Revealing hidden diversity among tropical cyanobacteria: the new genus Onodrimia (Synechococcales, Cyanobacteria) described using the polyphasic approach

Phytotaxa ◽  
2017 ◽  
Vol 326 (1) ◽  
pp. 28 ◽  
Author(s):  
EVA JAHODÁŘOVÁ ◽  
PETR DVOŘÁK ◽  
PETR HAŠLER ◽  
ALOISIE POULÍČKOVÁ
Keyword(s):  
New Genus ◽  
Sensu Stricto ◽  
Hot Water ◽  
Polyphasic Approach ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Peculiar Form ◽  
Morphological Differences ◽  
Trichome Morphology ◽  
The 16S Rrna Gene

Leptolyngbya represents a group of common mat forming cyanobacteria with very simple trichome morphology and a polyphyletic evolutionary origin. In this paper, we used a polyphasic approach to describe a new genus morphologically similar to Leptolyngbya. Three strains of Leptolyngbyaceae cyanobacteria were isolated from submersed bark of tree branches which fell into the Hot-water spring from a rainforest in West Java. A phylogeny of the 16S rRNA gene indicated that these strains fell into a well-supported clade separate from Leptolyngbya sensu stricto. Although our strains possessed only minor morphological differences from other similar Leptolyngbyaceae species, these new taxa may be differentiated based on a peculiar form of reproduction, where hormogonia and hormocytes form tree-like tuft structures. Thus, based on a phylogenetic position, morphological, and ecological evidence, we propose a new genus, Onodrimia.

scholarly journals Antricoccus suffuscus gen. nov., sp. nov., isolated from a natural cave

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4410-4416 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Type Strain ◽  
New Genus ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Diamino Acid ◽  
Unknown Phospholipid

A novel actinobacterium, designated strain C4-31T, was isolated from soil collected from a cave. Cells were aerobic, Gram-reaction-positive, oxidase-negative, catalase-positive and non-motile cocci. Comparison of 16S rRNA gene sequences showed that the organism occupied a distinct phylogenetic position within the suborder Frankineae, with sequence similarity values of less than 93.2 % to members of this suborder. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, an unknown aminophospholipid and an unknown phospholipid. The major fatty acids were iso-C16 : 0, C17 : 1ω6c and C16 : 0. The G+C content of the DNA was 62.8 mol%. On the basis of morphological and chemotaxonomic data as well as phylogenetic evidence, strain C4-31T ( = KCTC 39556T = DSM 100065T) is considered to represent the type strain of a novel species of a new genus in the suborder Frankineae, for which the name Antricoccus suffuscus gen. nov., sp. nov. is proposed.

A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3602-3608 ◽  
Author(s):  
Yasuko Yoneda ◽  
Takashi Yoshida ◽  
Hisato Yasuda ◽  
Chiaki Imada ◽  
Yoshihiko Sako
Keyword(s):  
Sediment Core ◽  
Marine Bacterium ◽  
New Genus ◽  
Gene Sequence ◽  
Ferric Iron ◽  
Core Sample ◽  
Rrna Gene ◽  
Content Type ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A hydrogenogenic, carboxydotrophic marine bacterium, strain KKC1T, was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile, Gram-stain-negative, 1.0–3.0 µm straight rods, often observed with round endospores. Strain KKC1T grew at 55–68 °C, pH 5.2–9.2 and 0.8–14 % (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0–7.5 and 2.46 % salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically, producing H2 from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g. sulfite, thiosulfate, fumarate, ferric iron and AQDS (9,10-anthraquinone 2,6-disulfonate). KKC1T grew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16 : 0 constituted almost half of the total cellular fatty acids. The DNA G+C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1T was most closely related to those of members of the genus Moorella with similarity ranging from 91 to 89 %. Based on physiological and phylogenetic novelty, we propose the isolate as a representative of a new genus and novel species with the name Calderihabitans maritimus gen. nov., sp. nov.; the type strain of the type species is KKC1T ( = DSM 26464T = NBRC 109353T).

scholarly journals Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum ‘Verrucomicrobia’ isolated from seawater in Japan

2007 ◽  
Vol 57 (5) ◽  
pp. 959-963 ◽  
Author(s):  
Jaewoo Yoon ◽  
Mina Yasumoto-Hirose ◽  
Atsuko Katsuta ◽  
Hiroshi Sekiguchi ◽  
Satoru Matsuda ◽  
...  
Keyword(s):  
Cell Wall ◽  
New Genus ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Hard Coral ◽  
The 16S Rrna Gene

An obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium, designated strain 04OKA010-24T, was isolated from seawater surrounding the hard coral Galaxea fascicularis L., collected at Majanohama, Akajima, Japan, and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain represented a member of the phylum ‘Verrucomicrobia’ and shared 84–95 % sequence similarity with cultivated strains of ‘Verrucomicrobia’ subdivision 4. Amino acid analysis of the cell-wall hydrolysate indicated the absence of muramic acid and diaminopimelic acid, which suggested that the strain did not contain peptidoglycan in the cell wall. The G+C content of the DNA was 53.9 mol%. MK-7 was the major menaquinone and C14 : 0, C18 : 1 ω9c and C18 : 0 were the major fatty acids. On the basis of these data, it was concluded that strain 04OKA010-24T represents a novel species in a new genus in subdivision 4 of the phylum ‘Verrucomicrobia’, for which the name Coraliomargarita akajimensis gen. nov., sp. nov. is proposed. The type strain of Coraliomargarita akajimensis is 04OKA010-24T (=MBIC06463T=IAM 15411T=KCTC 12865T).

scholarly journals Halotia gen. nov., a phylogenetically and physiologically coherent cyanobacterial genus isolated from marine coastal environments

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 663-675 ◽  
Author(s):  
Diego Bonaldo Genuário ◽  
Marcelo Gomes Marçal Vieira Vaz ◽  
Guilherme Scotta Hentschke ◽  
Célia Leite Sant’Anna ◽  
Marli Fátima Fiore
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
New Genus ◽  
Salinity Range ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Code Of Nomenclature ◽  
The Antarctic ◽  
The 16S Rrna Gene

Nostoc is a common and well-studied genus of cyanobacteria and, according to molecular phylogeny, is a polyphyletic group. Therefore, revisions of this genus are urged in an attempt to clarify its taxonomy. Novel strains isolated from underexplored environments and assigned morphologically to the genus Nostoc are not genetically related to the ‘true Nostoc’ group. In this study, four strains isolated from biofilms collected in Antarctica and five strains originated from Brazilian mangroves were evaluated. Despite their morphological similarities to other morphotypes of Nostoc , these nine strains differed from other morphotypes in ecological, physiological and genetic aspects. Based on the phylogeny of the 16S rRNA gene, the Antarctic sequences were grouped together with the sequences of the Brazilian mangrove isolates and Nostoc sp. Mollenhauer 1 : 1-067 in a well-supported cluster (74 % bootstrap value, maximum-likelihood). This novel cluster was separated phylogenetically from the ‘true Nostoc’ clade and from the clades of the morphologically similar genera Mojavia and Desmonostoc. The 16S rRNA gene sequences generated in this study exhibited 96 % similarity to sequences from the nostocacean genera mentioned above. Physiologically, these nine strains showed the capacity to grow in a salinity range of 1–10 % NaCl, indicating their tolerance of saline conditions. These results provide support for the description of a new genus, named Halotia gen. nov., which is related morphologically to the genera Nostoc , Mojavia and Desmonostoc. Within this new genus, three novel species were recognized and described based on morphology and internal transcribed spacer secondary structures: Halotia branconii sp. nov., Halotia longispora sp. nov. and Halotia wernerae sp. nov., under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants.

scholarly journals Proposal of Umezawaea gen. nov., a new genus of the Actinosynnemataceae related to Saccharothrix, and transfer of Saccharothrix tangerinus Kinoshita et al. 2000 as Umezawaea tangerina gen. nov., comb. nov.

2007 ◽  
Vol 57 (12) ◽  
pp. 2758-2761 ◽  
Author(s):  
D. P. Labeda ◽  
R. M. Kroppenstedt
Keyword(s):  
Type Strain ◽  
Type Species ◽  
New Genus ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Aerial Mycelium ◽  
Detailed Examination ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

In the course of phylogenetic analyses of the taxa within the suborder Pseudonocardineae, it was observed that Saccharothrix tangerinus MK27-91F2T was misplaced in the genus Saccharothrix. After a detailed examination of nucleotide signatures in the 16S rRNA gene sequence along with the morphological and chemotaxonomic characteristics of this strain, which are different from those of all species of Saccharothrix as well as the other genera within the suborder, it was concluded that this strain represents a new genus, for which the name Umezawaea gen. nov. is proposed. Pseudosporangia are produced on the aerial mycelium, the whole-cell sugar pattern consists of galactose, mannose and ribose, phosphatidylethanolamine, phosphatidylinositol and lyso-phosphatidylethanolamine are the predominant phospholipids and MK-9(H4) is the predominant menaquinone. The type species of the proposed new genus is Umezawaea tangerina gen. nov., comb. nov., with the type strain MK27-91F2T (=NRRL B-24463T =DSM 44720T =FERM P-16053T =JCM 10302T =NBRC 16184T).

scholarly journals Proposal to reclassify Streptobacillus hongkongensis into a novel genus as Pseudostreptobacillus hongkongensis gen. nov., comb. nov.

2020 ◽  
Vol 70 (4) ◽  
pp. 2366-2368 ◽  
Author(s):  
Tobias Eisenberg ◽  
Stefanie P. Glaeser ◽  
Jochen Blom ◽  
Peter Kämpfer
Keyword(s):  
Type Species ◽  
Core Genome ◽  
Housekeeping Genes ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Protein Coding ◽  
Content Type ◽  
Phenotypic Differences ◽  
Link Type ◽  
The 16S Rrna Gene

The reclassification of Streptobacillus hongkongensis as Pseudostreptobacillus hongkongensis gen. nov., comb. nov. is proposed because of the separate phylogenetic position on the basis of the 16S rRNA gene sequence phylogeny, the combined analysis of the three protein-coding housekeeping genes groEL, gyrB and recA and a core genome sequence phylogeny to all other Streptobacillus species that is supported by phenotypic differences. The species Pseudostreptobacillus hongkongensis is the type species of the genus. The type strain is HKU33T, JCM 18691T, NCTC 13659T, DSM 26322T.

scholarly journals Reclassification of Actinobacillus muris as Muribacter muris gen. nov., comb. nov.

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3344-3351 ◽  
Author(s):  
Werner Nicklas ◽  
Magne Bisgaard ◽  
Bent Aalbæk ◽  
Peter Kuhnert ◽  
Henrik Christensen
Keyword(s):  
16S Rrna ◽  
Dna Sequences ◽  
Type Strain ◽  
New Genus ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
New Combination ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Sequence Comparisons

To reinvestigate the taxonomy of [Actinobacillus] muris, 474 strains, mainly from mice and rats, were characterized by phenotype and 130 strains selected for genotypic characterization by 16S rRNA and partial rpoB gene sequencing. The type strain was further investigated by whole-genome sequencing. Phylogenetic analysis of the DNA sequences showed one monophyletic group with intragroup similarities of 96.7 and 97.2 % for the 16S rRNA and rpoB genes, respectively. The highest 16S rRNA gene sequence similarity to a taxon with a validly published name outside the group was 95.9 %, to the type strain of [Pasteurella] pneumotropica. The closest related taxon based on rpoB sequence comparison was ‘Haemophilus influenzae-murium’, with 88.4 % similarity. A new genus and a new combination, Muribacter muris gen. nov., comb. nov., are proposed based on a distinct phylogenetic position based on 16S rRNA and rpoB gene sequence comparisons, with major divergence from the existing genera of the family Pasteurellaceae. The new genus has the characteristics of [A.] muris with the emendation that acid formation from ( − )-d-mannitol and hydrolysis of aesculin are variable, while the α-glucosidase test is positive. There is no requirement for exogenously supplied NAD (V factor) for the majority of strains investigated; however, one strain was found to require NAD. The major fatty acids of the type strain of Muribacter muris were C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I, C16 : 1ω7c and C16 : 0, which is in line with most genera of the Pasteurellaceae. The type strain of Muribacter muris is CCUG 16938T ( = NCTC 12432T = ATCC 49577T).

scholarly journals Reclassification of the genus Natronolimnobius: proposal of two new genera, Natronolimnohabitans gen. nov. to accommodate Natronolimnobius innermongolicus and Natrarchaeobaculum gen. nov. to accommodate Natronolimnobius aegyptiacus and Natronolimnobius sulfurireducens

2020 ◽  
Vol 70 (5) ◽  
pp. 3399-3405 ◽  
Author(s):  
Dimitry Y. Sorokin ◽  
Alexander Y. Merkel ◽  
Enzo Messina ◽  
Mikhail M. Yakimov ◽  
Takashi Itoh ◽  
...  
Keyword(s):  
Type Strain ◽  
New Genus ◽  
Soda Lakes ◽  
Single Copy ◽  
Rrna Gene ◽  
Protein Markers ◽  
Content Type ◽  
Archaeal Protein ◽  
Link Type ◽  
The 16S Rrna Gene

The genus Natronolimnobius , currently including four species, is a member of the order Natrialbales , class Halobacteria, and consists of obligately alkaliphilic and extremely halophilic members found exclusively in highly alkaline hypersaline soda lakes. The species were classified into this genus mostly based on phylogenetic analysis of the 16S rRNA gene. However, a more advanced phylogenomic reconstruction based on 122 conserved single-copy archaeal protein markers clearly indicates a polyphyletic origin of the species included into this genus, thus warranting its reclassification into three separate genera. We therefore propose to transfer Nlb. innermongolicus (type strain N-1311) to a new genus Natronolimnohabitans as Nlh. innermongolicus comb. nov. and to transfer Nlb. aegyptiacus (type strain JW/NM-HA 15) and Nlb. sulfurireducens (type strain AArc1) to a new genus Natrarchaeobaculum as Nbl. aegyptiacum comb. nov. and Nbl. sulfurireducens comb. nov. The phylogenomic differentiation of these four species is also supported by the ANI/AAI distances and unique phenotypes. The most important physiological differences includes a previously unreported ability for cellulose and xylan utilization in Nlb. baerhuensis, thermophily in Nbl. aegyptiacus and anaerobic sulfur respiration in Nbl. sulfurireducens. We further present an emended description of Natronolimnobius baerhuensis .

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