Neptuniibacter pectenicola sp. nov. and Neptuniibacter marinus sp. nov., two novel species isolated from a Great scallop (Pecten maximus) hatchery in Norway and emended description of the genus Neptuniibacter.

Nine isolates obtained from a great scallop hatchery in Norway were characterized using a polyphasic approach. Strains were Gram-negative, aerobic and motile rods with oxidative metabolism. Phylogenetic analysis based on the sequences of 16S rRNA and rpoB genes showed that these strains formed two different groups associated with members of the genus Neptuniibacter. DNA–DNA hybridization (DDH) and Average Nucleotide Identity (ANI) demonstrated that the isolates constituted two novel species of this genus, which can be phenotypically differentiated from their closest relatives. The names Neptuniibacter marinus sp. nov. and Neptuniibacter pectenicola sp. nov are proposed, with ATR 1.1^T (=CECT 8938^T = DSM 100783^T) and LFT 1.8^T (=CECT 8936^T = DSM 100781^T) as respective type strains.     

Bifidobacterium primatium sp. nov., Bifidobacterium scaligerum sp. nov., Bifidobacterium felsineum sp. nov. and Bifidobacterium simiarum sp. nov.: Four novel taxa isolated from the faeces of the cotton top tamarin (Saguinus oedipus) and the emperor tamarin (Saguinus imperator)

Four novel Gram-stain-positive, non spore forming and fructose-6-phosphate phosphoketolase-positive strains were isolated from the faeces of a cotton top tamarin (Saguinus oedipus) and an emperor tamarin (Saguinus imperator). Phylogenetic analyses based on 16S rRNA revealed that bifidobacterial strains TRE 1^T exhibit close phylogenetic relatedness to Bifidobacterium catulorum DSM 103154 (96.0%) and Bifidobacterium tissieri DSM 100201 (96.0%); TRE D^T and TRE H^T were closely related to Bifidobacterium longum subsp. longum ATCC 15708^T with similarity values of 97.4% and 97.5%, respectively; TRI 7^T was closely related to Bifidobacterium tissieri DSM 100201 (96.0%). The Average Nucleotide Identity (ANI) and in silico DDH (isDDH) analysis with closest neighbour supported an independent phylogenetic position of all strains with values ranged from 74 to 85% for ANI and from 24 to 28% for isDDH. DNA base composition of the four strains was in the range of 58.3–63.5 mol% G + C. Based on the phylogenetic, genotypic and phenotypic data, the strains TRE 1^T, TRE D^T, TRE H^T and TRI 7^T clearly represent four novel taxa within the genus Bifidobacterium for which the names Bifidobacterium primatium sp. nov. (type strain TRE 1^T = DSM 100687^T = JCM 30945^T), Bifidobacterium scaligerum sp. nov. (type strain TRE D^T = DSM 103140^T = JCM 31792^T), Bifidobacterium felsineum sp. nov. (type strain TRE H^T = DSM 103139^T = JCM 31789^T) and Bifidobacterium simiarum sp. nov. (type strain TRI 7^T = DSM 103153^T = JCM 31793) are proposed.     

Polyphasic characterization of two novel Lactobacillus spp. isolated from blown salami packages: Description of Lactobacillus halodurans sp. nov. and Lactobacillus salsicarnum sp. nov.

Microbiota analysis of blown pack spoiled salami revealed five distinguishable Lactobacillus isolates we could not assign to a known species. Two of the isolates (TMW 1.2172^T and TMW 1.1920) are rod-shaped, whilst three isolates (TMW 1.2098^T, TMW 1.2118 and TMW 1.2188) appear coccus shaped or as short rods. All isolates are Gram-stain positive, facultative anaerobic, catalase and oxidase negative, non-motile and non-sporulating. Phylogenetic analysis of the 16S rRNA, dnaK, pheS and rpoA gene sequences revealed two distinct lineages within the genus Lactobacillus (L.). The isolates are members of the Lactobacillus alimentarius group with Lactobacillus ginsenosidimutans DSM 24154^T (99.4% 16S similarity), Lactobacillus versmoldensis DSM 14857^T (97.9%) and Lactobacillus furfuricola DSM 27174^T (97.7%) as phylogenetic closest related species and L. alimentarius DSM 20249^T (97.7%) and Lactobacillus paralimentarius DSM 13961^T (97.5%) as closest relatives, respectively. Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the isolates and their close related type strains are lower than 80% and 25%, respectively. For both designated type strains, the peptidoglycan type is A4α l-Lys-d-Asp and the major fatty acids are C_16:0, C_18:1ω9c and summed feature 7. Based on phylogenetic, phenotypic and chemotaxonomic analysis we demonstrated that the investigated isolates belong to two novel Lactobacillus species for which we propose the names Lactobacillus salsicarnum with the type strain TMW 1.2098^T = DSM 109451^T = LMG 31401^T and Lactobacillus halodurans with the type strain TMW 1.2172^T = DSM 109452^T = LMG 31402^T.     

Morphology and phylogeny of Bryophryoides ocellatus n. g., n. sp. (Ciliophora,Colpodea) from in situ soil percolates of Idaho,U.S.A.

We describe the morphology and 18S rDNA phylogeny of Bryophryoides ocellatus n. g., n. sp., a bryophryid ciliate inhabiting in situ soil percolates from Idaho, U.S.A. The new genus is distinguished from other bryophryid genera by a combination of the following features: (1) kreyellid (irregularly meshed) silverline pattern, (2) polymorphic adoral organelles in the preoral suture, (3) absence of vestibular kineties. In phylogenetic analyses, Bryophryoides ocellatus is most closely related to Bryophrya gemmea. The 18S rDNA sequence pairwise distance of 2% between these genera, while similar to that between many colpodidan species, exceeds that between some colpodidan genera (e.g. Mykophagophrys and Pseudoplatyophrya, 1.1%), further supporting establishment of the new genus. Topology hypothesis testing strongly supports the monophyly of the Colpodida including the bryophryids. Despite weak nodal support, tests of topology constraints narrowly reject the non-monophyly of the sequenced Bryophryidae (Bryophrya + Bryophryoides + Notoxoma). Likewise, the monophyletic origin of the sequenced Bryophryidae is indicated in the phylogenetic networks though with low support.     

Proposal of Desulfosarcina ovata subsp. sediminis subsp. nov., a novel toluene-degrading sulfate-reducing bacterium isolated from tidal flat sediment of Tokyo Bay

Strain 28bB2T^T is a sulfate-reducing bacterium isolated in a previous study, obtained from a p-xylene-degrading enrichment culture. Physiological, phylogenetic and genomic characterizations of strain 28bB2T^T were performed to establish the taxonomic status of the strain. Cells of strain 28bB2T^T were short oval-shaped (0.8–1.2 × 1.2–2.7 μm), motile, and Gram-negative. For growth, the optimum pH was pH 6.5–7.0 and the optimum temperature was 28–32 °C. Strain 28bB2T^T oxidized toluene but could not utilize p-xylene. Sulfate and thiosulfate were used as electron acceptors. The G + C content of the genomic DNA was 53.8 mol%. The genome consisted of an approximately 8.3 Mb of chromosome and two extrachromosomal elements. On the basis of 16S rRNA gene analysis, strain 28bB2T^T was revealed to belong to the genus Desulfosarcina, with high sequence identities to Desulfosarcina ovata oXyS1^T (99.5%) and Desulfosarcina cetonica DSM 7267^T (98.7%). Results of Average Nucleotide Identity (ANI) calculation and digital DNA–DNA hybridization (dDDH) analysis showed that the strain 28bB2T^T should be classified as a subspecies under D. ovata. Based on physiological and phylogenetic data, strain 28bB2T^T (=NBRC 106234 =DSM 23484) is proposed as the type strain of a novel species in genus Desulfosarcina, Desulfosarcina ovata subsp. sediminis subsp. nov.     

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).     

Avrilella dinanensis gen. nov., sp. nov., a novel bacterium of the family Flavobacteriaceae isolated from human blood

Polyphasic taxonomic analysis was performed on a novel bacterium, designated UR159^T, isolated in 2016 from human blood of a septic patient hospitalized in France. Preliminary 16S rRNA gene sequence-based phylogenetic analysis indicated that strain UR159^T belonged to the family Flavobacteriaceae, forming a distinct phyletic line distantly related (<94% sequence similarity) to known species of the family. Further phenotypic, chemotaxonomic and genomic analyses were performed. Cells were non-motile, oxidase-negative, catalase-positive Gram-negative rods. It was strictly aerobic yielding yellow-pigmented colonies, and was metabolically rather inert. Major fatty acids were iso-branched fatty acids, predominantly iso-C_15:0 (55.5%) and iso-C_17:1ω9c (8.8%). Whole genome sequencing revealed a 2.3-Mbp genome encoding a total of 2262 putative genes with a genomic DNA G + C content at 37.6 mol%. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between strain UR159^T and the most closely related members of the Flavobacteriaceae family were <75% and <39%, respectively, much below the established cut-offs for ANI (<95–96%) and isDDH (<70%) for species and genus delineation. Average Amino Acid Identity (AAI) percentages were also estimated and were lower than 65% (cut-off proposed for genus delineation for uncultivated prokaryotes) in all cases, except for F. marinum that was just at the limit (65.1%). Based on these findings, we propose it as a new genus and species, Avrilella dinanensis gen. nov., sp. nov. (type strain UR159^T = CIP 111616^T = DSM 105483^T).     

Vibrio aestivus sp. nov. and Vibrio quintilis sp. nov., related to Marisflavi and Gazogenes clades,respectively

Two new Vibrio species, Vibrio aestivus and Vibrio quintilis, are described after a polyphasic characterization of strains M22^T, M61 and M62^T, isolated from seawater collected off a beach on the East coast of Spain (Valencia). All three strains are Gram negative, mesophilic, slightly halophilic, fermentative rods. V. aestivus (M22^T = CECT 7558^T = CAIM 1861^T = KCTC 23860^T and M61 = CECT 7559 = CAIM 1862 = KCTC 23861) is oxidase positive, reduces nitrates to nitrites, is negative for Voges Proskauer, arginine dihydrolase and indole and non hydrolytic on most substrates tested. The 16S rRNA gene sequences of M22^T and M61 are most similar to Vibrio marisflavi (97.1–97.2%) but phylogenetic analysis using NJ, MP and ML methods display Vibrio stylophorae (96.2% similarity) as sibling species. The three species form a deep clade in the genus Vibrio. Average Nucleotide Identity (ANI) values, determined as a measure of overall genomic resemblance, confirmed that strains M22^T and M61 are members of the same species, different to V. marisflavi CECT 7928^T.V. quintilis (M62^T = CECT 7734^T = CAIM 1863^T = KCTC 23833^T) is aerogenic, arginine dihydrolase and Voges Proskauer positive, oxidase negative and unable to reduce nitrate, traits shared by most species in the Gazogenes clade. It is unpigmented and does not grow on TCBS Agar. 16S rRNA gene similarities to its nearest species, Vibrio aerogenes and Vibrio mangrovi, are 97.6% and 96.0% respectively. Strain M62^T and V. aerogenes CECT 7868^T display ANI values well below the 95% boundary for genomic species.     

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.     

Estimation of nuclear genome size of the genus Mycetophylax Emery, 1913: Evidence of no whole-genome duplication in Neoattini

Genome size estimates and their evolution can be useful for studying the phylogenetic relationships and taxonomy of a particular group. In the present study, the genome sizes of the three species that comprise the Mycetophylax genus were estimated by flow cytometry (FCM). There was little variation in genome size among them. The mean haploid genome size value of male and female individuals of Mycetophylax morschi was 312.96 Mbp (0.32 pg) and that of Mycetophylax conformis and Mycetophylax simplex females were 312.96 Mbp (0.32 pg) and 381.42 Mbp (0.39 pg), respectively. At first glance, this variation could be related with the heterochromatin content. Our results, together with other previous reports, have contributed to our knowledge about Attini genome size and will be useful to improve the understanding of the evolution of this tribe. It will help select potential model species in Attini for future genomic and sequencing projects.     

Phylogeny and biogeography of the Poecilia sphenops species complex (Actinopterygii,Poeciliidae) in Central America

We inferred the phylogenetic relationships among members of the Poecilia sphenops species complex to resolve the colonization process and radiation of this group in Central America. We analyzed 2550 base pairs (bp) of mitochondrial DNA (mtDNA), including ATP synthase 6 and 8, cytochrome oxidase subunit I and NADH dehydrogenase subunit 2 genes, and 906 bp of the nuclear S7 ribosomal protein of 86 ingroup individuals from 61 localities spanning most of its distribution from Mexico to Panama. Our mitochondrial data rendered a well-supported phylogeny for the P. sphenops complex that differed with the nuclear data set topology, which did not recover the monophyly of the P. mexicana mitochondrial lineage. Coalescent-based simulations tests indicated that, although hybridization cannot be completely ruled out, this incongruence is most likely due to incomplete lineage sorting in this group, which also showed the widest geographic distribution. A single colonization event of Central America from South America was estimated to have occurred between the early Paleocene and Oligocene (53–22 million years ago). Subsequently, two largely differentiated evolutionary lineages diverged around the Early Oligocene–Miocene (38–13 million years ago), which are considered two separate species complexes: P. sphenops and P. mexicana, which can also be distinguished by their tricuspid and unicuspid inner jaw teeth, respectively. Ultimately, within lineage diversification occurred mainly during the Miocene (22–5 million years ago). All major cladogenetic events predated the final closure of the Isthmus of Panama. The allopatric distribution of lineages together with the long basal internodes suggest that vicariance and long term isolations could be the main evolutionary forces promoting radiation in this group, although dispersal through water barriers might also have occurred. Lastly, our results suggest the need to review the current species distribution and taxonomy of the P. sphenops complex sensu lato.     

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.     

Morphological and molecular characterization of the name-bearing type species Rimaleptus binucleatus (Kahl, 1931), with a phylogenetic re-analysis of dileptid evolutionary history (Ciliophora: Litostomatea: Rhynchostomatia)

We collected Rimaleptus binucleatus from soil in the surroundings of the town of Ulsan, South Korea. Its morphology and 18S rRNA gene were studied using standard methods. This possibly widely distributed species is characterized by: (i) a size of about 170–400 × 20–65 μm; (ii) a narrowly to cylindrically dileptid body with proboscis occupying about 30–65% of body length; (iii) two dorsal contractile vacuoles; (iv) two size groups of rod-shaped extrusomes; and (v) about 18–29 ciliary rows, 4–6 of them anteriorly differentiated into a staggered dorsal brush. Phylogenetic analyses of five new rhynchostomatian 18S rRNA gene sequences supported monophylies of the orders Tracheliida and Dileptida, but revealed that the genera Rimaleptus and Pseudomonilicaryon are polyphyletic. Monophyly of genera with two macronuclear nodules was consistently rejected, but monophylies of dileptids with many scattered macronuclear nodules and of dileptids with moniliform macronucleus and multi-rowed dorsal brush could not be excluded by statistical topology tests. Nevertheless, phylogenetic network analyses indicated considerable conflict in the phylogenetic signal provided by the 18S rRNA gene to resolve unambiguously relationships among dileptid genera.     

Systematics and biogeography of the Neotropical genus Mabuya,with special emphasis on the Amazonian skink Mabuya nigropunctata (Reptilia,Scincidae)

Phylogenetic analyses using up to 1532 base pairs (bp) of mitochondrial DNA from 106 specimens of Neotropical Mabuya, including 18 of the 19 recognized South American and Mesoamerican species, indicate that most species of the genus are monophyletic, including M. nigropunctata that had previously been reported to be paraphyletic. The present results shows that this species includes three highly divergent and largely allopatric lineages restricted to occidental, meridional, and oriental Amazonia. Our dataset demonstrates that previous claims regarding the paraphyletic status of M. nigropunctata and the phylogenetic relationships within this species complex based on the analysis of three mitochondrial and four nuclear genes (approx. 5000 bp) were erroneous and resulted from two contaminated cytochrome b sequences.The phylogenetic results indicate that diversification in the Neotropical genus Mabuya started approximately in the Middle Miocene (15.5–13.4 Ma). The divergence dates estimated for the Mabuya nigropunctata species complex suggest that the major cladogenetic events that produced the three main groups (occidental (oriental + meridional)) occurred during the Late Miocene. These estimations show that diversification within the M. nigropunctata species complex was not triggered by the climatic changes that occurred during the Pleistocene, as has been suggested by several authors. Rather, our data support the hypothesis that the late tertiary (essentially Miocene epoch) was a period that played a very important role in the generation of biological diversity in the Amazonian forests.Speciation between Mabuya carvalhoi, endemic to the coastal mountain range of Venezuela, and M. croizati, restricted to the Guiana Shield, occurred during the Middle Miocene and may have been as the result of a vicariant event produced by the formation of the present day Orinoco river drainage basin and the consequent appearance of the Llanos del Orinoco, which acted as a barrier to dispersal between these two species. The split between M. bistriata and M. altamazonica and between the occidental and (meridional + oriental) clades of M. nigropunctata fits very well with the biogeographic split between the eastern and western Amazon basins reported for several other taxa.     

The oldest South American tuco-tuco (late Pliocene,northwestern Argentina) and the boundaries of the genus Ctenomys (Rodentia,Ctenomyidae)

A new species of Ctenomyidae from the late Pliocene of Uquía Formation (northwestern Argentina) is described. The new remains consist of a fragmentary rostrum, and a left mandible with partial lower dentition. Its phylogenetic affinity and morphological specializations for tooth-digging support its assignation to the South American rodent genus Ctenomys. In this context, we highlight the importance of unique morphological specializations for the delimitation of genera within an intrafamilial clade in which similar adaptive strategies could have evolved more than once. The new materials are the oldest fossils for the genus (ca. 3.5 Ma), and their finding in the central Andes agrees with previous hypotheses about the possible area of origin of Ctenomys. They precede by about one million years the presence of Ctenomys chapalmalensis in the Pliocene of the Pampean region of central Argentina, the oldest record previously known for the genus. Nevertheless, the new species does not contribute key information about ancestral character states for the genus beyond those already known through C. chapalmalensis. The phylogenetic, adaptive and even chronological information supplied by these new materials would be linked to the differentiation of the genus rather than to its origin.     

Description of a new anaerobic thermophilic bacterium,Thermoanaerobacterium butyriciformans sp. nov.

Strain USBA-019^T, an anaerobic and thermophilic strain, was identified as a new member of the genus Thermoanaerobacterium. USBA-019^T cells are gram-positive, strictly anaerobic, thermophilic, chemoorganotrophic, moderately acidophilic, non-motile, endospore-forming, slightly curved, and rod-shaped. Cells measure 0.4 × 3.0–7.0 μm. Optimal growth occurs at 50–55 °C (35–65 °C). Optimum pH is 5.0–5.5 (4.0–8.5). Thiosulfate, elemental sulfur and nitrate were utilized as electron acceptors. Fermentation of glucose, lactose, cellobiose, galactose, arabinose, xylose, starch and xylan primarily produced acetate and butyrate. Xylan, starch and cellobiose produced ethanol and starch, cellobiose, galactose, arabinose and mannose produced lactic acid. Phylogenetic analyses based on 16S rRNA gene sequence comparison and genomic relatedness indices show the close relation of USBA-019^T to Thermoanaerobacterium thermostercoris and Thermoanaerobacterium aotearoense (similarity value: 99%). Hybridization of USBA-019^T, Th. thermostercoris DSM22141^T and Th. aotearoense DMS10170^T found DNA–DNA relatedness of 33.2% and 18.2%, respectively. Based on phenotypic, chemotaxonomic and phylogenetic evidence, along with low identity at whole genome level, USBA-019^T is a novel species of the genus Thermoanaerobacterium which we propose to name Thermoanaerobacterium butyriciformans sp. nov. The type strain is USBA-019^T (=CMPUJ U-019^T = DSM 101588^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.     

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.     

The tropical African legume Scorodophloeus clade includes two undescribed Hymenostegia segregate genera and Micklethwaitia,a rare,monospecific genus from Mozambique

Legume subfamily Caesalpinioideae accommodates approximately 2250 species in 171 genera which traditionally are placed in four tribes: Caesalpinieae, Cassieae, Cercideae and Detarieae. The monophyletic tribe Detarieae includes the Amherstieae subclade which contains about 55 genera. Our knowledge of the relationships among those genera is good in some cases but for many other genera phylogenetic relationships have been unclear. The non-monophyletic nature of at least two amherstioid genera, Cynometra and Hymenostegia has also complicated the picture. During the course of a multi-disciplinary study of Hymenostegia sensu lato, which includes phylogenetic analyses based on matK and trnL data, we have recovered the “Scorodophloeus clade”, an exclusively tropical African clade of four genera which includes the eponymous genus Scorodophloeus, two undescribed generic segregates of Hymenostegia sensu lato, and the previously unsampled rare monospecific genus Micklethwaitia from Mozambique. Zenkerella is suggested as a possible sister genus to the Scorodophloeus clade. A distribution map is presented of the seven species that belong to the Scorodophloeus clade.     

Interannual patterns of the large free-living nematode assemblages in the Mexican Exclusive Economic Zone,NW Gulf of Mexico after the Deepwater Horizon oil spill

The presence and abundance of particular nematode genera in marine sediments are bioindicators of environmental disturbance. They can even reveal the existence of specific toxicants, such as trace-metals and hydrocarbons derived from fossil fuels. We studied this important infaunal component during a three-year monitoring program in Mexico’s Exclusive Economic Zone (EEZ) in the aftermath of a major oil spill in the northern Gulf of Mexico caused by the sinking of the Deepwater Horizon platform (DWH) in April of 2010. A closer look at the nematode composition and density values throughout and after the DWH oil spill revealed considerable changes. Continental shelf and upper slope sediments sampled in the summer of 2010 included 48 genera and a density of 44.45 ind/10 cm⁻². Eight months later in the winter of 2011, there was a critical decrement in genera number (23) and density (25.22 ind/10 cm⁻²). However, in 2012, the nematode community showed signs of recovery: genus diversity was 58 with a density of 91.45 ind/10 cm⁻². Significant differences were recorded between the first and the last sampling periods, driven by a remarkable turn-over in genera composition, and by an increase in density of the genera Sabatieria, Dorylaimopsis, and Cheironchus. Similarly, significant spatial differences between the nematofauna of the inner-middle shelf and the deepest zone (>2000 m) were detected. Correlation analyses confirmed the tolerant behavior of the above genera to Ni and Co, and their proliferation when hydrocarbon compounds presumably derived from the DWH oil spill increased throughout the study. The Maturity Index (MI) estimated for each survey ranged from 2.35 to 2.6. Environmental Quality Status conditions in the summer of 2010 were good while in the winter of 2011 were poor, and moderate towards the winter of 2012. Index of Trophic Diversity (ITD) values for each survey were high: 0.70, 0.68, and 0.74, respectively. A high predominance of feeding guilds 1B and 2B was recorded throughout the study.The estimated Index of Trophic Diversity (ITD) values resulted high (Table 5). These values apparently indicated that the four feeding types were proportionally distributed in the nematode assemblage. This fact was better reflected during the winter of 2012. Nonetheless, these results are not congruent with the high predominance of feeding guilds 1B and 2B observed throughout the study.