Characterization of Acinetobacter chengduensis sp. nov., isolated from hospital sewage and capable of acquisition of carbapenem resistance genes

Two strains of the genus Acinetobacter, WCHAc060005^T and WCHAc060007, were isolated from hospital sewage in China. The two strains showed different patterns of resistance to clinically important antibiotics and their taxonomic positions were investigated. Cells are Gram-negative, obligate aerobic, non-motile, catalase-positive and oxidase-negative coccobacilli. A preliminary analysis based on the 16S rRNA gene sequences indicated that the two strains had the highest similarity to Acinetobacter cumulans WCHAc060092^T (99.02%). Whole-genome sequencing of the two strains and genus-wide phylogeny reconstruction based on a set of 107 Acinetobacter core genes indicated that they formed a separate and internally cohesive clade within the genus. The average nucleotide identity based on BLAST and in silico DNA–DNA hybridization values between the two new genomes were 99.77% and 98.7% respectively, whereas those between the two genomes and the known Acinetobacter species were <88.93% and <34.0%, respectively. A total of 7 different genes were found in the two genome sequences which encode resistance to five classes of antimicrobial agents, including clinically important carbapenems, oxyimino-cephalosporins, and quinolones. In addition, the combination of their ability to assimilate gentisate, but not l-glutamate and d,l-lactate could distinguish the two strains from all known Acinetobacter species. Based on these combined data, we concluded that the two strains represent a novel species of the genus Acinetobacter, for which the name Acinetobacter chengduensis sp. nov. is proposed. The type strain is WCHAc060005^T (CCTCC AB 2019139 = GDMCC 1.1622 = JCM 33509).     

Oenococcus sicerae sp. nov., isolated from French cider

Two Gram-stain-positive, small ellipsoidal cocci, non-motile, oxidase- and catalase-negative, and facultative anaerobic strains (UCMA15228^T and UCMA17102) were isolated in France, from fermented apple juices (ciders). The 16S rRNA gene sequence was identical between the two isolates and showed 97 % similarity with respect to the closest related species Oenococcus oeni and O. kitaharae. Therefore, the two isolates were classified within the genus Oenococcus. The phylogeny based on the pheS gene sequences also confirmed the position of the new taxon. DNA–DNA hybridizations based on in silico genome-to-genome comparisons (GGDC) and Average Nucleotide Identity (ANI) values, as well as species-specific PCR, validated the novelty of the taxon. Various phenotypic characteristics such as the optimum temperature and pH for growth, the ability to metabolise sugars, the aptitude to perform the malolactic fermentation, and the resistance to ethanol and NaCl, revealed that the two strains are distinguishable from the other members of the Oenococcus genus. The combined genotypic and phenotypic data support the classification of strains UCMA15228^T and UCMA17102 into a novel species of Oenococcus, for which the name O. sicerae sp. nov. is proposed. The type strain is UCMA15228^T (=DSM107163^T = CIRM-BIA2288^T).     

Parendozoicomonas haliclonae gen. nov. sp. nov. isolated from a marine sponge of the genus Haliclona and description of the family Endozoicomonadaceae fam. nov. comprising the genera Endozoicomonas,Parendozoicomonas, and Kistimonas

Two Gram-stain-negative, facultative anaerobic, motile, rod-shaped strains, S-B4-1U^T and JOB-63a, forming small whitish transparent colonies on marine agar, were isolated from a sponge of the genus Haliclona. The strains shared 99.7% 16S rRNA gene sequence identity and a DNA-DNA hybridization value of 100%, but were differentiated by genomic fingerprinting using rep-PCRs. 16S rRNA gene sequence phylogeny placed the strains as a sister branch to the monophyletic genus Endozoicomonas (Oceanospirillales; Gammaproteobacteria) with 92.3–94.3% 16S rRNA gene sequence similarity to Endozoicomonas spp., 91.9 and 92.1% to Candidatus Endonucleobacter bathymodiolin, and 91.9 to 92.1% to the type strains of Kistimonas spp. Core genome based phylogeny of strain S-B4-1U^T confirmed the phylogenetic placement. Major fatty acids were summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) and 8 (C_18:1 ω7c/C_18:1 ω6c) followed by C_10:0 3-OH, C_16:0, and C_18:0. The G + C content was 50.1–51.4 mol%. The peptidoglycan diamino acid of strain S-B4-1U^T was meso-diaminopimelic acid, the predominant polyamine spermidine, the major respiratory quinone ubiquinone Q-9; phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine were major polar lipids. Based on the clear phylogenetic distinction, the genus Parendozoicomonas gen. nov. is proposed, with Parendozoicomonas haliclonae sp. nov. as type species and strain S-B4-1U^T (= CCM 8713^T = DSM 103671^T = LMG 29769^T) as type strain and JOB-63a as a second strain of the species. Based on the 16S rRNA gene sequence phylogeny of the Oceanospirillales within the Gammaproteobacteria, the Endozoicomonaceae fam. nov. is proposed including the genera Endozoicomonas, Parendozoicomonas, and Kistimonas as well as the Candidatus genus Endonucleobacter.     

Phylogeny,biogeography, and electric signal evolution of Neotropical knifefishes of the genus Gymnotus (Osteichthyes: Gymnotidae)

The Neotropical knifefish genus Gymnotus is the most broadly distributed and the most diverse (34 + species) gymnotiform genus. Its wide range includes both Central and South American drainages, including the Amazon, Orinoco, and La Plata Basins. Like all gymnotiforms, Gymnotus species produce weak electric fields for both navigation and communication, and these fields exhibit interspecific variation in electric waveform characteristics. Both biogeography and electric signal evolution can profitably be analyzed in a phylogenetic context. Here, we present a total evidence phylogeny for 19 Gymnotus species based on data from the mitochondrial cytochrome b and 16S genes (1558 bp), the nuclear RAG2 gene (1223 bp), and 113 morphological characters. Our phylogenetic hypothesis resolves five distinct Gymnotus lineages. In a previous morphology-based analysis, the Central American Gymnotus cylindricus lineage was hypothesized as the sister group to all other Gymnotus species. In our analysis, the G. cylindricus lineage is nested within South American species, and molecular age estimates support a relatively recent origin for the clade in Central America. Phylogenetic optimization of electric signal waveforms indicate that the ancestral state in Gymnotus is a multiphasic (4 + phases of alternating polarity) condition, and independent phase loss has occurred in multiple lineages. Gymnotus is a model group for understanding Neotropical diversification and the evolution of communication at a continental scale.     

A new species of Drepanocnemis (Diptera,Muscidae) from Andes in Peru,with an updated phylogenetic analysis of species

Drepanocnemis Stein (Diptera, Muscidae) is a small genus of flies that occur in high altitudes in the Colombian Andes, Ecuador, Peru and Bolivia. Herein we describe Drepanocnemis aurifronssp. nov. from Cuzco, Peru, which is found from high (2904 m) to lower altitudes (707 m). An updated phylogeny, key to species and map of species’ distributions are provided, together with images and illustrations of the male and the female terminalia.     

Agrobacterium rosae sp. nov., isolated from galls on different agricultural crops

The plant tumorigenic strain NCPPB 1650^T isolated from Rosa × hybrida, and four nonpathogenic strains isolated from tumors on grapevine (strain 384), raspberry (strain 839) and blueberry (strains B20.3 and B25.3) were characterized by using polyphasic taxonomic methods. Based on 16S rRNA gene phylogeny, strains were clustered within the genus Agrobacterium. Furthermore, multilocus sequence analysis (MLSA) based on the partial sequences of atpD, recA and rpoB housekeeping genes indicated that five strains studied form a novel Agrobacterium species. Their closest relatives were Agrobacterium sp. R89-1, Agrobacterium rubi and Agrobacterium skierniewicense. Authenticity of the novel species was confirmed by average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) comparisons between strains NCPPB 1650^T and B20.3, and their closest relatives, since obtained values were considerably below the proposed thresholds for the species delineation. Whole-genome-based phylogeny further supported distinctiveness of the novel species, that forms together with A. rubi, A. skierniewicense and Agrobacterium sp. R89-1 a well-delineated sub-clade of Agrobacterium spp. named “rubi”. As for other species of the genus Agrobacterium, the major fatty acid of the strains studied was 18:1 w7c (73.42–78.12%). The five strains studied were phenotypically distinguishable from other species of the genus Agrobacterium. Overall, polyphasic characterization showed that the five strains studied represent a novel species of the genus Agrobacterium, for which the name Agrobacterium rosae sp. nov. is proposed. The type strain of A. rosae is NCPPB 1650^T (=DSM 30203^T = LMG 230^T = CFBP 4470^T = IAM 13558^T = JCM 20915^T).     

Thaumasiovibrio occultus gen. nov. sp. nov. and Thaumasiovibrio subtropicus sp. nov. within the family Vibrionaceae,isolated from coral reef seawater off Ishigaki Island,Japan

Two phylogenetically distinct Vibrionaceae strains C4II189^T and C4V358^T isolated from reef seawater off Ishigaki Island, Japan, in 2014 were studied with advanced genome-based taxonomy approaches. All aspects of phylogenetic (16S rRNA phylogeny, MLSA), phenotypic and genetic (ANI, DDH, AAI, and the number of core genes) cohesions between the two identified species were high enough to propose them as members of a new genus within the family Vibrionaceae. Consequently, an eighth genus Thaumasiovibrio gen. nov. is proposed that contains two new species Thaumasiovibrio occultus sp. nov. strain C4II189^T (=DSM 101554^T = JCM 31629^T) (type species) and Thaumasiovibrio subtropicus sp. nov. strain C4V358^T (=DSM 101555^T = JCM 31630^T). Thaumasiovibrio species were phylogenetically distinct from the other Vibrionaceae species based on pyrH gene sequences. The combination of catalase negative, sensitivity to vibriostatic agent O/129, and green colony formation on TCBS for the phylogenetically affiliated strains was the diagnostic features for the current tentative identification of this genus.     

Genetic structure of Octopus vulgaris (Cephalopoda,Octopodidae) in the central Mediterranean Sea inferred from the mitochondrial COIII gene

The polymorphism of the mitochondrial gene cytochrome oxidase III was studied in the Mediterranean octopus, Octopus vulgaris Cuvier, 1797. A total of 202 specimens from seven sampling sites were analysed with the aim of elucidating patterns of genetic structure in the central Mediterranean Sea and to give an insight into the phylogeny of the Octopus genus. Phylogenetic analyses showed that individuals from the central Mediterranean belong to the O. vulgaris species whose limits should nevertheless be clarified. Concerning genetic structure, two high-frequency haplotypes were present in all locations. The overall genetic divergence (Φ_ST = 0.05, P < 0.05) indicated a significant genetic structuring in the study area and an AMOVA highlighted a significant break between western and eastern Mediterranean basins (Φ_CT = 0.094, P < 0.05). Possible explanations for the observed patterns of genetic structuring are discussed with reference to their relevance for fisheries management.     

Cyclestheria hislopi (Crustacea: Branchiopoda): A group of morphologically cryptic species with origins in the Cretaceous

Cyclestheria hislopi is thought to be the only extant species of Cyclestherida. It is the sister taxon of all Cladocera and displays morphological characteristics intermediate of Spinicaudata and Cladocera. Using one mitochondrial (COI) and two nuclear (EF1α and 28S rRNA) markers, we tested the hypothesis that C. hislopi represents a single circumtropic species. South American (French Guiana), Asian (India, Indonesia, Singapore) and several Australian populations were included in our investigation. Phylogenetic and genetic distance analyses revealed remarkable intercontinental genetic differentiation (uncorrected p-distances COI > 13%, EF1α > 3% and 28S > 4%). Each continent was found to have at least one distinct Cyclestheria species, with Australia boasting four distinct main lineages which may be attributed to two to three species. The divergence of these species (constituting crown group Cyclestherida) was, on the basis of phylogenetic analyses of COI and EF1α combined with molecular clock estimates using several fossil branchiopod calibration points or a COI substitution rate of 1.4% per million years, dated to the Cretaceous. This was when the South American lineage split from the Asian–Australian lineage, with the latter diverging further in the Paleogene. Today’s circumtropic distribution of Cyclestheria may be best explained by a combination of Gondwana vicariance and later dispersal across Asia and Australia when the tectonic plates of the two continents drew closer in the early Miocene. The lack of morphological differentiation that has taken place in this taxon over such a long evolutionary period contrasts with the high level of differentiation and diversification observed in its sister taxon the Cladocera. Further insights into the evolution of Cyclestheria may help us to understand the evolutionary success of the Cladocera.     

Tsuga seed cones from the late Paleogene of southwestern China and their biogeographical and paleoenvironmental implications

Six Tsuga ovuliferous/seed cone impression fossils were discovered from the late Eocene (34.6 ± 0.8 Ma) Lawula Formation in Mangkang County, eastern Tibet and the early Oligocene (32 ± 1 Ma) lacustrine deposits in Lühe Basin, Nanhua County, Yunnan Province. These two fossil sites are both located in southwestern China, ∼800 km apart from each other. These fossils represent the oldest records of this genus in southwestern China, even earliest reliable macrofossil records of this genus in the world. These well-preserved seed cones provide sufficient materials for the establishment of Tsuga asiatica Wu et Zhou n. sp. to accommodate five specimens, leaving one to be assigned to T. cf. dumosa Eichler (cf. Wu et Zhou). Both qualitative and quantitative comparisons with other cone fossils and cones of all living species of the genus suggested that T. asiatica shares more similarities with one of the basal species of the genus T. heterophylla. The discovery of late Paleogene macrofossil records of Tsuga in southwestern China supports the previous hypothesis of the early disposal routes of this coniferous genus predicted by phylogenetic analysis. The elevation ranges and the climate requirements of living species that are closely related to our fossils suggest that the southeastern edge of the Qinghai-Tibetan Plateau should be much warmer, and wetter in late Paleogene than nowadays.     

Molecular phylogeny of black fungus gnats (Diptera: Sciaroidea: Sciaridae) and the evolution of larval habitats

The phylogeny of the family Sciaridae is reconstructed, based on maximum likelihood, maximum parsimony, and Bayesian analyses of 4809 bp from two mitochondrial (COI and 16S) and two nuclear (18S and 28S) genes for 100 taxa including the outgroup taxa. According to the present phylogenetic analyses, Sciaridae comprise three subfamilies and two genus groups: Sciarinae, Chaetosciara group, Cratyninae, and Pseudolycoriella group + Megalosphyinae. Our molecular results are largely congruent with one of the former hypotheses based on morphological data with respect to the monophyly of genera and subfamilies (Sciarinae, Megalosphyinae, and part of postulated “new subfamily”); however, the subfamily Cratyninae is shown to be polyphyletic, and the genera Bradysia, Corynoptera, Leptosciarella, Lycoriella, and Phytosciara are also recognized as non-monophyletic groups. While the ancestral larval habitat state of the family Sciaridae, based on Bayesian inference, is dead plant material (plant litter + rotten wood), the common ancestors of Phytosciara and Bradysia are inferred to living plants habitat. Therefore, shifts in larval habitats from dead plant material to living plants may have occurred within the Sciaridae at least once. Based on the results, we discuss phylogenetic relationships within the family, and present an evolutionary scenario of development of larval habitats.     

Phylogeny and systematic revision of the karyorelictid genus Remanella (Ciliophora,Karyorelictea) with descriptions of two new species

We present here the systematic relationships and taxonomy of some newly collected karyorelictid ciliates from the genus Remanella isolated from the intertidal zone in China. Three species were investigated using observation in vivo and silver staining methods, of which two new species were identified: R. macrostoma sp. nov. and R. achroma sp. nov. Small subunit (SSU) rRNA genes were sequenced for six species and phylogenetic analyses indicated that the genus Remanella is paraphyletic, with three Loxodes species nesting within it. The monophyly of Remanella, however, could not be rejected through the approximately unbiased (AU) test (p = 0.311 > 0.05) and therefore we considered Remanella to be a valid genus. Based on a critical review of the literature, the validity of all nominal species of Remanella was discussed. Remanella unirugosa and R. multicorpusculata were regarded as junior synonyms of R. rugosa and R. granulosa respectively. We also presented here an illustrated taxonomic key based on morphologic and morphometric characteristics and containing all Remanella species considered identifiable in this revision.     

Acinetobacter cumulans sp. nov., isolated from hospital sewage and capable of acquisition of multiple antibiotic resistance genes

We studied the taxonomic position of six phenetically related strains of the genus Acinetobacter, which were recovered from hospital sewage in China and showed different patterns of resistance to clinically important antibiotics. Whole-genome sequencing of these strains and genus-wide phylogeny reconstruction based on a set of 107 Acinetobacter core genes indicated that they formed a separate and internally cohesive clade within the genus. The average nucleotide identity based on BLAST and digital DNA–DNA hybridization values between the six new genomes were 97.25–98.67% and 79.2–89.3%, respectively, whereas those between them and the genomes of the known species were ≤78.57% and ≤28.5%, respectively. The distinctness of the strains at the species level was also supported by the results of the cluster analysis of the whole-cell protein fingerprints generated by MALDI-TOF MS. Moreover, the strains displayed a catabolically unique profile and could be differentiated from the phylogenetically closest species at least by their inability to grow on d,l-lactate. A total of 18 different genes were found in the six genome sequences which encode resistance to seven classes of antimicrobial agents, including clinically important carbapenems, oxyimino-cephalosporins, or aminoglycosides. These genes occurred in five different combinations, with three to 10 different genes per strain. We conclude that the six strains represent a novel Acinetobacter species, for which we propose the name Acinetobacter cumulans sp. nov. to reflect its ability to acquire and cumulate diverse resistance determinants. The type strain is WCHAc060092^T (ANC 5797^T = CCTCC AB 2018119^T = GDMCC 1.1380^T = KCTC 62576^T).     

Argentinean native wood species: Physical and mechanical characterization of some Prosopis species and Acacia aroma (Leguminosae; Mimosoideae)

One of the problems in marketing the wood of Prosopis and Acacia is the lack of standardization of its qualities. The aim of this paper was to obtain a preliminary detection of some properties of the wood of four species of the genus Prosopis and one species from Acacia grown in Argentina. To accomplish this objective, the content of extractives and some physical and mechanical characteristics were analyzed.The density ρ₁₂ of all the species indicates that these woods range from heavy to very heavy (?0.69 g/cm³). The total volumetric shrinkage values are low, less than 10%, for all species. The parallel compression strength and the shear strength for all the species indicate a very resistant wood (?46.93 MPa and ?18.35 MPa, respectively). Brinell hardness was higher than 5 kg/mm² in all cases. The species with less content of extractives is P. ruscifolia (approximately 9% of anhydrous mass) whereas A. aroma was the one with the greatest content (approximately 25% of anhydrous mass in the heartwood).     

Intestinal ciliate fauna of the Asian elephant from Gaziantep,Turkey and the description of Brevitentaculum antebum n. g., n. sp.

The aims of this investigation were to identify and quantify ciliates inhabiting the large intestine of Asian elephants living in Gaziantep Zoo, Turkey, and to describe a new suctorian genus and species. Species composition and distribution of intestinal ciliates voided in the feces of two Asian elephants were examined. Fifteen species of intestinal ciliates, representing 7 genera, were identified. One new suctorian genus and species, Brevitentaculum antebum n. g., n. sp., was described. This new species has two short truncated terminal projections, with two longitudinally lined bands located between the two projections, near the convex surface of the cell. Short clavate-like tentacles are in two fascicles near each base of terminal projections on the flattened surface of the body. Ciliate densities in the two fecal samples were 4.5 × 10⁴ mL⁻¹ and 10 × 10⁴ mL⁻¹.     

A review of the phylogeny,ecology and toxin production of bloom-forming Aphanizomenon spp. and related species within the Nostocales (cyanobacteria)

The traditional genus Aphanizomenon comprises a group of filamentous nitrogen-fixing cyanobacteria of which several memebers are able to develop blooms and to produce toxic metabolites (cyanotoxins), including hepatotoxins (microcystins), neurotoxins (anatoxins and saxitoxins) and cytotoxins (cylindrospermopsin). This genus, representing geographically widespread and extensively studied cyanobacteria, is in fact heterogeneous and composed of at least five phylogenetically distant groups (Aphanizomenon, Anabaena/Aphanizomenon like cluster A, Cuspidothrix, Sphaerospermopsis and Chrysosporum) whose taxonomy is still under revision. This review provides a thorough insight into the phylogeny, ecology, biogeography and toxicogenomics (cyr, sxt, and ana genes) of the five best documented “Aphanizomenon” species with special relevance for water risk assessment: Aphanizomenon flos-aquae, Aphanizomenon gracile, Cuspidothrix issatschenkoi, Sphaerospermopsis aphanizomenoides and Chrysosporum ovalisporum. Aph. flos-aquae, Aph. gracile and C. issatschenkoi have been reported from temperate areas only whereas S. aphanizomenoides shows the widest distribution from the tropics to temperate areas. Ch. ovalisporum is found in tropical, subtropical and Mediterranean areas. While all five species show moderate growth rates (0.1–0.4 day⁻¹) within a wide range of temperatures (15–30 °C), Aph. gracile and A. flos-aquae can grow from around (or below) 10 °C, whereas Ch. ovalisporum and S. aphanizomenoides are much better competitors at high temperatures over 30 °C or even close to 35 °C. A. gracile has been confirmed as the producer of saxitoxins and cylindrospermopsin, C. issatschenkoi of anatoxins and saxitoxins and Ch. ovalisporum of cylindrospermopsin. The suspected cylindrospermopsin or anatoxin-a production of A. flos-aquae or microcystin production of S. aphanizomenoides is still uncertain. This review includes a critical discussion on the the reliability of toxicity reports and on the invasive potential of “Aphanizomenon” species in a climate change scenario, together with derived knowledge gaps and research needs. As a whole, this work is intended to represent a key reference for scientists and water managers involved in the major challenges of identifying, preventing and mitigating toxic Aphanizomenon blooms.     

New Middle Permian foraminifers (Chitralinidae) from the Karakaya Complex,in northwestern Turkey

One new foraminiferal genus, Rectoformata gen. nov., with two new species, has been described from a Permian limestone block in the Karakaya Complex in the South of the Balya district (Balikesir, northwestern Turkey). The type species of Rectoformata, Rectoformata tekini sp. nov., is characterized by a quadrangular transverse section having a calcareous microgranular wall with fine alveolar structures, whereas Rectoformata acari sp. nov. is recognized by a pentagonal transverse section having a calcareous microgranular wall with fine alveolar structures. The age of the described taxa is assigned as Midian ( = Capitanian) based on the association with small foraminifers and fusulinids. These new taxa are included in the family Chitralinidae, which is emended herein.