scholarly journals Phylogenetic Comparison of the Methanogenic Communities from an Acidic, Oligotrophic Fen and an Anaerobic Digester Treating Municipal Wastewater Sludge

2008 ◽  
Vol 74 (21) ◽  
pp. 6663-6671 ◽  
Author(s):  
Lisa M. Steinberg ◽  
John M. Regan
Keyword(s):  
16S Rrna ◽  
Municipal Wastewater ◽  
Anaerobic Digester ◽  
Wastewater Sludge ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Large Temperature ◽  
Clone Libraries ◽  
Average Sequence ◽  
Sequence Similarities

ABSTRACT Methanogens play a critical role in the decomposition of organics under anaerobic conditions. The methanogenic consortia in saturated wetland soils are often subjected to large temperature fluctuations and acidic conditions, imposing a selective pressure for psychro- and acidotolerant community members; however, methanogenic communities in engineered digesters are frequently maintained within a narrow range of mesophilic and circumneutral conditions to retain system stability. To investigate the hypothesis that these two disparate environments have distinct methanogenic communities, the methanogens in an oligotrophic acidic fen and a mesophilic anaerobic digester treating municipal wastewater sludge were characterized by creating clone libraries for the 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes. A quantitative framework was developed to assess the differences between these two communities by calculating the average sequence similarity for 16S rRNA genes and mcrA within a genus and family using sequences of isolated and characterized methanogens within the approved methanogen taxonomy. The average sequence similarities for 16S rRNA genes within a genus and family were 96.0 and 93.5%, respectively, and the average sequence similarities for mcrA within a genus and family were 88.9 and 79%, respectively. The clone libraries of the bog and digester environments showed no overlap at the species level and almost no overlap at the family level. Both libraries were dominated by clones related to uncultured methanogen groups within the Methanomicrobiales, although members of the Methanosarcinales and Methanobacteriales were also found in both libraries. Diversity indices for the 16S rRNA gene library of the bog and both mcrA libraries were similar, but these indices indicated much lower diversity in the 16S digester library than in the other three libraries.

scholarly journals Enumeration of Organohalide Respirers in Municipal Wastewater Anaerobic Digesters

2015 ◽  
Vol 8s2 ◽  
pp. MBI.S31445 ◽  
Author(s):  
Bryan J.K. Smith ◽  
Melissa A. Boothe ◽  
Brice A. Fiddler ◽  
Tania M. Lozano ◽  
Russel K. Rahi ◽  
...  
Keyword(s):  
16S Rrna ◽  
Municipal Wastewater ◽  
Wastewater Treatment Plants ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Municipal Wastewater Treatment ◽  
Anaerobic Digesters ◽  
Dehalococcoides Mccartyi ◽  
Halogenated Compound ◽  
Municipal Wastewater Treatment Plants

Organohalide contaminants such as triclosan and triclocarban have been well documented in municipal wastewater treatment plants (WWTPs), but the degradation of these contaminants is not well understood. One possible removal mechanism is organohalide respiration by which bacteria reduce the halogenated compound. The purpose of this study was to determine the abundance of organohalide-respiring bacteria in eight WWTP anaerobic digesters. The obligate organohalide respiring Dehalococcoides mccartyi was the most abundant and averaged 3.3 × 107 copies of 16S rRNA genes per gram, while the Dehalobacter was much lower at 2.6 × 104 copies of 16S rRNA genes per gram. The genus Sulfurospirillum spp. was also detected at 1.0 × 107 copies of 16S rRNA genes per gram. No other known or putatively organohalide-respiring strains in the Dehalococcoidaceae family were found to be present nor were the genera Desulfitobacterium or Desulfomonile.

scholarly journals Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease

2008 ◽  
Vol 57 (12) ◽  
pp. 1569-1576 ◽  
Author(s):  
Tanja Kuehbacher ◽  
Ateequr Rehman ◽  
Patricia Lepage ◽  
Stephan Hellmig ◽  
Ulrich R. Fölsch ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
16S Rrna ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Base Substitution ◽  
Clone Libraries ◽  
Bowel Diseases ◽  
Inflammatory Bowel ◽  
Almost All

TM7 is a recently described subgroup of Gram-positive uncultivable bacteria originally found in natural environmental habitats. An association of the TM7 bacterial division with the inflammatory pathogenesis of periodontitis has been previously shown. This study investigated TM7 phylogenies in patients with inflammatory bowel diseases (IBDs). The mucosal microbiota of patients with active Crohn's disease (CD; n=42) and ulcerative colitis (UC; n=31) was compared with that of controls (n=33). TM7 consortia were examined using molecular techniques based on 16S rRNA genes, including clone libraries, sequencing and in situ hybridization. TM7 molecular signatures could be cloned from mucosal samples of both IBD patients and controls, but the composition of the clone libraries differed significantly. Taxonomic analysis of the sequences revealed a higher diversity of TM7 phylotypes in CD (23 different phylotypes) than in UC (10) and non-IBD controls (12). All clone libraries showed a high number of novel sequences (21 for controls, 34 for CD and 29 for UC). A highly atypical base substitution for bacterial 16S rRNA genes associated with antibiotic resistance was detected in almost all sequences from CD (97.3 %) and UC (100 %) patients compared to only 65.1 % in the controls. TM7 bacteria might play an important role in IBD similar to that previously described in oral inflammation. The alterations of TM7 bacteria and the genetically determined antibiotic resistance of TM7 species in IBD could be a relevant part of a more general alteration of bacterial microbiota in IBD as recently found, e.g. as a promoter of inflammation at early stages of disease.

Halosimplex halophilum sp. nov. and Halosimplex salinum sp. nov., isolated from saline soil and a salt mine

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Xiao-Yan Yang ◽  
Xue-Meng Yin ◽  
Jing Hou ◽  
Lin Zhu ◽  
Heng-Lin Cui
Keyword(s):  
16S Rrna ◽  
In Silico ◽  
Saline Soil ◽  
Novel Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Threshold Values ◽  
Content Type ◽  
Link Type ◽  
Sequence Similarities

A polyphasic study was undertaken to determine the taxonomic position of two halophilic archaeal strains, TH32T and YPL4T, isolated from saline soil and a salt mine in PR China, respectively. Strains TH32T and YPL4T both have two dissimilar 16S rRNA genes. The two strains exhibited sequence similarities of 91.5–95.5 % for 16S rRNA genes and 90.9 % for the rpoB′ gene. Sequence similarities of 16S rRNA genes and the rpoB′ gene between the two strains and the current four members of Halosimplex were 90.6–97.4 % and 91.4–93.5 %, respectively. Phylogenetic analysis revealed that the two strains formed different branches separating them from the current Halosimplex members. Several phenotypic characteristics differentiate strains TH32T and YPL4T from current Halosimplex members. The polar lipids of the two strains are phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and four glycolipids. Two of the glycolipids are chromatographically identical to disulfated mannosyl glucosyl diether and sulfated mannosyl glucosyl diether, respectively, and the remaining two glycolipids are unidentified. The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) values between the two strains and the current members of Halosimplex (ANI 80.4–89.2 % and in silico DDH 24.0–41.8 %) were much lower than the threshold values proposed as a species boundary, suggesting that the two strains represent novel species of Halosimplex . The values between the two strains (ANI 81.3 % and in silico DDH 24.9 %) were also much lower than the recommended threshold values, which revealed that the two strains represent two genomically different species of Halosimplex . These results showed that strains TH32T (=CGMCC 1.15190T=JCM 30840T) and YPL4T (=CGMCC 1.15329T=JCM 31108T) represent two novel species of Halosimplex , for which the names Halosimplex halophilum sp. nov. and Halosimplex salinum sp. nov. are proposed.

scholarly journals Assessment of Microbial Diversity in Four Southwestern United States Soils by 16S rRNA Gene Terminal Restriction Fragment Analysis

2000 ◽  
Vol 66 (7) ◽  
pp. 2943-2950 ◽  
Author(s):  
John Dunbar ◽  
Lawrence O. Ticknor ◽  
Cheryl R. Kuske
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Restriction Fragment ◽  
Community Diversity ◽  
Detection Sensitivity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Clone Libraries

ABSTRACT The ability of terminal restriction fragment (T-RFLP or TRF) profiles of 16S rRNA genes to provide useful information about the relative diversity of complex microbial communities was investigated by comparison with other methods. Four soil communities representing two pinyon rhizosphere and two between-tree (interspace) soil environments were compared by analysis of 16S rRNA gene clone libraries and culture collections (Dunbar et al., Appl. Environ. Microbiol. 65:1662–1669, 1998) and by analysis of 16S rDNA TRF profiles of community DNA. The TRF method was able to differentiate the four communities in a manner consistent with previous comparisons of the communities by analysis of 16S rDNA clone libraries. TRF profiles were not useful for calculating and comparing traditional community richness or evenness values among the four soil environments. Statistics calculated from RsaI, HhaI, HaeIII, and MspI profiles of each community were inconsistent, and the combined data were not significantly different between samples. The detection sensitivity of the method was tested. In standard PCRs, a seeded population comprising 0.1 to 1% of the total community could be detected. The combined results demonstrate that TRF analysis is an excellent method for rapidly comparing the relationships between bacterial communities in environmental samples. However, for highly complex communities, the method appears unable to provide classical measures of relative community diversity.

scholarly journals Relationship of Temporal and Spatial Variabilities of Ammonia-Oxidizing Bacteria to Nitrification Rates in Monterey Bay, California

2005 ◽  
Vol 71 (2) ◽  
pp. 697-705 ◽  
Author(s):  
G. D. O'Mullan ◽  
B. B. Ward
Keyword(s):  
16S Rrna ◽  
Spatial Dynamics ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ammonia Oxidizing Bacteria ◽  
Monterey Bay ◽  
Strong Positive Correlation ◽  
Clone Libraries ◽  
Bacterial Populations ◽  
Temporal And Spatial

ABSTRACT Temporal and spatial dynamics of ammonia-oxidizing bacteria (AOB) were examined using genes encoding 16S rRNA and ammonia monooxygenase subunit A (AmoA) in Monterey Bay, Calif. Samples were collected from three depths in the water column on four dates at one mid-bay station. Diversity estimators for the two genes showed a strong positive correlation, indicating that overlapping bacterial populations had been sampled by both sets of clone libraries. Some samples that were separated by only 15 m in depth had less genetic similarity than samples that were collected from the same depth months apart. Clone libraries from the Monterey Bay AOB community were dominated by Nitrosospira-like sequences and clearly differentiated from the adjacent AOB community in Elkhorn Slough. Many Monterey Bay clones clustered with previously identified 16S rRNA and amoA groups composed entirely of marine sequences, supporting the hypothesis that these groups are specific to the marine environment and are dominant marine AOB. In addition, novel, phylogenetically distinct groups of AOB sequences were identified and compared to sequences in the database. Only one cluster of gammaproteobacterial AOB was detected using 16S rRNA genes. Although significant genetic variation was detected in AOB populations from both vertical and temporal samples, no significant correlation was detected between diversity and environmental variables or the rate of nitrification.

scholarly journals Differentiation of Bifidobacterium species using partial RNA polymerase β-subunit (rpoB) gene sequences

2010 ◽  
Vol 60 (12) ◽  
pp. 2697-2704 ◽  
Author(s):  
Byoung Jun Kim ◽  
Hee-Youn Kim ◽  
Yeo-Jun Yun ◽  
Bum-Joon Kim ◽  
Yoon-Hoh Kook
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rna Polymerase ◽  
Gene Sequence ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Gene Sequences ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Partial RNA polymerase β-subunit gene (rpoB) sequences (315 bp) were determined and used to differentiate the type strains of 23 species of the genus Bifidobacterium. The sequences were compared with those of the partial hsp60 (604 bp) and 16S rRNA genes (1475 or 1495 bp). The rpoB gene sequences showed nucleotide sequence similarities ranging from 84.1 % to 99.0 %, while the similarities of the hsp60 sequences ranged from 78.5 % to 99.7 % and the 16S rRNA gene sequence similarities ranged from 89.4 % to 99.2 %. The phylogenetic trees constructed from the sequences of these three genes showed similar clustering patterns, with the exception of several species. The Bifidobacterium catenulatum–Bifidobacterium pseudocatenulatum, Bifidobacterium pseudolongum subsp. pseudolongum–Bifidobacterium pseudolongum subsp. globosum and Bifidobacterium gallinarum–Bifidobacterium pullorum–Bifidobacterium saeculare groups were more clearly differentiated in the partial rpoB and hsp60 gene sequence trees than they were in the 16S rRNA gene tree. Based on sequence similarities and tree topologies, the newly determined rpoB gene sequences are suitable molecular markers for the differentiation of species of the genus Bifidobacterium and support various other molecular tools used to determine the relationships among species of this genus.

scholarly journals Methanogen Diversity Evidenced by Molecular Characterization of Methyl Coenzyme M Reductase A (mcrA) Genes in Hydrothermal Sediments of the Guaymas Basin

2005 ◽  
Vol 71 (8) ◽  
pp. 4592-4601 ◽  
Author(s):  
Ashita Dhillon ◽  
Mark Lever ◽  
Karen G. Lloyd ◽  
Daniel B. Albert ◽  
Mitchell L. Sogin ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gulf Of California ◽  
Pcr Amplification ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Coenzyme M ◽  
Clone Libraries ◽  
Guaymas Basin ◽  
Methanogen Community ◽  
Methyl Coenzyme M Reductase

ABSTRACT The methanogenic community in hydrothermally active sediments of Guaymas Basin (Gulf of California, Mexico) was analyzed by PCR amplification, cloning, and sequencing of methyl coenzyme M reductase (mcrA) and 16S rRNA genes. Members of the Methanomicrobiales and Methanosarcinales dominated the mcrA and 16S rRNA clone libraries from the upper 15 cm of the sediments. Within the H2/CO2- and formate-utilizing family Methanomicrobiales, two mcrA and 16S rRNA lineages were closely affiliated with cultured species of the genera Methanoculleus and Methanocorpusculum. The most frequently recovered mcrA PCR amplicons within the Methanomicrobiales did not branch with any cultured genera. Within the nutritionally versatile family Methanosarcinales, one 16S rRNA amplicon and most of the mcrA PCR amplicons were affiliated with the obligately acetate utilizing species Methanosaeta concilii. The mcrA clone libraries also included phylotypes related to the methyl-disproportionating genus Methanococcoides. However, two mcrA and two 16S rRNA lineages within the Methanosarcinales were unrelated to any cultured genus. Overall, the clone libraries indicate a diversified methanogen community that uses H2/CO2, formate, acetate, and methylated substrates. Phylogenetic affiliations of mcrA and 16S rRNA clones with thermophilic and nonthermophilic cultured isolates indicate a mixed mesophilic and thermophilic methanogen community in the surficial Guaymas sediments.

scholarly journals Community Composition of Marine Bacterioplankton Determined by 16S rRNA Gene Clone Libraries and Fluorescence In Situ Hybridization

2000 ◽  
Vol 66 (12) ◽  
pp. 5116-5122 ◽  
Author(s):  
Matthew T. Cottrell ◽  
David L. Kirchman
Keyword(s):  
In Situ Hybridization ◽  
16S Rrna ◽  
Fluorescence In Situ Hybridization ◽  
Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Clone Libraries ◽  
Marine Bacterioplankton ◽  
Bacterioplankton Communities

ABSTRACT We determined the compositions of bacterioplankton communities in surface waters of coastal California using clone libraries of 16S rRNA genes and fluorescence in situ hybridization (FISH) in order to compare the community structures inferred from these two culture-independent approaches. The compositions of two clone libraries were quite similar to those of clone libraries of marine bacterioplankton examined by previous studies. Clones from γ-proteobacteria comprised ca. 28% of the libraries, while approximately 55% of the clones came from α-proteobacteria, which dominated the clone libraries. TheCytophaga-Flavobacter group and three others each comprised 10% or fewer of the clone libraries. The community composition determined by FISH differed substantially from the composition implied by the clone libraries. The Cytophaga-Flavobacter group dominated 8 of the 11 communities assayed by FISH, including the two communities assayed using clone libraries. On average only 10% of DAPI (4′,6′-diamidino-2-phenylindole)-stained bacteria were detected by FISH with a probe for α-proteobacteria, but 30% of DAPI-stained bacteria appeared to be in the Cytophaga-Flavobacter group as determined by FISH. α-Proteobacteria were greatly overrepresented in clone libraries compared to their relative abundance determined by FISH, while the Cytophaga-Flavobacter group was underrepresented in clone libraries. Our data show that theCytophaga-Flavobacter group can be a numerically dominant component of coastal marine bacterioplankton communities.

Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning

1999 ◽  
Vol 65 (4) ◽  
pp. 1662-1669 ◽  
Author(s):  
John Dunbar ◽  
Shannon Takala ◽  
Susan M. Barns ◽  
Jody A. Davis ◽  
Cheryl R. Kuske
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Soil Samples ◽  
Community Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Clone Libraries ◽  
Bacterial Community Diversity

ABSTRACT Techniques based on amplification of 16S rRNA genes for comparing bacterial communities are now widely used in microbial ecology, but calibration of these techniques with traditional tools, such as cultivation, has been conspicuously absent. In this study, we compared levels of bacterial community diversity in two pinyon rhizosphere soil samples and two between-tree (interspace) soil samples by analyzing 179 cultivated bacterial isolates and 801 16S rRNA genes amplified from extracted soil DNA. Phylotypes were defined by performing a restriction fragment length polymorphism analysis of 16S rRNA gene sequences with the enzymes RsaI and BstUI. The average level of 16S rRNA gene sequence similarity of members of a phylotype was 86.6% based on an analysis of partial sequences. A total of 498 phylotypes were identified among the 16S ribosomal DNA (rDNA) clones, while 34 phylotypes occurred among the cultivated isolates. Analysis of sequences from a subset of the phylotypes showed that at least seven bacterial divisions were represented in the clone libraries, whereas the isolates represented only three. The phylotype richness, frequency distribution (evenness), and composition of the four culture collections and the four clone libraries were investigated by using a variety of diversity indices. Although cultivation and 16S rRNA cloning analyses gave contradictory descriptions of the relative phylotype richness for one of the four environments, the two methods identified qualitatively consistent relationships when levels of evenness were compared. The levels of phylotype similarity between communities were uniformly low (15 to 31%). Both methods consistently indicated that one environment was distinct from the other three. Our data illustrate that while 16S rDNA cloning and cultivation generally describe similar relationships between soil microbial communities, significant discrepancies can occur.

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