Identification and occurrence of tetrad-forming Alphaproteobacteria in anaerobic–aerobic activated sludge processes

Microbiology ◽  
2004 ◽  
Vol 150 (11) ◽  
pp. 3741-3748 ◽  
Author(s):  
Man-Tak Wong ◽  
Fea Mein Tan ◽  
Wun Jern Ng ◽  
Wen-Tso Liu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Organic Substrate ◽  
Rrna Gene ◽  
Soluble Phosphate ◽  
Biological Phosphorus Removal ◽  
Dominant Group ◽  
Chemical Profiles ◽  
Group A ◽  
Activated Sludge Processes

In an acetate-fed anaerobic–aerobic membrane bioreactor, a deteriorated enhanced biological phosphorus removal (EBPR) community was developed (as determined based on the chemical profiles of organic substrate, soluble phosphate, and intracellular carbohydrate and polyhydroxyalkanote (PHA) concentrations). Microscopic observations revealed the dominance of tetrad-forming organisms (TFOs), of which the majority stained positively for PHA under anaerobic conditions. Fluorescence in situ hybridization (FISH) confirmed that the Alphaproteobacteria (85·0±7·0 % of total cells) were the most dominant group. A 16S rRNA gene clone library specific for the Alphaproteobacteria indicated that most 16S rRNA gene clones (61 % of total clones) were closely affiliated with ‘Defluvicoccus vanus’, forming a cluster within subgroup 1 of the Alphaproteobacteria. Combined PHA staining and FISH with specific probes designed for the members of the ‘Defluvicoccus’ cluster suggested diversity within this TFO cluster, and that these TFOs were newly identified glycogen-accumulating organisms in EBPR systems. However, these ‘Defluvicoccus’-related TFOs were only seen in low abundance in 12 different EBPR and non-EBPR systems, suggesting that they were not the key populations responsible for the deterioration of full-scale EBPR processes.

scholarly journals Diversity of NC10 bacteria associated with sediments of submergedPotamogeton crispus(Alismatales: Potmogetonaceae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6041 ◽  
Author(s):  
Binghan Wang ◽  
Shanshan Huang ◽  
Liangmao Zhang ◽  
Jianwei Zhao ◽  
Guanglong Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Diversity ◽  
Rrna Gene ◽  
Dominant Group ◽  
Potamogeton Crispus ◽  
Carbon And Nitrogen ◽  
Operational Taxonomic Units ◽  
Group A ◽  
Group B

BackgroundThe nitrite-dependent anaerobic methane oxidation (N-DAMO) pathway, which plays an important role in carbon and nitrogen cycling in aquatic ecosystems, is mediated by “CandidatusMethylomirabilis oxyfera” (M. oxyfera) of the NC10 phylum.M. oxyfera-like bacteria are widespread in nature, however, the presence, spatial heterogeneity and genetic diversity ofM. oxyferain the rhizosphere of aquatic plants has not been widely reported.MethodIn order to simulate the rhizosphere microenvironment of submerged plants,Potamogeton crispuswas cultivated using the rhizobox approach. Sediments from three compartments of the rhizobox: root (R), near-rhizosphere (including five sub-compartments of one mm width, N1–N5) and non-rhizosphere (>5 mm, Non), were sampled. The 16S rRNA gene library was used to investigate the diversity ofM. oxyfera-like bacteria in these sediments.ResultsMethylomirabilis oxyfera-like bacteria were found in all three sections, with all 16S rRNA gene sequences belonging to 16 operational taxonomic units (OTUs). A maximum of six OTUs was found in the N1 sub-compartment of the near-rhizosphere compartment and a minimum of four in the root compartment (R) and N5 near-rhizosphere sub-compartment. Indices of bacterial community diversity (Shannon) and richness (Chao1) were 0.73–1.16 and 4–9, respectively. Phylogenetic analysis showed that OTU1-11 were classified into group b, while OTU12 was in a new cluster of NC10.DiscussionOur results confirmed the existence ofM. oxyfera-like bacteria in the rhizosphere microenvironment of the submerged plantP. crispus. Group b ofM. oxyfera-like bacteria was the dominant group in this study as opposed to previous findings that both group a and b coexist in most other environments. Our results indicate that understanding the ecophysiology ofM. oxyfera-like bacteria group b may help to explain their existence in the rhizosphere sediment of aquatic plant.

scholarly journals Flavobacterium croceum sp. nov., isolated from activated sludge

2006 ◽  
Vol 56 (10) ◽  
pp. 2443-2447 ◽  
Author(s):  
Minjeong Park ◽  
Shipeng Lu ◽  
Seung Hyun Ryu ◽  
Bok Sil Chung ◽  
Woojun Park ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Batch Reactor ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Biological Phosphorus Removal ◽  
Rrna Gene Sequence

A Gram-negative, non-motile, rod-shaped bacterium, designated strain EMB47T, was isolated from activated sludge performing enhanced biological phosphorus removal in a sequencing batch reactor. Growth was observed between 10 and 40 °C (optimum, 25–35 °C) and between pH 5.0 and 8.5 (optimum, pH 7.5–8.0). The predominant fatty acids of strain EMB47T were iso-C16 : 0 3-OH, iso-C15 : 1 G, C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0 and it contained phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylcholine as polar lipids. The G+C content of the genomic DNA was 40.8 mol% and the major quinone was MK-6. Comparative 16S rRNA gene sequence analyses showed that strain EMB47T formed a distinct phyletic line within the genus Flavobacterium. The levels of 16S rRNA gene sequence similarity with respect to Flavobacterium species were below 94.7 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB47T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium croceum sp. nov. is proposed. The type strain is EMB47T (=KCTC 12611T=DSM 17960T).

scholarly journals Hydrogenophaga caeni sp. nov., isolated from activated sludge

2007 ◽  
Vol 57 (5) ◽  
pp. 1126-1130 ◽  
Author(s):  
Bok Sil Chung ◽  
Seung Hyun Ryu ◽  
Minjeong Park ◽  
Yeji Jeon ◽  
Young Ryun Chung ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Batch Reactor ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Biological Phosphorus Removal ◽  
Rrna Gene Sequence

A Gram-negative bacterium, designated strain EMB71T, was isolated from activated sludge used for enhanced biological phosphorus removal in a sequencing batch reactor. The cells of the isolate were facultatively aerobic, motile rods with single polar flagella. Growth was observed to occur at 15–35 °C (optimally at 30 °C) and at pH 6.0–9.0 (optimally at pH 7.0–8.0). The predominant fatty acids of strain EMB71T were C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), and the polar lipids comprised a large amount of phosphatidylethanolamine and a small amount of diphosphatidylglycerol. The G+C content of the genomic DNA was 61.6 mol % and the major quinone was Q-8. Comparative 16S rRNA gene sequence analyses showed that strain EMB71T formed a phyletic lineage with the genus Hydrogenophaga within the family Comamonadaceae. The levels of 16S rRNA gene sequence similarity with respect to the type strains of Hydrogenophaga species ranged from 95.1 to 96.9 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB71T represents a novel species of the genus Hydrogenophaga, for which the name Hydrogenophaga caeni sp. nov. is proposed. The type strain is EMB71T (=KCTC 12613T=DSM 17962T).

scholarly journals Brevundimonas aveniformis sp. nov., a stalked species isolated from activated sludge

2007 ◽  
Vol 57 (7) ◽  
pp. 1561-1565 ◽  
Author(s):  
Seung Hyun Ryu ◽  
Minjeong Park ◽  
Jung Ro Lee ◽  
Pil-Yong Yun ◽  
Che Ok Jeon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Batch Reactor ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Biological Phosphorus Removal ◽  
Rrna Gene Sequence

A Gram-negative, rod-like, stalk-producing bacterium, designated strain EMB102T, was isolated from activated sludge that performed enhanced biological phosphorus removal in a sequencing batch reactor. Cells without stalks were motile with single polar flagella, but cells that did produce stalks were non-motile and lacked polar flagella. Growth of strain EMB102T was observed at temperatures between 15 and 35 °C (optimum, 30 °C) and between pH 6.0 and 9.0 (optimum, pH 7.5–8.5). The predominant fatty acids of strain EMB102T were C18 : 1 ω7c, C16 : 0 and C15 : 0. The predominant polar lipid was phosphatidylglycerol. The G+C content of the genomic DNA was 64.1 mol% and the major quinone was Q-10. Comparative 16S rRNA gene sequence analyses showed that strain EMB102T formed a distinct phyletic lineage within the genus Brevundimonas. The levels of 16S rRNA gene sequence similarity between the type strains of Brevundimonas species ranged from 95.8 to 97.5 %. DNA–DNA relatedness levels between the EMB102T and closely related Brevundimonas species were below 15.0 %. On the basis of chemotaxonomic data and molecular properties, strain EMB102T represents a novel species within the genus Brevundimonas, for which the name Brevundimonas aveniformis sp. nov. is proposed. The type strain is EMB102T (=KCTC 12609T=DSM 17977T).

Culture-dependent and -independent approaches establish the complexity of a PAH-degrading microbial consortium

2005 ◽  
Vol 51 (11) ◽  
pp. 897-909 ◽  
Author(s):  
Marc Viñas ◽  
Jordi Sabaté ◽  
Caterina Guasp ◽  
Jorge Lalucat ◽  
Anna M Solanas
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Consortium ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Sole Source ◽  
Rrna Gene ◽  
Dominant Group ◽  
Clone Libraries ◽  
Variable Regions ◽  
Culture Dependent

A microbial consortium (AM) obtained by sequential enrichment in liquid culture with a polycyclic aromatic hydrocarbon (PAH) mixture of three- and four-ringed PAHs as a sole source of carbon and energy was examined using a triple-approach method based on various cultivation strategies, denaturing gradient gel electrophoresis (DGGE), and the screening of 16S and 18S rRNA gene clone libraries. Eleven different sequences by culture-dependent techniques and seven by both DGGE and clone libraries were obtained. The comparison of three variable regions (V3–V5) of the 16S rRNA gene between the sequences obtained yielded 19 different microbial components. Proteobacteria were the dominant group, representing 83% of the total, while the Cytophaga–Flexibacter–Bacteroides group (CFB) was 11% and the Ascomycota fungi 6%. β-Proteobacteria were predominant in the DGGE and clone library methods, whereas they were a minority in culturable strains. The highest diversity and number of noncoincident sequences were achieved by the cultivation method that showed members of the α-, β-, and γ-Proteobacteria; CFB bacterial group; and Asco mycota fungi. Only six of the 11 strains isolated showed PAH-degrading capability. The bacterial strain (AMS7) and the fungal strain (AMF1), which were similar to Sphingomonas sp. and Fusarium sp., respectively, achieved the greatest PAH depletion. The results indicate that polyphasic assessment is necessary for a proper understanding of the composition of a microbial consortium.Key words: microbial consortium, microbial diversity, PAHs, DGGE, 16S rRNA gene.

scholarly journals Reassessment of the Role of Rapid Antigen Detection Tests in Diagnosis of Invasive Group A Streptococcal Infections

2016 ◽  
Vol 54 (4) ◽  
pp. 994-999 ◽  
Author(s):  
Vincent Gazzano ◽  
Anne Berger ◽  
Yvonne Benito ◽  
Anne-Marie Freydiere ◽  
Anne Tristan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Point Of Care ◽  
Test Strip ◽  
Antigen Detection ◽  
Rrna Gene ◽  
Invasive Group ◽  
Life Threatening ◽  
Group A

Rapid antigen detection tests (RADTs) for group A streptococci (GAS) are widely used for diagnosing acute pharyngitis, which has led to a considerable reduction in antibiotic prescriptions over the past decade. Beyond this intended use, their reassessment on invasive samples may be relevant in the management of life-threatening GAS infections. To this end, we evaluated the performances of three RADTs, culture, GAS PCR, and 16S rRNA gene PCR assays, and compared them with a composite gold standard (GAS-PCR assay and/or culture) for the diagnosis of severe GAS infection. A total of 192 specimens from deep-tissue (mostly normally sterile) sites enriched for 75 GAS-positive samples were enrolled in the study. The three evaluated RADTs showed sensitivities ranging from 88.0% to 94.7% versus 98.7% for GAS PCR, 84% for 16S rRNA gene PCR, and 77.3% for culture. The sensitivities of the ImmunoCardSTAT! Strep A test (Meridian Bioscience) and the NADAL Strep A strip (Nal Von Minden) were similar to that of GAS PCR (P= 0.25 and 0.03, respectively) and higher than that of culture (P= 0.001 and 0.006, respectively), whereas the SD Bioline Strep A test strip (Standard Diagnostics) showed a performance similar to that of culture (P= 0.02). The three RADTs detected 10 distinctemmtypes, including a predominance ofemm1 (33.3%),emm89 (10.6%), andemm12 (7.6%). No false-positive results were observed, leading to a specificity of 100% for all the evaluated RADTs. The GAS RADTs turned out to be sensitive, specific, and easy-to-use tools that may aid in the management of invasive GAS infections in 24/7 point-of-care laboratories by enabling early diagnosis and focused therapy.

Improved Sensitivity of PCR for Diagnosis of Human Granulocytic Ehrlichiosis Using epank1 Genes of Ehrlichia phagocytophila -Group Ehrlichiae

2000 ◽  
Vol 38 (1) ◽  
pp. 354-356
Author(s):  
Jennifer J. Walls ◽  
Patrizio Caturegli ◽  
Johan S. Bakken ◽  
Kristin M. Asanovich ◽  
J. Stephen Dumler
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Ankyrin Repeat ◽  
Rrna Gene ◽  
Gene Target ◽  
Granulocytic Ehrlichiosis ◽  
Ehrlichia Phagocytophila ◽  
Human Granulocytic Ehrlichiosis ◽  
Group A ◽  
Group B

ABSTRACT The agent of human granulocytic ehrlichiosis (HGE), Ehrlichia phagocytophila , and Ehrlichia equi probably comprise variants of a single Ehrlichia species now called the Ehrlichia phagocytophila genogroup. These variants share a unique 153-kDa protein antigen with ankyrin repeat motifs encoded by the epank1 gene. The epank1 gene was investigated as an improved target for PCR diagnosis of HGE compared with the currently used 16S rRNA gene target. Primers for epank1 flanking a region that spans part of the 5′ ankyrin repeat coding region and part of the unique 3′ region were synthesized. Blood samples from 31 patients with suspected HGE who were previously tested by 16S rRNA gene (16S) PCR and indirect immunofluorescent antibody test (IFA) were retrospectively tested with the epank1 primers. Eleven patients were 16S PCR positive and had a seroconversion detected by IFA (group A), 10 patients were 16S PCR negative but had a seroconversion detected by IFA (group B), and 10 patients were 16S PCR negative and seronegative (group C). Ten of the 11 group A patients were epank1 PCR positive, all 10 of the group B patients were epank1 PCR positive, and all of the PCR-negative and seronegative patients (group C) were epank1 PCR negative. The epank1 primers are more sensitive than the previously used 16S rRNA gene primers and therefore may be more useful in diagnostic testing for HGE.

scholarly journals Oligotyping and Genome-Resolved Metagenomics Reveal DistinctCandidatusAccumulibacter Communities in Full-Scale Side-Stream versus Conventional Enhanced Biological Phosphorus Removal (EBPR) Configurations

2019 ◽  
Author(s):  
Varun N. Srinivasan ◽  
Guangyu Li ◽  
Dongqi Wang ◽  
Nicholas B. Tooker ◽  
Zihan Dai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phosphorus Removal ◽  
Full Scale ◽  
Rrna Gene ◽  
Enhanced Biological Phosphorus Removal ◽  
Biological Phosphorus Removal ◽  
Side Stream ◽  
First Time ◽  
Biological Phosphorus

AbstractCandidatusAccumulibacter phosphatis (CAP) and its sub-clades-level diversity has been associated and implicated in successful phosphorus removal performance in enhanced biological phosphorus removal (EBPR). Development of high-throughput untargeted methods to characterize clades of CAP in EBPR communities can enable a better understanding of Accumulibacter ecology at a higher-resolution beyond OTU-level in wastewater resource recovery facilities (WRRFs). In this study, for the first time, using integrated 16S rRNA gene sequencing, oligotyping and genome-resolved metagenomics, we were able to reveal clade-level differences in Accumulibacter communities and associate the differences with two different full-scale EBPR configurations. The results led to the identification and characterization of a distinct and dominant Accumulibacter oligotype - Oligotype 2 (belonging to Clade IIC) and its matching MAG (RC14) associated with side-stream EBPR configuration. We are also able to extract MAGs belonging to CAP clades IIB (RCAB4-2) and II (RC18) which did not have representative genomes before. This study demonstrates and validates the use of a high-throughput approach of oligotyping analysis of 16S rRNA gene sequences to elucidate CAP clade-level diversity. We also show the existence of a previously uncharacterized diversity of CAP clades in full-scale EBPR communities through extraction of MAGs, for the first time from full-scale facilities.

scholarly journals Putative glycogen-accumulating organisms belonging to the Alphaproteobacteria identified through rRNA-based stable isotope probing

Microbiology ◽  
2006 ◽  
Vol 152 (2) ◽  
pp. 419-429 ◽  
Author(s):  
Rikke Louise Meyer ◽  
Aaron Marc Saunders ◽  
Linda Louise Blackall
Keyword(s):  
Stable Isotope ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Phosphorus Removal ◽  
Stable Isotope Probing ◽  
Metabolic Phenotype ◽  
Rrna Gene ◽  
Biological Phosphorus Removal ◽  
16S Rrna Gene Analysis

Deterioration of enhanced biological phosphorus removal (EBPR) has been linked to the proliferation of glycogen-accumulating organisms (GAOs), but few organisms possessing the GAO metabolic phenotype have been identified. An unidentified GAO was highly enriched in a laboratory-scale bioreactor and attempts to identify this organism using conventional 16S rRNA gene cloning had failed. Therefore, rRNA-based stable isotope probing followed by full-cycle rRNA analysis was used to specifically identify the putative GAOs based on their characteristic metabolic phenotype. The study obtained sequences from a group of Alphaproteobacteria not previously shown to possess the GAO phenotype, but 90 % identical by 16S rRNA gene analysis to a phylogenetic clade containing cloned sequences from putative GAOs and the isolate Defluvicoccus vanus. Fluorescence in situ hybridization (FISH) probes (DF988 and DF1020) were designed to target the new group and post-FISH chemical staining demonstrated anaerobic–aerobic cycling of polyhydroxyalkanoates, as per the GAO phenotype. The successful use of probes DF988 and DF1020 required the use of unlabelled helper probes which increased probe signal intensity up to 6·6-fold, thus highlighting the utility of helper probes in FISH. The new group constituted 33 % of all Bacteria in the lab-scale bioreactor from which they were identified and were also abundant (51 and 55 % of Bacteria) in two other similar bioreactors in which phosphorus removal had deteriorated. Unlike the previously identified Defluvicoccus-related organisms, the group identified in this study were also found in two full-scale treatment plants performing EBPR, suggesting that this group may be industrially relevant.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

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