scholarly journals Quantification of Syntrophic Fatty Acid-β-Oxidizing Bacteria in a Mesophilic Biogas Reactor by Oligonucleotide Probe Hybridization

1999 ◽  
Vol 65 (11) ◽  
pp. 4767-4774 ◽  
Author(s):  
Kaare H. Hansen ◽  
Birgitte K. Ahring ◽  
Lutgarde Raskin
Keyword(s):  
Fatty Acid ◽  
Saturated Fatty Acid ◽  
Small Subunit ◽  
Most Probable Number ◽  
Small Subunit Rrna ◽  
Probable Number ◽  
Syntrophomonas Wolfei ◽  
The Family ◽  
Syntrophic Bacteria ◽  
Biogas Reactor

Small-subunit rRNA sequences were obtained for two saturated fatty acid-β-oxidizing syntrophic bacteria, Syntrophomonas sapovorans and Syntrophomonas wolfei LYB, and sequence analysis confirmed their classification as members of the family Syntrophomonadaceae. S. wolfei LYB was closely related to S. wolfei subsp. wolfei, butS. sapovorans did not cluster with the other members of the genus Syntrophomonas. Five oligonucleotide probes targeting the small-subunit rRNA of different groups within the familySyntrophomonadaceae, which contains all currently known saturated fatty acid-β-oxidizing syntrophic bacteria, were developed and characterized. The probes were designed to be specific at the family, genus, and species levels and were characterized by temperature-of-dissociation and specificity studies. To demonstrate the usefulness of the probes for the detection and quantification of saturated fatty acid-β-oxidizing syntrophic bacteria in methanogenic environments, the microbial community structure of a sample from a full-scale biogas plant was determined. Hybridization results with probes for syntrophic bacteria and methanogens were compared to specific methanogenic activities and microbial numbers determined with most-probable-number estimates. Most of the methanogenic rRNA was comprised of Methanomicrobiales rRNA, suggesting that members of this order served as the main hydrogen-utilizing microorganisms. Between 0.2 and 1% of the rRNA was attributed to theSyntrophomonadaceae, of which the majority was accounted for by the genus Syntrophomonas.

The Relationships among Microorganisms in Paddy Soil of Rice Varieties at Sanamchaikate, Chachoengsao

2017 ◽  
Vol 866 ◽  
pp. 144-147
Author(s):  
Duongruitai Nicomrat ◽  
Paisan Kanthang ◽  
Siriphatrc Chamutpong
Keyword(s):  
Paddy Soil ◽  
Small Subunit ◽  
Organic Fertilizers ◽  
Rrna Genes ◽  
Most Probable Number ◽  
Small Subunit Rrna ◽  
Rice Varieties ◽  
Probable Number ◽  
Jasmine Rice ◽  
Ph Range

The research was conducted to understand the diversity of microbial communities in the rice cultivars KDM 105 in the rice fields at Sanamchaikate, Chachoengsao Province. The culturing bacterial community in paddy soil before planting, during the planting and sowing of rice, and after rice collection as well as isolation of free nitrogen fixing bacteria under aerobic and anaerobic conditions were identified by molecular comparision of 16S small subunit rRNA genes as well as species diversity and their richness by Most Probable Number (MPN) method. Culturable bacterial isolates in the soil around the roots of rice varieties were determined for their physical appearances on the solid culture (Plate culturing method) and the microscopic observation under light microscope. It was found that bacteria in the paddy soil complemented with organic fertilizers and no pesticide application for over five years had a pH range from 5.2 to 5.5 cultivated jasmine rice, 8-9 log Units of free N2-fixing bacteria near the roots compared with those in other area having 4-5 log Units. Most of them were identified to be Pseudomonas sp. Microbacterium sp. Bacillus sp. Stenotrophomonas sp. and Burkholderia sp., by homology comparison of 16S rDNA gene at 98, 97, 99, 99.5, and 99%, respectively. This research revealed the recognizable complex and change in soil bacteria presented in paddy ecosystem. In any critical change of to the soil, the study of microbial diversity, compositions and their richness can be further useful for indicating proper soil management.

scholarly journals Development and Application of a Most-Probable-Number–PCR Assay To Quantify Flagellate Populations in Soil Samples

2001 ◽  
Vol 67 (4) ◽  
pp. 1613-1618 ◽  
Author(s):  
Line Fredslund ◽  
Flemming Ekelund ◽  
Carsten Suhr Jacobsen ◽  
Kaare Johnsen
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Small Subunit ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Heterotrophic Flagellates ◽  
Small Subunit Rrna ◽  
Pcr Assay ◽  
Probable Number ◽  
Soil Protozoa

ABSTRACT This paper reports on the first successful molecular detection and quantification of soil protozoa. Quantification of heterotrophic flagellates and naked amoebae in soil has traditionally relied on dilution culturing techniques, followed by most-probable-number (MPN) calculations. Such methods are biased by differences in the culturability of soil protozoa and are unable to quantify specific taxonomic groups, and the results are highly dependent on the choice of media and the skills of the microscopists. Successful detection of protozoa in soil by DNA techniques requires (i) the development and validation of DNA extraction and quantification protocols and (ii) the collection of sufficient sequence data to find specific protozoan 18S ribosomal DNA sequences. This paper describes the development of an MPN-PCR assay for detection of the common soil flagellate Heteromita globosa, using primers targeting a 700-bp sequence of the small-subunit rRNA gene. The method was tested by use of gnotobiotic laboratory microcosms with sterile tar-contaminated soil inoculated with the bacterium Pseudomonas putida OUS82 UCB55 as prey. There was satisfactory overall agreement between H. globosa population estimates obtained by the PCR assay and a conventional MPN assay in the three soils tested.

scholarly journals Description of Eurystomatella sinica n. gen., n. sp., with establishment of a new family Eurystomatellidae n. fam. (Protista, Ciliophora, Scuticociliatia) and analyses of its phylogeny inferred from sequences of the small-subunit rRNA gene

2010 ◽  
Vol 60 (2) ◽  
pp. 460-468 ◽  
Author(s):  
Miao Miao ◽  
Yangang Wang ◽  
Weibo Song ◽  
John C. Clamp ◽  
Khaled A. S. Al-Rasheid
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
New Family ◽  
Small Subunit Rrna Gene ◽  
The Family ◽  
Great Divergence

Recently, an undescribed marine ciliate was isolated from China. Investigation of its morphology and infraciliature revealed it as an undescribed species representing a new genus, Eurystomatella n. gen., the type of the new family Eurystomatellidae n. fam. The new family is defined by close-set, apically positioned oral membranelles and a dominant buccal field that is surrounded by an almost completely circular paroral membrane. The new genus is defined by having a small oral membranelle 1 (M1), bipartite M2 and well-developed M3, a body surface faintly sculptured with a silverline system in a quadrangular, reticulate pattern and a cytostome located at the anterior third of a large buccal field. The type species of the new genus, Eurystomatella sinica n. sp., is a morphologically unique form that is defined mainly by the combination of a conspicuously flattened body, several caudal cilia, extremely long cilia associated with the buccal apparatus and a contractile vacuole located subcaudally. According to phylogenetic analyses of small-subunit (SSU) rRNA gene sequences, Eurystomatella clusters with the genus Cyclidium, as a sister group to the family Pleuronematidae. The great divergence in both buccal and somatic ciliature between Eurystomatella and all other known scuticociliates supports the establishment of a new family for Eurystomatella.

Detection of fatty acid beta-oxidizing syntrophic bacteria by fluorescence in situ hybridization

2006 ◽  
Vol 54 (2) ◽  
pp. 33-39 ◽  
Author(s):  
R.J. Menes ◽  
D. Travers
Keyword(s):  
In Situ Hybridization ◽  
Fatty Acid ◽  
Fluorescence In Situ Hybridization ◽  
Upflow Anaerobic Sludge Blanket ◽  
Anaerobic Sludge ◽  
Enrichment Cultures ◽  
The Family ◽  
Syntrophic Bacteria ◽  
Anaerobic Sludge Blanket

A new 16S rRNA-targeted oligonucleotide probe, specific for the cluster of fatty acid β-oxidizing syntrophic bacteria of the family Syntrophomonadaceae was designed for fluorescence in situ hybridization. This probe was evaluated with target as well as non-target cultures. Moreover this probe was assessed with butyrate and oleate degrading enrichment cultures and methanogenic sludges from full-scale plants. The results showed that the probe revealed the presence of fatty acid β-oxidizing syntrophic bacteria in some of the samples analyzed. However, cell quantification was possible only in enrichment cultures and in a flocculent sludge from a reactor that treats lipid-rich wastewaters, but not in methanogenic granular sludges from upflow anaerobic sludge blanket reactors.

Small-subunit rRNA gene sequences from representatives of selected families of the Gigartinales and Rhodymeniales (Rhodophyta). 1. Evidence for the Plocamiales ord.nov.

1994 ◽  
Vol 72 (9) ◽  
pp. 1250-1263 ◽  
Author(s):  
G. W. Saunders ◽  
G. T. Kraft
Keyword(s):  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Chain Reaction ◽  
Small Subunit Rrna Gene ◽  
New Information ◽  
The Family ◽  
Close Relationship ◽  
Polymerase Chain

Nucleotide sequences of the nuclear, small-subunit (SSU) ribosomal RNAs, as inferred from polymerase chain reaction (PCR)-amplified products, are presented for Areschougia congesta (Turner) J. Agardh (Solieriaceae), Dasyphloea insignis Montagne (Dumontiaceae), Sarcothalia crassifolia (C. Agardh) Edyvane & Womersley (Gigartinaceae), Nizymenia australis Sonder (Nizymeniaceae), Phacelocarpus peperocarpos (Poiret) Wynne, Ardré & Silva (Phacelocarpaceae), Plocamiocolax pulvinata Setchell, Plocamium angustum (J. Agardh) J.D. Hooker, Plocamium cartilagineum (Linnaeus) Dixon (Plocamiaceae), Rhodymenia linearis J. Agardh (Rhodymeniaceae), and Sphaerococcus coronopifolius Stackhouse (Sphaerococcaceae). Phylogenetic analyses of the SSU sequences between the Plocamiaceae and members of the Sphaerococcaceae, Phacelocarpaceae, and Nizymeniaceae, with which the Plocamiaceae has been associated historically, show SSU differences of between 87 and 105 nucleotides and do not indicate a close relationship. A review of anatomical knowledge of the Plocamiaceae and Pseudoanemoniaceae and new information on vegetative and tetrasporangial development in Plocamium and Plocamiocolax are presented to buttress a case for the Plocamiales ord.nov. Representatives of the Nizymeniaceae and Phacelocarpaceae differ from one another by only nine nucleotides, suggesting that these two taxa are very closely related and perhaps not distinct at the family rank. Key words: Gigartinales, PCR, phylogeny, Plocamiales ord.nov., Pseudoanemoniaceae, Rhodophyta, small-subunit rRNA, systematics.

scholarly journals The phylogeny of the Schistosomatidae based on three genes with emphasis on the interrelationships of Schistosoma Weinland, 1858

Parasitology ◽  
2003 ◽  
Vol 126 (3) ◽  
pp. 203-224 ◽  
Author(s):  
A. E. LOCKYER ◽  
P. D. OLSON ◽  
P. ØSTERGAARD ◽  
D. ROLLINSON ◽  
D. A. JOHNSTON ◽  
...  
Keyword(s):  
Ribosomal Subunit ◽  
Good Deal ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Small Subunit ◽  
Small Subunit Rrna ◽  
Asian Origin ◽  
The Family ◽  
Veterinary Importance

Schistosomes are digenean flukes, parasitic of birds, mammals and crocodiles. The family Schistosomatidae contains species of considerable medical and veterinary importance, which cause the disease schistosomiasis. Previous studies, both morphological and molecular, which have provided a good deal of information on the phylogenetics of this group, have been limited in the number of species investigated or the type or extent of molecular data used. This paper presents the most comprehensive phylogeny to date, based on the sequences of 3 genes, complete ribosomal small subunit rRNA and large ribosomal subunit rRNA, and mitochondrial cytochrome oxidase 1, sequenced from 30 taxa including at least 1 representative from 10 of the 13 known genera of the Schistosomatidae and 17 of the 20 recognized Schistosoma species. The phylogeny is examined using morphological characters, intermediate and definitive host associations and biogeography. Theories as to the origins and spread of Schistosoma are also explored. The principal findings are that Ornithobilharzia and Austrobilharzia form a sister group to the Schistosoma; mammalian schistosomes appear paraphyletic and 2 Trichobilharzia species, T. ocellata and T. szidati, seem to be synonymous. The position of Orientobilharzia within the Schistosoma is confirmed, as is an Asian origin for the Schistosoma, followed by subsequent dispersal through India and Africa.

Morphology and molecular phylogeny of four Frontonia species from Turkey (Protista, Ciliophora)

Zootaxa ◽  
2019 ◽  
Vol 4609 (3) ◽  
pp. 548
Author(s):  
SIBEL KIZILDAG ◽  
ISMAIL YILDIZ
Keyword(s):  
Phylogenetic Trees ◽  
Turkish Population ◽  
Small Subunit ◽  
The Other ◽  
Aquatic Environments ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Small Subunit Rrna Gene ◽  
The Family ◽  
Systematic Relationships

In this study, Frontonia leucas, Frontonia acuminata, Frontonia angusta, and Frontonia anatolica species isolated from aquatic environments of Van in Turkey were investigated in detail using morphological, morphometrical, and molecular methods. Although there were minor differences, the Frontonia populations were morphologically similar to the other previously reported populations of the 4 species. Frontonia leucas differed from the other populations by the following combination of characters: about 200 somatic and only 3 vestibular kineties, and a single micronucleus. The Turkish population of Frontonia acuminata had just 4 vestibular kineties and the large micronucleus was always located to the anterior of the carrot-shaped macronucleus. The ratio of the oral apparey size to the cell size of Frontonia angusta in this study was about 18%, with 3 vestibular kineties, and 1 excretory pore. Phylogenetic trees based on small-subunit rRNA gene sequences were constructed using Bayesian inference and maximum-likelihood. Frontonia anatolica was more closely related to Apofrontonia dohrni and Paramecium spp. than to its congeners, while F. acuminata, like F. terricola, was also more closely related to the family Stokesiidae. The results indicated that Frontonia is a non-monophyletic genus consisting of 3 groups. We presented the systematic relationships of the genera and families of Peniculida with new data of genus Frontonia herein. 

scholarly journals Disentangling the Taxonomy of Rickettsiales and Description of Two Novel Symbionts (“Candidatus Bealeia paramacronuclearis” and “Candidatus Fokinia cryptica”) Sharing the Cytoplasm of the Ciliate Protist Paramecium biaurelia

2016 ◽  
Vol 82 (24) ◽  
pp. 7236-7247 ◽  
Author(s):  
Franziska Szokoli ◽  
Michele Castelli ◽  
Elena Sabaneyeva ◽  
Martina Schrallhammer ◽  
Sascha Krenek ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Sensu Stricto ◽  
The Other ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Taxonomic Assignment ◽  
Content Type ◽  
The Family ◽  
Critical Revision

ABSTRACTIn the past 10 years, the number of endosymbionts described within the bacterial orderRickettsialeshas constantly grown. Since 2006, 18 novelRickettsialesgenera inhabiting protists, such as ciliates and amoebae, have been described. In this work, we characterize two novel bacterial endosymbionts fromParameciumcollected near Bloomington, IN. Both endosymbiotic species inhabit the cytoplasm of the same host. The Gram-negative bacterium “CandidatusBealeia paramacronuclearis” occurs in clumps and is frequently associated with the host macronucleus. With its electron-dense cytoplasm and a distinct halo surrounding the cell, it is easily distinguishable from the second smaller symbiont, “CandidatusFokinia cryptica,” whose cytoplasm is electron lucid, lacks a halo, and is always surrounded by a symbiontophorous vacuole. For molecular characterization, the small-subunit rRNA genes were sequenced and used for taxonomic assignment as well as the design of species-specific oligonucleotide probes. Phylogenetic analyses revealed that “CandidatusBealeia paramacronuclearis” clusters with the so-called “basal”Rickettsiales, and “CandidatusFokinia cryptica” belongs to “CandidatusMidichloriaceae.” We obtained tree topologies showing a separation ofRickettsialesinto at least two groups: one represented by the familiesRickettsiaceae,Anaplasmataceae, and “CandidatusMidichloriaceae” (RAM clade), and the other represented by “basalRickettsiales,” including “CandidatusBealeia paramacronuclearis.” Therefore, and in accordance with recent publications, we propose to limit the orderRickettsialesto the RAM clade and to raise “basalRickettsiales” to an independent order,Holosporalesord. nov., insideAlphaproteobacteria, which presently includes four family-level clades. Additionally, we define the family “CandidatusHepatincolaceae” and redefine the familyHolosporaceae.IMPORTANCEIn this paper, we provide the characterization of two novel bacterial symbionts inhabiting the sameParameciumhost (Ciliophora, Alveolata). Both symbionts belong to “traditional”Rickettsiales, one representing a new species of the genus “CandidatusFokinia” (“CandidatusMidichloriaceae”), and the other representing a new genus of a “basal”Rickettsiales. According to newly characterized sequences and to a critical revision of recent literature, we propose a taxonomic reorganization of “traditional”Rickettsialesthat we split into two orders:Rickettsiales sensu strictoandHolosporalesord. nov. This work represents a critical revision, including new records of a group of symbionts frequently occurring in protists and whose biodiversity is still largely underestimated.

Spencermartinsiella europaea gen. nov., sp. nov., a new member of the family Trichomonascaceae

2011 ◽  
Vol 61 (4) ◽  
pp. 993-1000 ◽  
Author(s):  
Gábor Péter ◽  
Dénes Dlauchy ◽  
Judit Tornai-Lehoczki ◽  
Motofumi Suzuki ◽  
Cletus P. Kurtzman
Keyword(s):  
Novel Species ◽  
Large Subunit ◽  
Elongation Factor ◽  
Small Subunit ◽  
The Novel ◽  
Small Subunit Rrna ◽  
Gene Sequences ◽  
Rotten Wood ◽  
The Family ◽  
Large Subunit Rrna

Ten strains of a novel heterothallic yeast species were isolated from rotten wood collected at different locations in Hungary. Analysis of gene sequences for the D1/D2 domain of the large subunit rRNA, as well as analysis of concatenated gene sequences for the nearly complete nuclear large subunit rRNA, nuclear small subunit rRNA and translation elongation factor 1-α, placed the novel species in the family Trichomonascaceae, but showed that it was distinct from all currently recognized genera. The name Spencermartinsiella europaea gen. nov., sp. nov. is proposed to accommodate the new genus and novel species. The novel species could be distinguished from recognized species of neighbouring genera on the basis of standard phenotypic characteristics. The type and isotype strains of Spencermartinsiella europaea are NCAIM Y.01817T ( = NRRL Y-48265T =  CBS 11730T) and NCAIM Y.01819I ( = NRRL Y-48266I = CBS 11731I), respectively.

scholarly journals Cryptosporidium Genotypes and Subtypes in Lambs and Goat Kids in Spain

2008 ◽  
Vol 74 (19) ◽  
pp. 6026-6031 ◽  
Author(s):  
Joaqu�n Qu�lez ◽  
Eucaris Torres ◽  
Rachel M. Chalmers ◽  
Stephen J. Hadfield ◽  
Emilio del Cacho ◽  
...  
Keyword(s):  
Potential Role ◽  
Geographical Area ◽  
Small Ruminants ◽  
Small Subunit ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Single Nucleotide ◽  
The Family ◽  
Pcr Products

ABSTRACT To provide information on the transmission dynamics of cryptosporidial infections in domestic small ruminants and the potential role of sheep and goats as a source for human cryptosporidiosis, Cryptosporidium-positive isolates from 137 diarrheic lambs and 17 goat kids younger than 21 days of age were examined by using genotyping and subtyping techniques. Fecal specimens were collected between 2004 and 2006 from 71 sheep and 7 goat farms distributed throughout Arag�n (northeastern Spain). Cryptosporidium parvum was the only species identified by restriction analyses of PCR products from small-subunit rRNA genes from all 154 microscopy-positive isolates and the sequencing of a subset of 50 isolates. Sequence analyses of the glycoprotein (GP60) gene revealed extensive genetic diversity within the C. parvum strains in a limited geographical area, in which the isolates from lambs exhibited 11 subtypes in two subtype families (IId and IIa) and those from goat kids displayed four subtypes within the family IId. Most isolates (98%) belonged to the subtype family IId, whereas only three isolates belonged to the most widely distributed family, IIa. Three of the four most prevalent subtypes (IIdA17G1a, IIdA19G1, and IIdA18G1) were previously identified in humans, and five subtypes (IIdA14G1, IIdA15G1, IIdA24G1, IIdA25G1, and IIdA26G1) were novel subtypes. All IId subtypes were identical to each other in the nonrepeat region, except for subtypes IIdA17G1b and IIdA22G1, which differed by a single nucleotide polymorphism downstream of the trinucleotide repeats. These findings suggest that lambs and goat kids are an important reservoir of the zoonotic C. parvum subtype family IId for humans.

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