A single extremely halophilic strain was isolated from salt brine produced when a fresh water lake flooded a large salt mine located beneath the lake. The water that entered this mine contained less ...than 0.34 M NaCl, but over time, this sealed brine became saturated by Cenozoic age salt (121–125 million-year BCE). The isolated strain requires at least 1.7 M NaCl for survival and grows optimally in 3.1 M NaCl. Therefore, it could not have survived or been present in the waters that flooded this salt mine. The strain grows at a pH range from 6.5 to 9.0 and has a wide tolerance to temperatures from 25 ℃ to at least 60 ℃. The comparison of 16S rRNA and
rpoB′
genes revealed that strain 1–13-28
T
is related to
Halorubrum tebenquichense
DSM 14210
T
showing 98.6% and 98.1% similarities, respectively. Phylogenetic analyses based on 16S rRNA,
rpoB′
genes and 122 concatenated archaeal genes show that the strain 1–13-28
T
consistently forms a cluster with
Halorubrum tebenquichense
of the genus
Halorubrum.
Strain 1–13-28
T
contained sulfated mannosyl glucosyl diether, and the polar lipid profile was identical to those of most
Halorubrum
species. Based on the overall combination of physiological, phylogenetic, polar lipids and phylogenomic characteristics, strain 1–13-28
T
(= ATCC 700083
T
= CGMCC 1.62627
T
) represents a newly identified species within the genus
Halorubrum
for which the name
Halorubrum hochsteinianum
is proposed.
Full text
Available for:
EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Bacteria have been found associated with a variety of ancient samples, however few studies are generally accepted due to questions about
sample quality and contamination. When Cano and Borucki ...isolated
a strain of Bacillus sphaericus from an extinct bee trapped in 25-30
million-year-old amber, careful sample selection and stringent sterilization
techniques were the keys to acceptance. Here we report the isolation and growth
of a previously unrecognized spore-forming bacterium (Bacillus species,
designated 2-9-3) from a brine inclusion within a 250 million-year-old
salt crystal from the Permian Salado Formation. Complete gene sequences of
the 16S ribosomal DNA show that the organism is part of the lineage of
Bacillus marismortui and Virgibacillus pantothenticus. Delicate
crystal structures and sedimentary features indicate the salt has not recrystallized
since formation. Samples were rejected if brine inclusions showed physical
signs of possible contamination. Surfaces of salt crystal samples were sterilized
with strong alkali and acid before extracting brines from inclusions. Sterilization
procedures reduce the probability of contamination to less than 1 in 10
9.
Full text
Available for:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Halophilic archaea of the class
are the most salt-requiring prokaryotes within the domain
. In 1997, minimal standards for the description of new taxa in the order
were proposed. From then on, the ...taxonomy of the class
provides an excellent example of how changing concepts on prokaryote taxonomy and the development of new methods were implemented. The last decades have witnessed a rapid expansion of the number of described taxa within the class
coinciding with the era of genome sequencing development. The current members of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of
propose these revisions to the recommended minimal standards and encourage the use of advanced technologies in the taxonomic description of members of the
. Most previously required and some recommended minimal standards for the description of new taxa in the class
were retained in the present revision, but changes have been proposed in line with the new methodologies. In addition to the 16S rRNA gene, the
gene is an important molecular marker for the identification of members of the
. Phylogenomic analysis based on concatenated conserved, single-copy marker genes is required to infer the taxonomic status of new taxa. The overall genome relatedness indexes have proven to be determinative in the classification of the taxa within the class
. Average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values should be calculated for rigorous comparison among close relatives.
1 Spanish Type Culture Collection (CECT) and Department of Microbiology and Ecology, University of Valencia, 46100 Valencia, Spain
2 Ancient Biomaterials Institute and Department of Biology, West ...Chester University, West Chester, PA 19383, USA
3 Department of Environmental Science and Policy, George Mason University, Manassas, VA 20110, USA
4 Department of Biological Sciences, University of Missouri-Rolla, Rolla, MO 65401, USA
5 German Collection of Microorganisms and Cell Cultures (DSMZ), Inhoffenstrasse 7b, 38124 Braunschweig, Germany
6 The Institute of Life Sciences and the Moshe Shilo Minerva Center for Marine Biogeochemistry, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
7 Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
8 Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
Correspondence Antonio Ventosa ventosa{at}us.es
Following Recommendation 30b of the Bacteriological Code (1990 Revision), a proposal of minimal standards for describing new taxa within the family Halomonadaceae is presented. An effort has been made to evaluate as many different approaches as possible, not only the most conventional ones, to ensure that a rich polyphasic characterization is given. Comments are given on the advantages of each particular technique. The minimal standards are considered as guidelines for authors to prepare descriptions of novel taxa. The proposals presented here have been endorsed by the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halomonadaceae .
This book is designed to be a long term career reference. The chapters present modern procedures. This is a how-to-book with a difference. These chapters: - reveal the background information about ...working with salt loving organisms, - are loaded with information about how experiments are conducted under high salt, - provide information about analyses that work under these conditions and those that may not, - present a wide range of details from laboratory designs to equipment used and even to simple anecdotal hints that can only come from experience. Microbiological training focuses largely on the growth, the handling and the study of the microbes associated with humans and animals. Yet the largest proportion of the Earths microbiota lives in saline environments such as the Oceans, saline deserts and terminal hypersaline environments. This need for salt can be intimidating for those interested in entering the field or for those interested in understanding how such research is accomplished.
Full text
Available for:
FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
1 Graduate School of Biosphere Science, Hiroshima University, Kagamiyama, Higashi-hiroshima 739-8528, Japan
2 Unit de Recherche 09-03, Ecotoxicologie Marine, Institut Préparatoire aux Etudes ...d'Ingénieurs de Sfax, Université de Sfax, IPEIS BP 805, 3018 Sfax, Tunisia
3 Ancient Biomaterials Institute and Department of Biology, West Chester University, West Chester, PA 19383, USA
4 Alliance for Research on Northern Africa, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8572, Japan
Correspondence Takeshi Naganuma takn{at}hiroshima-u.ac.jp
A Gram-positive, endospore-forming, rod-shaped and moderately halophilic bacterium was isolated from a salt-crust sample collected from Gharsa salt lake (Chott el Gharsa), Tunisia. The newly isolated bacterium, designated SA-Vb1 T , was identified based on polyphasic taxonomy including genotypic, phenotypic and chemotaxonomic characterization. Strain SA-Vb1 T was closely related to the type strains of Virgibacillus marismortui and Virgibacillus olivae , with 16S rRNA gene sequence similarities of 99.7 and 99.4 %, respectively. However, strain SA-Vb1 T was distinguished from these two type strains on the basis of phenotypic characteristics and DNA–DNA relatedness (29.4 and 5.1 %, respectively). The genetic relationship between strain SA-Vb1 T and Virgibacillus pantothenticus IAM 11061 T (the type strain of the type species) and other type strains of the genus was 96–98 % based on 16S rRNA gene sequence similarity and 18.3–22.3 % based on DNA–DNA hybridization. Biochemical analysis resulted in determination of major fatty acids iso-C 15 : 0 , anteiso-C 15 : 0 and anteiso-C 17 : 0 (33.3, 29.2 and 9.8 %, respectively); phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine were the main polar lipids and MK-7 was the predominant menaquinone ( 100 %). The distinct characteristics demonstrated by strain SA-Vb1 T represent properties of a novel species of the genus Virgibacillus , for which the name Virgibacillus salarius sp. nov. is proposed. The type strain is SA-Vb1 T (=JCM 12946 T =DSM 18441 T ).
Abbreviations: CZE, capillary zone electrophoresis
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain SA-Vb1 T is AB197851 .
Fatty acid profiles of strain SA-Vb1 T and related type strains and detailed 16S rRNA gene sequence similarity and DNA–DNA hybridization results are available as supplementary material with the online version of this paper.
A halophilic archaeon has been isolated from unsterilized salt crystals taken from the 250-million-year-old Salado formation in southeastern New Mexico. This microorganism grows only on defined media ...supplemented with either a combination of acetate and glycerol, glycerol and pyruvate, or pyruvate alone. The archaeon is unable to grow on complex media or to use carbohydrates, amino acids, fats, proteins, or nucleic acids for growth. Unlike other halophilic microbes, this organism possesses four glycolipids, two of which may be novel. The microbe is unique in that it has three dissimilar 16S rRNA genes. Two of the three genes show only 97% similarity to one another, while the third gene possesses only 92%-93% similarity to the other two. Inferred phylogenies indicate that the organism belongs to a deep branch in the line of Haloarcula and Halorhabdus. All three lines of taxonomic evidence: phenotype, lipid patterns, and phylogeny, support creation of a new genus and species within the halophilic Archaea. The name suggested for this new genus and species is Halosimplex carlsbadense. The type strain is 2-9-1(T) (= ATCC BAA-75 and JCM 11222) as written in the formal description.
Full text
Available for:
EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
The isolation of living microorganisms from primary 250-million-year-old (MYA) salt crystals has been questioned by several researchers. The most intense discussion has arisen from questions about ...the texture and age of the crystals used, the ability of organisms to survive 250 million years when exposed to environmental factors such as radiation and the close similarity between 16S rRNA sequences in the Permian and modern microbes. The data in this manuscript are not meant to provide support for the antiquity of the isolated bacterial strains. Rather, the data presents several comparisons between the Permian microbes and other isolates to which they appear related. The analyses include whole cell fatty acid profiling, DNA-DNA hybridizations, ribotyping, and random amplified polymorphic DNA amplification (RAPD). These data show that the Permian strains, studied here, differ significantly from their more modern relatives. These differences are accumulating in both phenotypic and molecular areas of the cells. At the fatty acid level the differences are approaching but have not reached separate species status. At the molecular level the variation appears to be distributed across the genome and within the gene regions flanking the highly conserved 16S rRNA itself. The data show that these bacteria are not identical and help to rule out questions of contamination by putatively modern strains.
Full text
Available for:
EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
PDF
