Culturable diversity of lithotrophic haloalkaliphilic sulfate-reducing bacteria in soda lakes and the description of Desulfonatronum thioautotrophicum sp. nov., Desulfonatronum thiosulfatophilum sp. nov., Desulfonatronovibrio thiodismutans sp. nov., and Desulfonatronovibrio magnus sp. nov

Soda lake sediments usually contain high concentrations of sulfide indicating active sulfate reduction. Monitoring of sulfate-reducing bacteria (SRB) in soda lakes demonstrated a dominance of two groups of culturable SRB belonging to the order Desulfovibrionales specialized in utilization of inorganic electron donors, such as formate, H₂ and thiosulfate. The most interesting physiological trait of the novel haloalkaliphilic SRB isolates was their ability to grow lithotrophically by dismutation of thiosulfate and sulfite. All isolates were obligately alkaliphilic with a pH optimum at 9.5–10 and moderately salt tolerant. Among the fifteen newly isolated strains, four belonged to the genus Desulfonatronum and the others to the genus Desulfonatronovibrio. None of the isolates were closely related to previously described species of these genera. On the basis of phylogenetic, genotypic and phenotypic characterization of the novel soda lake SRB isolates, two novel species each in the genera Desulfonatronum and Desulfonatronovibrio are proposed.     

Ancylobacter lacus sp. nov. and Ancylobacter plantiphilus sp. nov., Novel Aerobic Facultative Methylotrophic Bacteria

Microbiology - Novel aerobic facultatively methylotrophic bacteria were isolated from the water of a freshwater lake (strain F30LT), soil sample of rhizosphere of white clover Trifolium repens L....     

Alkalisalibacterium limincola gen. nov., sp. nov., an Alkaliphilic Bacterium Isolated from an Alkaline,Saline Lake of Buryatia in Russia

Microbiology - A gram-stain-negative, aerobic, rod-shaped and motile bacterium, designated Alg18-2.2T, was isolated from a bottom sediment of the highly alkaline-saline lake in Buryatia, Russia....     

Halegenticoccus tardaugens sp. nov., an extremely halophilic archaeon isolated from a saline soil

Extremophiles - Two extremely halophilic archaea, isolates SYSU A00711T and SYSU A00630, were isolated from a sediment soil sample collected from the Aiding lake, China. Cells of these isolates...     

Fontisphaera persica gen. nov., sp. nov., a thermophilic hydrolytic bacterium from a hot spring of Baikal lake region,and proposal of Fontisphaeraceae fam. nov., and Limisphaeraceae fam. nov. within the Limisphaerales ord. nov. (Verrucomicrobiota)

A novel facultatively anaerobic moderately thermophilic bacterium, strain B-154 ^T, was isolated from a terrestrial hot spring in the Baikal lake region (Russian Federation). Gram-negative, motile, spherical cells were present singly, in pairs, or aggregates, and reproduced by binary fission. The strain grew at 30–57 °C and within a pH range of 5.1–8.4 with the optimum at 50 °C and pH 6.8–7.1. Strain B-154 ^T was a chemoorganoheterotroph, growing on mono-, di- and polysaccharides (xylan, starch, galactan, galactomannan, glucomannan, xyloglucan, pullulan, arabinan, lichenan, beta-glucan, pachyman, locust bean gum, xanthan gum). It did not require sodium chloride or yeast extract for growth. Major cellular fatty acids were anteiso-C_15:0, iso-C_16:0 and iso-C_14:0. The respiratory quinone was MK-7. The complete genome of strain B-154 ^T was 4.73 Mbp in size; its G + C content was 61%. According to the phylogenomic analysis strain B-154 ^T forms a separate family-level phylogenetic lineage. Moreover, together with Limisphaera ngatamarikiensis and “Pedosphaera parvula” this strain forms a separate order-level phylogenetic lineage within Verrucomicrobiae class. Hence, we propose a novel order, Limisphaerales ord. nov., with two families Limisphaeraceae fam. nov. and Fontisphaeraceae fam. nov., and a novel genus and species Fontisphaera persica gen. nov., sp. nov. with type strain B-154 ^T. Ecogenomic analysis showed that representatives of the Limisphaerales are widespread in various environments. Although some of them were detected in hot springs the majority of Limisphaerales (54% of the studied metagenome-assembled genomes) were found in marine habitats. This study allowed a better understanding of physiology and ecology of Verrucomicrobiota – a rather understudied bacterial phylum.     

Ectothiorhodosinus mongolicum gen. nov., sp. nov., a New Purple Bacterium from a Soda Lake in Mongolia

A new nonmotile purple sulfur bacterium (strain M9) was isolated from the steppe soda lake Lake Dzun Uldziin Nur (pH 9.4; mineralization, 3.3%) situated in southeastern Mongolia. Individual cells appear as vibrios 0.3–0.5 × 0.7–1 m 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 additional sources of carbon in anoxygenic photosynthesis. Vitamins 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°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 sulfur bacterium was assigned to a new species of a new genus of the family Ectothiorhodospiraceae, Ectothiorhodosinus mongolicum gen. nov., sp. nov.     

Natranaeroarchaeum sulfidigenes gen. nov., sp. nov., carbohydrate-utilizing sulfur-respiring haloarchaeon from hypersaline soda lakes,a member of a new family Natronoarchaeaceae fam. nov. in the order Halobacteriales

A pure culture of alkaliphilic haloarchaeon strain AArc-S^T capable of anaerobic growth by carbohydrate-dependent sulfur respiration was obtained from hypersaline lakes in southwestern Siberia. According to phylogenetic analysis, AArc-S^T formed a new genus level branch most related to the genus Natronoarchaeum in the order Halobacteriales. The strain is facultatively anaerobic with strictly respiratory metabolism growing either by anaerobic respiration with elemental sulfur and thiosulfate as the electron acceptors or by aerobic respiration at microoxic conditions. Thiosulfate is reduced partially to sulfide and sulfite. It is a first sulfur-reducing alkaliphilic haloarchaeon utilizing sugars, starch and glycerol as substrates for anaerobic growth. It is extremely halophilic (optimum at 3.5 M total Na⁺) and obligately alkaliphilic (optimum at pH 9.5). The dominant polar lipids include PG and PGP-Me with the archaeol (C₂₀-C₂₀) or extended archaeol (C₂₀-C₂₅) cores. The dominant respiratory lipoquinone is MK-8:8. On the basis of unique physiological properties and results of phylogenetic analysis, the soda lake isolate is suggested to be classified into a novel genus and species Natranaeroarchaeum sulfidigenes gen. nov., sp. nov. (=JCM 34033^T = UNIQEM U1000^T). Furthermore, on the bases of phylogenomic reconstruction, a new family Natronoarchaeaceae fam. nov. is proposed within the order Halobacteriales incorporating Natranaeroarchaeum and three related genera: Natronoarchaeum, Salinarchaeum and Halostella.     

Lacipirellula parvula gen. nov., sp. nov., representing a lineage of planctomycetes widespread in low-oxygen habitats,description of the family Lacipirellulaceae fam. nov. and proposal of the orders Pirellulales ord. nov., Gemmatales ord. nov. and Isosphaerales ord. nov.

Pirellula-like planctomycetes are ubiquitous aquatic bacteria, which are often detected in anoxic or micro-oxic habitats. By contrast, the taxonomically described representatives of these bacteria, with very few exceptions, are strict aerobes. Here, we report the isolation and characterization of the facultatively anaerobic planctomycete, strain PX69^T, which was isolated from a boreal lake. Its 16S rRNA gene sequence is affiliated with the Pirellula-related Pir4 clade, which is dominated by environmental sequences retrieved from a variety of low-oxygen habitats. Strain PX69^T was represented by ellipsoidal cells that multiplied by budding and grew on sugars, some polysaccharides and glycerol. Anaerobic growth occurred by means of fermentation. Strain PX69^T grew at pH 5.5–7.5 and at temperatures between 10 and 30 °C. The major fatty acids were C18:1ω9c, C16:0 and C16:1ω7c; the major intact polar lipid was dimethylphosphatidylethanolamine. The complete genome of strain PX69^T was 6.92 Mb in size; DNA G + C content was 61.7 mol%. Among characterized planctomycetes, the highest 16S rRNA gene similarity (90.4%) was observed with ‘Bythopirellula goksoyri’ Pr1d, a planctomycete from deep-sea sediments. We propose to classify PX69^T as a novel genus and species, Lacipirellula parvula gen. nov., sp. nov.; the type strain is strain PX69^T (=KCTC 72398^T = CECT 9826^T = VKM B-3335^T). This genus is placed in a novel family, Lacipirellulaceae fam. nov., which belongs to the order Pirellulales ord. nov. Based on the results of comparative genome analysis, we also suggest establishment of the orders Gemmatales ord. nov. and Isosphaerales ord. nov. as well as an emendation of the order Planctomycetales.     

Natronobacillus azotifigens gen. nov., sp. nov., an anaerobic diazotrophic haloalkaliphile from soda-rich habitats

Gram-positive bacteria capable of nitrogen fixation were obtained in microoxic enrichments from soda soils in south-western Siberia, north-eastern Mongolia, and the Lybian desert (Egypt). The same organisms were obtained in anoxic enrichments with glucose from soda lake sediments in the Kulunda Steppe (Altai, Russia) using nitrogen-free alkaline medium of pH 10. The isolates were represented by thin motile rods forming terminal round endospores. They are strictly fermentative saccharolytic anaerobes but tolerate high oxygen concentrations, probably due to a high catalase activity. All of the strains are obligately alkaliphilic and highly salt-tolerant natronophiles (chloride-independent sodaphiles). Growth was possible within a pH range from 7.5 to 10.6, with an optimum at 9.5–10, and within a salt range from 0.2 to 4 M Na⁺, with an optimum at 0.5–1.5 M for the different strains. The nitrogenase activity in the whole cells also had an alkaline pH optimum but was much more sensitive to high salt concentrations compared to the growing cells. The isolates formed a compact genetic group with a high level of DNA similarity. Phylogenetic analysis based on 16S-rRNA gene sequences placed the isolates into Bacillus rRNA group 1 as a separate lineage with Amphibacillus tropicus as the nearest relative. In all isolates the key functional nitrogenase gene nifH was detected. A new genus and species, Natronobacillus azotifigens gen. nov., sp. nov., is proposed to accommodate the novel diazotrophic haloalkaliphiles. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. The GenBank accession numbers for the 16S rRNA gene of the novel strains are EU143681-EU143690 and EU850814-EU850816; for the nifH gene the accession numbers are EU542601, EU563380-EU563386 and EU850817-EU850819.     

Silicibacter lacuscaerulensis gen. nov., sp. nov., a mesophilic moderately halophilic bacterium characteristic of the Blue Lagoon geothermal lake in Iceland

Mesophilic, moderately halophilic bacteria were isolated from a silica-rich geothermal lake, the Blue Lagoon in Iceland. The isolates are strictly aerobic, but reduce nitrate to nitrite, and are oxidase- and catalase-positive. The nonsporeforming and nonmotile Gram negative rods are 0.6–0.8 μm in diameter and variable in length (9–18 μm), and contain gas vacuoles. The GC content in their DNA is 66.15%. The minimum, optimum, and maximum temperatures for growth are 22°C, 45°:C, and 50°C, respectively. The isolates do not grow without added salt in the medium and can grow at up to 7% NaCl (w/v). The optimal salinity for growth is 3.5%–4% NaCl. The pH range for growth is 6.5–8.5, with the optimal pH at 7.0. At optimal conditions the bacterium has a doubling time of 80 min. The main cytochrome is a membrane-bound cytochrome c with an α-peak at 549 nm. Sequencing of 16S rRNA from the type strain ITI-1157 revealed it to be a proteobacterium of the α-subclass with the closest relatives being Roseobacter litoralis and Paracoccus kocurii. The new isolates do not contain bacteriochlorophyll a and are considered to represent a new genus and a new species, Silicibacter lacuscaerulensis. Received: September 17, 1996 / Accepted: December 10, 1996     

Fontivita pretiosa gen. nov., sp. nov., a thermophilic planctomycete of the order Tepidisphaerales from a hot spring of Baikal lake region

A novel facultatively anaerobic moderately thermophilic bacterium, strain B-254^T, was isolated from a terrestrial hot spring near the town of Goryachinsk in the Baikal lake region (Russian Federation). Motile spherical cells of the strain were present as single cocci, in pairs, or aggregates. The cells had a Gram negative cell wall and reproduced by binary fission. The isolate grew at 30–57 °C (opt. 50–54 °C) and at pH 5.1–8.4 (opt. 6.6–7.1). Strain B-254^T was a chemoorganoheterotroph, growing on mono-, di- and polysaccharides (xylan, starch, galactan, galactomannan, xyloglucan, arabinan, curdlan, beta-glucan, locust bean gum, xanthan gum). Sodium chloride or yeast extract were not required for growth. Major cellular fatty acids were iso-C_16:0, anteiso-C_17:0, and C_20:0; major polar lipid was phosphatidylethanolamine. The complete genome of strain B-254^T was 5.54 Mb; its GC content was 64 %. According to the results of 16S rRNA gene sequence-based phylogenetic analysis and the conserved proteins sequences-based phylogenomic analysis strain B-254^T was on a separate lineage within the order Tepidisphaerales (Phycisphaerae, Planctomycetes). Based on phylogenetic and phylogenomic analyses of Phycisphaerae, whole genome comparisons of Tepidisphaerales as well as distinctive phenotypic features of the strain, it was assigned to a novel genus and species for which the name Fontivita pretiosa gen. nov. sp. nov. is proposed. Strain B-254^T = KCTC 82380^T = VKM B-3507^T.     

Kaistia adipata gen. nov., sp. nov., a novel alpha-proteobacterium

A taxonomic study was carried out on Chj404T, a bacterial strain isolated from a soil sample collected in an industrial stream near the Chung-Ju industrial complex in Korea. The strain was a gram-negative, aerobic, short rod to coccus-shaped bacterium. It grew well on nutrient agar medium and utilized a broad spectrum of carbon sources. The G+C content of the DNA was 67.4 mol% and the major composition of ubiquinone was Q-10. The major fatty acid was C18:1. Comparative 16S rDNA studies showed a clear affiliation of this bacterium to alpha-Proteobacteria. Comparison of phylogenetic data indicated that it was most closely related to Prosthecomicrobium pneumaticum (92.7% similarity in 16S rDNA sequence). Since strain Chj404 is clearly distinct from closely related species, we propose the name Kaistia adipata gen. nov., sp. nov. for this strain Chj404T (=IAM 15023T=KCTC 12095T).     

Disproportionation of inorganic sulfur compounds by the sulfate-reducing bacterium Desulfocapsa thiozymogenes gen. nov., sp. nov.

A new strictly anaerobic, gram-negative bacterium was isolated from the sediment of a freshwater lake after enrichment with thiosulfate as the energy source. The strain, named Bra2 (DSM 7269), is able to grow by disproportionation of thiosulfate or sulfite to sulfate plus sulfide. Elemental sulfur is also disproportionated to sulfate and sulfide, but this only supports growth if free sulfide is chemically removed from the culture, e.g., by precipitation with amorphous ferric hydroxide. Growth is also possible by coupling the reduction of sulfate to sulfide with the oxidation of ethanol, propanol, or butanol to the corresponding fatty acid. The cells are rod-shaped, motile, and have genomic DNA with a mol% G+C content of 50.7. Cytochromes are present, but desulfoviridin is not. The new strain was shown to be related to, but distinct from members of the genus Desulfobulbus on the basis of physiological characteristics and by comparative sequence analysis of its 16S rDNA. Strain Bra2 is described as the type strain of a new taxon, Desulfocapsa thiozymogenes gen. nov., sp. nov. Received: 29 January 1996 / Accepted: 31 May 1996     

Agromonas oligotrophica gen. nov., sp. nov., a nitrogen-fixing oligotrophic bacterium

Phenotypic and chemotaxonomic characteristics of five isolates of acetylenereducing (nitrogen-fixing) oligotrophic bacteria from a paddy soil were investigated. They showed similar phenotypic characteristics: they were aerobic, asporogenous, gram-negative, motile by a polar flagellum, and irregular rods. On full strength nutrient broth (NB) growth was severely suppressed, but well supported on 10-to 10000-fold diluted NB. They consumed glucose but produced no acid, and also utilized phenolic acids such as ferulic acid or p-coumaric acid. The cellular fatty acid composition, quinone system and DNA base composition of the isolates were investigated. Cellular fatty acids mainly consisted of straightchain unsaturated C_{18 : 1} (62–81% of total fatty acids). Ubiquinone Q-10 and a high guanine-plus-cytosine content (65.1–66.0 mol%) were found. The taxonomic status of the isolates is discussed and a new genus, Agromonas, with a single species Agromonas oligotrophica sp. nov., is proposed for these isolates. The type strain of A. oligotrophica is JCM 1494.     

Acidibacter ferrireducens gen. nov., sp. nov.: an acidophilic ferric iron-reducing gammaproteobacterium

An acidophilic gammaproteobacterium, isolated from a pit lake at an abandoned metal mine in south-west Spain, was shown to be distantly related to all characterized prokaryotes, and to be the first representative of a novel genus and species. Isolate MCF85 is a Gram-negative, non-motile, rod-shaped mesophilic bacterium with a temperature growth optimum of 32–35 °C (range 8–45 °C). It was categorized as a moderate acidophile, growing optimally at pH 3.5–4.0 and between pH 2.5 and 4.5. Under optimum conditions its culture doubling time was around 75 min. Only organic electron donors were used by MCF85, and the isolate was confirmed to be an obligate heterotroph. It grew on a limited range of sugars (hexoses and disaccharides, though not pentoses) and some other small molecular weight organic compounds, and growth was partially or completely inhibited by small concentrations of some aliphatic acids. The acidophile grew in the presence of >100 mM ferrous iron or aluminium, but was more sensitive to some other metals, such as copper. It was also much more tolerant of arsenic (V) than arsenic (III). Isolate MCF85 catalysed the reductive dissolution of the ferric iron mineral schwertmannite when incubated under micro-aerobic or anaerobic conditions, causing the culture media pH to increase. There was no evidence, however, that the acidophile could grow by ferric iron respiration under strictly anoxic conditions. Isolate MCF85 is the designated type strain of the novel species Acidibacter ferrireducens (=DSM 27237^T = NCCB 100460^T).     

Heliorestis daurensis, gen. nov. sp. nov., an alkaliphilic rod-to-coiled-shaped phototrophic heliobacterium from a Siberian soda lake

A novel alkaliphilic heliobacterium was isolated from microbial mats of a low-salt alkaline Siberian soda lake. Cells of the new organism were tightly coiled when grown in coculture with a rod-shaped bacterium, but grew as short filaments when finally obtained in pure culture. The new phototroph, designated strain BT-H1, produced bacteriochlorophyll g and a neurosporene-like pigment, and lacked internal photosynthetic membranes. Similar to other heliobacteria, strain BT-H1 grew photoheterotrophically on a limited range of organic compounds including acetate and pyruvate. Sulfide was oxidized to elemental sulfur and polysulfides under photoheterotrophic conditions; however, photoautotrophic growth was not observed. Cultures of strain BT-H1 were alkaliphilic, growing optimally at pH 9, and unlike other heliobacteria, they grew optimally at a temperature of 25 °C rather than at 40 °C or above. Analysis of the 16S rRNA gene sequence of the new organism showed that it groups within the heliobacterial clade. However, its branching order was phylogenetically basal to all previously investigated species of heliobacteria. The G+C content of the DNA of strain BT-H1 (44.9 mol%) was also quite distinct from that of other heliobacteria. This unique assemblage of properties implicates strain BT-H1 as a new genus and species of the heliobacteria, Heliorestis daurensis, named for its unusual morphology (“restis” is Latin for “rope”) and for the Daur Steppe in Russia in which these soda lakes are located. Received: 15 March 1999 / Accepted: 25 June 1999     

Isolation and characterization of Cytophaga flevensis sp. nov., a new agarolytic flexibacterium

The occurrence of agarolytic microorganisms in a variety of natural environments was investigated using enrichment culture techniques. From samples taken from the IJsselmeer, and adjacent areas in the central part of The Netherlands a new agarolytic flexibacterium was isolated. Enrichments inoculated with samples from other sources were unsuccessful. The yellow-pigmented organism exhibits gliding motility, but spreading was only occasionally detected. Since neither fruiting bodies nor microcysts were observed, the organism was placed into the genus Cytophaga and designated as Cytophaga flevensis sp. nov. The occurrence of this species is probably restricted to the IJsselmeer, a fresh-water lake that was in open contact with the North Sea until 1932, and some other lakes which are in direct contact with the IJsselmeer. The organism utilizes only carbohydrates as a carbon and energy source for growth and is strictly aerobic. When the organism is grown on agar, on its components or on melibiose, an extracellular agarase is produced. This enzyme is highly specific for polysaccharides containing neoagarobiose units and hydrolyzes neoagaro-oligosaccharides with a degree of polymerization of more than four.     

Paenibacillus turpanensis sp. nov., isolated from a salt lake of Turpan city in Xinjiang province,north-west China

Archives of Microbiology - Strain YIM B00363T, a Gram-positive, aerobic, non-motile, rod-shaped, spore-forming bacterium, was isolated from saline soil samples collected from a salt lake in...     

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.