scholarly journals Revision of the Synechococcales (Cyanobacteria) through recognition of four families including Oculatellaceae fam. nov. and Trichocoleaceae fam. nov. and six new genera containing 14 species

Phytotaxa ◽  
2018 ◽  
Vol 365 (1) ◽  
pp. 1 ◽  
Author(s):  
TRUC MAI ◽  
JEFFREY R. JOHANSEN ◽  
NICOLE PIETRASIAK ◽  
MARKÉTA BOHUNICKÁ ◽  
MICHAEL P. MARTIN
Keyword(s):  
16S Rrna ◽  
Large Family ◽  
The Other ◽  
Rrna Gene ◽  
New Genera ◽  
Filamentous Cyanobacteria ◽  
Family Level ◽  
Gene Data ◽  
The 16S Rrna Gene ◽  
Rpoc1 Gene

A total of 48 strains of thin, filamentous cyanobacteria in Synechococcales were studied by sequencing 16S rRNA and rpoC1 sequence fragments. We also carefully characterized a subset of these by morphology. Phylogenetic analysis of the 16S rRNA gene data using Bayesian inference of a large Synechococcales alignment (345 OTU’s) was in agreement with the phylogeny based on the rpoC1 gene for 59 OTU’s. Both indicated that the large family-level grouping formerly classified as the Leptolyngbyaceae could be further divided into four family-level clades. Two of these family-level clades have been recognized previously as Leptolyngbyaceae and Prochlorotrichaceae. Oculatellaceae fam. nov. and Trichocoleaceae fam. nov. are proposed for the other two families. The Oculatellaceae was studied in greater detail, and six new genera containing 14 species were characterized and named. These new taxa are: Pegethrix botrychoides, P. olivacea, P. convoluta, P. indistincta, Drouetiella lurida, D. hepatica, D. fasciculata, Cartusia fontana, Tildeniella torsiva, T. nuda, Komarkovaea angustata, Kaiparowitsia implicata, Timaviella obliquedivisa, and T. radians.

scholarly journals Lake Superior Supports Novel Clusters of Cyanobacterial Picoplankton

2007 ◽  
Vol 73 (12) ◽  
pp. 4055-4065 ◽  
Author(s):  
Natalia V. Ivanikova ◽  
Linda C. Popels ◽  
R. Michael L. McKay ◽  
George S. Bullerjahn
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Lake Superior ◽  
Abundant Species ◽  
Rrna Gene ◽  
Neighbor Joining ◽  
16S Rrna Gene Sequences ◽  
The World ◽  
Gene Data ◽  
The 16S Rrna Gene

ABSTRACT Very little is known about the biodiversity of freshwater autotrophic picoplankton (APP) in the Laurentian Great Lakes, a system comprising 20% of the world's lacustrine freshwater. In this study, the genetic diversity of Lake Superior APP was examined by analyzing 16S rRNA gene and cpcBA PCR amplicons from water samples. By neighbor joining, the majority of 16S rRNA gene sequences clustered within the “picocyanobacterial clade” consisting of freshwater and marine Synechococcus and Prochlorococcus. Two new groups of Synechococcus spp., the pelagic Lake Superior clusters I and II, do not group with any of the known freshwater picocyanobacterial clusters and were the most abundant species (50 to 90% of the sequences) in samples collected from offshore Lake Superior stations. Conversely, at station Portage Deep (PD), located in a nearshore urbanized area, only 4% of the sequences belonged to these clusters and the remaining clones reflected the freshwater Synechococcus diversity described previously at sites throughout the world. Supporting the 16S rRNA gene data, the cpcBA library from nearshore station PD revealed a cosmopolitan diversity, whereas the majority of the cpcBA sequences (97.6%) from pelagic station CD1 fell within a unique Lake Superior cluster. Thus far, these picocyanobacteria have not been cultured, although their phylogenetic assignment suggests that they are phycoerythrin (PE) rich, consistent with the observation that PE-rich APP dominate Lake Superior picoplankton. Lastly, flow cytometry revealed that the summertime APP can exceed 105 cells ml−1 and suggests that the APP shifts from a community of PE and phycocyanin-rich picocyanobacteria and picoeukaryotes in winter to a PE-rich community in summer.

scholarly journals Myroides albus sp. nov., isolated from the gut of plastic-eating larvae of the coleopteran insect Zophobas atratus

2020 ◽  
Vol 70 (10) ◽  
pp. 5460-5466 ◽  
Author(s):  
Mengli Xia ◽  
Lin Hu ◽  
Yi-Xin Huo ◽  
Yu Yang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Coleopteran Insect ◽  
Zophobas Atratus ◽  
The 16S Rrna Gene

A bacterial strain, BIT-d1T, was isolated from the gut of plastic-eating larvae of the coleopteran insect Zophobas atratus. Its taxonomic position was analysed using a polyphasic approach. Cells were white-pigmented, Gram-stain-negative, non-motile, long rods without flagella. The 16S rRNA gene sequence (1401 bp) of strain BIT-d1T showed highest similarity (98.0%) to Myroides pelagicus SM1T and 96.6~92.6 % similarity to the other species of the genus Myroides . The results of phylogenetic analyses, based on the 16S rRNA gene, concatenated sequences of six housekeeping genes (gyrB, dnaK, tuf, murG, atpA and glyA) and genome sequences, placed strain BIT-d1T in a separate lineage among the genus Myroides , family Flavobacteriaceae . The major isoprenoid quinone was menaquinone-6 (MK-6) and the major fatty acids were C15 : 0 iso, C17 : 0 iso 3-OH and summed feature 9 (comprising iso-C17 : 1  ω9c and/or C16 : 0 10-methyl), which were similar to other members in the genus Myroides. In silico DNA–DNA hybridization and average nucleotide identity calculations plus physiological and biochemical tests exhibited the genotypic and phenotypic differentiation of strain BIT-d1T from the other members of the genus Myroides . Therefore, strain BIT-d1T is considered to represent a novel species within the genus Myroides , for which the name Myroides albus sp. nov is proposed. The type strain is BIT-d1T (=CGMCC 1.17043T=KCTC 72447T).

scholarly journals Resolving a taxonomic and nomenclatural puzzle in mantellid frogs: synonymization of Gephyromantis azzurrae with G. corvus, and description of Gephyromantis kintana sp. nov. from the Isalo Massif, western Madagascar

ZooKeys ◽  
2020 ◽  
Vol 951 ◽  
pp. 133-157
Author(s):  
Walter Cocca ◽  
Franco Andreone ◽  
Francesco Belluardo ◽  
Gonçalo M. Rosa ◽  
Jasmin E. Randrianirina ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
New Records ◽  
Molecular Data ◽  
The Other ◽  
Rrna Gene ◽  
Museum Specimens ◽  
Rich Family ◽  
Frog Species ◽  
The 16S Rrna Gene

The genus Gephyromantis belongs to the species-rich family Mantellidae and is currently divided in six subgenera. Among these is the subgenus Phylacomantis, which currently includes four described species: Gephyromantis pseudoasper, G. corvus, G. azzurrae, and G. atsingy. The latter three species are distributed in western Madagascar, and two of them (G. azzurrae and G. corvus) occur in the Isalo Massif. Based on the analysis of molecular data (a fragment of the 16S rRNA gene), morphological inspection of museum specimens, and photographic comparisons, G. azzurrae is synonymised with G. corvus and the second Phylacomantis lineage of Isalo is described as G. kintanasp. nov. This medium-sized frog species (adult snout-vent length 35–44 mm) is assigned to this subgenus according to genetic and morphological similarities to the other known species of Phylacomantis. Gephyromantis kintanasp. nov. is known only from the Isalo Massif, while new records for G. corvus extend its range to ca. 200 km off its currently known distribution. These two taxa seem to occur in syntopy in at least one locality in Isalo, and the easiest way to distinguish them is the inspection of the ventral colouration, dark in G. corvus and dirty white in G. kintana.

scholarly journals Identification of New Single Nucleotide Polymorphism-Based Markers for Inter- and Intraspecies Discrimination of Obligate Bacterial Parasites (Pasteuria spp.) of Invertebrates

2011 ◽  
Vol 77 (18) ◽  
pp. 6388-6394 ◽  
Author(s):  
Tim H. Mauchline ◽  
Rachel Knox ◽  
Sharad Mohan ◽  
Stephen J. Powers ◽  
Brian R. Kerry ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
The Other ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Single Nucleotide ◽  
Content Type ◽  
Protein Encoding ◽  
Encoding Genes ◽  
The 16S Rrna Gene

ABSTRACTProtein-encoding and 16S rRNA genes ofPasteuria penetranspopulations from a wide range of geographic locations were examined. Most interpopulation single nucleotide polymorphisms (SNPs) were detected in the 16S rRNA gene. However, in order to fully resolve all populations, these were supplemented with SNPs from protein-encoding genes in a multilocus SNP typing approach. Examination of individual 16S rRNA gene sequences revealed the occurrence of “cryptic” SNPs which were not present in the consensus sequences of anyP. penetranspopulation. Additionally, hierarchical cluster analysis separatedP. penetrans16S rRNA gene clones into four groups, and one of which contained sequences from the most highly passaged population, demonstrating that it is possible to manipulate the population structure of this fastidious bacterium. The other groups were made from representatives of the other populations in various proportions. Comparison of sequences among threePasteuriaspecies, namely,P. penetrans,P. hartismeri, andP. ramosa, showed that the protein-encoding genes provided greater discrimination than the 16S rRNA gene. From these findings, we have developed a toolbox for the discrimination ofPasteuriaat both the inter- and intraspecies levels. We also provide a model to monitor genetic variation in other obligate hyperparasites and difficult-to-culture microorganisms.

Morphological and molecular studies of Neosynechococcus sphagnicola, gen. et sp. nov. (Cyanobacteria, Synechococcales)

Phytotaxa ◽  
2014 ◽  
Vol 170 (1) ◽  
pp. 024 ◽  
Author(s):  
PETR DVOŘÁK ◽  
FRANTIŠEK HINDÁK ◽  
PETR HAŠLER ◽  
ALICA HINDÁKOVÁ ◽  
ALOISIE POULÍČKOVÁ
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
New Genus ◽  
Peat Bog ◽  
Rrna Gene ◽  
Filamentous Cyanobacteria ◽  
Ecological Features ◽  
Close Proximity ◽  
Molecular Studies ◽  
The 16S Rrna Gene

The genus Synechococcus represents an enigmatic group of cyanobacteria with very simple unicellular morphology and polyphyletic evolutionary origin. Here, we describe a new genus based on strain of Synechococcus-like cyanobacterium. The strain was isolated from the peat bog Klin (Slovakia), where it occupies different niches such as hyaline cells of Sphagnum, sheaths of cyanobacteria, dead cells of desmids, carapaces of dead crustaceans, and solitary in detritus. We describe this new genus using a combination of molecular, morphological and ecological features. A phylogeny of the 16S rRNA gene, 16S-23S ITS and rbcL loci showed a separate position of the investigated strain and its close proximity to filamentous cyanobacteria. Therefore, it is a novel lineage of Synechococcus-like cyanobacteria illustrating the polyphyletic nature of the genus Synechococcus. Moreover, the strain exhibits unique morphological and ecological features, which allow us to erect the new monospecific genus Neosynechococcus.

scholarly journals How conserved are the conserved 16S-rRNA regions?

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3036 ◽  
Author(s):  
Marcel Martinez-Porchas ◽  
Enrique Villalpando-Canchola ◽  
Luis Enrique Ortiz Suarez ◽  
Francisco Vargas-Albores
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Frequency Analysis ◽  
Universal Primers ◽  
Rrna Gene ◽  
Conserved Regions ◽  
Hypervariable Regions ◽  
Prokaryotic Diversity ◽  
Gene Data ◽  
The 16S Rrna Gene

The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123) were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers) were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%). Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker.

scholarly journals Two Distinct Mechanisms Cause Heterogeneity of 16S rRNA

1999 ◽  
Vol 181 (1) ◽  
pp. 78-82 ◽  
Author(s):  
Kumiko Ueda ◽  
Tatsuji Seki ◽  
Takuji Kudo ◽  
Toshiomi Yoshida ◽  
Masakazu Kataoka
Keyword(s):  
Secondary Structure ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
16S Rrna ◽  
Direct Sequencing ◽  
The Other ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The 16S Rrna Gene

ABSTRACT To investigate the frequency of heterogeneity among the multiple 16S rRNA genes within a single microorganism, we determined directly the 120-bp nucleotide sequences containing the hypervariable α region of the 16S rRNA gene from 475 Streptomyces strains. Display of the direct sequencing patterns revealed the existence of 136 heterogeneous loci among a total of 33 strains. The heterogeneous loci were detected only in the stem region designated helix 10. All of the substitutions conserved the relevant secondary structure. The 33 strains were divided into two groups: one group, including 22 strains, had less than two heterogeneous bases; the other group, including 11 strains, had five or more heterogeneous bases. The two groups were different in their combinations of heterogeneous bases. The former mainly contained transitional substitutions, and the latter was mainly composed of transversional substitutions, suggesting that at least two mechanisms, possibly misincorporation during DNA replication and horizontal gene transfer, cause rRNA heterogeneity.

scholarly journals Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Eric J. Raes ◽  
Kristen Karsh ◽  
Swan L. S. Sow ◽  
Martin Ostrowski ◽  
Mark V. Brown ◽  
...  
Keyword(s):  
16S Rrna ◽  
Metabolic Pathways ◽  
Low Cost ◽  
Marker Gene ◽  
South Pacific ◽  
Rrna Gene ◽  
South Pacific Ocean ◽  
Bacterial Marker ◽  
Gene 16S Rrna ◽  
Gene Data

AbstractGlobal oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

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