scholarly journals Molecular Comparison of Bacterial Communities within Iron-Containing Flocculent Mats Associated with Submarine Volcanoes along the Kermadec Arc

2008 ◽  
Vol 75 (6) ◽  
pp. 1650-1657 ◽  
Author(s):  
Tyler W. Hodges ◽  
Julie B. Olson
Keyword(s):  
Bacterial Communities ◽  
Fragment Length Polymorphism ◽  
Phylogenetic Analyses ◽  
Clone Libraries ◽  
Site Specific ◽  
Operational Taxonomic Units ◽  
Molecular Comparison ◽  
Flocculent Material ◽  
Hydrothermal Environments

ABSTRACT Iron oxide sheaths and filaments are commonly found in hydrothermal environments and have been shown to have a biogenic origin. These structures were seen in the flocculent material associated with two submarine volcanoes along the Kermadec Arc north of New Zealand. Molecular characterization of the bacterial communities associated with the flocculent samples indicated that no known Fe-oxidizing bacteria dominated the recovered clone libraries. However, clones related to the recently described Fe-oxidizing bacterium Mariprofundus ferrooxydans were obtained from both the iron-containing flocculent (Fe-floc) and sediment samples, and peaks corresponding to Mariprofundus ferrooxydans, as well as the related clones, were observed in several of our terminal restriction fragment length polymorphism profiles. A large group of epsilonproteobacterial sequences, for which there is no cultured representative, dominated clones from the Fe-floc libraries and were less prevalent in the sediment sample. Phylogenetic analyses indicated that several operational taxonomic units appeared to be site specific, and statistical analyses of the clone libraries found that all samples were significantly different from each other. Thus, the bacterial communities in the Fe-floc samples were not more closely related to each other than to the sediment communities.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

scholarly journals Characterization of Microbial Community Structure in Gulf of Mexico Gas Hydrates: Comparative Analysis of DNA- and RNA-Derived Clone Libraries

2005 ◽  
Vol 71 (6) ◽  
pp. 3235-3247 ◽  
Author(s):  
Heath J. Mills ◽  
Robert J. Martinez ◽  
Sandra Story ◽  
Patricia A. Sobecky
Keyword(s):  
Phylogenetic Analysis ◽  
Microbial Community ◽  
Gulf Of Mexico ◽  
Gas Hydrate ◽  
Phylogenetic Analyses ◽  
Active Fraction ◽  
Clone Libraries ◽  
Dna And Rna ◽  
Rna And Dna

ABSTRACT The characterization of microbial assemblages within solid gas hydrate, especially those that may be physiologically active under in situ hydrate conditions, is essential to gain a better understanding of the effects and contributions of microbial activities in Gulf of Mexico (GoM) hydrate ecosystems. In this study, the composition of the Bacteria and Archaea communities was determined by 16S rRNA phylogenetic analyses of clone libraries derived from RNA and DNA extracted from sediment-entrained hydrate (SEH) and interior hydrate (IH). The hydrate was recovered from an exposed mound located in the northern GoM continental slope with a hydrate chipper designed for use on the manned-submersible Johnson Sea Link (water depth, 550 m). Previous geochemical analyses indicated that there was increased metabolic activity in the SEH compared to the IH layer (B. N. Orcutt, A. Boetius, S. K. Lugo, I. R. Macdonald, V. A. Samarkin, and S. Joye, Chem. Geol. 205:239-251). Phylogenetic analysis of RNA- and DNA-derived clones indicated that there was greater diversity in the SEH libraries than in the IH libraries. A majority of the clones obtained from the metabolically active fraction of the microbial community were most closely related to putative sulfate-reducing bacteria and anaerobic methane-oxidizing archaea. Several novel bacterial and archaeal phylotypes for which there were no previously identified closely related cultured isolates were detected in the RNA- and DNA-derived clone libraries. This study was the first phylogenetic analysis of the metabolically active fraction of the microbial community extant in the distinct SEH and IH layers of GoM gas hydrate.

scholarly journals Characterization of a Phytoplasma Associated with Cabbage Yellows in Iran

Plant Disease ◽  
2007 ◽  
Vol 91 (5) ◽  
pp. 625-630 ◽  
Author(s):  
M. Salehi ◽  
K. Izadpanah ◽  
M. Siampour
Keyword(s):  
Nested Pcr ◽  
Fragment Length Polymorphism ◽  
Phylogenetic Analyses ◽  
Fars Province ◽  
Beet Leafhopper ◽  
Circulifer Haematoceps ◽  
Pcr Products ◽  
Disease Agent ◽  
Polymerase Chain

In 2001, a disease tentatively named Iranian cabbage yellows (ICY) was observed in cabbage fields of Zarghan (Fars Province, Iran). The major symptoms of the disease were yellowing, little leaves, plant stunting, opening of the head, and proliferation of the buds at the base of the stem into a witches'-broom. Among leafhoppers collected in cabbage fields, only Circulifer haematoceps transmitted the ICY agent. The disease agent was transmitted by the leafhopper from cabbage to cabbage, cauliflower, rape, and periwinkle, causing phytoplasma-type symptoms in these plants. Polymerase chain reaction (PCR) using phytoplasma-specific primer pair P1/P7 and nested PCR using P1/P7 and R16F2n/R16R2 primer pairs amplified products of expected size (1.8 and 1.2 kb, respectively) from symptomatic cabbage plants. Both restriction fragment length polymorphism (RFLP) of nested PCR products (1.2 kb) and phylogenetic analyses of 16S–23S rDNA spacer region sequence indicated that the ICY phytoplasma had the closest relationship to subgroup A members of the clover proliferation group, including beet leafhopper-transmitted virescence agent, ‘Candidatus Phytoplasma trifolii’, Columbia Basin potato purple top phytoplasma, and vinca virescence phytoplasma. Cabbage is reported as a new natural host to the 16SrVI group of phytoplasmas.

scholarly journals Characterization of a Bacterial Community in an Abandoned Semiarid Lead-Zinc Mine Tailing Site

2008 ◽  
Vol 74 (12) ◽  
pp. 3899-3907 ◽  
Author(s):  
Monica O. Mendez ◽  
Julia W. Neilson ◽  
Raina M. Maier
Keyword(s):  
Bacterial Communities ◽  
Phylogenetic Analyses ◽  
Control Sample ◽  
Mine Tailing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Semiarid Environment ◽  
Lead Zinc ◽  
Zinc Mine

ABSTRACT Bacterial diversity in mine tailing microbial communities has not been thoroughly investigated despite the correlations that have been observed between the relative microbial diversity and the success of revegetation efforts at tailing sites. This study employed phylogenetic analyses of 16S rRNA genes to compare the bacterial communities present in highly disturbed, extremely (pH 2.7) and moderately (pH 5.7) acidic lead-zinc mine tailing samples from a semiarid environment with those from a vegetated off-site (OS) control sample (pH 8). Phylotype richness in these communities decreased from 42 in the OS control to 24 in the moderately acidic samples and 8 in the extremely acidic tailing samples. The clones in the extremely acidic tailing sample were most closely related to acidophiles, none of which were detected in the OS control sample. The comparison generated by this study between the bacteria present in extremely acidic tailing and that in moderately acidic tailing communities with those in an OS control soil provides a reference point from which to evaluate the successful restoration of mine tailing disposal sites by phytostabilization.

scholarly journals Analysis of Soil Fungal and Bacterial Communities in Tianchi Volcano Crater, Northeast China

Life ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 280
Author(s):  
Xiao Wang ◽  
Lorenzo Pecoraro
Keyword(s):  
High Altitude ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Northeast China ◽  
Extreme Environments ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Operational Taxonomic Units ◽  
Tianchi Volcano

High-altitude volcanoes, typical examples of extreme environments, are considered of particular interest in biology as a possible source of novel and exclusive microorganisms. We analyzed the crater soil microbial diversity of Tianchi Volcano, northeast China, by combining molecular and morphological analyses of culturable microbes, and metabarcoding based on Illumina sequencing, in order to increase our understanding of high-altitude volcanic microbial community structure. One-hundred and seventeen fungal strains belonging to 51 species and 31 genera of Ascomycota, Basidiomycota and Mucoromycota were isolated. Penicillium, Trichoderma, Cladosporium, Didymella, Alternaria and Fusarium dominated the culturable fungal community. A considerable number of isolated microbes, including filamentous fungi, such as Aureobasidium pullulans and Epicoccum nigrum, yeasts (Leucosporidium creatinivorum), and bacteria (Chryseobacterium lactis and Rhodococcus spp.), typical of high-altitude, cold, and geothermal extreme environments, provided new insights in the ecological characterization of the investigated environment, and may represent a precious source for the isolation of new bioactive compounds. A total of 1254 fungal and 2988 bacterial operational taxonomic units were generated from metabarcoding. Data analyses suggested that the fungal community could be more sensitive to environmental and geographical change compared to the bacterial community, whose network was characterized by more complicated and closer associations.

scholarly journals Molecular Characterization of Functional and Phylogenetic Genes from Natural Populations of Methanotrophs in Lake Sediments

1999 ◽  
Vol 65 (11) ◽  
pp. 5066-5074 ◽  
Author(s):  
Andria M. Costello ◽  
Mary E. Lidstrom
Keyword(s):  
16S Rrna ◽  
Phylogenetic Analyses ◽  
Natural Populations ◽  
Restriction Enzymes ◽  
Clone Libraries ◽  
Operational Taxonomic Units ◽  
Methane Oxidizing Bacteria ◽  
Lake Washington ◽  
Pcr Products ◽  
Total Community

ABSTRACT The 16S rRNA and pmoA genes from natural populations of methane-oxidizing bacteria (methanotrophs) were PCR amplified from total community DNA extracted from Lake Washington sediments obtained from the area where peak methane oxidation occurred. Clone libraries were constructed for each of the genes, and approximately 200 clones from each library were analyzed by using restriction fragment length polymorphism (RFLP) and the tetrameric restriction enzymesMspI, HaeIII, and HhaI. The PCR products were grouped based on their RFLP patterns, and representatives of each group were sequenced and analyzed. Studies of the 16S rRNA data obtained indicated that the existing primers did not reveal the total methanotrophic diversity present when these data were compared with pure-culture data obtained from the same environment. New primers specific for methanotrophs belonging to the generaMethylomonas, Methylosinus, andMethylocystis were developed and used to construct more complete clone libraries. Furthermore, a new primer was designed for one of the genes of the particulate methane monooxygenase in methanotrophs, pmoA. Phylogenetic analyses of both the 16S rRNA and pmoA gene sequences indicated that the new primers should detect these genes over the known diversity in methanotrophs. In addition to these findings, 16S rRNA data obtained in this study were combined with previously described phylogenetic data in order to identify operational taxonomic units that can be used to identify methanotrophs at the genus level.

scholarly journals Genotyping of Malassezia pachydermatis disclosed genetic variation in isolates from dogs in Colombia

2019 ◽  
Vol 39 (11) ◽  
pp. 915-922
Author(s):  
Adriana Marcela Celis-Ramírez ◽  
Marcela Guevara-Suarez ◽  
Juan Camilo Galvis-Marín ◽  
María Ximena Rodríguez-Bocanegra ◽  
Rubiela Castañeda-Salazar ◽  
...  
Keyword(s):  
Otitis Externa ◽  
Fragment Length Polymorphism ◽  
Phylogenetic Analyses ◽  
Population Data ◽  
Rflp Pattern ◽  
Malassezia Pachydermatis ◽  
Canine Population ◽  
26S Rrna ◽  
Sequence Types

ABSTRACT: Malassezia pachydermatis is a lipophilic and lipid-dependent yeast mostly isolated from animals’ skin; hence, it is regarded as a zoophilic species causing otitis externa in dogs. Aspects associated with its epidemiology and pathogenicity is a matter of interest. This study aimed to conduct a molecular characterization of 43 isolates of M. pachydermatis obtained from dogs with otitis externa. For this purpose, the 5.8S internal transcribed spacer 2 (ITS2) and D1/D2 26S rRNA regions were amplified, sequenced and analyzed using restriction fragment length polymorphism (RFLP) with AluI, CfoI, and BstF5I endonucleases. Phylogenetic analyses revealed that these isolates grouped with the sequence types I, IV and V, previously proposed for M. pachydermatis. Interestingly, we found a new polymorphic RFLP pattern using BstF5I, these isolates were associated with the sequence types IV and V, nevertheless an association between polymorphic RFLP patterns, and fosfolipase activity or canine population data was not observed. These findings underline the genetic diversity of M. pachydermatis and provide new insights about the epidemiology of this species in the analyzed population.

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