Pseudomonas caspiana sp. nov., a citrus pathogen in the Pseudomonas syringae phylogenetic group

In a screening by multilocus sequence analysis of Pseudomonas strains isolated from diverse origins, 4 phylogenetically closely related strains (FBF58, FBF102^T, FBF103, and FBF122) formed a well-defined cluster in the Pseudomonas syringae phylogenetic group. The strains were isolated from citrus orchards in northern Iran with disease symptoms in the leaves and stems and its pathogenicity against citrus plants was demonstrated. The whole genome of the type strain of the proposed new species (FBF102^T = CECT 9164^T = CCUG 69273^T) was sequenced and characterized. Comparative genomics with the 14 known Pseudomonas species type strains of the P. syringae phylogenetic group demonstrated that this strain belonged to a new genomic species, different from the species described thus far. Genome analysis detected genes predicted to be involved in pathogenesis, such as an atypical type 3 secretion system and two type 6 secretion systems, together with effectors and virulence factors. A polyphasic taxonomic characterization demonstrated that the 4 plant pathogenic strains represented a new species, for which the name Pseudomonas caspiana sp. nov. is proposed.     

Methylosulfonomonas methylovora gen. nov., sp. nov., and Marinosulfonomonas methylotropha gen. nov., sp. nov.: novel methylotrophs able to grow on methanesulfonic acid

Two novel genera of restricted facultative methylotrophs are described; both Methylosulfonomonas and Marinosulfonomonas are unique in being able to grow on methanesulfonic acid as their sole source of carbon and energy. Five identical strains of Methylosulfonomonas were isolated from diverse soil samples in England and were shown to differ in their morphology, physiology, DNA base composition, molecular genetics, and 16S rDNA sequences from the two marine strains of Marinosulfonomonas, which were isolated from British coastal waters. The marine strains were almost indistinguishable from each other and are considered to be strains of one species. Type species of each genus have been identified and named Methylosulfonomonas methylovora (strain M2) and Marinosulfonomonas methylotropha (strain PSCH4). Phylogenetic analysis using 16S rDNA sequencing places both genera in the α-Proteobacteria. Methylosulfonomonas is a discrete lineage within the α-2 subgroup and is not related closely to any other known bacterial genus. The Marinosulfonomonas strains form a monophyletic cluster in the α-3 subgroup of the Proteobacteria with Roseobacter spp. and some other partially characterized marine bacteria, but they are distinct from these at the genus level. This work shows that the isolation of bacteria with a unique biochemical character, the ability to grow on methanesulfonic acid as energy and carbon substrate, has resulted in the identification of two novel genera of methylotrophs that are unrelated to any other extant methylotroph genera. Received: 19 July 1996 / Accepted: 7 October 1996     

Rhodotorula lamellibrachii sp. nov., a new yeast species from a tubeworm collected at the deep-sea floor in Sagami Bay and its phylogenetic analysis

A new species of the genus Rhodotorula was isolated from a tubeworm (Lamellibrachia sp.) collected at a depth of 1156 m in Sagami Bay, Japan. Strain SY-89 had physiological properties quite similar to R. aurantiaca. Two phylogenetic trees, one based on internal transcribed spacer (ITS) regions and 5.8S rDNA sequences and the other based on the D1/D2 region of the large subunit (26S) rDNA sequences, united strain SY-89 to the type strain of Sakaguchia dacryoides through a considerable evolutionary distance. Strain SY-89 was differentiated from S. dacryoides by the G+C content of the nuclear DNA and differences in the ability to utilize specific carbon and nitrogen compounds. The low complementarity of strain SY-89 DNA to that of the type strain of S. dacryoides confirmed that this strain was genetically unrelated to previously known species. The tubeworm isolates are described as R. lamellibrachii sp. nov. The type strain of R. lamellibrachii is strain SY-89 (= JCM 10907). R. lamellibrachii formed a cluster with Erythrobasidium hasegawianum, R. lactosa, S. dacryoides and Sporobolomyces elongatus on the ITS and 5.8S rDNA phylogenetic tree. These five species shared a signature sequence in 26S rDNA, although this relationship was not supported by phylogeny based on the D1/D2 region of 26S rDNA.     

A new obligately chemolithoautotrophic,nitrite-oxidizing bacterium,Nitrospira moscoviensis sp. nov. and its phylogenetic relationship

A gram-negative, non-motile, non-marine, nitrite-oxidizing bacterium was isolated from an enrichment culture initiated with a sample from a partially corroded area of an iron pipe of a heating system in Moscow, Russia. The cells were 0.9–2.2 μm × 0.2–0.4 μm in size. They were helical- to vibroid-shaped and often formed spirals with up to three turns 0.8–1.0 μm in width. The organism possessed an enlarged periplasmic space and lacked intracytoplasmic membranes and carboxysomes. The cells tended to excrete extracellular polymers, forming aggregates. The bacterium grew optimally at 39°C and pH 7.6– 8.0 in a mineral medium with nitrite as sole energy source and carbon dioxide as sole carbon source. The optimal nitrite concentration was 0.35 mM. Nitrite was oxidized to nitrate stoichiometrically. The doubling time was 12 h in a mineral medium with 7.5 mM nitrite. The cell yield was low; only 0.9 mg protein/l was formed during oxidation of 7.5 mM nitrite. Under anoxic conditions, hydrogen was used as electron donor with nitrate as electron acceptor. Organic matter (yeast extract, meat extract, peptone) supported neither mixotrophic nor heterotrophic growth. At concentrations as low as 0.75 g organic matter/l or higher, growth of nitrite-oxidizing cells was inhibited. The cells contained cytochromes of the b- and c-type. The G+C content of DNA was 56.9 ± 0.4 mol%. The chemolithoautotrophic nitrite-oxidizer differed from the terrestrial members of the genus Nitrobacter with regard to morphology and substrate range and equaled Nitrospira marina in both characteristics. The isolated bacterium is designated as a new species of the genus Nitrospira. Comparative analysis of 16S rRNA gene sequences revealed a moderate phylogenetic relationship to Nitrospira marina, leptospirilla, Thermodesulfovibrio yellowstonii, "Magnetobacterium bavaricum," and the isolate OPI-2. Initial evidence is given that these organisms represent a new phylum of the domain bacteria. Received: 17 February 1995 / Accepted: 18 April 1995     

Trichosporon mycotoxinivorans sp. nov., a new yeast species useful in biological detoxification of various mycotoxins

A yeast strain isolated from the hindgut of the lower termite Mastotermes darwiniensis (Mastotermitidae) was found to represent a new member of the genus Trichosporon. Trichosporon mycotoxinivorans is closely related to T. loubieri on the basis of the phylogenetic trees based on the D1/D2 region of 26S rDNA, an approx. 600 bp fragment of the 18S rDNA and both ITS regions. However, the two species differ at nine positions in the D1/D2 region of 26S rDNA. The IGS1 region of T. mycotoxinivorans is 401 bp long. T. mycotoxinivorans is distinguished from T. loubieri by its ability to assimilate inulin and galactitol, and its inability to grow at 40 °C. The name of this newly isolated strain refers to an important characteristics of T. mycotoxinivorans to detoxify mycotoxins such as ochratoxin A and zearalenone. Therefore this strain can be used for the deactivation of the respective mycotoxins in animal feeds.     

Photobacterium malacitanum sp. nov., and Photobacterium andalusiense sp. nov., two new bacteria isolated from diseased farmed fish in Southern Spain

Three strains, H01100409B^T, H01100413B, and H27100402H^T, were isolated from several internal organs of diseased redbanded seabream (Pagrus auriga) reared in Andalusia (Southern Spain). All strains were studied by phenotypic, including chemotaxonomy, and genomic characteristics. Phylogenetic analysis based on concatenated sequences of six housekeeping genes (gyrB, ftsZ, topA, mreB, gapA, and 16S rRNA) supported the inclusion of the strains within the clade Phosphoreum of the genus Photobacterium, and two of the strains (H27100402H^T and H01100409B^T) formed a tight group separated from the closest species P. aquimaris. Genomic analyses, including average nucleotide identity (ANIb and ANIm) and DNA–DNA hybridization (DDH), clearly separated strains H27100402H^T and H01100409B^T from the other species within the clade Phosphoreum with values below the thresholds for species delineation. The chemotaxonomic features (including FAME analysis and MALDI-TOF-MS) of H27100402H^T and H01100409B^T strains confirmed their differentiation from the related taxa. The results demonstrated that strain H01100413B was classified as P. aquimaris and the strains H27100402H^T and H01100409B^T represented a new species each in the genus Photobacterium, for which we propose the names Photobacterium malacitanum sp. nov., type strain H27100402H^T (=CECT 9190^T = LMG 29992^T), and Photobacterium andalusiense sp. nov., type strain H01100409B^T (=CECT 9192^T = LMG 29994^T).     

Arachnophora dinghuensis sp. nov. and Websteromyces inaequale sp. nov., and two new records of anamorphic fungi from dead branches of broad-leaved trees in China

Two new species of hyphomycetes, Arachnophora dinghuensis and Websteromyces inaequale, are described and illustrated from specimens collected on dead branches of unidentified plants in China. Arachnophora dinghuensis is characterized by monoblastic, integrated, terminal, occasionally percurrently extending conidiogenous cells that produce solitary, acrogenous, staurosporous conidia. The conidia are two-celled, irregular, brown, 21–27.5 × 10–17 μm, with a central body that bears 2 or more fertile, brown to pale brown lateral cells, which in turn give rise to 1–3 fertile, conical, hyaline to pale brown arm-cells, 4–6.5 × 3.5–4.5 μm. A microconidial, Selenosporella-like synanamorph occurs at the apex of the arms. Websteromyces inaequale is recognized as the second species in the genus, and differs from the type species, W. verruculosus, in possessing naviculiform, obclavate to ellipsoidal, smooth, larger conidia in unbranched acropetal chains. The hyphomycetes Rhexoacrodictys queenslandica and Solicorynespora sylvatica are reported from China for the first time. A key to Arachnophora species is provided.     

Cyst‐theca relationship of a new dinoflagellate with a spiny round brown cyst,Protoperidinium lewisiae sp. nov., and its comparison to the cyst of Oblea acanthocysta

Round spiny brown cysts with apiculocavate processes were isolated from sediments of Lake Saroma, Japan, Changle Harbor, East China Sea, China, Jinzhou Harbor, Bohai Sea, China, and San Pedro Harbor, California, USA. Superficially similar round spiny brown cysts of the species, Oblea acanthocysta were, for comparison, restudied through light microscopy and scanning electron microscopy (SEM) and by sequencing of small subunit (SSU) and large subunit (LSU) rDNA obtained through a single cyst from Lake Saroma. These morphological measurements and SEM observations showed that the new cysts can be discriminated from O. acanthocysta by the archeopyle, number of processes, shape of process bases and its apiculocavate processes. Based on LSU sequences, the most closely related species was Protoperidinium monovelum, for which no cyst stage has been described so far. However, the thecal morphology of the specimens found in this study differed from P. monovelum in details of the sulcal plates and shape of apical pore and 2a plate. We therefore describe Protoperidinium lewisiae sp. nov., which can be found in estuarine subtropical to temperate waters of the Pacific Ocean.     

The flagellin gene of Borrelia miyamotoi sp. nov. and its phylogenetic relationship among Borrelia species

Abstract We have cloned and sequenced the flagellin gene from Borrelia miyamotoi strain HT31 and compared it with previously published flagellin sequences. Sequence similarity analysis demonstrated that strain HT31 is phylogenetically distant from the three species of Lyme disease borreliae and is deeply branched into the relapsing fever borrelia cluster. The result was in full agreement with the classification of Borrelia strains using 16S rRNA sequences. This finding indicates that a phylogenetic analysis using flagellin gene sequences might be useful for classification of Borrelia strains.     

Gambierdiscus (Gonyaulacales,Dinophyceae) diversity in Vietnamese waters with description of G. vietnamensis sp. nov.

Viet Nam has a coastline of 3200 km with thousands of islands providing diverse habitats for benthic harmful algal species including species of Gambierdiscus. Some of these species produce ciguatera toxins, which may accumulate in large carnivore fish potentially posing major threats to public health. This study reports five species of Gambierdiscus from Vietnamese waters, notably G. australes, G. caribaeus, G. carpenteri, G. pacificus, and G. vietnamensis sp. nov. All species are identified morphologically by LM and SEM, and identifications are supported by molecular analyses of nuclear rDNA (D1–D3 and D8–D10 domains of LSU, SSU, and ITS1-5.8S-ITS2 region) based on cultured material collected during 2010–2021. Statistical analyses of morphometric measurements may be used to differentiate some species if a sufficiently large number of cells are examined. Gambierdiscus vietnamensis sp. nov. is morphologically similar to other strongly reticulated species, such as G. belizeanus and possibly G. pacificus; the latter species is morphologically indistinguishable from G. vietnamensis sp. nov., but they are genetically distinct, and molecular analysis is deemed necessary for proper identification of the new species. This study also revealed that strains denoted G. pacificus from Hainan Island (China) should be included in G. vietnamensis sp. nov.     

A combined morphological and molecular approach to Nitzschia varelae sp. nov., with discussion of symmetry in Bacillariaceae

A previously unknown member of the Bacillariaceae was discovered almost simultaneously in four different brackish coastal wetlands on the Atlantic and Mediterranean coasts of the Iberian Peninsula. It appears to tolerate a wide range of salinities but was never common in samples where it occurred. The frustules were consistently hantzschioid (i.e. with the raphe systems always on the same side of the frustule) and the valve outline was asymmetrical about the apical plane, two features that have until recently been considered characteristic of Hantzschia. Molecular phylogenies based on rbcL and LSU rDNA indicated, however, that the new species does not belong in Hantzschia but among the several disparate lineages that comprise the paraphyletic genus Nitzschia. This finding, coupled with the recent discovery of other diatoms with constant hantzschioid symmetry but with a morphology very similar to the type species of Nitzschia, is discussed in relation to the status and characterization of Hantzschia as an independent genus. It is concluded that, while a core of hantzschioid species may exist that can be classified together, corresponding to the traditional understanding of the genus Hantzschia, there is no single morphological feature common to all of them that can be used to diagnose the group and differentiate it from the various hantzschioid lineages that are separate from true Hantzschia and currently placed in e.g. Nitzschia or Cymbellonitzschia. Testing whether a hantzschioid species does or does not belong to Hantzschia will in many cases require molecular evidence. Although the new coastal species does not belong to the same lineage as the type species of Nitzschia, N. sigmoidea, it is described for the moment as N. varelae Carballeira, D.G. Mann & Trobajo, sp. nov., until there is a better understanding of generic limits in the Bacillariaceae following a wider molecular and morphological survey of that family.     

A new oomycete species parasitic in nematodes, Chlamydomyzium dictyuchoides sp. nov.: Developmental biology and phylogenetic studies

The genus Chlamydomyzium is a little studied holocarpic oomycete parasite of nematodes of uncertain phylogenetic and taxonomic position. A new holocarpic species, Chlamydomyzium dictyuchoides, is described which has usually refractile cytoplasm and a dictyuchoid pattern of spore release. This new species infects bacteriotrophic rhabditid nematodes and was isolated from diverse geographical locations. Infection was initiated by zoospore encystment on the host surface and direct penetration of the cuticle. A sparsely branched, constricted, refractile thallus was formed which eventually occupied almost the entire host body cavity, often accompanied by complete dissolution of the host cuticle. Walled primary cysts formed throughout the thallus and each cyst released a single zoospore via an individual exit papillum, leaving a characteristic dictyuchoid wall net behind. At later stages of infection some thalli formed thick-walled stellate resting spores in uniseriate rows. Resting spore formation appeared to be parthenogenetic and was not accompanied by the formation of antheridial compartments. These spores had ooplast-like vacuoles and thick multi-layered walls, both of which suggest they were oospores. The maximum likelihood tree of sequences of the small ribosomal subunit (SSU) gene placed this new isolate in a clade before the main saprolegnialean and peronosporalean lines diverge. A second undescribed Chlamydomyzium sp., which has direct spore release forms a paraphyletic clade, close to C. dictyuchoides and Sapromyces. The fine structure of other documented Chlamydomyzium species was compared, including an undescribed (but sequenced) isolate, SL02, from Japan, Chlamydomyzium anomalum and Chlamydomyzium oviparasiticum. Chlamydomyzium as currently constituted is a paraphyletic genus that is part of a group of phylogenetically problematic early diverging clades that lie close to both the Leptomitales and Rhipidiales.     

Tsukamurella spumae sp. nov., a novel actinomycete associated with foaming in activated sludge plants

A polyphasic taxonomic study was undertaken to establish the taxonomic position of six representative strains isolated from activated sewage sludge foam. The organisms were found to have chemical and morphological properties consistent with their assignment to the genus Tsukamurella. DNA:DNA relatedness studies showed that five out of the six isolates formed a distinct genomic species, the remaining strain was most closely associated with this taxon. The five isolates had a unique phenotypic profile that served to distinguish them from representatives of the validly described species of Tsukamurella. The combination of the genotypic and phenotypic data indicated that the five strains should be classified as a new species in the genus Tsukamurella. The name proposed for this taxon is Tsukamurella spumae, the type strain is N1171T (= DSM 44.113T = NCIMB 13947T). It was also shown that some of the reference strains were misclassified as Tsukamurella paurometabola.     

Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the Iheya Ridge

An extremely halotolerant and alkaliphilic bacterium was isolated previously from deep-sea sediment collected at a depth of 1050 m on the Iheya Ridge. The strain, designated HTE831 (JCM 11309, DSM 14371), was Gram-positive, strictly aerobic, rod-shaped, motile by peritrichous flagella, and spore-forming. Strain HTE831 grew at salinities of 0-21% (w/v) NaCl at pH 7.5 and 0-18% at pH 9.5. The optimum concentration of NaCl for growth was 3% at both pH 7.5 and 9.5. The G+C content of its DNA was 35.8%.Low level (12-30%) of DNA-DNA relatedness between strain HTE831 and the species of these genera was found, indicating that HTE831 could not be classified as a member of a new species belonging to known genera. Based on phylogenetic analysis using 16S rDNA sequencing, chemotaxonomy, and the physiology of strain HTE831, it is proposed that this organism is a member of a new species in a new genus, for which the name Oceanobacillus iheyensis is proposed.     

Studies on woloszynskioid dinoflagellates VII. Description of Borghiella andersenii sp. nov.: light and electron microscopy and phylogeny based on LSU rDNA

Freshwater woloszynskioid dinoflagellates were collected independently in Scotland and Portugal and found to belong to a previously unknown species of the genus Borghiella, here described as B. andersenii. The new species differs in morphology and nuclear-encoded LSU rDNA and ITS sequences from B. dodgei and B. tenuissima, the two species presently comprising the genus Borghiella. Unusual features of the new species were observed particularly during asexual reproduction, which took place in the motile stage – as in many other dinoflagellates – or in a so-called division cyst, recalling cell division in the family Tovelliaceae. Such diversity in cell division is rarely reported in dinoflagellates. Morphologically Borghiella andersenii differs from B. tenuissima in being only slightly compressed dorsoventrally whereas the latter species is flat. The slight compression is also visible in lateral view. Borghiella andersenii and B. dodgei are more challenging to discriminate but the apical structure complex is only half the length in B. andersenii compared with B. dodgei (3–4 vs 6 µm). This difference can only be accounted for in the scanning electron microscope. At the light microscopy level the epicone in B. andersenii is rounded whereas it is conical in B. dodgei. Sexual reproduction in Borghiella andersenii was homothallic by formation of planozygotes, followed by apparent resting cysts. Phylogenetic studies on woloszynskioids have recently shown that they comprise a polyphyletic assemblage, which has been divided into the three families Borghiellaceae, Tovelliaceae and Suessiaceae. New species of the three families are now being found rapidly in many parts of the world, proving that the techniques required to investigate these small, morphologically similar dinoflagellates are now in place and proving that such ‘gymnodinioids’ or ‘woloszynskioids’ comprise an often overlooked biological entity in both marine and freshwater biotopes. Based on LSU rDNA, B. andersenii is most closely related to B. tenuissima.     

New dinoflagellate species Protoperidinium haizhouense sp. nov. (Peridiniales,Dinophyceae), its cyst‐theca relationship and phylogenetic position within the Monovela group

The number of cingular plates has been used to differentiate Protoperidinium from Peridinium and related genera. Protoperidinium is characterized by the presence of three cingular plates plus a transitional plate (3C+t). However, many Protoperidinium species have been described that exhibit different cingular plate tabulations. How these species should be classified within the genus remains unclear. To address this question, the phylogenetic relationship of four Protoperidinium species, with three or four cingular plates and lacking a transitional plate, were examined in relationship to other Protoperidinium species. These four species were germinated from cysts deposited in surface sediments collected from the East China Sea, the Bohai Sea and the Yellow Sea. Three of the isolated species, P. tricingulatum, P. americanum and P. parthenopes, were described previously. The fourth is here described as P. haizhouense sp. nov. with the plate formula Po, X, 4′, 3a, 7′′, 3C, 6S, 5′′′, 2′′′′. Differences in the cyst stages of these four species, which can be taxonomically informative, were compared. Partial large subunit ribosomal DNA sequences were obtained by single‐cell polymerase chain reaction. Maximum‐likelihood and Bayesian inference showed that these four species, P. fukuyoi and Islandinium minutum form a monophyletic clade with maximal support. The genus as a whole, however, appeared polyphyletic. Our results suggest that the presence/absence of a transitional plate is significant in the phylogeny of Protoperidinium.