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1.
Luciana Albuquerque Catarina Ferreira David Tomaz Igor Tiago António Veríssimo Milton S. da Costa M. Fernanda Nobre 《Systematic and applied microbiology》2009
Four red-pigmented isolates, with optimum growth temperatures of approximately 55–60 °C and an optimum pH for growth between 7.5 and 8.5, were recovered from hot springs in Central France. Phylogenetic analysis of the 16S rRNA gene sequences showed that these organisms represented a new species of the genus Meiothermus. The new isolates could be distinguished from other strains of the species of the genus Meiothermus primarily by the glycolipid profile and fatty acid composition because these organisms lacked the hydroxy fatty acids and the glycolipid variant GL-1a found in all other isolates of the species of Meiothermus examined. On the basis of the results presented here we propose the name Meiothermus rufus for the new species, which is represented by strains CAL-4T (=DSM 22234T=LMG 24878T) and CAL-12 (=DSM 22235=LMG 24879). We also propose emending the genus Meiothermus to include strains that have only one glycolipid instead of two glycolipid variants. 相似文献
2.
Peltola M Kanto Oqvist C Ekman J Kosonen M Jokela S Kolari M Korhonen P Salkinoja-Salonen M 《Journal of industrial microbiology & biotechnology》2008,35(12):1651-1657
Deinococcus geothermalis has frequently been isolated from pink colored deposits of paper industry processes. Laboratory studies have shown that D. geothermalis is capable of forming on nonliving surfaces patchy biofilms that are resistant to adverse agents such as extreme pH, desiccation,
solubilising detergents and biocides. This study was done to quantitatively assess the role of D. geothermalis as a biofouler in paper industry. Colored deposits were collected from 24 European and North American paper and board machines
and the densities of the bacterial 16S rRNA genes and those of the red slime producers D. geothermalis and Meiothermus spp. were measured by QPCR (quantitative real time PCR). D. geothermalis was found at nine machines, usually from splash area deposits, but its contribution was minor, 0.001–1%, to the total bacterial
burden of 8.3 to log 10.5 log units per gram wet-weight of the deposits. When D. geothermalis was found in a measurable quantity, Meiothermus spp. also was found, often in bulk quantity (7–100% of the total bacteria). The data are in line with the properties of D. geothermalis known from laboratory biofilm studies, indicating this species is a pioneer coloniser of machine surfaces and may help other
bacteria to adhere and grown into biofilms, rather than competing with them. 相似文献
3.
Luciana Albuquerque Fred A. Rainey M. Fernanda Nobre Milton S. da Costa 《Systematic and applied microbiology》2010
Two red-pigmented isolates, with optimum growth temperatures between 45 and 50 °C, were recovered from a hot spring in the Furnas, Área da Fonte 1825 on the Island of São Miguel in the Azores. Phylogenetic analysis of the 16S rRNA gene sequences showed that these organisms represented a new species of the genus Meiothermus. These new isolates could be distinguished from other strains of the species of the genus Meiothermus primarily by the fatty acid composition and polar lipid pattern, since they did not possess 2-OH fatty acids or glycolipid variant GL-1a. Moreover, the two new isolates had the lowest growth temperature range of any of the known species of the genus Meiothermus. On the basis of the results presented here we propose the name Meiothermus granaticius for the new species represented by strains AF-68T (=DSM 23260T = LMG 25524T) and AF-49 (=DSM 23259 = LMG 25525). 相似文献
4.
Early succession of bacterial biofilms in paper machines 总被引:1,自引:0,他引:1
Marja Tiirola Tomi Lahtinen Matti Vuento Christian Oker-Blom 《Journal of industrial microbiology & biotechnology》2009,36(7):929-937
Formation of biofilms causes severe problems in paper machines, and hence financial costs. It would be preferable to prevent
attachment of the primary-colonizing bacteria than to control the growth of secondary communities, which are sheltered by
exopolysaccharide slime layers. We have therefore investigated the early succession of paper-machine biofilms by incubating
stainless-steel test coupons in the process water-flow lines in two paper machines operating in slightly alkaline conditions
in temperatures (45 and 49°C) supporting thermophilic microbes. Microbial succession was profiled using length heterogeneity
analysis of PCR-amplified 16S rRNA genes (LH-PCR) and linking the sequence data of the created 16S rRNA gene libraries to
the dominant LH-PCR peaks. Although the bacterial fingerprints obtained from the attached surface communities varied slightly
in different samples, the biomarker signals of the dominating primary-colonizing bacterial groups remained high over time
in each paper machine. Most of the 16S rRNA gene copies in the early biofilms were assigned to the genera Rhodobacter, Tepidimonas, and Cloacibacterium. The dominance of these sequence types decreased in the developing biofilms. Finally, as phylogenetically identical primary-colonizers
were detected in the two different paper mills, the machines evidently had similar environmental conditions for bacterial
growth and potentially a common source of contamination. 相似文献
5.
Suihko ML Kroppenstedt RM Stackebrandt E 《Journal of industrial microbiology & biotechnology》2006,33(3):183-191
The aim of this study was to characterize the actinobacterial population present in pulps and boards containing recycled fibres.
A total of 107 isolates was identified on the basis of their pigmentation, morphological properties, fatty acid profiles and
growth temperature. Of the wet pulp and water sample isolates (n=87), 74.7% belonged to the genus Streptomyces, 17.2% to Nocardiopsis and 8.0% to thermoactinomycetes, whereas all the board sample isolates (n=20) were thermoactinomycetes. The identification of 53 isolates was continued by molecular methods. Partial 16S rDNA sequencing
and automated ribotyping divided the Streptomyces isolates (n=31) into 14 different taxa. The most common streptomycetes were the mesophilic S. albidoflavus and moderately thermophilic S. thermocarboxydus. The Nocardiopsis isolates (n=11) belonged to six different taxa, whereas the thermoactinomycetes were mainly members of the species Laceyella sacchari (formerly Thermoactinomyces sacchari). The results indicated the probable presence of one or more new species within each of these genera. Obviously, the drying
stage used in the board making processes had eliminated all members of the species Streptomyces and Nocardiopsis present in the wet recycled fibre pulp samples. Only the thermotolerant endospores of L. sacchari were still present in the final products. The potential of automated ribotyping for identifying actinobacteria was indicated,
as soon as comprehensive identification libraries became available. 相似文献
6.
Culturable Actinobacteria from the Marine Sponge Hymeniacidon perleve: Isolation and Phylogenetic Diversity by 16S rRNA gene-RFLP Analysis 总被引:1,自引:0,他引:1
A total of 106 actinobacteria associated with the marine sponge Hymeniacidon perleve collected from the Yellow Sea, China were isolated using eight different media. The number of species and genera of actinobacteria recovered from the different media varied significantly, underlining the importance of optimizing the isolation conditions. The phylogenetic diversity of the actinobacteria isolates was assessed using 16S rRNA gene amplification–restriction fragment length polymorphism (RFLP) analysis of the 106 strains with different morphologies. The RFLP fingerprinting of selected strains by HhaI-digestion of the 16S rRNA genes resulted in 11 different patterns. The HhaI-RFLP analysis gave good resolution for the identification of the actinobacteria isolates at the genus level. A phylogenetic analysis using 16S rRNA gene sequences revealed that the isolates belonged to seven genera of culturable actinobacteria including Actinoalloteichus, Micromonospora, Nocardia, Nocardiopsis, Pseudonocardia, Rhodococcus, and Streptomyces. The dominant genus was Streptomyces, which represented 74% of the isolates. Three of the strains identified are candidates for new species. 相似文献
7.
Márquez MC Carrasco IJ de la Haba RR Jones BE Grant WD Ventosa A 《Systematic and applied microbiology》2011,34(6):424-428
A polyphasic taxonomic study was performed on seven Bacillus-like bacteria isolated from three hypersaline and alkaline lakes located in China, Kenya and Tanzania. All strains were moderately halophilic and alkaliphilic, Gram positive, motile rods. The DNA G+C content from the seven isolates ranged from 42.2 to 43.4 mol% and their major fatty acid was anteiso-C15:0. Strain CG1T, selected as representative strain of the isolates, possesses meso-diaminopimelic acid in the cell wall peptidoglycan, MK-7 as the predominant menaquinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. Comparative 16S rRNA gene sequence analysis indicated that the isolates belonged to the genus Bacillus. The seven isolates shared 97.7–99.9% 16S rRNA gene sequence similarity, and formed a branch that was distinct from the type strains of the recognized species of the genus Bacillus. They were most closely related to Bacillus agaradhaerens DSM 8721T (92.6–93.8% 16S rRNA sequence similarity). DNA–DNA hybridization values between the seven isolates were 85–100%. According to the polyphasic characterization, the strains represent a novel species, for which the name Bacillus locisalis sp. nov. is proposed. The type strain is CG1T (CCM 7370T = CECT 7152T = CGMCC 1.6286T = DSM 18085T). 相似文献
8.
Rasimus S Kolari M Rita H Hoornstra D Salkinoja-Salonen M 《Journal of industrial microbiology & biotechnology》2011,38(9):1379-1390
Biofilms cause runnability problems in paper machines and are therefore controlled with biocides. Peracetic acid is usually
effective in preventing bulky biofilms. This study investigated the microbiological status of a paper machine where low concentrations
(≤15 ppm active ingredient) of peracetic acid had been used for several years. The paper machine contained a low amount of
biofilms. Biofilm-forming bacteria from this environment were isolated and characterized by 16S rRNA gene sequencing, whole-cell
fatty acid analysis, biochemical tests, and DNA fingerprinting. Seventy-five percent of the isolates were identified as members
of the subclades Sphingomonas
trueperi and S. aquatilis, and the others as species of the genera Burkholderia (B. cepacia complex), Methylobacterium, and Rhizobium. Although the isolation media were suitable for the common paper machine biofoulers Deinococcus, Meiothermus, and Pseudoxanthomonas, none of these were found, indicating that peracetic acid had prevented their growth. Spontaneous, irreversible loss of the
ability to form biofilm was observed during subculturing of certain isolates of the subclade S. trueperi. The Sphingomonas isolates formed monoculture biofilms that tolerated peracetic acid at concentrations (10 ppm active ingredient) used for
antifouling in paper machines. High pH and low conductivity of the process waters favored the peracetic acid tolerance of
Sphingomonas sp. biofilms. This appears to be the first report on sphingomonads as biofilm formers in warm water using industries. 相似文献
9.
Two Phosphate- and Potassium-solubilizing Bacteria Isolated from Tianmu Mountain, Zhejiang, China 总被引:1,自引:0,他引:1
Xiufang Hu Jishuang Chen Jiangfeng Guo 《World journal of microbiology & biotechnology》2006,22(9):983-990
Summary Two phosphate- and potassium-solubilizing strains (KNP413 and KNP414) were isolated from the soil of Tianmu Mountain, Zhejiang Province (China) and they were phenotypically and phylogenetically characterized. Both isolates effectively dissolved mineral phosphate and potassium, while strain KNP414 showed higher dissolution capacity even than Bacillus mucilaginosus AS1.153, the inoculant of potassium fertilizer widely used in China. When grown on Aleksandrov medium, both strains were rod-shaped spore-formers with a large capsule, and they formed slimy and translucent colonies. The DNA G+C contents were 57.7 mol% for strain KNP413 and 56.1 mol% for strain KNP414. Strain KNP413 shared a 16S rRNA gene sequence similarity of more than 99.1% with strain KNP414 and Bacillus mucilaginosus strains HSCC 1605 and YNUC0001, and a 94.6% similarity with Bacillus mucilaginosus VKM B-1480D, the type strain of Bacillus mucilaginosus. Strains KNP413 and KNP414 together with other Bacillus mucilaginosus were clustered with Paenibacillus strains in a group. The use of a specific PCR primer PAEN515F designed for differentiating the genus Paenibacillus from other members of the Bacillaceae showed that strains KNP413 and KNP414 had the same amplified 16S rRNA gene fragment (0.9-kb) as members of the genus Paenibacillus. In conclusion, phosphate- and potassium-solubilizing strains KNP413 and KNP414 should be integrated into the same species different from strain VKM B-1480D and they might be transferred to the genus of Paenibacillus, i.e. Paenibacillus mucilaginosus.The GenBank accession numbers of the 16S rRNA gene sequences are AY646227 for KNP413 and AY646228 for KNP414. 相似文献
10.
The aim of this study was to compare the ability of commonly used conventional biochemical tests, sequencing analysis of 16S
rRNA genes and tDNA-intergenic spacer length polymorphism (tDNA-PCR) to identify species of the genus Bacillus recovered from marine sediments. While biochemical tests were not sufficiently sensitive to distinguish between the 23 marine
strains analyzed, partial 16S rRNA gene sequences allowed a correct identification, clustering them into four species belonging
to Bacillus licheniformis (n = 6), Bacillus cereus (n = 9), Bacillus subtilis (n = 7) and Bacillus pumilus (n = 1). The identification results obtained with 16S rRNA sequencing were validated by tDNA-PCR analysis of 23 marine isolates
that were identified by the similarities of their fingerprints to those of reference strains. tDNA-PCR fingerprinting was
as discriminatory as 16S rRNA sequencing analysis. Although it was not able to distinguish among the species of the B. cereus and B. subtilis groups, it should be considered a rapid and easy approach for the reliable identification of unknown Bacillus isolates or at least for the primary differentiation of Bacillus groups. 相似文献
11.
Strain B31T is a Gram-staining-negative, motile, and extremely halophilic archaeon that was isolated from salt-fermented seafood. Its
morphology, physiology, biochemical features, and 16S rRNA gene sequence were determined. Phylogenetic analysis of its 16S
rRNA gene sequence and composition of its major polar lipids placed this archaeon in the genus Halorubrum of the family Halobacteriaceae. Strain B31T showed 97.3, 97.2, and 96.9 % 16S rRNA similarity to the type strains of Halorubrum alkaliphilum, Hrr. tibetense, and Hrr. vacuolatum, respectively. Its major polar lipids were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me)
and sulfated diglycosyl diether (S-DGD). Genomic DNA from strain B31T has a 61.7 mol% G+C content. Analysis of 16S rRNA gene sequences, as well as physiological and biochemical tests, identified
genotypic and phenotypic differences between strain B31T and other Halorubrum species. The type strain of the novel species is B31T (=JCM 15757T =DSM 19504T). 相似文献
12.
A culture-independent, nested PCR procedure based on genus-specific oligonucleotide primers detected the presence of members of the genus Dactylosporangium in 14 out of 21 diverse environmental samples. Clones generated from the 14 positive environmental samples formed distinct phyletic lines in the dactylosporangial 16S rRNA gene tree. Presumptive dactylosporangiae were isolated from 7 of these samples using a medium designed to be selective for members of the genus Dactylosporangium, namely Streptomyces Isolation Medium supplemented with gentamicin and antifungal antibiotics. One hundred and two out of 219 representative presumptive dactylosporangiae were considered as authentic members of the genus Dactylosporangium as they gave PCR amplification products using the genus-specific primers and had chemical features typical of dactylosporangiae. Representative of the Dactylosporangium isolates formed distinctive phyletic lines in the dactylosporangial 16S rRNA gene tree, contained the non-ribosomal peptide and type-I polyketide synthase genes and inhibited the growth of Bacillus subtilis, Kocuria rhizophila and Staphylococcus aureus strains. It is evident from these results that the genus Dactylosporangium is underspeciated, widely distributed in natural habitats and is a potentially rich source of novel secondary metabolites. 相似文献
13.
Comparative 16S rRNA gene sequence and genomic DNA reassociation analyses were used to assess the phylogenetic relationships
of Methanobrevibacter fecal isolates. The 16S rRNA gene sequences of Methanobrevibacter smithii strain PS and the human fecal isolates B181 and ALI were essentially identical, and their genomic DNA reassociated at values
greater than 94%. The analysis of 16S rRNA sequences of the horse, pig, cow, rat, and goose fecal isolates confirm that they
are members of the genus Methanobrevibacter. They had a high degree of sequence similarity (97–98%) with the 16S rRNA gene of M. smithii, indicating that they share a common line of descent. The 16S rRNA genes of the horse and pig isolates had 99.3% sequence
similarity. Sequence analysis of the 16S rRNA gene of the sheep fecal isolate showed that it formed a separate line of descent
in the genus Methanobrevibacter. Genomic DNA reassociation studies indicate that the horse, pig, cow, and goose fecal isolates represent at least three new
species. The horse and pig isolates were the only animal isolates that had > 70% genomic DNA reassociation and represent strains
of a single species. The cow, goose, and sheep isolates had little or no genomic DNA reassociation with M. smithii or with each other. The relationship of the rat isolate to the other animal isolates was not determined. An evaluation of
the relationship of 16S rRNA gene sequence similarity and genomic DNA reassociation of Methanobrevibacter and other methanogenic archaea indicated that genomic DNA reassociation studies are necessary to establish that two methanogenic
organisms belong to the same species.
Received: 17 November 1997 / Accepted: 16 January 1998 相似文献
14.
Santillana N Ramírez-Bahena MH García-Fraile P Velázquez E Zúñiga D 《Archives of microbiology》2008,189(3):239-247
In this study 17 isolates from effective nodules of Vicia faba and Pisum sativum var. macrocarpum growing in different soils from Peru were isolated and characterized. The isolates, presenting 11 different
RAPD profiles, were distributed in three groups on the basis of their 16S-RFLP patterns. The 16S rRNA gene sequences of strains
from 16S-RFLP groups I, II and III were closely related (identities higher than 99.5%) to Rhizobium leguminosarum bv. trifolii DSM 30141 (=ATCC 14480), R. leguminosarum bv. viciae DSM 30132T and Rhizobium etli CFN42T (=USDA 9032T), respectively. The analysis of the 16S–23S intergenic spacer (ITS) and two housekeeping genes, atpD and recA, confirmed the identification of strains from group I, however those from groups II and III were phylogenetically divergent
to strains DSM 30132T and CFN42T. These results support the fact that the 16S rRNA gene is not adequate for identification at species level within genus Rhizobium and suggest the existence of putative new species within the phylogenetic group of R. leguminosarum. They also confirm the need of a taxonomic revision of R. leguminosarum since the reference strains of the three biovars included in this study are phylogenetically divergent according to their
ITS, atpD and recA gene sequences. 相似文献
15.
Phylogenetic relations within the genus Gordonia were analyzed using partial gyrB and secA1 gene sequences of 23 type species in comparison with those of 16S rRNA gene. The gyrB and secA1 phylogenies showed agreement with that constructed using 16S rRNA gene sequences. The degrees of divergence of the gyrB and secA1 genes were approximately 3.4 and 1.7 times greater, respectively, than that of 16S rRNA gene. The gyrB gene showed more discriminatory power than either the secA1 or 16S rRNA gene, facilitating clear differentiation of any two Gordonia species using gyrB gene analysis. Our data indicate that gyrB and secA1 gene sequences are useful as markers for phylogenetic study and identification at the species level of the genus Gordonia. 相似文献
16.
Perevalova A. A. Lebedinsky A. V. Bonch-Osmolovskaya E. A. Chernyh N. A. 《Microbiology》2003,72(3):340-346
Based on the analysis of nucleotide sequences of 16S rRNA, oligonucleotide probes were designed for the detection and identification of representatives of the genus Desulfurococcus (kingdom Crenarchaeota of the domain Archaea). The detection procedure included obtaining PCR products on DNA isolated from pure cultures, enrichments, or natural samples with a designed Crenarchaeota-specific primer pair: Cren 7F (5"-TTCCGGTTGATCCYGCCGGACC-3") and Cren 518R (5"-GCTGGTWTTACCGCGGCGGCTGA-3"). The PCR products were hybridized with Dig-11-dUTP–labeled oligonucleotide probes targeting the genus Desulfurococcus (Dco 198, 5"-CGTTAACYCCYGCCACACC-3") and its species D. mobilis (Dco_mob 198, 5"-CGTTAACCCCTGCCACACC-3") and D. amylolyticus (Dco_amy 198, 5"-CGTTAACCCCCGCCACACC-3"). With the use of these primers and probes, four new strains isolated from hydrotherms of Kamchatka and Kunashir Island were identified as members of the speciesDesulfurococcus amylolyticus. Desulfurococcus representatives were detected in several natural samples, including a sample taken from a marine hydrotherm at Kunashir Island; this demonstrates that representatives of this genus occur not only in terrestrial but also in marine environments. 相似文献
17.
Comparison of 16S rRNA gene sequences of genus <Emphasis Type="Italic">Methanobrevibacter</Emphasis>
Abhijit?S?Dighe Kamlesh?Jangid José?M?González Vyankatesh?J?Pidiyar Milind?S?Patole Dilip?R?Ranade Yogesh?S?Shouche
Background
The phylogeny of the genus Methanobrevibacter was established almost 25 years ago on the basis of the similarities of the 16S rRNA oligonucleotide catalogs. Since then, many 16S rRNA gene sequences of newly isolated strains or clones representing the genus Methanobrevibacter have been deposited. We tried to reorganize the 16S rRNA gene sequences of this genus and revise the taxonomic affiliation of the isolates and clones representing the genus Methanobrevibacter. 相似文献18.
19.
Phylogenetic diversity among filamentous sulfur-oxidizing bacteria of the genus Thioploca inhabiting freshwater/brackish environments was analyzed in detail. The 16S rRNA gene sequence of Thioploca found in a freshwater lake in Japan, Lake Okotanpe, was identical to that of Thioploca from Lake Ogawara, a brackish lake. The samples of the two lakes could be differentiated by the sequences of their 23S rRNA
genes and 16S–23S rRNA internal transcribed spacer (ITS) regions. The 23S rRNA-based phylogenetic relationships between Thioploca samples from four lakes (Lake Okotanpe, Lake Ogawara, Lake Biwa, and Lake Constance) were similar to those based on the 16S
rRNA gene sequences. In addition, multiple types of the ITS sequences were obtained from Thioploca inhabiting Lake Okotanpe and Lake Constance. Variations within respective Thioploca populations were also observed in the analysis of the soxB gene, involved in sulfur oxidation. As major members of the sheath-associated microbial community, bacteria of the phylum
Chloroflexi were consistently detected in the samples from different lakes. Fluorescence in situ hybridization revealed that they were
filamentous and abundantly distributed within the sheaths of Thioploca. 相似文献
20.
Little is known about the genus Verrucosispora though it does contain organisms which produce novel antibiotics. A set of genus-specific oligonucleotide primers was generated
to gain an insight into the presence, distribution and taxonomic diversity of members of this genus in diverse samples taken
from marine habitats. In silico and pure culture studies showed that the primers matched perfectly with target sequences of
the 16S rRNA genes of representatives of the genus Verrucosispora. The primers, designated S-G-Verr-0195-a-S-20 and S-G-Verr-1152-a-A-18, amplified an ≈960 bp stretch of the 16S rRNA genes
of Verrucosispora strains but not those of representatives of other genera classified in the family Micromonosporaceae. Genus-specific amplicons were detected from 17 out of 20 community DNA samples prepared from diverse marine sediments and
coastal soils. Phylogenetic analysis of over 40% of clones derived from five of the samples indicated they belonged to novel
Verrucosispora species. The primers were also used to confirm the identity of Verrucosispora-like strains isolated from two of the environmental samples. The primers can be used to facilitate the isolation of novel
Verrucosispora strains by allowing prescreening of environmental samples and the subsequent identification of verrucosisporae on selective
isolation plates. For this purpose, a novel medium facilitating the recovery of Verrucosispora strains was formulated and used to recover novel isolates validated using the novel PCR primers. This medium may be useful
as the basis for development of a selective medium. 相似文献