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rRNA Gene Sequences (rrna + gene_sequence)
Terms modified by rRNA Gene Sequences Selected AbstractsPhylogenetic Analysis of Complete rRNA Gene Sequence of Nosema philosamiae Isolated from the Lepidopteran Philosamia cynthia riciniTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 3 2010FENG ZHU ABSTRACT. The microsporidian Nosema philosamiae is a pathogen that infects the eri-silkworm Philosamia cynthia ricini. The complete sequence of rRNA gene (4,314 bp) was obtained by polymerase chain reaction amplification with specific primers and sequencing. The sequence analysis showed that the organization of the rRNA of N. philosamiae was similar to the pattern of Nosema bombycis. Phylogenetic analysis of rRNA gene sequences revealed that N. philosamiae had a close relationship with other Nosema species, confirming that N. philosamiae is correctly assigned to the genus Nosema. [source] Taxonomic Redescriptions of Two Ciliates, Protogastrostyla pulchra n. g., n. comb. and Hemigastrostyla enigmatica (Ciliophora: Spirotrichea, Stichotrichia), with Phylogenetic Analyses Based on 18S and 28S rRNA Gene SequencesTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 6 2007JUN GONG ABSTRACT. The morphology and infraciliature of two stichotrichid ciliates, Gastrostyla pulchra(Perejaslawzewa 1886) Kahl, 1932 and Hemigastrostyla enigmatica(Dragesco and Dragesco-Kernéis 1986) Song & Wilbert, 1997, collected from marine and brackish sediments, were investigated by using living observations and protargol impregnations. Both 18S and 28S rRNA genes of these two species were sequenced. The 18S rDNA show high similarities (98.4%,99.7%) among populations of each species. There is about 94% similarity in 18S rDNA genes between G. pulchra and Gastrostyla steinii, the type species of the genus, which has been confirmed to be an oxytrichid by previous studies. In the phylogenetic trees of 18S, 28S, and combined 18S and 28S rDNA, both G. pulchra and H. enigmatica are consistently placed outside the well-established oxytrichid clade. Based on our analyses and previous ontogenetic data, we conclude that these two species may represent some lower groups in the subclass Stichotrichia, and that G. pulchra should represent a new genus, Protogastrostyla n. g. This new genus, which is morphologically similar to Gastrostyla, differs in its morphogenesis: the apical part of the old AZM is retained combining with the newly built membranelles that develop from the proter's oral primordium; the primary primordia of the dorsal kinety; and marginal primordia commence de novo without a definite contribution from the old structure. [source] Reevaluation of the Phylogenetic Relationship between Mobilid and Sessilid Peritrichs (Ciliophora, Oligohymenophorea) Based on Small Subunit rRNA Genes SequencesTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 5 2006YING-CHUN GONG ABSTRACT. Based on morphological characters, peritrich ciliates (Class Olygohymenophorea, Subclass Peritrichia) have been subdivided into the Orders Sessilida and Mobilida. Molecular phylogenetic studies on peritrichs have been restricted to members of the Order Sessilida. In order to shed more light into the evolutionary relationships within peritrichs, the complete small subunit rRNA (SSU rRNA) sequences of four mobilid species, Trichodina nobilis, Trichodina heterodentata, Trichodina reticulata, and Trichodinella myakkae were used to construct phylogenetic trees using maximum parsimony, neighbor joining, and Bayesian analyses. Whatever phylogenetic method used, the peritrichs did not constitute a monophyletic group: mobilid and sessilid species did not cluster together. Similarity in morphology but difference in molecular data led us to suggest that the oral structures of peritrichs are the result of evolutionary convergence. In addition, Trichodina reticulata, a Trichodina species with granules in the center of the adhesive disc, branched separately from its congeners, Trichodina nobilis and Trichodina heterodentata, trichodinids without such granules. This indicates that granules in the adhesive disc might be a phylogenetic character of high importance within the Family Trichodinidae. [source] Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragmentsENVIRONMENTAL MICROBIOLOGY, Issue 12 2005Takuro Nunoura Summary Within a phylum Crenarchaeota, only some members of the hyperthermophilic class Thermoprotei, have been cultivated and characterized. In this study, we have constructed a metagenomic library from a microbial mat formation in a subsurface hot water stream of the Hishikari gold mine, Japan, and sequenced genome fragments of two different phylogroups of uncultivated thermophilic Crenarchaeota: (i) hot water crenarchaeotic group (HWCG) I (41.2 kb), and (ii) HWCG III (49.3 kb). The genome fragment of HWCG I contained a 16S rRNA gene, two tRNA genes and 35 genes encoding proteins but no 23S rRNA gene. Among the genes encoding proteins, several genes for putative aerobic-type carbon monoxide dehydrogenase represented a potential clue with regard to the yet unknown metabolism of HWCG I Archaea. The genome fragment of HWCG III contained a 16S/23S rRNA operon and 44 genes encoding proteins. In the 23S rRNA gene, we detected a homing-endonuclease encoding a group I intron similar to those detected in hyperthermophilic Crenarchaeota and Bacteria, as well as eukaryotic organelles. The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota. [source] Isolation and properties of methanesulfonate-degrading Afipia felis from Antarctica and comparison with other strains of A. felisENVIRONMENTAL MICROBIOLOGY, Issue 1 2005S. Azra Moosvi Summary Three novel strains of methylotrophic Afipia felis were isolated from several locations on Signy Island, Antarctica, and a fourth from estuary sediment from the River Douro, Portugal. They were identified as strains of the ,-2 proteobacterium A. felis by 16S rRNA gene sequence, analysis., Two, strains, tested, were, shown to contain the fdxA gene, diagnostic for A. felis. All strains grew with methanesulfonate (and two strains with dimethylsulfone) as sole carbon substrate. Growth on methanesulfonate required methanesulfonate monooxygenase (MSAMO), using NADH as the reductant and stimulated by reduced flavin nucleotides and Fe(II). Polymerase chain reaction amplification of DNA from an Antarctic strain showed a typical msmA gene for the ,-hydroxylase of MSAMO, and both Antarctic and Portuguese strains contained mxaF, the methanol dehydrogenase large subunit gene. This is the first report of methanesulfonate-degrading bacteria from the Antarctic and of methylotrophy in Afipia, and the first description of any bacterium able to use both methanesulfonate and dimethylsulfone. In contrast, the type strain of A. felis DSM 7326T was not methylotrophic, but grew in defined mineral medium with a wide range of single simple organic substrates. Free-living Afipia strains occurring widely in the natural environment may be significant as methylotrophs, degrading C1 -sulfur compounds, including the recalcitrant organosulfur compound methanesulfonate. [source] Early diagnosis of rhinocerebral mucormycosis by cerebrospinal fluid analysis and determination of 16s rRNA gene sequenceEUROPEAN JOURNAL OF NEUROLOGY, Issue 9 2007D. Bengel A 40-year-old diabetic woman was diagnosed with rhinocerebral mucormycosis. Cerebral mucormycosis is an acute life-threatening disease, which is caused by fungi of the class Phycomycetae. Clinical suspicion and detection of the fungal hyphae in cerebrospinal fluid (CSF) led to early diagnosis, subsequently confirmed by immunohistochemistry and molecular analysis of fungal RNA. Early infiltration of the infectious agent into the central nervous system resulted in septic thrombosis of the cavernous sinus, mycotic meningoencephalitis, brain infarctions as well as intracerebral and subarachnoidal hemorrhages. Despite immediate high-dose antimycotic treatment, surgical debridement of necrotic tissue, and control of diabetes as a predisposing factor, the woman died 2 weeks after admission. Although fungal organisms are rarely detectable in CSF specimens from patients with mycotic infections of the central nervous system, comprehensive CSF examination is beneficial in the diagnosis of rhinocerebral mucormycosis. Furthermore, a concerted team approach, systemic antifungal agents and early surgical intervention seem to be crucial for preventing rapid disease progression. [source] Isolation and characterization of a bacterial strain of the genus Ochrobactrum with methyl parathion mineralizing activityJOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2006X.-H. Qiu Abstract Aims:, To isolate and characterize a methyl parathion (MP)-mineralizing bacterium, and to elucidate the degradative pathway of MP and localize the responsible degrading genes. Methods and Results:, A bacterial strain, designated B2, capable of mineralizing MP was isolated from the MP-polluted soil. Analysis of the 16S rRNA gene sequence and phenotypic analysis suggested that strain B2 had a close relationship with Ochrobactrum anthropi. B2 could totally degrade MP and four metabolites [p -nitrophenol (PNP), 4-nitrocatechol (4-NC), 1,2,4-benzenetriol (BT) and hydroquinone (HQ)] were identified by HPLC and gas chromatography-mass spectrometry analyses. Plasmid curing of strain B2 resulted in the loss of ability of B2 to degrade PNP, but not the ability to hydrolyse MP. Conclusions:,Ochrobactrum sp. B2 can mineralize MP rapidly via PNP, 4-NC, BT and HQ pathway. B2 harbours a plasmid encoding the ability to degrade PNP, while MP-hydrolysing activity is encoded on the bacterial chromosome. Significance and Impact of the Study:, This new bacterial strain (B2) capable of mineralizing MP will be useful in a pure-culture remediation process of organophosphate pesticides and their metabolites such as nitroaromatics. [source] Physiological characterization of Mycobacterium sp. strain 1B isolated from a bacterial culture able to degrade high-molecular-weight polycyclic aromatic hydrocarbonsJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2004C.E. Dandie Abstract Aim:, The aim of this study was to further characterize a bacterial culture (VUN 10,010) capable of benzo[a]pyrene cometabolism. Methods and Results:, The bacterial culture, previously characterized as a pure culture of Stenotrophomonas maltophilia (VUN 10,010), was found to also contain another bacterial species (Mycobacterium sp. strain 1B), capable of degrading a similar range of PAH substrates. Analysis of its 16S rRNA gene sequence and growth characteristics revealed the strain to be a fast-growing Mycobacterium sp., closely related to other previously isolated PAH and xenobiotic-degrading mycobacterial strains. Comparison of the PAH-degrading characteristics of Mycobacterium sp. strain 1B with those of S. maltophilia indicated some similarities (ability to degrade phenanthrene and pyrene), but some differences were also noted (S. maltophilia able to degrade fluorene, but not fluoranthene, whereas Mycobacterium sp. strain 1B can degrade fluoranthene, but not fluorene). Unlike the S. maltophilia culture, there was no evidence of benzo[a]pyrene degradation by Mycobacterium sp. strain 1B, even in the presence of other PAHs (ie pyrene) as co-metabolic substrates. Growth of Mycobacterium sp. strain 1B on other organic carbon sources was also limited compared with the S. maltophilia culture. Conclusions:, This study isolated a Mycobacterium strain from a bacterial culture capable of benzo[a]pyrene cometabolism. The Mycobacterium strain displays different PAH-degrading characteristics to those described previously for the PAH-degrading bacterial culture. It is unclear what role the two bacterial strains play in benzo[a]pyrene cometabolism, as the Mycobacterium strain does not appear to have endogenous benzo[a]pyrene degrading ability. Significance and Impact of the Study:, This study describes the isolation and characterization of a novel PAH-degrading Mycobacterium strain from a PAH-degrading culture. Further studies utilizing this strain alone, and in combination with other members of the consortium, will provide insight into the diverse roles different bacteria may play in PAH degradation in mixed cultures and in the environment. [source] HETEROGENEITY OF THE CYANOBACTERIAL GENUS SYNECHOCYSTIS AND DESCRIPTION OF A NEW GENUS, GEMINOCYSTIS,JOURNAL OF PHYCOLOGY, Issue 4 2009Jana Korelusová The study and revision of the unicellular cyanobacterial genus Synechocystis was based on the type species S. aquatilis Sauv. and strain PCC 6803, a reference strain for this species. Uniformity in rRNA gene sequence, morphology, and ultrastructure was observed in all available Synechocystis strains, with the exception of the strain PCC 6308, which has been considered by some to be a model strain for Synechocystis. This strain differs substantially from the typical Synechocystis cluster according to both molecular (<90% of similarity, differences in 16S,23S rRNA internal transcribed spacer [ITS] secondary structure) and phenotypic criteria (different ultrastructure of cells). This strain is herein classified into the new genus Geminocystis gen. nov., as a sister taxon to the genus Cyanobacterium. Geminocystis differs from Cyanobacterium by genetic position (<94.4% of similarity) and more importantly by its different type of cell division. Because strain PCC 6308 was designated as a reference strain of the Synechocystis cluster 1 in Bergey's Manual, the members of this genetic cluster have to be revised and reclassified into Geminocystis gen. nov. Only the members of the Synechocystis cluster 2 allied with PCC 6803 correspond both genetically and phenotypically to the type species of the genus Synechocystis (S. aquatilis). [source] 16S rDNA targeted PCR for the detection of Paenibacillus maceransLETTERS IN APPLIED MICROBIOLOGY, Issue 5 2003R.E. Vollú Abstract Aims: To develop a PCR detection method, which could be used for the detection of Paenibacillus macerans in environmental samples or to help the identification of strains suspected to belong to this species. Methods and Results: Primers specific for P. macerans were developed based on the 16S rRNA gene sequence and were evaluated by PCR performed with genomic DNA from other Paenibacillus, other bacteria and DNA from soil as templates. The primers were shown to be specific for P. macerans strains and to amplify a 981-bp amplicon. Vegetative cells of P. macerans LMD 24.10T were tracked in Cerrado soil in 24-h experiments and PCR allowed the detection of 103 introduced cells per gram of dry soil. Conclusions: This PCR detection method was adequate to assess the presence of P. macerans in Cerrado soil. Significance and Impact of the Study: It can also be used after culturing to rapid confirm the identity of isolates suspected to belong to P. macerans. [source] The colonization of Europe by the freshwater crustacean Asellus aquaticus (Crustacea: Isopoda) proceeded from ancient refugia and was directed by habitat connectivityMOLECULAR ECOLOGY, Issue 14 2005R. VEROVNIK Abstract Recent continental-scale phylogeographic studies have demonstrated that not all freshwater fauna colonized Europe from the classic Mediterranean peninsular refugia, and that northern or central parts of the continent were occupied before, and remained inhabited throughout the Pleistocene. The colonization history of the ubiquitous aquatic isopod crustacean Asellus aquaticus was assessed using mitochondrial COI and a variable part of nuclear 28S rDNA sequences. Phylogeographic analysis of the former suggested that dispersion proceeded possibly during late Miocene from the western part of the Pannonian basin. Several areas colonized from here have served as secondary refugia and/or origins of dispersion, well before the beginning of the Pleistocene. Postglacial large-scale range expansion was coupled with numerous separate local dispersions from different refugial areas. Connectivity of the freshwater habitat has played an important role in shaping the current distribution of genetic diversity, which was highest in large rivers. The importance of hydrographic connections for the maintenance of genetic contact was underscored by a discordant pattern of mtDNA and nuclear rDNA differentiation. Individuals from all over Europe, differing in their mtDNA to a level normally found between species or even genera (maximal within population nucleotide divergence reached 0.16 ± 0.018), shared the same 28S rRNA gene sequence. Only populations from hydrographically isolated karst water systems in the northwestern Dinaric Karst had distinct 28S sequences. Here isolation seemed to be strong enough to prevent homogenization of the rRNA gene family, whereas across the rest of Europe genetic contact was sufficient for concerted evolution to act. [source] Phylogenetic diversity and metagenomics of candidate division OP3ENVIRONMENTAL MICROBIOLOGY, Issue 5 2010Jana Glöckner Summary Except for environmental 16S rRNA gene sequences, no information is available for members of the candidate division OP3. These bacteria appear to thrive in anoxic environments, such as marine sediments, hypersaline deep sea, freshwater lakes, aquifers, flooded paddy soils and methanogenic bioreactors. The 16S rRNA phylogeny suggests that OP3 belongs to the Planctomycetes/Verrucomicrobia/Chlamydiae (PVC) superphylum. Metagenomic fosmid libraries were constructed from flooded paddy soil and screened for 16S rRNA gene-containing fragments affiliated with the PVC superphylum. The screening of 63 000 clones resulted in 23 assay-positive fosmids, of which three clones were affiliated with OP3. The 16S rRNA gene sequence divergence between the fragments OP3/1, OP3/2 and OP3/3 ranges from 18% to 25%, indicating that they belong to different OP3 subdivisions. The 23S rRNA phylogeny confirmed the membership of OP3 in the PVC superphylum. Sequencing the OP3 fragments resulted in a total of 105 kb of genomic information and 90 ORFs, of which 47 could be assigned a putative function and 11 were conserved hypothetical. Using BLASTP searches, a high proportion of ORFs had best matches to homologues from Deltaproteobacteria, rather than to those of members of the PVC superphylum. On the fragment OP3/3, a cluster of nine ORFs was predicted to encode the bacterial NADH dehydrogenase I. Given the high proportion of homologues present in deltaproteobacteria and anoxic conditions in the natural environment of OP3 bacteria, the detection of NADH dehydrogenase I may suggest an anaerobic respiration mode. Oligonucleotide frequencies calculated for OP3/1, OP3/2 and OP/3 show high intraphylum correlations. This novel sequence information could therefore be used to identify OP3-related fragments in large metagenomic data sets using marker gene-independent procedures in the future. In addition to the OP3 fragments, a single metagenomic fragment affiliated with the candidate division BRC1 was obtained and analysed. [source] Linking microbial oxidation of arsenic with detection and phylogenetic analysis of arsenite oxidase genes in diverse geothermal environmentsENVIRONMENTAL MICROBIOLOGY, Issue 2 2009N. Hamamura Summary The identification and characterization of genes involved in the microbial oxidation of arsenite will contribute to our understanding of factors controlling As cycling in natural systems. Towards this goal, we recently characterized the widespread occurrence of aerobic arsenite oxidase genes (aroA -like) from pure-culture bacterial isolates, soils, sediments and geothermal mats, but were unable to detect these genes in all geothermal systems where we have observed microbial arsenite oxidation. Consequently, the objectives of the current study were to measure arsenite-oxidation rates in geochemically diverse thermal habitats in Yellowstone National Park (YNP) ranging in pH from 2.6 to 8, and to identify corresponding 16S rRNA and aroA genotypes associated with these arsenite-oxidizing environments. Geochemical analyses, including measurement of arsenite-oxidation rates within geothermal outflow channels, were combined with 16S rRNA gene and aroA functional gene analysis using newly designed primers to capture previously undescribed aroA -like arsenite oxidase gene diversity. The majority of bacterial 16S rRNA gene sequences found in acidic (pH 2.6,3.6) Fe-oxyhydroxide microbial mats were closely related to Hydrogenobaculum spp. (members of the bacterial order Aquificales), while the predominant sequences from near-neutral (pH 6.2,8) springs were affiliated with other Aquificales including Sulfurihydrogenibium spp., Thermocrinis spp. and Hydrogenobacter spp., as well as members of the Deinococci, Thermodesulfobacteria and ,- Proteobacteria. Modified primers designed around previously characterized and newly identified aroA -like genes successfully amplified new lineages of aroA- like genes associated with members of the Aquificales across all geothermal systems examined. The expression of Aquificales aroA- like genes was also confirmed in situ, and the resultant cDNA sequences were consistent with aroA genotypes identified in the same environments. The aroA sequences identified in the current study expand the phylogenetic distribution of known Mo-pterin arsenite oxidase genes, and suggest the importance of three prominent genera of the order Aquificales in arsenite oxidation across geochemically distinct geothermal habitats ranging in pH from 2.6 to 8. [source] Active bacterial community structure along vertical redox gradients in Baltic Sea sedimentENVIRONMENTAL MICROBIOLOGY, Issue 8 2008Anna Edlund Summary Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179, ,64 and ,337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labelled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labelled DNA and DNA from reverse transcription polymerase chain reaction showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences, indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths. [source] Patterns of bacterial diversity across a range of Antarctic terrestrial habitatsENVIRONMENTAL MICROBIOLOGY, Issue 11 2007Etienne Yergeau Summary Although soil-borne bacteria represent the world's greatest source of biological diversity, it is not well understood whether extreme environmental conditions, such as those found in Antarctic habitats, result in reduced soil-borne microbial diversity. To address this issue, patterns of bacterial diversity were studied in soils sampled along a > 3200 km southern polar transect spanning a gradient of increased climate severity over 27° of latitude. Vegetated and fell-field plots were sampled at the Falkland (51°S), South Georgia (54°S), Signy (60°S) and Anchorage Islands (67°S), while bare frost-sorted soil polygons were examined at Fossil Bluff (71°S), Mars Oasis (72°S), Coal Nunatak (72°S) and the Ellsworth Mountains (78°S). Bacterial 16S rRNA gene sequences were recovered subsequent to direct DNA extraction from soil, polymerase chain reaction amplification and cloning. Although bacterial diversity was observed to decline with increased latitude, habitat-specific patterns appeared to also be important. Namely, a negative relationship was found between bacterial diversity and latitude for fell-field soils, but no such pattern was observed for vegetated sites. The Mars Oasis site, previously identified as a biodiversity hotspot within this region, proved exceptional within the study transect, with unusually high bacterial diversity. In independent analyses, geographical distance and vegetation cover were found to significantly influence bacterial community composition. These results provide insight into the factors shaping the composition of bacterial communities in Antarctic terrestrial habitats and support the notion that bacterial diversity declines with increased climatic severity. [source] Heterotrophic symbionts of phototrophic consortia: members of a novel diverse cluster of Betaproteobacteria characterized by a tandem rrn operon structureENVIRONMENTAL MICROBIOLOGY, Issue 11 2007Kristina R. Pfannes Summary Phototrophic consortia represent the most highly developed type of interspecific association of bacteria and consist of green sulfur bacterial epibionts attached around a central colourless rod-shaped bacterium. Based on 16S rRNA gene sequencing, the central bacterium of the consortium ,Chlorochromatium aggregatum' was recently shown to represent a novel and phylogenetically isolated lineage of the Comamonadaceae within the ,-subgroup of the Proteobacteria. To date, 19 types of phototrophic consortia are distinguished based on the different 16S rRNA gene sequences of their epibionts, but the diversity and phylogenetic relationships of the heterotrophic partner bacteria are still unknown. We developed an approach based on the specific rrn (ribosomal RNA) operon structure of the central bacterium of ,C. aggregatum' to recover 16S rRNA gene sequences of other central bacteria and their close relatives from natural consortia populations. Genomic DNA of the central bacterium of ,C. aggregatum' was first enriched several hundred-fold by employing a selective method for growth of consortia in a monolayer biofilm followed by a purification of the genome of the central bacterium by cesium chloride-bisbenzimidazole equilibrium density gradient centrifugation. A combination of inverse PCR, cloning and sequencing revealed that two rrn operons of the central bacterium are arranged in a tandem fashion and are separated by an unusually short intergenic region of 195 base pairs. This rare gene order was exploited to screen various natural microbial communities by PCR. We discovered a diverse and previously unknown subgroup of Betaproteobacteria in the chemoclines of freshwater lakes. This group was absent in other freshwater and soil samples. All the 16S rRNA gene sequences recovered are related to that of the central bacterium of ,C. aggregatum'. Fluorescence in situ hybridization indicated that two of these sequences originated from central bacteria of different phototrophic consortia, which, however, were only distantly related to the central bacterium of ,C. aggregatum'. Based on a detailed phylogenetic analysis, these central bacterial symbionts of phototrophic consortia have a polyphyletic origin. [source] Methanogenesis and methanogenic pathways in a peat from subarctic permafrostENVIRONMENTAL MICROBIOLOGY, Issue 4 2007Martina Metje Summary Few studies have dealt so far with methanogenic pathways and populations in subarctic and arctic soils. We studied the effects of temperature on rates and pathways of CH4 production and on the relative abundance and structure of the archaeal community in a mildly acidic peat from a permafrost region in Siberia (67°N). We monitored the production of CH4 and CO2 over time and measured the consumption of Fe(II), ethanol and volatile fatty acids. All experiments were performed with and without specific inhibitors [2-bromoethanesulfonate (BES) for methanogenesis and CH3F for acetoclastic methanogenesis]. The optimum temperature for methanogenesis was between 26°C and 28°C [4.3 ,mol CH4 (g dry weight),1 day,1], but the activity was high even at 4°C [0.75 ,mol CH4 (g dry weight),1 day,1], constituting 17% of that at 27°C. The population structure of archaea was studied by terminal restriction fragment length polymorphism analysis and remained constant over a wide temperature range. Acetoclastic methanogenesis accounted for about 70% of the total methanogenesis. Most 16S rRNA gene sequences clustered with Methanosarcinales, correlating with the prevalence of acetoclastic methanogenesis. In addition, sequences clustering with Methanobacteriales were recovered. Fe reduction occurred in parallel to methanogenesis. At lower and higher temperatures Fe reduction was not affected by BES. Because butyrate was consumed during methanogenesis and accumulated when methanogenesis was inhibited (BES and CH3F), it is proposed to serve as methanogenic precursor, providing acetate and H2 by syntrophic oxidation. In addition, ethanol and caproate occurred as intermediates. Because of thermodynamic constraints, homoacetogenesis could not compete with hydrogenotrophic methanogenesis. [source] Identification and characterization of ectosymbionts of distinct lineages in Bacteroidales attached to flagellated protists in the gut of termites and a wood-feeding cockroachENVIRONMENTAL MICROBIOLOGY, Issue 1 2006Satoko Noda Summary Bacterial attachments to nearly the entire surface of flagellated protists in the guts of termites and the wood-feeding cockroach Cryptocercus are often observed. Based on the polymerase chain reaction-amplified 16S rRNA gene sequences, we investigated the phylogenetic relationships of the rod-shaped, attached bacteria (ectosymbionts) of several protist species from five host taxa and confirmed their identity by fluorescence in situ hybridizations. These ectosymbionts are affiliated with the order Bacteroidales but formed three distinct lineages, each of which may represent novel bacterial genera. One lineage consisted of the closely related ectosymbionts of two species of the protist genus Devescovina (Cristamonadida). The second lineage comprised three phylotypes identified from the protist Streblomastix sp. (Oxymonadida). The third lineage included ectosymbionts of the three protist genera Hoplonympha, Barbulanympha and Urinympha in the family Hoplonymphidae (Trichonymphida). The ultrastructural observations indicated that these rod-shaped ectosymbionts share morphological similarities of their cell walls and their point of attachment with the protist but differ in shape. Elongated forms of the ectosymbionts appeared in all the three lineages. The protist cells Streblomastix sp. and Hoplonympha sp. display deep furrows and vane-like structures, but these impressive structures are probably evolutionarily convergent because both the host protists and their ectosymbionts are distantly related. [source] Bacterial diversity in the bacterioneuston (sea surface microlayer): the bacterioneuston through the looking glassENVIRONMENTAL MICROBIOLOGY, Issue 5 2005Mark P. Franklin Summary The bacterioneuston is defined as the community of bacteria present within the neuston or sea surface microlayer. Bacteria within this layer were sampled using a membrane filter technique and bacterial diversity was compared with that in the underlying pelagic coastal seawater using molecular ecological techniques. 16S rRNA gene libraries of , 500 clones were constructed from both bacterioneuston and the pelagic water samples and representative clones from each library were sequenced for comparison of bacterial diversity. The bacterioneuston was found to have a significantly lower bacterial diversity than the pelagic seawater, with only nine clone types (ecotaxa) as opposed to 46 ecotaxa in the pelagic seawater library. Surprisingly, the bacterioneuston clone library was dominated by 16S rRNA gene sequences affiliated to two groups of organisms, Vibrio spp. which accounted for over 68% of clones and Pseudoalteromonas spp. accounting for 21% of the library. The dominance of these two 16S rRNA gene sequence types within the bacterioneuston clone library was confirmed in a subsequent gene probing experiment. 16S rRNA gene probes specific for these groups of bacteria were designed and used to probe new libraries of 1000 clones from both the bacterioneuston and pelagic seawater DNA samples. This revealed that 57% of clones from the bacterioneuston library hybridized to a Vibrio sp.-specific 16S rRNA gene probe and 32% hybridized to a Pseudoalteromonas sp.-specific 16S rRNA gene probe. In contrast, the pelagic seawater library resulted in only 13% and 8% of 16S rRNA gene clones hybridizing to the Vibrio sp. and Pseudoalteromonas sp. probes respectively. Results from this study suggest that the bacterioneuston contains a distinct population of bacteria and warrants further detailed study at the molecular level. [source] Characterization of bacterial pectinolytic strains involved in the water retting processENVIRONMENTAL MICROBIOLOGY, Issue 9 2003Elena Tamburini Summary Pectinolytic microorganisms involved in the water retting process were characterized. Cultivable mesophilic anaerobic and aerobic bacteria were isolated from unretted and water-retted material. A total of 104 anaerobic and 23 aerobic pectinolytic strains were identified. Polygalacturonase activity was measured in the supernatant of cell cultures; 24 anaerobic and nine aerobic isolates showed an enzymatic activity higher than the reference strains Clostridium felsineum and Bacillus subtilis respectively. We performed the first genotypic characterization of the retting microflora by a 16S amplified ribosomal DNA restriction analysis (ARDRA). Anaerobic isolates were divided into five different groups, and the aerobic isolates were clustered into three groups. 84.6% of the anaerobic and 82.6% of the aerobic isolates consisted of two main haplotypes. Partial 16S rRNA gene sequences were determined for 12 strains, representative of each haplotype. All anaerobic strains were assigned to the Clostridium genus, whereas the aerobic isolates were assigned to either the Bacillus or the Paenibacillus genus. Anaerobic isolates with high polygalacturonase (PG) activity belong to two clearly distinct phylogenetic clusters related to C. acetobutylicum,C. felsineum and C. saccharobutylicum species. Aerobic isolates with high PG activity belong to two clearly distinct phylogenetic clusters related to B. subtilisT and B. pumilusT. [source] Physiological and molecular characterization of anaerobic benzene-degrading mixed culturesENVIRONMENTAL MICROBIOLOGY, Issue 2 2003Ania C. Ulrich Summary Nine distinct anaerobic benzene-degrading cultures were enriched from sediment samples from four different sites. These cultures used nitrate, sulphate or CO2 as electron acceptors. The shortest doubling times were observed in nitrate-reducing cultures, although cell yield was lowest in these cultures. The highest substrate concentration utilized and maximum absolute rates of benzene degraded (in µM day,1) were observed in methanogenic cultures. The microbial compositions of a methanogenic and nitrate-reducing culture were determined from a clone library of 16S rRNA genes. Five Bacterial 16S rRNA sequences, one of which resembled a clone previously found in a sulphate-reducing, benzene-degrading culture and four Archaeal 16S rRNA sequences were identified in a methanogenic culture. Four Bacterial and no Archaeal 16S rRNA sequences were identified in a nitrate-reducing culture. The relative abundance of the four nitrate-reducing putative species was determined by slot blot hybridization. Two green sulphur bacteria together formed 52% of the clone library, but were found to be less than 4% of the culture by slot blot analysis. One of the cloned 16S rRNA gene sequences comprised 70% of the culture and was phylogenetically 93% similar to both Azoarcus and Dechloromonas species, which have been shown to degrade aromatic compounds, including benzene, under nitrate-reducing conditions. [source] Changes in microbial community composition following treatment of methanogenic granules with chloroformENVIRONMENTAL PROGRESS & SUSTAINABLE ENERGY, Issue 1 2009Bo Hu Abstract Eliminating hydrogen consuming bacteria is a critical step in anaerobic fermentation for biohydrogen production. Treatment of anaerobic granular sludge with chloroform was reported as effective in transforming a methane-producing system into a hydrogen-producing system by eliminating methane production. This study, using 16S rRNA gene sequences, further assessed changes in microbial community composition as a result of chloroform treatment and during continuous cultivation of chloroform-treated granules in a continuous upflow reactor employing immobilized cells. Profiles of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes sequences cloned from samples before and after chloroform treatment showed that methanogenic hydrogen consumers and Methanosaeta harundinacea sp. were eliminated. Methanosaeta concilii, however, was not eliminated from the hydrogen-producing system, which might explain, in part, the granulation phenomena in the anaerobic hydrogen fermentation system. The results also showed that Clostridium butyricum dominated the hydrogen-production system. © 2009 American Institute of Chemical Engineers Environ Prog, 2009 [source] Phylogenetic diversity of Synechococcus strains isolated from the East China Sea and the East SeaFEMS MICROBIOLOGY ECOLOGY, Issue 3 2009Dong Han Choi Abstract Phylogenetic relationships among 33 Synechococcus strains isolated from the East China Sea (ECS) and the East Sea (ES) were studied based on 16S rRNA gene sequences and 16S,23S rRNA gene internal transcribed spacer (ITS) sequences. Pigment patterns of the culture strains were also examined. Based on 16S rRNA gene and ITS sequence phylogenies, the Synechococcus isolates were clustered into 10 clades, among which eight were previously identified and two were novel. Half of the culture strains belonged to clade V or VI. All strains that clustered into novel clades exhibited both phycoerythrobilin and phycourobilin. Interestingly, the pigment compositions of isolates belonging to clades V and VI differed from those reported for other oceanic regions. None of the isolates in clade V showed phycourobilin, whereas strains in clade VI exhibited both phycourobilin and phycoerythrobilin, which is in contrast to previous studies. The presence of novel lineages and the different pigment patterns in the ECS and the ES suggests the possibility that some Synechococcus lineages are distributed only in geographically restricted areas and have evolved in these regions. Therefore, further elucidation of the physiological, ecological, and genetic characteristics of the diverse Synechococcus strains is required to understand their spatial and geographical distribution. [source] Genomic and phenotypic heterogeneity of Acidithiobacillus spp. strains isolated from diverse habitats in ChinaFEMS MICROBIOLOGY ECOLOGY, Issue 2 2008Yong-Qing Ni Abstract The genetic variability among 32 Chinese Acidithiobacillus spp. environmental isolates and four reference strains representing three recognized species of the genus Acidithiobacillus was characterized by using a combination of molecular methods, namely restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes and 16S,23S rRNA gene intergenic spacers, repetitive element PCR, arbitrarily primed PCR and 16S rRNA gene sequence analyses. 16S rRNA gene sequences revealed that all Acidithiobacillus spp. strains could be assigned to seven groups, three of which encompassed the Acidithiobacillus ferrooxidans strains from various parts of the world. A comparative analysis of the phylogenetic Group 1 and 2 was undertaken. Restriction fragment length polymorphism results allowed us to separate the 35 Acidithiobacillus strains into 15 different genotypes. An integrated phenotypic and genotypic analysis indicated that the distribution of A. ferrooxidans strains among the physiological groups were in agreement with their distribution among the genomic groups, and that no clear correlation was found between the genetic polymorphism of the Acidithiobacillus spp. strains and either the geographic location or type of habitats from which the strains were isolated. In addition, five unidentified sulfur-oxidizing isolates may represent one or two novel species of the genus Acidithiobacillus. The results showed that the Chinese Acidithiobacillus spp. isolates exhibited a high degree of genomic and phenotypic heterogeneity. [source] Tracking temporal changes of bacterial community fingerprints during the initial stages of compostingFEMS MICROBIOLOGY ECOLOGY, Issue 1 2003Patrick D Schloss Abstract The initial phase of composting is the most dynamic part of the process and is characterized by rapid increases in temperature, large swings in pH, and the degradation of simple organic compounds. DNA samples were taken from an active compost system to determine the microbial 16S rRNA gene sequences that were present during this phase. We observed two significant shifts in the composition of the microbial community, one between 12 and 24 h and the other between 60 and 72 h into the process using automated 16S,23S rRNA intergenic spacer amplification (ARISA). The 16S rRNA gene sequences adjoining the most common ARISA fragments at each time point were determined. We found that sequences related to lactic acid bacteria were most common during the first 60 h and Bacillus -type sequences were most common between 72 and 96 h. While the temperature increased steadily over the first 96 h, the pH dropped after 12 h and increased after 60 h correlating with the shift from Bacillus to lactic acid sequences and the later return to Bacillus -type sequences. [source] Mucilaginibacter dorajii sp. nov., isolated from the rhizosphere of Platycodon grandiflorumFEMS MICROBIOLOGY LETTERS, Issue 2 2010Byung-Chun Kim Abstract A Gram-negative, nonmotile and rod-shaped bacterial strain was isolated from the rhizosphere of Platycodon grandiflorum in a study of bacterial diversity, and its taxonomic position was investigated by a genotypic and phenotypic analysis. This isolate, designated as DR-f4, grew at 4,30 °C (optimally at 20,25 °C) and in the presence of 0,1% (w/v) NaCl. It contained MK-7 as the predominant menaquinone. The isolate had activities of catalase, oxidase and ,-galactosidase and hydrolyzed aesculin, casein, carboxymethyl-cellulose, starch and l -tyrosine. The major cellular fatty acids were summed feature 3 (C16:1,7c and/or iso-C15:0 2OH) and iso-C15:0. The DNA G+C content was 42.6 mol%. This isolate belonged to the genus Mucilaginibacter based on phylogenetic analysis using 16S rRNA gene sequences. The nearest phylogenetic neighbors of strain DR-f4T were Mucilaginibacter lappiensis ANJL12T and Mucilaginibacter rigui WPCB133T, with 16S rRNA gene sequence similarity levels of 96.9% and 96.4%, respectively. The genotypic and phenotypic evidence suggests that strain DR-f4T should be classified as a novel species, for which the name Mucilaginibacter dorajii sp. nov. is proposed. The type strain for the novel species is DR-f4T (=KACC 14556T=JCM 16601T). [source] Phylogenetic relationship of 16 Oedipodidae species (Insecta: Orthoptera) based on the 16S rRNA gene sequencesINSECT SCIENCE, Issue 2 2006HUI-MENG LU Abstract The sequences of the mitochondrial 16S rRNA gene of 16 Oedipodidae species were amplified and sequenced. All sequences were aligned and analyzed and the phylogenetic relationships were inferred. The properties of 16S gene in Oedipodidae showed typical patterns of many insects such as a high A+T content and variable distance-dependent transition/transversion ratios. The 0.2 weight for sites of loops may be advisable for phylogeny reconstruction using the maximum parsimony method. The phylogenetic analysis results do not support the current subfamily classification systems of Oedipodidae. Bryodemellinae and Bryodeminae are closely related and should be merged as one subfamily. The status of Oedipodinae and Locustinae is also problematic. [source] Application of recA and rpoB sequence analysis on phylogeny and molecular identification of Geobacillus speciesJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2009F.Y. Weng Abstract Aims:, Some Geobacillus species have highly similar 16S rRNA gene sequences, making 16S rDNA sequence analysis-based identification problematic. To overcome this limitation, recA and rpoB sequence analysis was evaluated as an alternative for distinguishing Geobacillus species. Methods and Results:, The phylogram of 16S rRNA gene sequences inferred from the neighbour-joining method showed that nine clusters of Geobacillus species were characterized with bootstrap values >90%. The recA and rpoB sequences of 10 reference strains in clusters V, VIb and VIc were amplified and sequenced using consensus primers. Alignment of recA sequences in clusters V, VIb and VIc revealed three types of recA genes, consistent with the putative amino acid sequences and in vivo recA splicing analysis. The phylogram constructed from rpoB sequences showed more divergence than that constructed from 16S rRNA gene sequences. Conclusions:,recA and rpoB sequence analysis differentiated closely-related Geobacillus species and provided direct evidence for reclassifying some species dubiously categorized as Geobacilli. Additionally, this study revealed three types of recA genes in the different Geobacillus species. Significance and Impact of the Study:, This study highlights the advantage of recA and rpoB sequence analysis to supplement 16S rRNA gene sequence analysis for efficient and convenient determination of Geobacillus species. [source] The molecular diversity of the methanogenic community in a hypereutrophic freshwater lake determined by PCR-RFLPJOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2004C. Whitby Abstract Aims:, To combine database-held sequence information with a programme of experimental molecular ecology to define the methanogenic community of a hypereutrophic lake by a PCR-restriction fragment length polymorphism (RFLP) analysis. Methods and Results:, Methanogen diversity in a hypereutrophic freshwater lake was analysed using 16S rDNA PCR-RFLP. Database-held 16S rRNA gene sequences for 76 diverse methanogens were analysed for specific restriction sites that permitted unequivocal differentiation of methanogens. Restriction digestion and agarose gel electrophoresis of the 16S rDNA from selected methanogen pure cultures generated observed restriction profiles that corroborated the expected patterns. This method was then tested by analysing methanogen diversity in samples obtained over 1 year from sediment and water samples taken from the same sampling site. Conclusions:, Restriction analysis of the 16S rRNA gene sequences from 157 methanogen clones generated from lakewater and sediment samples showed that over 50% were similar to Methanoculleus spp. Furthermore, a total of 16 RFLP types (1,16) were identified, eight of which contained no cultured representative archaeal 16S rRNA gene sequences. Significance and Impact of the Study:, This RFLP strategy provides a robust and reliable means to rapidly identify methanogens in the environment. [source] Molecular characterization of early colonizer bacteria from wastes in a steel plantLETTERS IN APPLIED MICROBIOLOGY, Issue 4 2008D.B. Freitas Abstract Aims:, Forty-nine bacteria isolated from four newly-produced waste samples of a steel industry, which had a high content of CaO, MgO, Cr and P2O5, were characterized molecularly and phenotypically by susceptibility testing against heavy metals. Methods and Results:, Phylogenetic analysis using 16S rRNA gene sequences revealed that the isolates belonged to nine genera, Pseudomonas, Micrococcus, Acinetobacter, Bacillus, Dietzia, Kocuria, Diaphorobacter, Staphylococcus and Brevibacillus. Besides, some isolates could be affiliated to species: M. luteus, Ac. junii, Ac. schindleri, B. cereus, K. marina, D. nitroreducens and Staph. warneri. The bacteria that were characterized are taxonomically diverse, and Pseudomonas and Micrococcus predominated. Fingerprinting BOX-PCR revealed high genomic heterogeneity among the isolates. Among the heavy metal compounds Zn, Ni, Pb and Cu were least toxic to the bacterial isolates, whereas Ag inhibited all isolates at 0·001 mmol l,1. Conclusions:, Heterotrophic bacteria, affiliated with several phylogentic groups, were able to colonize different wastes of a steel industry. Significance and Impact of the Study:, This study extends our knowledge of the early colonizers bacteria populating siderurgic environments. Some of these bacteria could have potential for recycling siderurgic waste for steel production. [source] | ||||||||||||||||||||||||||||