Gwendolyn R. Drake

Bacillus infernus sp. nov., an Fe(III)- and Mn(IV)-reducing anaerobe from the deep terrestrial subsurface.

Bacillus infernus sp. nov. was isolated from ca. 2,700 m below the land surface in the Taylorsville Triassic Basin in Virginia. B. infernus was a strict anaerobe that grew on formate or lactate with Fe(III), MnO2, trimethylamine oxide, or nitrate (reduced to nitrite) as an electron acceptor, and it also grew fermentatively on glucose. Type strain TH-23 and five reference strains were gram-positive rods that were thermophilic (growth occurred at 61 degrees C), halotolerant (good growth occurred in the presence of Na+ concentrations up to 0.6 M), and very slightly alkaliphilic (good growth occurred at pH 7.3 to 7.8). A phylogenetic analysis of its 16S rRNA indicated that B. infernus should be classified as a new species of the genus Bacillus. B. infernus is the only strictly anaerobic species in the genus Bacillus.

Characterization of the anaerobic propionate-degrading syntrophs Smithella propionica gen. nov., sp. nov. and Syntrophobacter wolinii.

A strain of anaerobic, syntrophic, propionate-oxidizing bacteria, strain LYPT (= OCM 661T; T = type strain), was isolated and proposed as representative of a new genus and new species, Smithella propionica gen. nov., sp. nov. The strain was enriched from an anaerobic digestor and isolated. Initial isolation was as a monoxenic propionate-degrading co-culture containing Methanospirillum hungateii JF-1T as an H2- and formate-using partner. Later, an axenic culture was obtained by using crotonate as the catabolic substrate. The previously described propionate-degrading syntrophs of the genus Syntrophobacter also grow in co-culture with methanogens such as Methanospirillum hungateii, forming acetate, CO2 and methane from propionate. However, Smithella propionica differs by producing less methane and more acetate; in addition, it forms small amounts of butyrate. Smithella propionica and Syntrophobacter wolinii grew within similar ranges of pH, temperature and salinity, but they differed significantly in substrate ranges and catabolic products. Unlike Syntrophobacter wolinii, Smithella propionica grew axenically on crotonate, although very slowly. Co-cultures of Smithella propionica grew on propionate, and grew slowly on crotonate or butyrate. Syntrophobacter wolinii and Syntrophobacter pfennigii grow on propionate plus sulfate, whereas Smithella propionica did not. Comparisons of 16S rDNA genes indicated that Smithella propionica is most closely related to Syntrophus, and is more distantly related to Syntrophobacter.

Taxonomic Study of Aromatic-Degrading Bacteria from Deep- Terrestrial-Subsurface Sediments and Description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov.

Phylogenetic analyses of 16S rRNA gene sequences by distance matrix and parsimony methods indicated that six strains of bacteria isolated from deep saturated Atlantic coastal plain sediments were closely related to the genus Sphingomonas. Five of the strains clustered with, but were distinct from, Sphingomonas capsulata, whereas the sixth strain was most closely related to Blastobacter natatorius. The five strains that clustered with S. capsulata, all of which could degrade aromatic compounds, were gram-negative, non-spore-forming, non-motile, rod-shaped organisms that produced small, yellow colonies on complex media. Their G + C contents ranged from 60.0 to 65.4 mol%, and the predominant isoprenoid quinone was ubiquinone Q-10. All of the strains were aerobic and catalase positive. Indole, urease, and arginine dihydrolase were not produced. Gelatin was not liquified, and glucose was not fermented. Sphingolipids were present in all strains; 2OH14:0 was the major hydroxy fatty acid, and 18:1 was a major constituent of cellular lipids. Acid was produced oxidatively from pentoses, hexoses, and disaccharides, but not from polyalcohols and indole. All of these characteristics indicate that the five aromatic-degrading strains should be placed in the genus Sphingomonas as currently defined. Phylogenetic analysis of 16S rRNA gene sequences, DNA-DNA reassociation values, BOX-PCR genomic fingerprinting, differences in cellular lipid composition, and differences in physiological traits all indicated that the five strains represent three previously undescribed Sphingomonas species. Therefore, we propose the following new species: Sphingomonas aromaticivorans (type strain, SMCC F199), Sphingomonas subterranea (type strain, SMCC B0478), and Sphingomonas stygia (type strain, SMCC B0712).

Temporal Shifts in the Geochemistry and Microbial Community Structure of an Ultradeep Mine Borehole Following Isolation

A borehole draining a water-bearing dyke fracture at 3.2-km depth in a South African Au mine was isolated from the open mine environment. Geochemical, stable isotopic, nucleic acid-based, and phospholipid fatty acid (PLFA) analyses were employed as culture-independent means for assessing shifts in the microbial community and habitat as the system equilibrated with the native rock-water environment. Over a two-month period, the pH increased from 5.5 to 7.4, concurrent with a drop in pe from −2 to −3. Whereas rDNAs related to Desulfotomaculum spp. represented the major clone type encountered throughout, lipid biomarker profiling along with 16S rDNA clone library and terminal restriction fragment length polymorphism (T-RFLP) analyses indicated the emergence of other Gram-positive and deeply-branching lineages in samples during the later stages of the equilibration period. A biofilm that formed on the mine wall below the borehole produced abundant rDNAs related to the α Proteobacteria. β- and γ −Proteobacteria appeared to transiently bloom in the borehole shortly after isolation. Chemical modeling and sulfur isotope analyses of the borehole effluent indicated that microbial sulfate reduction was the major terminal electron-accepting process shortly after isolation, whereas Fe+3 reduction dominated towards the end of the experiment. The persistence of Desulfotomaculum-like bacteria throughout suggests that these organisms adapted to changing geochemical conditions as the redox decreased and pH increased following the isolation of the borehole from the mine atmosphere. The restoration of anaerobic aquatic chemistry to this borehole environment may have allowed microbiota indigenous to the local basalt aquifer to become more dominant among the diverse collection of bacterial lineages present in the borehole.

Description of Two New Thermophilic Desulfotomaculum spp., Desulfotomaculum putei sp. nov., from a Deep Terrestrial Subsurface, and Desulfotomaculum luciae sp. nov., from a Hot Spring

Six strains of thermophilic, endospore-forming, sulfate-reducing bacteria were enriched and isolated from 2.7 km below the earths surface in the Taylorsville Triassic Basin in Virginia. The cells of these strains were motile rods that were 1 to 1.1 μ in diameter and 2 to 5 μ long. The cells grew by oxidizing H2, formate, methanol (weakly), lactate (incompletely, to acetate and CO2), or pyruvate (incompletely) while reducing sulfate to sulfide; acetate did not serve as a catabolic substrate. Thiosulfate or sulfite could replace sulfate as an electron acceptor. The results of a phylogenetic analysis of the 16S rRNA gene indicated that these strains belong to the genus Desulfotomaculum, but are distinct from previously described Desulfotomaculum species. Thus, we propose a new species, Desulfotomaculum putei, for them, with strain TH-11 (= SMCC W459) as the type strain. The results of our phylogenetic analysis also indicated that strain SLTT, which was isolated from a hot spring and has been described previously (T. M. Karnauchow, S. F. Koval, and K. F. Jarrell, Syst. Appl. Microbiol. 15:296-310, 1992), is also a member of the genus Desulfotomaculum and is distinct from other species in this genus. We therefore propose the new species Desulfotomaculum luciae for this organism; strain SLT (= SMCC W644) is the type strain of D. luciae.

Desulfovibrio carbinoliphilus sp. nov., a benzyl alcohol-oxidizing, sulfate-reducing bacterium isolated from a gas condensate-contaminated aquifer

Phenotypic and phylogenetic studies were performed on a novel sulfate-reducing bacterium, strain D41(T), isolated as part of a methanogenic syntrophic culture from a gas condensate-contaminated aquifer undergoing intrinsic bioremediation. The bacterium was a Gram-negative, non-spore-forming, curved rod, motile by a single polar flagellum, which oxidized several alcohols incompletely, including methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, 2-butanol, 3-methyl-1-butanol (isoamyl alcohol), ethylene glycol, 1,2-propanediol, 1,3-propanediol, 1,4-butanediol, phenylethanol and benzyl alcohol. Additionally, the strain oxidized H(2)/CO(2), formate, lactate, pyruvate, maleate, malate and fumarate. Sulfate, thiosulfate and sulfite were used as electron acceptors. The DNA G+C content was 63 mol%. Based on phylogenetic and phenotypic evidence, the novel species Desulfovibrio carbinoliphilus sp. nov. is proposed. The type strain is D41(T) (=ATCC BAA-1241(T) =DSM 17524(T)).

The naturally transformable marine bacterium WJT-1C formally identified as "Vibrio" is a pseudomonad.

Abstract. A marine bacterial isolate, previously identified as Vibrio WJT-1C (ATCC 55351) and used as a model for investigating the process of natural transformation in the marine environment, has been further examined to determine its taxonomic identity. API 20E test strips, phenotypic testing, and flagellar staining had previously assigned the strain to the genus Vibrio, most closely related to V. campbelli. 16S rRNA analysis indicated that WJT-1C was in the Pseudomonas subgroup of the gamma proteobacteria. Bacteriophage typing and natural transformation with chromosomal DNA indicated that it was distinct from previously described marine transforming pseudomonads including Pseudomonas stutzeri strain JM300. The importance and abundance of the Pseudomonas subgroup of the gamma proteobacteria in the environment suggest that these marine strains are well suited as model organisms for describing the process and importance of natural transformation in nature.