scholarly journals Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization

Toxins ◽  
2015 ◽  
Vol 7 (7) ◽  
pp. 2514-2533 ◽  
Author(s):  
Vitor Ramos ◽  
Daniele Salvi ◽  
João Machado ◽  
Micaela Vale ◽  
Joana Azevedo ◽  
...  
Keyword(s):  
Late Stage ◽  
Independent Study ◽  
Genetic Differences ◽  
Species Level ◽  
Structure Characterization ◽  
Toxic Dinoflagellate ◽  
Culture Independent

scholarly journals PseudomonasDiversity in Crude-Oil-Contaminated Intertidal Sand Samples Obtained after thePrestigeOil Spill

2010 ◽  
Vol 77 (3) ◽  
pp. 1076-1085 ◽  
Author(s):  
Magdalena Mulet ◽  
Zoyla David ◽  
Balbina Nogales ◽  
Rafael Bosch ◽  
Jorge Lalucat ◽  
...  
Keyword(s):  
Carbon Sources ◽  
Species Level ◽  
Gene Library ◽  
Direct Plating ◽  
Selective Media ◽  
Dna Library ◽  
Culture Independent ◽  
Northwestern Spain ◽  
Pcr Method ◽  
Culture Dependent

ABSTRACTThe Galicia seashore, in northwestern Spain, was one of the shorelines affected by thePrestigeoil spill in November 2002. The diversity of autochthonousPseudomonaspopulations present at two beaches (Carnota municipality) was analyzed using culture-independent and culture-dependent methods. The first analysis involved the screening of anrpoDgene library. The second involved the isolation of 94Pseudomonasstrains that were able to grow on selective media by direct plating or after serial enrichments on several carbon sources: biphenyl, gentisate, hexadecane, methylnaphthalene, naphthalene, phenanthrene, salicylate, xylene, and succinate. Eight denitrifyingPseudomonasstrains were also isolated by their ability to grow anaerobically with nitrate. The calculated coverage index forPseudomonasspecies was 89% when clones and isolates were considered together, and there were 29 phylospecies detected. The most abundant were members of the speciesP. stutzeri,P.putida,P. anguilliseptica, andP. oleovorans. Thirty-one isolates could not be identified at the species level and were considered representatives of 16 putative novelPseudomonasspecies. One isolate was considered representative of a novelP. stutzerigenomovar. Concordant results were obtained when the diversities of the cloned DNA library and the cultured strains were compared. The clone library obtained by therpoDPCR method was a useful tool for evaluatingPseudomonascommunities and also for microdiversity studies ofPseudomonaspopulations.

scholarly journals Bioacoustic investigations and taxonomic considerations on the Cicadetta montana species complex (Homoptera: Cicadoidea: Tibicinidae)

2004 ◽  
Vol 76 (2) ◽  
pp. 316-324 ◽  
Author(s):  
Matija Gogala ◽  
Tomi Trilar
Keyword(s):  
Cryptic Species ◽  
Species Complex ◽  
Similar Case ◽  
Genetic Differences ◽  
Species Level ◽  
Sister Species ◽  
Type Locality

Recent bioacoustic investigations have shown that Cicadetta montana Scopoli 1772 is a complex of morphologically similar sister species that are best characterized by their song patterns. At the type locality of C. montana, only mountain cicadas with simple, long lasting song phrases were heard, recorded and collected. Therefore, we have good reasons to suggest that this type of song is characteristic for C. montana s. str. Boulard described a song of C. montana from France with phrases composed of a long and a short echeme; this type of song is characteristic for cicadas morphologically corresponding to C. montana var. brevipennis Fieber 1876; we suggest to raise this taxon to species level. On the basis of specific song, Puissant and Boulard described C. cerdaniensis from Pyrénées. A similar case was the discovery and description of C. montana macedonica Schedl 1999 from Macedonia; since these Macedonian cicadas are sympatric with at least two other cryptic species in the C. montana group and molecular investigations showed substantial genetic differences between C. macedonica and C. montana or C. brevipennis, we conclude that this taxon should also be raised to species level. Songs of closely related C. podolica and Korean mountain cicada are presented as well.

scholarly journals Finally, Bulk Typing of Bacterial Species down to Strain Level using ON-rep-seq

2018 ◽  
Author(s):  
Łukasz Krych ◽  
Josué L. Castro-Mejía ◽  
Daniel N. Moesby ◽  
Morten B. Mikkelsen ◽  
Morten A. Rasmussen ◽  
...  
Keyword(s):  
High Speed ◽  
Bacterial Species ◽  
Cost Effective ◽  
Species Level ◽  
Strain Level ◽  
Read Length ◽  
High Quality ◽  
Sequencing Platform ◽  
Culture Independent ◽  
Single Flow

AbstractDespite the massive developments within culture-independent methods for detection and quantification of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (< 24h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation takes less than 5h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting the random error of reads within peaks of LCp generates a set (∼10 contigs per sample; 300bp - 3Kb) of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation. With benchmarked 288 isolates identified on a single flow cell and a theoretical throughput to evaluate over 1000 isolates, our method allows for detailed bacterial identification for less than 2$ per sample at very high speed.

scholarly journals Detection and phylogenetic analysis of coastal bioaerosols using culture dependent and independent techniques

2011 ◽  
Vol 8 (2) ◽  
pp. 301-309 ◽  
Author(s):  
R. Urbano ◽  
B. Palenik ◽  
C. J. Gaston ◽  
K. A. Prather
Keyword(s):  
Atmospheric Chemistry ◽  
Cloud Droplet ◽  
Independent Study ◽  
Rrna Gene ◽  
Monitoring Site ◽  
Microbial Composition ◽  
Atmospheric Processes ◽  
Erosion Processes ◽  
Culture Independent ◽  
Culture Dependent

Abstract. Bioaerosols are emerging as important yet poorly understood players in atmospheric processes. Microorganisms can impact atmospheric chemistry through metabolic reactions and can potentially influence physical processes by participating in ice nucleation and cloud droplet formation. Microbial roles in atmospheric processes are thought to be species-specific and potentially dependent on cell viability. Using a coastal pier monitoring site as a sampling platform, culture-dependent (i.e. agar plates) and culture-independent (i.e. DNA clone libraries from filters) approaches were combined with 18S rRNA and 16S rRNA gene targeting to obtain insight into the local atmospheric microbial composition. From 13 microbial isolates and 42 DNA library clones, a total of 55 sequences were obtained representing four independent sampling events. Sequence analysis revealed that in these coastal samples two fungal phyla, Ascomycota and Basidiomycota, predominate among eukaryotes while Firmicutes and Proteobacteria predominate among bacteria. Furthermore, our culture-dependent study verifies the viability of microbes from all four phyla detected through our culture-independent study. Contrary to our expectations and despite oceanic air mass sources, common marine planktonic bacteria and phytoplankton were not typically found. The abundance of terrestrial and marine sediment-associated microorganisms suggests a potential importance for bioaerosols derived from beaches and/or coastal erosion processes.

scholarly journals Culture-independent study of bacterial communities in tropical river sediment

2016 ◽  
Vol 81 (1) ◽  
pp. 200-209 ◽  
Author(s):  
Honglada Thoetkiattikul ◽  
Wuttichai Mhuantong ◽  
Onruthai Pinyakong ◽  
Worachart Wisawapipat ◽  
Atsushi Yamazoe ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
River Sediment ◽  
Independent Study ◽  
Tropical River ◽  
Culture Independent

scholarly journals The Human Oral Microbiome

2010 ◽  
Vol 192 (19) ◽  
pp. 5002-5017 ◽  
Author(s):  
Floyd E. Dewhirst ◽  
Tuste Chen ◽  
Jacques Izard ◽  
Bruce J. Paster ◽  
Anne C. R. Tanner ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Level ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
16S Rrna Gene Sequences ◽  
Culture Independent ◽  
Health And Disease

ABSTRACT The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org ). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.

scholarly journals Culture-Dependent and Culture-Independent Diversity within the Obligate Marine Actinomycete Genus Salinispora

2005 ◽  
Vol 71 (11) ◽  
pp. 7019-7028 ◽  
Author(s):  
Tracy J. Mincer ◽  
William Fenical ◽  
Paul R. Jensen
Keyword(s):  
Marine Sediments ◽  
Environmental Dna ◽  
Species Level ◽  
Sequence Diversity ◽  
Biologically Active ◽  
Intraspecific Diversity ◽  
Rrna Gene ◽  
The Bahamas ◽  
Clone Libraries ◽  
Culture Independent

ABSTRACT Salinispora is the first obligate marine genus within the order Actinomycetales and a productive source of biologically active secondary metabolites. Despite a worldwide, tropical or subtropical distribution in marine sediments, only two Salinispora species have thus far been cultivated, suggesting limited species-level diversity. To further explore Salinispora diversity and distributions, the phylogenetic diversity of more than 350 strains isolated from sediments collected around the Bahamas was examined, including strains cultured using new enrichment methods. A culture-independent method, using a Salinispora-specific seminested PCR technique, was used to detect Salinispora from environmental DNA and estimate diversity. Overall, the 16S rRNA gene sequence diversity of cultured strains agreed well with that detected in the environmental clone libraries. Despite extensive effort, no new species level diversity was detected, and 97% of the 105 strains examined by restriction fragment length polymorphism belonged to one phylotype (S. arenicola). New intraspecific diversity was detected in the libraries, including an abundant new phylotype that has yet to be cultured, and a new depth record of 1,100 m was established for the genus. PCR-introduced error, primarily from Taq polymerase, significantly increased clone library sequence diversity and, if not masked from the analyses, would have led to an overestimation of total diversity. An environmental DNA extraction method specific for vegetative cells provided evidence for active actinomycete growth in marine sediments while indicating that a majority of sediment samples contained predominantly Salinispora spores at concentrations that could not be detected in environmental clone libraries. Challenges involved with the direct sequence-based detection of spore-forming microorganisms in environmental samples are discussed.

scholarly journals Identifying the Source of Unknown Microcystin Genes and Predicting Microcystin Variants by Comparing Genes within Uncultured Cyanobacterial Cells

2009 ◽  
Vol 75 (11) ◽  
pp. 3598-3604 ◽  
Author(s):  
Christopher J. Allender ◽  
Gary R. LeCleir ◽  
Johanna M. Rinta-Kanto ◽  
Randall L. Small ◽  
Michael F. Satchwell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Great Lakes ◽  
Water Samples ◽  
Independent Study ◽  
Laurentian Great Lakes ◽  
Dna Fragments ◽  
The Novel ◽  
Multiple Markers ◽  
Culture Independent

ABSTRACT While multiple phylogenetic markers have been used in the culture-independent study of microcystin-producing cyanobacteria, in only a few instances have multiple markers been studied within individual cells, and in all cases these studies have been conducted with cultured isolates. Here, we isolate and evaluate large DNA fragments (>6 kb) encompassing two genes involved in microcystin biosynthesis (mcyA2 and mcyB1) and use them to identify the source of gene fragments found in water samples. Further investigation of these gene loci from individual cyanobacterial cells allowed for improved analysis of the genetic diversity within microcystin producers as well as a method to predict microcystin variants for individuals. These efforts have also identified the source of the novel mcyA genotype previously termed Microcystis-like that is pervasive in the Laurentian Great Lakes and they predict the microcystin variant(s) that it produces.

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