Milton S. da Costa

Extensive Diversity of Ionizing-Radiation-Resistant Bacteria Recovered from Sonoran Desert Soil and Description of Nine New Species of the Genus Deinococcus Obtained from a Single Soil Sample

ABSTRACT The ionizing-radiation-resistant fractions of two soil bacterial communities were investigated by exposing an arid soil from the Sonoran Desert and a nonarid soil from a Louisiana forest to various doses of ionizing radiation using a 60Co source. The numbers of surviving bacteria decreased as the dose of gamma radiation to which the soils were exposed increased. Bacterial isolates surviving doses of 30 kGy were recovered from the Sonoran Desert soil, while no isolates were recovered from the nonarid forest soil after exposure to doses greater than 13 kGy. The phylogenetic diversities of the surviving culturable bacteria were compared for the two soils using 16S rRNA gene sequence analysis. In addition to a bacterial population that was more resistant to higher doses of ionizing radiation, the diversity of the isolates was greater in the arid soil. The taxonomic diversity of the isolates recovered was found to decrease as the level of ionizing-radiation exposure increased. Bacterial isolates of the genera Deinococcus, Geodermatophilus, and Hymenobacter were still recovered from the arid soil after exposure to doses of 17 to 30 kGy. The recovery of large numbers of extremely ionizing-radiation-resistant bacteria from an arid soil and not from a nonarid soil provides further ecological support for the hypothesis that the ionizing-radiation resistance phenotype is a consequence of the evolution of other DNA repair systems that protect cells against commonly encountered environmental stressors, such as desiccation. The diverse group of bacterial strains isolated from the arid soil sample included 60 Deinococcus strains, the characterization of which revealed nine novel species of this genus.

Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater.

Two recently reported bacterial strains that are able to reductively dehalogenate polychlorinated aliphatic alkanes, including 1,2,3-trichloropropane, 1,2-dichloropropane, 1,1,2,2-tetrachloroethane, 1,1,2-trichloroethane and 1,2-dichloroethane, were further characterized to clarify their taxonomic position. The two strains, designated BL-DC-8 and BL-DC-9(T), were mesophilic, non-spore-forming, non-motile, Gram-negative staining and strictly anaerobic. Cells were irregular cocci, 0.3-0.6 mum in diameter. The two strains were resistant to ampicillin and vancomycin. Hydrogen was utilized as an electron donor. The genomic DNA G+C content of strains BL-DC-8 and BL-DC-9(T) was 54.0 and 53.8 mol%, respectively. The major cellular fatty acids were C(18 : 1)omega9c, C(16 : 1)omega9c, C(16 : 0) and C(14 : 0). Phylogenetic analyses based on 16S rRNA gene sequences indicated that the strains cluster within the phylum Chloroflexi, but are related only distantly to all recognized taxa in the phylum. Morphological, physiological and chemotaxonomic traits as well as phylogenetic analysis support the conclusion that these two strains represent a novel species of a new genus in the phylum Chloroflexi, for which the name Dehalogenimonas lykanthroporepellens gen. nov., sp. nov. is proposed. The type strain of Dehalogenimonas lykanthroporepellens is BL-DC-9(T) (=ATCC BAA-1523(T) =JCM 15061(T)).

Combined effect of the growth temperature and salinity of the medium on the accumulation of compatible solutes by Rhodothermus marinus and Rhodothermus obamensis

Abstract In this study we propose revised structures for the two major compatible solutes of Rhodothermus marinus. We have also examined the accumulation of compatible solutes by the type strains of the slightly halophilic and thermophilic species Rhodothermus marinus and Rhodothermus obamensis at several growth temperatures and salinities. The major solutes of R. marinus were identified as α-mannosylglycerate (α-MG) and α-mannosylglyceramide (α-MGA), whereas R. obamensis accumulated only α-mannosylglycerate. The total osmolyte content was higher during the early exponential phase and decreased abruptly as growth continued into the stationary phase. At low growth temperatures, R. marinus responded to water stress by accumulation of α-mannosylglycerate and its amide, in addition to low levels of trehalose, glutamate, and glucose. At the highest growth temperature, α-mannosylglycerate was the major compatible solute and α-mannosylglyceramide was not detected. When both compounds were present, an increase in the salinity of the growth medium favored the accumulation of α-mannosylglyceramide over α-mannosylglycerate. The absence of α-mannosylglyceramide in R. obamensis at all growth temperatures and salinities constituted the most pronounced difference in the profiles of compatible solute accumulation by the two strains. Trehalose was also a prominent solute in this organism. Both organisms accumulated higher levels of α-mannosylglycerate as the temperature was raised. The importance of the two compounds in the mechanisms of thermoadaptation and osmoadaptation is discussed.

Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.

Halorhabdus tiamatea sp. nov., a non-pigmented, extremely halophilic archaeon from a deep-sea, hypersaline anoxic basin of the Red Sea, and emended description of the genus Halorhabdus.

An extremely halophilic archaeon was isolated from a sample of the brine-sediment interface of the Shaban Deep in the northern Red Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed a close proximity to Halorhabdus utahensis (99.3%), the sole species of the genus Halorhabdus. Strain SARL4B(T) formed non-pigmented colonies and showed optimum growth at 45 degrees C, in 27% (w/v) NaCl and at pH 6.5-7.0. This organism utilized a few complex substrates, such as yeast extract and starch, for growth. Strain SARL4B(T) grew under anaerobic and microaerophilic conditions but grew extremely poorly under aerobic conditions. The ether lipids were diphytanyl derivatives. The DNA G+C content of the type strain was 61.7 mol%. On the basis of the phylogenetic data and physiological and biochemical characteristics, strain SARL4B(T) represents a novel species of the genus Halorhabdus, for which the name Halorhabdus tiamatea is proposed. The type strain is SARL4B(T) (=DSM 18392(T)=JCM 14471(T)). An emended description of the genus Halorhabdus is also proposed.

Numerical Taxonomy of Thermus Isolates from Hot Springs in Portugal

Summary Forty-two strains of the eubacterial genus Thermus isolated from two sites on mainland Portugal and several sites on the Island of S. Miguel, Azores, as well as two reference strains were subjected to a numerical classification study based on 48 characters. Unweighted average linkage analysis (UPGMA) using simple matching (S SM ) and Jaccard similarity (S J ) coefficients, produced slightly different phenograms. Test error was estimated at 2.7%. The S SM /UPGMA phenogram formed six clusters which reflected, to some extent, the geographical sources of the isolates: clusters A and B were composed of isolates from S. Miguel, the Caldas de Vizela strains from the mainland formed two clusters (C and D), cluster F was composed of some of the isolates from S. Pedro do Sul, also on the mainland, while cluster E comprised a mixture of isolates from S. Miguel and S. Pedro do Sul.

Description of four novel psychrophilic, ionizing radiation-sensitive Deinococcus species from alpine environments.

Five psychrophilic bacterial strains were isolated from soil samples collected above the treeline of alpine environments. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these organisms represent four novel species of the genus Deinococcus; levels of sequence similarity to the type strains of recognized Deinococcus species were in the range 89.3-94.7 %. Strains PO-04-20-132T, PO-04-20-144, PO-04-19-125T, ME-04-01-32T and ME-04-04-52T grew aerobically, with optimum growth at 10 degrees C and at pH 6-9. The major respiratory menaquinone was MK-8. The fatty acid profiles of strains PO-04-20-132T, PO-04-20-144, PO-04-19-125T and ME-04-01-32T were dominated by 16 : 1omega7c, 17 : 0 iso and 15 : 1omega6c, whereas 16 : 1omega7c, 17 : 0 cyclo and 16 : 0 predominated in strain ME-04-04-52T. The DNA G+C contents of strains PO-04-20-132T, PO-04-19-125T, ME-04-01-32T and ME-04-04-52T were 63.2, 63.1, 65.9 and 62.6 mol%, respectively. Strains PO-04-20-132T, PO-04-19-125T, ME-04-01-32T and ME-04-04-52T had gamma radiation D10 (dose required to reduce the bacterial population by 10-fold) values of < or =4 kGy. These four strains showed sensitivity to UV radiation and extended desiccation as compared with Deinococcus radiodurans. On the basis of the phylogenetic analyses, and chemotaxonomic and phenotypic data, it is proposed that strains PO-04-20-132T (=LMG 24019T=NRRL B-41950T; Deinococcus radiomollis sp. nov.), PO-04-19-125T (=LMG 24282T=NRRL B-41949T; Deinococcus claudionis sp. nov.), ME-04-01-32T (=LMG 24022T=NRRL B-41947T; Deinococcus altitudinis sp. nov.) and ME-04-04-52T (=LMG 24283T=NRRL B-41948T; Deinococcus alpinitundrae sp. nov.) represent the type strains of four novel species of the genus Deinococcus.

[26] Organic solutes from thermophiles and hyperthermophiles

Publisher Summary Research on thermophilic and hyperthermophilic bacteria and archaea has intensified for several years primarily because of the biotechnological importance of their thermostable enzymes. However, the diversity of these organisms, their physiology and biochemistry, and our perception that they represent ancient lines of evolution are sufficient to justify research on these fascinating organisms. Although there is no biological definition that distinguishes a thermophile from a byperthermophile, as a general rule, a thermophile can be described as an organism with optimum growth between 60° and 80° and a hyperthermophile as one that grows optimally at 80° or above. Many thermophilic and hyperthermophilic organisms originate from inland geothermal areas where the salinity of the water is very low, but increasingly, the isolation and description of novel microorganisms has shifted to marine geothermal areas where the levels of NaCl can reach those of seawater. The same interest that fuels research into so many aspects of life at extremely high temperatures also fuels research into osmotic adaptation in thermophilic and hyperthermophilic organisms, leading to the rapid increase in the knowledge of the compatible solutes themselves, their role in the protection of macromolecules, and the mechanisms of osmotic adaptation.

Effect of Growth Temperature on the Lipid Composition of two Strains of Thermus sp.

Summary: Growth-temperature-dependent alterations in the total extractable lipid and polar lipid components of two strains of Thermus sp. isolated from a Portuguese hot spring were studied between 50°C and 78°C. The total extractable lipid varied between 8.0 and 10.6% of the cell dry weight; there were no alterations in the phosphorus and carotenoid content of the lipid extract, but the carbohydrate content increased as the growth temperature was raised. Three glycolipids and the four phospholipids were separated by thin-layer chromatography. The relative concentration of the major glycolipid (GL1) of strain SPS 17 (yellow-pigmented) increased with the growth temperature, whereas the relative concentration of a minor glycolipid (GL2) decreased. There were no temperature-dependent alterations in the relative concentrations of GL1 and GL2 from strain SPS 11 (colourless). The proportion of the major phospholipid (PL2) decreased in both strains as the growth temperature increased, whereas that of a minor phospholipid (PL1) increased. The major fatty acyl chains of both strains were 13-methyltetradecanoate (iso-C15) and 15-methylhexadecanoate (iso-C17). The GL1 in strains SPS 11 and SPS 17 had a glucose:glucosamine:glycerol:long fatty acyl chain ratio of 3:1:1:3.

Presence and Persistence of Legionella spp. in Groundwater

ABSTRACT Groundwater samples (111) from six different boreholes located in two geographical areas were examined for the presence of legionellae over a 7-year period. The number of Legionella isolates detected was generally low. The colonization of the aquifers was not uniform, and the persistence of Legionella was independent of the hydraulic pumps and the plumbing system present in the borehole. A total of 374 isolates identified by fatty acid methyl ester analysis belonged to Legionella pneumophila, L. oakridgensis, L. sainthelensi, and L. londiniensis. In area 1, L. oakridgensis constituted the major population detected, exhibiting only one random amplified polymorphic DNA (RAPD)-PCR profile. L. sainthelensi strains were less frequently isolated and also displayed a single RAPD profile, while L. pneumophila was only sporadically detected. In contrast, L. pneumophila comprised the vast majority of the isolates in area 2 and exhibited six distinct RAPD patterns, indicating the presence of different genetic groups; three L. londiniensis RAPD types were also detected. Two of the L. pneumophila and one of the L. londiniensis RAPD types were persistent in this environment for at least 12 years. The genetic structure of L. pneumophila groundwater populations, inferred from rpoB and dotA gene sequences, was peculiar, since the majority of the isolates were allied in a discrete group different from the lineages containing most of the type and reference strains of the three subspecies of L. pneumophila. Furthermore, gene exchange events related to the dotA allele could be envisioned.