Reinvestigations of Three “Well-known” Marine Scuticociliates: Uronemella filificum (Kahl, 1931) nov. gen., nov. comb., Pseud cohnilembus hargisi Evans & Thompson, 1964 and Cyclidium citrullus Cohn 1865, with Description of the New Genus Uronemella (Protozoa, Ciliophora, Scuticociliatida)

The living morphology, infraciliature and silverline system of 3 “well-known” marine scuticociliates, Uronemella filificum (Kahl, 1931) nov. gen., nov. comb. (formerly Uronema filificum Kahl, 1931), Pseudocohnilembus hargisi Evans & Thompson, 1964 and Cyclidium citrullus Cohn 1865 are reinvestigated and redescribed.

Based on the data obtained, we suggest an establishment of a new genus Uronemella. The diagnosis for the new taxon: thigmotactic Uronematidae with generally pear-shaped body and subequatorially positioned cytostome; apical plate dominant; oral apparatus Uronema-like, one-rowed membranelle 1 about as long as membranelle 2; paroral membrane extending anteriorly to about mid-level of membrane 2; one caudal cilium; in vivo exhibiting typical rotatory movement with help of a caudal-cilium-associated sticky thread; generally in marine habitats. According to this definition, three nominal species as new combinations are transferred into this genus: Uronemella binucleata (Song, 1993) nov. comb. (= Homalogastra binucleata Song, 1993), Uronemella filificum (Kahl, 1931) nov. comb. (= Uronema filificum Kahl, 1931) and Uronemella cymruensis (Pérez-Uz & Hope, 1997) nov. comb. (=Urocyclon cymruensis Pérez-Uz & Hope, 1997). For comparison with Uronemella, some other closely-related taxa are also briefly outlined in the present paper.     

Two new subspecies of Photorhabdus luminescens, isolated from Heterorhabditis bacteriophora (Nematoda: Heterorhabditidae): Photorhabdus luminescens subsp. kayaii subsp. nov. and Photorhabdus luminescens subsp. thracensis subsp. nov

Bacterial isolates from nematodes from Turkish soil samples were initially characterized by molecular methods and seven members of the genus Photorhabdus identified to the species level, using riboprint analyses and metabolic properties. Strain 07-5 (DSM 15195) was highly related to the type strain of Photorhabdus luminescens subsp. laumondii DSM 15139T, and was regarded a strain of this subspecies. Strains 1121T (DSM 15194T), 68-3 (DSM 15198) and 47-10 (DSM 15197) formed one, strain 39-8T (DSM 15199T), 39-7 (DSM 15196) and 01-12 (DSM 15193) formed a second cluster that branched intermediate the three subspecies of Photorhabdus luminescens. Based upon moderate 16S rRNA gene sequence similarities and differences in metabolic properties among themselves and with type strains of the three subspecies we consider the two clusters to represent two new subspecies of Photorhabdus luminescens for which the names Photorhabdus luminescens subsp. kayaii, type strain 1121T (DSM 15194T, NCIMB 13951T), and Photorhabdus luminescens subsp. thracensis subsp. nov., type strain 39-8T (DSM 15199T, NCIMB 13952T) are proposed.     

Geminicoccus roseus gen. nov., sp. nov., an aerobic phototrophic Alphaproteobacterium isolated from a marine aquaculture biofilter

A Gram-negative, strictly aerobic, diplococcoid bacterium (strain D2-3^T) was isolated from the biofilter of a recirculating marine aquaculture system. Phylogenetic analysis of the 16S rRNA gene sequence of D2-3^T indicated that the new organism occupied a novel lineage within the -1 subclass of Proteobacteria and was related to the genera Rhodothalassium, Azospirillum, Craurococcus, Acidiphilium, and Tistrella. The highest sequence similarity (90.8%) of the 16S rRNA gene sequence of D2-3^T was to that of Candidatus “Alysiosphaera europaea”. D2-3^T was mesophilic, heterotrophic, required sea salt, and had a pH optimum of 8.0. Growth in the presence of light resulted in the formation of pink colonies, a 25% increased cell yield, and a slightly increased growth rate. D2-3^T contained carotenoids and low amounts of bacteriochlorophyll a. Membranes of D2-3^T contained b-type cytochromes. The G+C content of the DNA was 60.3±0.1 mol%. Phylogenetic, morphological, physiological, and biochemical analyses demonstrated that D2-3^T represented a new aerobic phototrophic genus, for which the name Geminicoccus roseus gen. nov., sp. nov. is proposed for the type species (D2-3^T=DSM 18922^T=ATCC BAA-1445^T).     

Syntrophomonas wolfei subsp. methylbutyratica subsp. nov., and assignment of Syntrophomonas wolfei subsp. saponavida to Syntrophomonas saponavida sp. nov. comb. nov

A spore-forming bacterium strain 4J5(T) was isolated from rice field mud. When co-cultured with Methanobacterium formicicum DSM 1535(T), strain 4J5(T) could syntrophically degrade saturated fatty acids with 4-8 carbon atoms, including 2-methylbutyrate. Phylogenetic analysis based on 16S rRNA gene similarity showed that strain 4J5(T) was most closely related to Syntrophomonas wolfei subsp. wolfei DSM 2245(T) (98.9% sequence similarity); however, it differed from the latter in the substrates utilized and its genetic characteristics. Therefore, a new subspecies Syntrophomonas wolfei subsp. methylbutyratica is proposed. The type strain is 4J5(T) (=CGMCC 1.5051(T)=JCM 14075(T)). Furthermore, based on 16S rRNA sequence divergence and substrate utilization, we propose the assignment of Syntrophomonas wolfei subsp. saponavida DSM 4212(T) to Syntrophomonas saponavida sp. nov. comb. nov.     

Proposal of Mycobacterium peregrinum sp. nov., nom. rev., and elevation of Mycobacterium chelonae subsp. abscessus (Kubica et al.) to species status: Mycobacterium abscessus comb. nov.

We studied the taxonomic positions of the rapidly growing organism Mycobacterium fortuitum and phenotypically related organisms. We confirmed that "Mycobacterium peregrinum" ATCC 14467T (T = type strain) is genetically independent of M. fortuitum ATCC 6841T by using various DNA hybridization conditions. Strains that were genetically identified as "M. peregrinum" were phenotypically differentiated from M. fortuitum ATCC 6841T. Thus, we propose that "M. peregrinum" should be revived as an independent species, Mycobacterium peregrinum sp. nov., nom. rev. The type strain is strain ATCC 14467. M. fortuitum subsp. acetamidolyticum ATCC 35931T exhibited a high level of DNA relatedness to M. fortuitum ATCC 6841T. The hybridized DNAs maintained stable heteroduplexity at high stringency; thus, we confirmed that M. fortuitum subsp. acetamidolyticum is identical to M. fortuitum ATCC 6841T. We found that M. chelonae subsp. abscessus ATCC 19977T is genetically different from M. chelonae subsp. chelonae NCTC 946T on the basis of the results of quantitative hybridization even under optimal conditions. There was no reason to maintain this organism as a subspecies of M. chelonae. Thus, we propose that M. chelonae subsp. abscessus should be elevated to species status as Mycobacterium abscessus (Kubica et al.) comb. nov. The type strain is strain ATCC 19977.     

Salinivibrio costicola subsp. alcaliphilus subsp. nov., a haloalkaliphilic aerobe from Campania Region (Italy)

Phenotypic and phylogenetic studies were performed on unidentified Gram-negative staining, haloalkaliphilic aerobe and protease producer Salinivibrio-like organism recovered from a saltish spring with algal mat in the “Pozzo del Sale” site (Salt's Well) in the Campania Region (South Italy). Phylogenetic analysis based on comparison of 16S rRNA gene sequences demonstrated that the isolate was related to species of Salinivibrio genus. The DNA–DNA hybridization of the type strain 18AG^T with the most related Salinivibrio costicola subsp. costicola showed a re-association value of 72%. Based on the phenotypic distinctiveness of 18AG^T strain and molecular, chemical and genetic evidence, it is proposed that strain 18AG^T can be classified as S. costicola subsp. alcaliphilus, subsp. nov. The type strain of S. costicola subsp. alcaliphilus, is ATCC BAA-952^T; DSM 16359^T.     

Xylella fastidiosa subspecies: X. fastidiosa subsp. [correction] fastidiosa [correction] subsp. nov., X. fastidiosa subsp. multiplex subsp. nov., and X. fastidiosa subsp. pauca subsp. nov

Xylella fastidiosa, a fastidious bacterium causing disease in over 100 plant species, is classified as a single species, although genetic studies support multiple taxons. To determine the taxonomic relatedness among strains of X. fastidiosa, we conducted DNA-DNA relatedness assays and sequenced the 16S-23S intergenic spacer (ITS) region using 26 strains from 10 hosts. Under stringent conditions (Tm -15 degrees C), the DNA relatedness for most X. fastidiosa strains was *70%. However, at high stringency (Tm -8 degrees C), three distinct genotypes (A, B, and C) were revealed. Taxon A included strains from cultivated grape, alfalfa, almond (two), and maple, interrelated by 85% (mean); taxon B included strains from peach, elm, plum, pigeon grape, sycamore, and almond (one), interrelated by 84%; and taxon C included only strains from citrus, interrelated by 87%. The mean reciprocal relatedness between taxons A and B, A and C, and B and C, were 58, 41, and 45%, respectively. ITS results also indicated the same grouping; taxons A and B, A and C, and B and C had identities of 98.7, 97.9, and 99.2%, respectively. Previous and present phenotypic data supports the molecular data. Taxon A strains grow faster on Pierce's disease agar medium whereas B and C strains grow more slowly. Taxon B and C strains are susceptible to penicillin and resistant to carbenicillin whereas A strains are opposite. Each taxon can be differentiated serologically as well as by structural proteins. We propose taxons A, B, and C be named X. fastidiosa subsp. fastidiosa [correction] subsp. nov, subsp. multiplex, subsp. nov., and subsp. pauca, subsp. nov., respectively. The type strains of the subspecies are subsp. fastidiosa [correction] ICPB 50025 (= ATTC 35879T and ICMP 15197), subsp. multiplex ICPB 50039 (= ATTC 35871 and ICMP 15199), and subsp. pauca ICPB 50031 (= ICMP 15198).     

Molecular phylogeny and taxonomic revision of Chlamydomonas (Chlorophyta). I. Emendation of Chlamydomonas Ehrenberg and Chloromonas Gobi, and description of Oogamochlamys gen. nov. and Lobochlamys gen. nov

The genus Chlamydomonas (including Chloromonas) is one of the largest green algal genera comprising more than 600 species. To initiate a comprehensive analysis of the phylogeny and systematics of the genus, we determined nuclear-encoded SSU rRNA sequences from 32 strains of Chlamydomonas, Chloromonas and Chlorogonium with emphasis on oogamous taxa and related strains, and incorporated these into global molecular phylogenetic analyses of 132 strains of Chlorophyceae. In addition, we studied the morphology and reproduction of oogamous and related strains by light microscopy. We recognize and designate 18 monophyletic lineages (clades) within the Chlorophyceae, 11 of which are confined to the CW (basal bodies displaced clockwise) subgroup. The majority of clades recognized within the Chlorophyceae do not correspond to any of the traditional classification systems, which are still largely based on the organization level. Strains assigned to Chlamydomonas and Chloromonas were found in seven different clades confirming the polyphyly of the two genera as presently conceived. To initiate the taxonomic revision of Chlamydomonas, C. reinhardtii is proposed as the conserved type of the genus. In consequence, species in clades other than the clade containing C. reinhardtii must be transferred to other genera, a process initiated in this contribution. The oogamous strains studied represent a monophyletic lineage, which is described as Oogamochlamys gen. nov. comprising three species (O. gigantea, O. zimbabwiensis and O. ettlii spec. nov.). The sister clade to Oogamochlamys consists of isogamous strains characterized by chloroplasts with incisions and is described as Lobochlamys gen. nov. with two species (L. culleus and L. segnis). Another clade is characterized by asteroid or perforated, parietal chloroplasts and contains the type species of Chloromonas (C. reticulata). Thus, the polyphyletic Chloromonas (traditionally defined as “Chlamydomonas without pyrenoids”) can be legitimized as a monophyletic genus by restriction to this clade and is here emended on the basis of chloroplast characters (the clade contains strains with or without pyrenoids thus rejecting the character “absence of pyrenoids”).     

Vibrio tetraodonis subsp. pristinus subsp. nov., isolated from the coral Acropora cytherea at Palmyra Atoll,and creation and emended description of Vibrio tetraodonis subsp. tetraodonis subsp. nov

Strain OCN044^T was isolated from the homogenised tissue and mucus of an apparently healthy Acropora cytherea coral fragment collected from the western reef terrace of Palmyra Atoll in the Northern Line Islands and was taxonomically evaluated with a polyphasic approach. The morphological and chemotaxonomic properties are consistent with characteristics of the genus Vibrio: Gram-stain-negative rods, oxidase- and catalase-positive, and motile by means of a polar flagellum. Strain OCN044^T can be differentiated as a novel subspecies based on 21 differences among chemotaxonomic features (e.g., fatty acids percentages for C_12:0 and C_18:1 ω7c), enzymatic activities (e.g., DNase and cystine arylamidase), and carbon sources utilized (e.g., L-xylose and D-melezitose) from its nearest genetic relative. Phylogenetic analysis and genomic comparisons show close evolutionary relatedness to Vibrio tetraodonis A511^T but the overall genomic relatedness indices identify strain OCN044^T as a distinct subspecies. Based on a polyphasic characterisation, differences in genomic and taxonomic data, strain OCN044^T represents a novel subspecies of V. tetraodonis A511^T, for which the name Vibrio tetraodonis subsp. pristinus subsp. nov. is proposed. The type strain is OCN044^T (=?LMG 31895^T?=?DSM 111778^T).

     

Cochliopodium barki n. sp. (Rhizopoda, Himatismenida) re-isolated from soil 30 years after its initial description

A strain of Cochliopodium isolated from grassland soil at Sourhope Research Station (Scotland, UK) was found to be identical to the strain “Cochliopodium sp.2” studied by Bark in 1973. We name it Cochliopodium barki. It belongs to a group of species (comprising also C. minus and Cochliopodium sp. “NYS strain”) with very similar scale pattern.     

Photorhabdus temperata subsp. stackebrandtii subsp. nov. (Enterobacteriales: Enterobacteriaceae)

The bacterial symbiont of the entomopathogenic nematode Heterorhabditis bacteriophora strain GPS11 was characterized by 16S rRNA gene sequence and physiological traits. The phylogenetic tree built upon 16S rRNA gene sequences clustered the GPS11 bacterial isolate with Photorhabdus temperata strains which have been previously isolated from Heterorhabditis species. The phylogenetic tree further identified four subgroups in P. temperata, and the relationships among these subgroups were confirmed by gyrase subunit B (gyrB) gene sequence analysis. The subgroup containing the GPS11 bacterial isolate differs from other subgroups in sequences of 16S rRNA and gyrB gene, physiological traits, nematode host species, and geographic origin. Therefore, the subgroup comprising the GPS11 bacterial isolate is proposed here as a new subspecies: Photorhabdus temperata subsp. stackebrandtii subsp. nov. (type strain GPS11). The type strain has been deposited in ATCC and DSMZ collections.     

Growth and siderophore production of Xylella fastidiosa under iron-limited conditions

In this study, the production of siderophores by Xylella fastidiosa from the citrus bacteria isolate 31b9a5c (FAPESP – ONSA, Brazil) was investigated. The preliminary evidence supporting the existence of siderophore in X. fastidiosa was found during the evaluation of sequencing data generated in our lab using the BLAST-X tool, which indicated putative open reading frames (ORFs) associated with iron-binding proteins. In an iron-limited medium siderophores were detected in the supernatant of X. fastidiosa cultures. The endophytic bacterium Methylobacterium extorquens was also evaluated. Capillary electrophoresis was used to separate putative siderophores produced by X. fastidiosa. The bacterial culture supernatants of X. fastidiosa were identified negative for hydroxamate and catechol and positive for M. extorquens that secreted hydroxamate-type siderophores.     

Population differentiation and phylogeography of Hygrophila pogonocalyx based on RAPDs fingerprints

Genetic variation of the endangered species, Hygrophila pogonocalyx Hayata (Acanthaceae), was estimated based on RAPD fingerprints. According to the criteria of the International Union for Conservation of Nature and Nature Resources, H. pogonocalyx is on the Red List Category due to its endangered status. Entomophilous plants of H. pogonocalyx are mostly pollinated by honeybees. Gene flow between populations is constrained by the migratory capacity of the pollinators. A survey based on RAPD fingerprinting using 50 random primers revealed the distribution of genetic variation following an “isolation by distance” model. A hierarchical AMOVA analyses indicated significant differentiation between geographical regions (Φ_ct=0.934; P=0.048), among populations (Φ_st=0.945; P<0.001), and among populations within region (Φ_sc=0.169; P<0.001). The differentiation between geographic populations may be ascribed to a long isolation since the formation of the Central Mountain Range 1 million years ago. In contrast to low levels of genetic variation in many endangered species, some genetic processes avoiding selfing may have evolved in H. pogonocalyx. Somatic mutation also possibly contributed to the variability maintenance within populations with limited size.     

Alcaligenes faecalis subsp. parafaecalis subsp. nov., a bacterium accumulating poly-beta-hydroxybutyrate from acetone-butanol bioprocess residues

The authors have previously isolated a solvent tolerant bacterium, strain G(T), (T = type strain) capable to convert acetone-butanol bioprocess residues into poly-beta-hydroxybutyrate. Strain G(T) was initially identified as Alcaligenes spp by standard bacteriological tests. In this study the taxonomic position of the bacterium was investigated in detail. The 165 rDNA sequence analysis, the G + C content of DNA (56 mol%) and the presence of ubiquinone Q-8 confirmed strain G(T) as a representative of the genus Alcaligenes. In the polyamine pattern of the bacterium putrescine and cadaverine were detected, but only trace amounts of 2-hydroxyputrescine. The extremely low content of 2-hydroxyputrescine is remarkable, since this unique diamine is a common marker for beta-proteobacteria. Phylogenetic analyses of 16S rDNA demonstrated that Alcaligenes sp. G(T) is most closely related to the species Alcaligenes faecalis (99.6% sequence similarity to A. faecalis HR4 and 98.7% sequence similarity to A. faecalis [ATCC 8750T = DSM 30030T]. On the basis of DNA-DNA relatedness (56% similarity), the unique polyamine pattern, the physiological and biochemical differences strain G(T) could be distinguished from the species A. faecalis. Therefore, a new subspecies for the species Alcaligenes faecalis is proposed; Alcaligenes faecalis subsp. parafaecalis subsp. nov.     

Characterization of Desulfomicrobium salsuginis sp. nov. and Desulfomicrobium aestuarii sp. nov., two new sulfate-reducing bacteria isolated from the Adour estuary (French Atlantic coast) with specific mercury methylation potentials

Three strains of sulfate-reducing bacteria (ADR21, ADR26 and ADR28) were isolated from Adour estuary sediments (French South Atlantic coast). Cells of these isolates were rod-shaped, motile and stained Gram-negative. The 16S rRNA and dsrAB genes sequence analyses indicated that these three strains belonged to the genus Desulfomicrobium within the delta Proteobacteria, with Desulfomicrobium escambiense strain DSM10707^T as their closest relative. According to phenotypic characteristics, strains ADR21 and ADR28 could be considered as members of the same species. The relatedness values, based on DNA–DNA hybridization studies, between strains ADR21/DSM10707^T, ADR26/DSM10707^T and ADR21/ADR26 ranged between 30.6–40.8%, 45.2–43.0% and 19.0–26.4%, respectively. Strains ADR21 and ADR28 grew well on lactate, fumarate, malate, formate, ethanol and H₂/acetate in the presence of sulfate as an electron acceptor. Thiosulfate, nitrate, fumarate and DMSO were alternative electron acceptors. Malate was well fermented but pyruvate and fumarate only poorly. Strain ADR26 could not grow on ethanol or fumarate and was unable to use DMSO or fumarate as electron acceptors. The three new strains exhibited differences compared to the type strain of D. escambiense, such as temperature optima, substrate utilization and mercury methylation capacities. On the basis of both genetic and phenotypic evidences, strain ADR21 is proposed as the type strain of the species Desulfomicrobium salsuginis sp. nov., and strain ADR26 as the type strain of the species Desulfomicrobium aestuarii sp. nov.     

Staphylococcus petrasii sp. nov. including S. petrasii subsp. petrasii subsp. nov. and S. petrasii subsp. croceilyticus subsp. nov., isolated from human clinical specimens and human ear infections

Thirteen coagulase-negative, oxidase-negative, and novobiocin-susceptible staphylococci were isolated from human clinical specimens. The isolates were differentiated from known staphylococcal species on the basis of 16S rRNA, hsp60, rpoB, dnaJ, tuf, and gap gene sequencing, automated ribotyping, (GTG)₅-PCR fingerprinting, and MALDI-TOF MS analysis. Phylogenetic analysis based on the 16S rRNA gene sequence indicated phylogenetic relatedness of the analyzed strains to Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus devriesei, and Staphylococcus lugdunensis. DNA–DNA hybridization experiments between representative strains CCM 8418^T, CCM 8421^T, and the closest phylogenetic neighbors confirmed that the isolates represent novel Staphylococcus species, for which the name Staphylococcus petrasii sp. nov. is proposed. Genotypic and phenotypic analyses unambiguously split the strains into two closely related subclusters. Based on the results, two novel subspecies S. petrasii subsp. petrasii subsp. nov. and S. petrasii subsp. croceilyticus subsp. nov. are proposed, with type strains CCM 8418^T (=CCUG 62727^T) and CCM 8421^T (=CCUG 62728^T), respectively.     

A review of fossil cycad megasporophylls, with new evidence of Crossozamia pomel and its associated leaves from the lower permian of Taiyuan, China

Four species of cycad megasporophyll from the Lower Permian of Taiyuan, China, are described as Crossozamia chinensis (Zhu and Du) comb. nov., C. minor sp. nov., C. spadicia sp. nov. and C. cucullata comb. nov. together with the associated leaves Tianbaolinia circinalis gen. et sp. nov., Yuania chinensis Zhu and Du and Taeniopteris taiyuanensis Halle. An axis bearing megasporophylls in organic connection is described for the first time. Two possible evolutionary pathways from this structure to those of the female reproductive organs of extant cycads are proposed, involving either the reduction of the megasporophylls and their compaction on the axis, or the reduction of the “strobilus” axis. It is suggested that migration of cycads from North China to Europe might have occurred through transportation of their buoyant seeds by the palaeoceanic currents of the Tethys sea.