinilabilia salmonicolor as the closest relative, is described as a new genus and species, Alkaliflexus imshenetskii. This is the first cultivated alkaliphilic anaerobic member of the Cytophaga/Flavobacterium/Bacteroides phylum.Dedicated to Prof. Dr. Hans Günter Schlegel on the occasion of his 80th birthday.     

Geoalkalibacter ferrihydriticus gen. nov. sp. nov., the first alkaliphilic representative of the family Geobacteraceae, isolated from a soda lake

Investigation of iron reduction in bottom sediments of alkaline soda lakes resulted in the isolation of a new obligately anaerobic iron-reducing bacterium, strain Z-0531, from Lake Khadyn (Tuva, Russia) sediment samples. The cells of strain Z-0531 are short (1.0–1.5 by 0.3–0.5 μm), motile, non-spore-forming, gram-negative rods. The isolate is an obligate alkaliphile, developing in the pH range of 7.8–10.0, with an optimum at pH 8.6. It does not require NaCl but grows at NaCl concentrations of 0–50 g/l. It can oxidize acetate with such electron acceptors as amorphous Fe(III) hydroxide (AFH), EDTA-Fe(III), anthraquinone-2,6-disulfonate (quinone), Mn(IV), and S⁰. On medium with EDTA-Fe(III), the isolate can oxidize, apart from acetate, ethanol, pyruvate, oxalate, arginine, tartrate, lactate, propionate, and serine. H₂ is not utilized. The reduced products formed during growth with AFH are siderite or magnetite, depending on the growth conditions. The isolate is incapable of fermenting sugars, peptides, and amino acids. Yeast extract or vitamins are required as growth factors. The organism is capable of dinitrogen fixation and harbors the nifH gene. The DNA G+C content is 55.3 mol %. 16S rRNA analysis places strain Z-0531 into the family Geobacteraceae. Its closest relative (93% similarity) is Desulfuromonas palmitatis. Based on phenotypic distinctions and phylogenetic position, it is proposed that this strain be assigned to the new genus and species Geoalkalibacter ferrihydriticus gen. nov., sp. nov. (Z-0531^T-DSMZ-17813-VKMB-2401). Original Russian Text ? D.G. Zavarzina, T.V. Kolganova, E.S. Boulygina, N.A. Kostrikina, T.P. Tourova, G.A. Zavarzin, 2006, published in Mikrobiologiya, 2006, Vol. 75, No. 6, pp. 775–785.     

Ferribacterium limneticum, gen. nov., sp. nov., an Fe(III)-reducing microorganism isolated from mining-impacted freshwater lake sediments

A dissimilatory Fe(III)-reducing bacterium was isolated from mining-impacted lake sediments and designated strain CdA-1. The strain was isolated from a 4-month enrichment culture with acetate and Fe(III)-oxyhydroxide. Strain CdA-1 is a motile, obligately anaerobic rod, capable of coupling the oxidation of acetate and other organic acids to the reduction of ferric iron. Fe(III) reduction was not observed using methanol, ethanol, isopropanol, propionate, succinate, fumarate, H₂, citrate, glucose, or phenol as potential electron donors. With acetate as an electron donor, strain CdA-1 also grew by reducing nitrate or fumarate. Growth was not observed with acetate as electron donor and O₂, sulfoxyanions, nitrite, trimethylamine N-oxide, Mn(IV), As(V), or Se(VI) as potential terminal electron acceptors. Comparative 16 S rRNA gene sequence analyses show strain CdA-1 to be most closely related (93.6% sequence similarity) to Rhodocyclus tenuis. However, R. tenuis did not grow heterotrophically by Fe(III) reduction, nor did strain CdA-1 grow photrophically. We propose that strain CdA-1 represents a new genus and species, Ferribacterium limneticum. Strain CdA-1 represents the first dissimilatory Fe(III) reducer in the β subclass of Proteobacteria, as well as the first Fe(III) reducer isolated from mine wastes. Received: 14 July 1998 / Accepted: 14 December 1998     

Anaerotalea alkaliphila gen. nov., sp. nov., an alkaliphilic,anaerobic, fermentative bacterium isolated from a terrestrial mud volcano

Extremophiles - Diversity of extremophilic microorganisms in mud volcanoes is largely unexplored. Here, we report the isolation of a novel alkaliphilic, mesophilic, fermentative bacterium (strain...     

Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov., sp. nov., non-phototrophic Rhodobacteraceae from the biofilter of a marine aquaculture

Three Gram-negative bacterial strains were isolated from the biofilter of a recirculating marine aquaculture. They were non-pigmented rods, mesophiles, moderately halophilic, and showed chemo-organoheterotrophic growth on various sugars, fatty acids, and amino acids, with oxygen as electron acceptor; strains D9-3^T and D11-58 were in addition able to denitrify. Phototrophic or fermentative growth could not be demonstrated. Phylogenetic analysis of the 16S rRNA gene sequences placed D9-3^T and D11-58, and D1-19^T on two distinct branches within the alpha-3 proteobacterial Rhodobacteraceae, affiliated with, but clearly separate from, the genera Rhodobacter, Rhodovulum, and Rhodobaca. Based on morphological, physiological, and 16S rRNA-based phylogenetic characteristics, the isolated strains are proposed as new species of two novel genera, Defluviimonas denitrificans gen. nov., sp. nov. (type strain D9-3^T = DSM 18921^T = ATCC BAA-1447^T; additional strain D11-58 = DSM19039 = ATCC BAA-1448) and Pararhodobacter aggregans gen. nov., sp. nov (type strain D1-19^T = DSM 18938^T = ATCC BAA-1446^T).     

Anaerofustis stercorihominis gen. nov., sp. nov., from human feces

Phenotypic and phylogenetic studies were performed on an unidentified Gram-positive, strictly anaerobic, non-spore-forming, rod-shaped bacterium isolated from human feces. The organism was catalase-negative, resistant to 20% bile, produced acetic and butyric acids as end products of glucose metabolism, and possessed a G+C content of approximately 70 mol%. Comparative 16S rRNA gene sequencing demonstrated that the unidentified bacterium was a member of the Clostridium sub-phylum of the Gram-positive bacteria, and formed a loose association with rRNA cluster XV. Sequence divergence values of 12% or greater were observed between the unidentified bacterium and all other recognized species within this and related rRNA clusters. Treeing analysis showed the unknown anaerobe formed a deep line branching near to the base of rRNA cluster XV and phylogenetically represents a hitherto unknown taxon, distinct from Acetobacterium, Eubacterium sensu stricto, Pseudoramibacter and other related organisms. Based on both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from feces be classified in a new genus Anaerofustis, as Anaerofustis stercorihominis sp. nov. The type strain of Anaerofustis stercorihominis is ATCC BAA-858(T)=CCUG 47767(T).     

Propionispora vibrioides, nov. gen., nov. sp., a new gram-negative, spore-forming anaerobe that ferments sugar alcohols

Anaerobic enrichment cultures, with erythritol as substrate, resulted in the isolation of a strain with properties not yet found in an existing genus in this combination. The strain, FKBS1, was strictly anaerobic, stained gram-negative and formed spores. Cells were small motile vibrios with flagella inserted at the concave side of the cell. Spores were located terminally and caused only slight swelling of the cells if compared to related spore-forming genera. FKBS1 fermented fructose, mannitol, sorbitol, xylitol and erythritol to propionic acid, acetic acid, CO2 and small amounts of H2 to balance the difference in the oxidation-reduction value between substrate and cell mass. The 16S rDNA sequence revealed relationship to the Sporomusa-Pectinatus-Selenomonas group. However, the phylogenetic distance to any of its members was too great to allow it to be placed in one of the existing genera. Morphologically the strain resembled Sporomusa, which, however, performs an acetogenic type of fermentation. The propionic-acid-forming genera of the group are either not spore-formers or, in the case of Dendrosporobacter quercicolus (syn. Clostridium quercicolum), morphologically different. It is therefore proposed to classify strain FKBS1 as a new genus and species, Propionispora vibrioides.     

Natronolimnobius baerhuensis gen. nov., sp. nov. and Natronolimnobius innermongolicus sp. nov., novel haloalkaliphilic archaea isolated from soda lakes in Inner Mongolia, China

Three novel isolates of haloalkaliphilic archaea, strains IHC-005^T, IHC-010, and N-1311^T, from soda lakes in Inner Mongolia, China, were characterized to elucidate their taxonomic positions. The three strains were aerobic, Gram-negative chemoorganotrophs growing optimally at 37–45°C, pH 9.0–9.5, and 15–20% NaCl. Cells of strains IHC-005^T/IHC-010 were motile rods, while those of strain N-1311^T were non-motile pleomorphic flats or cocci. The three strains contained diphytanyl and phytanyl-sesterterpanyl diether derivatives of phosphatidylglycerol and phosphatidylglycerophosphate methyl ester. No glycolipids were detected. On phylogenetic analysis of 16S rRNA gene sequences, they formed an independent cluster in the Natro group of the family Halobacteriaceae. Comparison of their morphological, physiological, and biochemical properties, DNA G+C content and 16S rRNA gene sequences, and DNA-DNA hybridization study support the view that strains IHC-005^T/IHC-010 and strain N-1311^T represent separate species. Therefore, we propose Natronolimnobius baerhuensis gen. nov., sp. nov. for strains IHC-005^T (=CGMCC 1.3597^T =JCM 12253^T)/IHC-010 (=CGMCC 1.3598=JCM 12254) and Natronolimnobius innermongolicus sp. nov. for N-1311^T (=CGMCC 1.2124^T =JCM 12255^T).     

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).     

Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov.

Senegalemassilia anaerobia strain JC110^T sp.nov. is the type strain of Senegalemassilia anaerobia gen. nov., sp. nov., the type species of a new genus within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,383,131 bp long genome contains 1,932 protein-coding and 58 RNA genes.     

Neoscardovia arbecensis gen. nov., sp. nov., isolated from porcine slurries

Three Gram-positive, anaerobic, pleomorphic strains (PG10(T), PG18 and PG22), were selected among five strains isolated from pig slurries while searching for host specific bifidobacteria to track the source of fecal pollution in water. Analysis of the 16S rRNA gene sequence showed a maximum identity of 94% to various species of the family Bifidobacteriaceae. However, phylogenetic analyses of 16S rRNA and HSP60 gene sequences revealed a closer relationship of these strains to members of the recently described Aeriscardovia, Parascardovia and Scardovia genera, than to other Bifidobacterium species. The names Neoscardovia gen. nov. and Neoscardovia arbecensis sp. nov. are proposed for a new genus and for the first species belonging to this genus, respectively, and for which PG10(T) (CECT 8111(T), DSM 25737(T)) was designated as the type strain. This new species should be placed in the Bifidobacteriaceae family within the class Actinobacteria, with Aeriscardovia aeriphila being the closest relative. The prevailing cellular fatty acids were C(16:0) and C(18:1)ω9c, and the major polar lipids consisted of a variety of glycolipids, diphosphatidyl glycerol, two unidentified phospholipids, and phosphatidyl glycerol. The peptidoglycan structure was A1γmeso-Dpm-direct. The GenBank accession numbers for the 16S rRNA gene and HSP60 gene sequences of strains PG10(T), PG18 and PG22 are JF519691, JF519693, JQ767128 and JQ767130, JQ767131, JQ767133, respectively.     

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).     

Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment

A novel Gram-stain-negative, rod-to-spiral-shaped, oxidase- and catalase- positive and facultatively aerobic bacterium, designated HS6^T, was isolated from marine sediment of Yellow Sea, China. It can reduce nitrate to nitrite and grow well in marine broth 2216 (MB, Hope Biol-Technology Co., Ltd) with an optimal temperature for growth of 30–33 °C (range 12–45 °C) and in the presence of 2–3 % (w/v) NaCl (range 0.5–7 %, w/v). The pH range for growth was pH 6.2–9.0, with an optimum at 6.5–7.0. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the novel isolate was 93.3 % similar to the type strain of Neptunomonas antarctica, 93.2 % to Neptunomonas japonicum and 93.1 % to Marinobacterium rhizophilum, the closest cultivated relatives. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol and some other unknown lipids. Major cellular fatty acids were summed feature 3 (C_16:1 ω7c/iso-C_15:0 2-OH), C_18:1 ω7c and C_16:0 and the main respiratory quinone was Q-8. The DNA G+C content of strain HS6^T was 61.2 mol %. Based on the phylogenetic, physiological and biochemical characteristics, strain HS6^T represents a novel genus and species and the name Motiliproteus sediminis gen. nov., sp. nov., is proposed. The type strain is HS6^T (=ATCC BAA-2613^T=CICC 10858^T).     

Anaerobic utilization of pectinous substrates at extremely haloalkaline conditions by Natranaerovirga pectinivora gen. nov., sp. nov., and Natranaerovirga hydrolytica sp. nov., isolated from hypersaline soda lakes

Anaerobic enrichments at pH 10, with pectin and polygalacturonates as substrates and inoculated with samples of sediments of hypersaline soda lakes from the Kulunda Steppe (Altai, Russia) demonstrated the potential for microbial pectin degradation up to soda-saturating conditions. The enrichments resulted in the isolation of six strains of obligately anaerobic fermentative bacteria, which represented a novel deep lineage within the order Clostridiales loosely associated with the family Lachnospiraceae. The isolates were rod-shaped and formed terminal round endospores. One of the striking features of the novel group is a very narrow substrate spectrum for growth, restricted to galacturonic acid and its polymers (e.g. pectin). Acetate and formate were the final fermentation products. Growth was possible in a pH range from 8 to 10.5, with an optimum at pH 9.5–10, and in a salinity range from 0.2 to 3.5 M Na⁺. On the basis of unique phenotypic properties and distinct phylogeny, the pectinolytic isolates are proposed to be assigned to a new genus Natranaerovirga with two species N. hydrolytica (APP2^T=DSM24176^T=UNIQEM U806^T) and N. pectinivora (AP3^T=DSM24629^T=UNIQEM U805^T).