Phylogenetic Data Research Articles

Kekerabatan Zeylanicobdella arugamensis pada Ikan Kerapu Cantang dengan Pendekatan Molekuler di Jawa Timur dan Lombok

Giant grouper is a highly sought-after cultivated fish in Indonesia due to its high market value. One of the challenges in grouper aquaculture is the infestation of the sea leech ektoparasite Zeylanicobdella arugamensis. The prevalence rate of ektoparasite infestation reaches up to 100%. An effective method to manage ektoparasite infestation is through molecular profiling, serving as preliminary literature in the development of molecular biology efforts to overcome cultivation challenges in giant grouper. This research aims to study the homology and relationship of Zeylanicobdella arugamensis on giant grouper in East Java, specifically in Lamongan, Mandangin, Situbondo, and Lombok. The method used is RT-PCR with mtDNA COI gene primers. Molecular sequence data were collected from samples and compared with data from NCBI GenBank, and analyzed using Neighbor-joining phylogenetic tree method and homology data analysis on BLAST. The research results indicate clinical symptoms in giant grouper including swelling, lesions/wounds, pale skin, decreased appetite, and fin erosion. Electrophoresis results from PCR products show a single band at 750bp for samples from Lamongan, Situbondo, Mandangin, and Lombok. DNA sequencing results on NCBI BLAST and homology analysis against the reference gene were conducted. Homology analysis results between samples from Situbondo and Lamongan show the highest similarity at 98.28%, whereas the lowest similarity is between samples from Mandangin and Situbondo at 88.51%. Based on phylogenetic tree analysis, samples from Lamongan and Situbondo waters show a close relationship with a genetic distance of 0.009272.

A new species of Thamnophis (Serpentes, Colubridae) from Jalisco, Mexico, with a discussion on the phylogeny, taxonomy, and distribution of snakes related to Thamnophis scalaris

Garter snakes in the genus Thamnophis from Mexico have a long and convoluted taxonomic history. From 2015 to 2022, we conducted a comprehensive sampling of Mexican Thamnophis species, aiming to link molecular phylogenies with the recognized species related to T. scalaris in the highlands of Mexico. Here, we present an analysis of mitochondrial DNA to resolve the status of two enigmatic highland Thamnophis populations. Our research resulted in the identification and morphological characterization of a previously undescribed Thamnophis species from the state of Jalisco in western Mexico. We also clarify the identity and relationships of several previously enigmatic populations of Thamnophis. This work presents new data for Thamnophis phylogenetics from the Mexican highlands and offers a framework for future conservation efforts.

Svornostia abyssi gen. nov., sp. nov. isolated from the world's deepest silver-uranium mine currently devoted to the extraction of radon-saturated water.

A Gram-stain-positive, rod-shaped, aerobic, motile bacterium, J379T, was isolated from radioactive water spring C1, located in a former silver-uranium mine in the Czech Republic. This slow-growing strain exhibited optimal growth at 24-28 °C on solid media with <1 % salt concentration and alkaline pH 8-10. The only respiratory quinone found in strain J379T was MK-7(H4). C18 : 1 ω9c (60.9 %), C18 : 0 (9.4 %), C16 : 0 and alcohol-C18 : 0 (both 6.2 %) were found to be the major fatty acids. The peptidoglycan contained directly cross-linked meso-diaminopimelic acid. Phylogenetic reconstruction based on the 16S rRNA gene sequences and the core-genome analysis revealed that strain J379T forms a separate phylogenetic lineage within the recently amended order Solirubrobacterales. A comparison of the 16S rRNA gene sequences between strain J379T and other members of the order Solirubrobacterales showed <96 % similarity. This analysis revealed that the closest type strains were Parviterribacter kavangonensis D16/0 /H6T (95.2 %), Capillimicrobium parvum 0166_1T (94.9 %) and Conexibacter arvalis KV-962T (94.5 %). Whole-genome analysis showed that the closest type strain was Baekduia soli BR7-21T with an average nucleotide identity of 78 %, average amino acid identity of 63.2 % and percentage of conserved proteins of 48.2 %. The G+C content of the J379T genomic DNA was 71.7 mol%. Based on the phylogenetic and phylogenomic data, as well as its physiological characteristics, strain J379T is proposed to represent a type strain (DSM 113746T=CCM 9300T) of Svornostia abyssi gen. nov. sp. nov. within the family Baekduiaceae.

Colletotrichum paridis sp. nov., a novel endophytic species on Paris polyphylla var. chinensis

The genus Paris is a crucial medicinal herb, widely cultivated in East Asia and Europe. In 2017 a novel Colletotrichum species was isolated from leaf lesions with grey mould of Paris polyphylla var. chinensis in Sichuan Province of China. Through single-spore technique, four isolates were obtained for characterization. Phylogeny inferred from multi-locus sequences of ITS, gapdh, act, tub2, chs-1, and his3, showed that these isolates represented a novel sister species to C. jinshuiense within the C. dematium complex. Morphologically, this new species produces larger conidia than those of C. jinshuiense and cultures on PDA show a noticeable pink ring. Tests showed that this species had no pathogenicity to the host plants. Based on phylogenetic, morphological, and pathogenicity data, we propose the name C. paridis sp. nov. for this new endophyte from P. polyphylla in China.

Orobanche dagestanica (Orobanchaceae): a new species from the Greater Caucasus

A new, probably endemic species, Orobanche dagestanica is described from Dagestan in Russia (the Greater Caucasus). The species grows in alpine shale scree slopes, and is a parasite of the roots of species from the genus Lophiolepis (Asteraceae). Based on morphological and phylogenetic data, the newly-described species belongs to Orobanche subsect. Curvatae, and specifically to O. ser. Krylowianae, however it is distinct from all other taxa in this group. A detailed description, diagnosis, illustrations, a comparison with related species, as well as phylogenetic analysis are provided.

Mangrovimonas cancribranchiae sp. nov., a novel bacterial species associated with the gills of the fiddler crab Cranuca inversa (Brachyura, Ocypodidae) from Red Sea mangroves.

Two bacteria, UG2_1T and UG2_2, were isolated from the gill tissues of the mangrove fiddler crab Cranuca inversa collected on the east coast of the Red Sea (Thuwal, Saudi Arabia). The cells are Gram-negative, rod-shaped, orange-pigmented, motile by gliding with no flagella, strictly aerobic, and grow at 20-37 °C (optimum, 28-35 °C), at pH 5.0-9.0 (optimum, pH 6.0-7.0), and with 1-11 % (w/v) NaCl (optimum, 2-4 %). They were positive for oxidase and catalase activity. Phylogenetic analysis based on 16S rRNA gene sequences indicated that isolates UG2_1T and UG2_2 belong to the genus Mangrovimonas, showing the highest similarity to Mangrovimonas spongiae HN-E26T (99.4 %). Phylogenomic analysis based on the whole genomes, independently using 49 and 120 concatenated genes, showed that strains UG2_1T and UG2_2 formed a monophyletic lineage in a different cluster from other type strain species within the genus Mangrovimonas. The genome sizes were 3.08 and 3.07 Mbp for UG2_1T and UG2_2, respectively, with a G+C content of 33.8 mol% for both strains. Values of average nucleotide identity and digital DNA-DNA hybridization between the strains and closely related species were 91.0 and 43.5 %, respectively. Chemotaxonomic analysis indicated that both strains had iso-C15 : 0 and iso-C15 : 1 G as dominant fatty acids, and the primary respiratory quinone was identified as MK-6. The major polar lipids comprised phosphatidylethanolamine, one unidentified glycolipid, one unidentified phospholipid, two unidentified aminolipids, and four unidentified lipids. Based on phylogenetic, phylogenomic, genome relatedness, phenotypic, and chemotaxonomical data, the two isolates represent a novel species within the genus Mangrovimonas, with the proposed name Mangrovimonas cancribranchiae sp. nov., and the type strain UG2_1T (=KCTC 102158T=DSM 117025T).

Clostridium omnivorum sp. nov., isolated from anoxic soil under the treatment of reductive soil disinfestation.

Reductive soil disinfestation (RSD), also known as biological soil disinfestation, is a bioremediation method used to suppress soil-borne plant pathogens by stimulating the activity of indigenous anaerobic bacteria in the soil. An anaerobic bacterial strain (E14T) was isolated from an anoxic soil sample subjected to RSD treatment and then comprehensively characterized. Cells of the strain were Gram-stain-positive, curved to sigmoid, and spore-forming rods. Cells were motile with a polar flagellum. Strain E14T grew in peptone-yeast extract broth, indicating that it utilized proteinous compounds. Strain E14T was also saccharolytic and produced acetate, isobutyrate, butyrate, isovalerate and gases (H2 and CO2) as fermentation products. The strain did not decompose any of examined polysaccharides except for starch. The major cellular fatty acids of strain E14T were iso-C15:0 and iso-C15:0 DMA. The closest relative to strain E14T, based on 16S rRNA gene sequences, was Clostridium thermarum SYSU GA15002T (96.2 %) in the Clostridiaceae. Whole-genome analysis of strain E14T showed that its genome was 4.66 Mb long with a genomic DNA G+C content of 32.5 mol%. The average nucleotide identity (ANIb) between strain E14T and C. thermarum SYSU GA15002T was 69.0 %. The presence of the genes encoding glycolysis and butyrate production via the acetyl-CoA pathway was confirmed through genome analysis. Based on the obtained phylogenetic, genomic and phenotypic data, we propose that strain E14T should be assigned to the genus Clostridium in the family Clostridiaceae as Clostridium omnivorum sp. nov. The type strain is E14T (=NBRC 115133T=DSM 114974T).

Molecular insights into fungal diversity reveal three novel species of Leucocoprinus from southern Punjab, Pakistan

ABSTRACT Three novel species of the genus Leucocoprinus, named Lc. cinnamomeodiscus, Lc. dahranwalanus, and Lc. iqbalii, are described from unexplored regions of southern Punjab, Pakistan, based on comprehensive analyses of morphoanatomical characteristics and molecular phylogenetic data. We provide illustrations of freshly collected basidiomata and detailed line drawings highlighting key anatomical features. The molecular phylogenetic analyses, which are based on the internal transcribed spacer (ITS) region and combined ITS-28S sequences, consistently position these newly described species within the genus Leucocoprinus. Additionally, this study also introduces new taxonomic combinations for previously reported Leucoagaricus species.

Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages

Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and a single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signal or low phylogenetic noise. For some previously contentious relationships, we find a variety of analyses and gene filtering criteria consistently unite previously unstable groupings with strong statistical support. For example, we recovered a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister-lineage to Pinguiophyceae. Selecting genes with high phylogenetic signal or data quality recovered more stable topologies. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving phylogenetic relationships, and discrete gene properties affect lineages of stramenopiles differently. This is something which may be explored to further our understanding of the molecular evolution of stramenopiles.

Lysobacter stagni sp. nov. and Limnohabitans lacus sp. nov., isolated from a pond.

Two Gram-negative bacteria, designated as strains LF1T and HM2-2T, were isolated from an artificial pond in a honey farm at Hoengseong-gun, Gangwon-do, Republic of Korea. The 16S rRNA sequence analysis results revealed that strain LF1T belonged to the genus Lysobacter and had the highest sequence similarity to Lysobacter niastensis GH41-7T (99.0 %), Lysobacter panacisoli CJ29T (98.9 %), and Lysobacter prati SYSU H10001T (98.2 %). Its growth occurred at 20-37 °C, at pH 5.0-12.0, and in the presence of 0-2% NaCl. The major fatty acids were iso-C15 : 0, iso-C16 : 0, and summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The DNA G+C content was 67.5 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain LF1T and species of the genus Lysobacter were 79.1-84.4% and 22.0-27.5 %, respectively. The 16S rRNA sequence analysis results revealed that strain HM2-2T belonged to the genus Limnohabitans and was most closely related to Limnohabitans planktonicus II-D5T (98.9 %), Limnohabitans radicicola JUR4T (98.4%), and Limnohabitans parvus II-B4T (98.4 %). Its growth occurred at 10-35 °C, at pH 5.0-11.0, and in the presence of 0-2% NaCl. The major fatty acids were C16 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). The major polar lipid was phosphatidylethanolamine. The DNA G+C content was 59.9 mol%. The ANI and dDDH values between strain HM2-2T and its closely related strains were 75.1-83.0% and 20.4-26.4 %, respectively. Phenotypic, genomic, and phylogenetic data revealed that strains LF1T and HM2-2T represent novel species in the genera Lysobacter and Limnohabitans, for which the names Lysobacter stagni sp. nov. and Limnohabitans lacus sp. nov. are proposed, respectively. The type strain of Lys. stagni is LF1T (=KACC 23251T=TBRC 17648T), and that of Lim. lacus is HM2-2T (=KACC 23250T=TBRC 17649T).

Hwangdonia lutea sp. nov., isolated from the Haima cold seep, South China Sea.

A Gram-stain-negative, orange-yellow, rod-shaped bacterium, designated strain SCSIO 19198T, was isolated from sediment of the Haima cold seep in the South China Sea, PR China. The strain was aerobic and non-motile. Growth of strain SCSIO 19198T occurred at pH 7-9 (optimum, pH 7), 15-37 °C (optimum, 25-32 °C) and with 3-8 % (w/v) NaCl (optimum, 3-6 % NaCl). Phylogenetic analyses based on 16S rRNA sequences revealed that strain SCSIO 19198T belonged to the genus Hwangdonia, having the highest similarity to Hwangdonia seohaensis HD-3T (98.35 %), followed by Algibacter aquimarinus KYW589T (95.17 %) and Gelatiniphilus marinus GYP-24T (94.89 %). The DNA G+C content was 35.92 mol%. The average nucleotide identity value between the genome of strain SCSIO 19198T and that of H. seohaensis HD-3T was 88.49 %. The digital DNA-DNA hybridization value between strain SCSIO 19198T and H. seohaensis HD-3T was 36 %. The major fatty acids (>10 %) of strain SCSIO 19198T were iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c) and anteiso-C15 : 0. MK-6 was the only detected respiratory quinone. The polar lipids of strain SCSIO 19198T included phosphatidylethanolamine, two aminolipids, glycolipid and two unidentified lipids. The phenotypic, phylogenetic, chemotaxonomic and genomic data clearly suggest that strain SCSIO 19198T represents a novel species of the genus Hwangdonia, for which the name Hwangdonia lutea sp. nov. is proposed. The type strain is SCSIO 19198T (=MCCC 1K08674T=KCTC 102078T).

A novel method for predicting ecological interactions with an unsupervised machine learning algorithm

Abstract This gap in knowledge regarding ecological interactions has prompted the development of various predictive approaches. Traditionally, ecological interactions have been inferred using traits. However, the lack of trait information for numerous organisms necessitates using phylogenetic data and statistical insights from interaction matrices for prediction. Previous studies have overlooked the validation of model‐predicted interactions. This study used a novel method in predicting ecological interactions using a self‐organizing map (SOM), an unsupervised machine learning algorithm. The SOM learns from the input interaction matrix by grouping the nodes into output layers based on their interactions. Subsequently, the trained model predicts the interactions as scores. To distinguish between interactions and non‐interactions, we employed F1 score maximization, setting scores above a specific threshold as interactions and the remainder as non‐interactions. We applied this method to three unipartite metawebs and one bipartite metaweb and subsequently validated the predicted interactions using two innovative approaches: taxonomic and interaction recovery validation. Our method exhibited outstanding predictive performance, particularly for large networks. Various binary classification performance indicators, including F1 score (0.84–0.97) and accuracy (0.97–0.99), indicated high performance. Moreover, the method generated minimal predicted interactions, signifying low noise in the predictions, particularly for large networks. Taxonomic validation excels in metawebs with a connectance &gt;0.1 but performs poorly in metawebs with very low connectance. In contrast, interaction recovery was most effective in larger metawebs. Our proposed method excels at making highly accurate predictions of ecological interactions with minimal noise, solely utilizing input interaction data without relying on traits or phylogenetic information regarding interacting nodes. These predictions are particularly precise for large networks, underscoring their potential to address knowledge gaps in emerging extensive metawebs. Notably, taxonomic validation and interaction recovery methods are sensitive to connectance and network size, respectively, suggesting prospects for developing robust interaction validation methods.

Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of Photinia and its allies in the Old World

This study addresses the longstanding absence of a comprehensive phylogenetic backbone for the apple tribe Maleae, a deficiency attributed to limited taxon and marker sampling. We conducted an extensive taxon sampling, incorporating 563 plastomes from a diverse range of 370 species encompassing 26 presently recognized genera. Employing a range of phylogenetic inference methods, including RAxML and IQ-TREE2 for Maximum Likelihood (ML) analyses, we established a robust phylogenetic framework for the Maleae tribe. Our phylogenomic investigations provided compelling support for three major clades within Maleae. By integrating nuclear phylogenetic data with morphological and chromosomal evidence, we propose an updated infra-tribal taxonomic system, comprising subtribe Malinae Reveal, subtribe Lindleyinae Reveal, and subtribe Vauqueliniinae B.B.Liu (subtr. nov.). Plastid phylogenetic analysis also confirmed the monophyly of most genera, except for Amelanchier, Malus, Sorbus sensu lato, and Stranvaesia. In addition, we present a comprehensive taxonomic synopsis of Photinia and its morphological allies in the Old World, recognizing 27 species and ten varieties within Photinia, three species and two varieties within Stranvaesia, and two species and three varieties within Weniomeles. Furthermore, we also lectotypified 12 names and made two new combinations, Photinia microphylla (J.E.Vidal) B.B.Liu and Weniomeles atropurpurea (P.L.Chiu ex Z.H.Chen &amp; X.F.Jin) B.B.Liu.

A Novel View on the Taxonomy of Sulfate-Reducing Bacterium 'Desulfotomaculum salinum' and a Description of a New Species Desulfofundulus salinus sp. nov.

Two thermophilic spore-forming sulfate-reducing strains, 435T and 781, were isolated from oil and gas reservoirs in Western Siberia (Russia) about 50 years ago. Both strains were found to be neutrophilic, chemoorganotrophic, anaerobic bacteria, growing at 45-70 °C (optimum, 55-60 °C) and with 0-4.5% (w/v) NaCl (optimum, 0.5-1% NaCl). The major fatty acids were iso-C15:0, iso-C17:0, C16:0, and C18:0. In sulfate-reducing conditions, the strains utilized H2/CO2, formate, lactate, pyruvate, malate, fumarate, succinate, methanol, ethanol, propanol, butanol, butyrate, valerate, and palmitate. In 2005, based on phenotypic characteristics and a 16S rRNA gene sequence analysis, the strains were described as 'Desulfotomaculum salinum' sp. nov. However, this species was not validly published because the type strain was not deposited in two culture collections. In this study, a genomic analysis of strain 435T was carried out to determine its taxonomic affiliation. The genome size of strain 435T was 2.886 Mb with a 55.1% genomic G + C content. The average nucleotide identity and digital DNA-DNA hybridization values were highest between strain 435T and members of the genus Desulfofundulus, 78.7-93.3% and 25.0-52.2%, respectively; these values were below the species delineation cut-offs (<95-96% and <70%). The cumulative phenotypic and phylogenetic data indicate that two strains represent a novel species within the genus Desulfofundulus, for which the name Desulfofundulus salinus sp. nov. is proposed. The type strain is 435T (=VKM B-1492T = DSM 23196T). A genome analysis of strain 435T revealed the genes for dissimilatory sulfate reduction, autotrophic carbon fixation via the Wood-Ljungdahl pathway, hydrogen utilization, methanol and organic acids metabolism, and sporulation, which were confirmed by cultivation studies.

Climatic niche evolution and niche conservatism of Nymphaea species in Africa, South America, and Australia

BackgroundInterest in the evolution of climatic niches, particularly in understanding the potential adaptive responses of species under climate change, has increased both theoretically and within macroecological studies. These studies have provided valuable insights into how climatic traits of species influence their niche evolution. In this study, we aim to investigate whether niche conservatism plays a role in the species diversification of Nymphaea, a group of aquatic plants with a cosmopolitan distribution that is facing severe habitat loss. We will use climatic models and phylogenetic data for 23 species to reconstruct Nymphaea’s niche evolution, measure niche overlap, and assess disparity through time while testing for evolutionary models.ResultsThere was a lot of overlap in niches both within and between groups, especially for species that can be found in many places. The breadth and peaks of the niche profile varied depending on the bioclimatic variables, which suggested that the species evolved differently to cope with changes in climate. The analysis also showed that evolutionary changes happened across the phylogeny, with weak to moderate signals. The morphological disparity index (MDI) values indicated that there were disparities within subclades over time but not between or among them. Niche reconstruction and evolution analysis revealed both convergent and divergent evolution among various variables. For example, N. immutabilis, N. atrans, N. violancea, and N. nouchali evolved towards intermediate temperatures for bio2 and bio3 (isothermity) while moving towards extreme temperatures for bio8 and bio9 (wettest and driest average quarterly temperatures).ConclusionOur study will improve our understanding of how changes in climatic niches are potentially driving the evolution of Nymphaea. It has significant scientific implications for the limits, assemblages, evolution, and diversification of species. This information is crucial for the ongoing efforts of conservation and management, particularly considering the inevitable effects of climate change.

Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov., two novel actinobacteria isolated from mangrove sediments and leaves of halophyte Sesuvium portulacastrum in Thailand.

A polyphasic approach was used to characterize two novel actinobacterial strains, designated PKS22-38T and LSe1-13T, which were isolated from mangrove soils and leaves of halophyte Sesuvium portulacastrum (L.), respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that they belonged to the genus Gordonia and were most closely related to three validly published species with similarities ranging from 98.6 to 98.1 %. The genomic DNA G+C contents of strains PKS22-38T and LSe1-13T were 67.3 and 67.2 mol%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 93.3 and 54.9 %, respectively, revealing that they are independent species. Meanwhile, the ANI and dDDH values between the two novel strains and closely related type strains were below 80.5 and 24.0 %, respectively. Strains PKS22-38T and LSe1-13T contained C16 : 0, C18 : 1 ω9c and C18 : 0 10-methyl (TBSA) as the major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as the main phospholipids. The predominant menaquinone was MK-9(H2). Based on phenotypic, chemotaxonomic, phylogenetic and genomic data, strains PKS22-38T and LSe1-13T are considered to represent two novel species within the genus Gordonia, for which the names Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov. are proposed, with strain PKS22-38T (=TBRC 17540T=NBRC 116256T) and strain LSe1-13T (=TBRC 17706T=NBRC 116396T) as the type strains, respectively.

Deinococcus arenicola sp. nov., a novel radiation-resistant bacterium isolated from sandy soil in Antarctica.

A Gram-stain-positive, aerobic, non-mobile and spherical strain, designated ZS9-10T, belonging to the genus Deinococcus was isolated from soil sampled at the Chinese Zhong Shan Station, Antarctica. Growth was observed in the presence of 0-4 % (w/v) NaCl, at pH 7.0-8.0 and at 4-25 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZS9-10T formed a lineage in the genus Deinococcus. It exhibited highest sequence similarity (97.4 %) to Deinococcus marmoris DSM 12784T. The major phospholipids of ZS9-10T were unidentified phosphoglycolipid, unidentified glycolipids and unidentified lipids. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C16 : 1 ω7c. MK-8 was the predominant respiratory quinone. The digital DNA-DNA hybridization and average nucleotide identity values between strain ZS9-10T and its close relative D. marmoris DSM 12784T were 27.4 and 83.9 %, respectively. Based on phenotypic, phylogenetic and genotypic data, a novel species, named Deinococcus arenicola sp. nov., is proposed. The type strain iis ZS9-10T (=CCTCC AB 2019392T=KCTC43192T).

New species of Argythamnia (Euphorbiaceae) restricted to Seasonal Forest of Brazil, with morphological and phylogenetic support

Argythamnia (Acalyphoideae, Euphorbiaceae) is a monophyletic genus with approximately 70 species exclusive to the New World, distributed from the southern United States to Patagonia. The greatest diversity of the genus occurs in southern North America, Central America and the Caribbean. The distribution of the genus is strongly related to seasonally dry vegetation, mainly in Seasonally Dry Tropical Forests and Woodlands in the Neotropics. Based on morphological and phylogenetic data, here we describe the eleventh species of the genus for Brazil and the fourth for the state of Bahia, where the greatest diversity of the genus in the country is concentrated. We present a description, distribution map, illustration, table with the main diagnostic characters, preliminary conservation status, palynological data, as well as the phylogenetic position for the new species.

Catenovulum adriaticum sp. nov., isolated from algae in the harbour of Susak, Croatia.

The use of algae as feedstock for industrial purposes, such as in bioethanol production, is desirable. During a search for new agarolytic marine bacteria, a novel Gram-stain-negative, strictly aerobic, and agarolytic bacterium, designated as TS8T, was isolated from algae in the harbour of the island of Susak, Croatia. The cells were rod-shaped and motile. The G+C content of the sequenced genome was 38.6 mol%. Growth was observed at 11-37 °C, with 0.5-13 % (w/v) NaCl, and at pH 6.0-9.0. The main fatty acids were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), and C16 : 0. The main respiratory quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Analysis of 16S rRNA gene sequences indicated that the newly isolated strain belongs to the genus Catenovulum. Based on 16S rRNA gene sequence data, strain TS8T is closely related to Catenovulum sediminis D2T (95.7 %), Catenovulum agarivorans YM01T (95.0 %), and Catenovulum maritimum Q1T (93.2 %). Digital DNA-DNA hybridization values between TS8T and the other Catenovulum strains were below 25 %. Based on genotypic, phenotypic, and phylogenetic data, strain TS8T represents a new species of the genus Catenovulum, for which the name Catenovulum adriaticum sp. nov. is proposed. The type strain is TS8T (=DSM 114830T=NCIMB 15451T).

Shewanella phaeophyticola sp. nov. and Vibrio algarum sp. nov., isolated from marine brown algae.

Two Gram-stain-negative, rod-shaped bacteria, designated as strains KJ10-1T and KJ40-1T, were isolated from marine brown algae. Both strains were catalase-positive, oxidase-positive, and facultative aerobic. Strain KJ10-1T exhibited optimal growth at 25 °C, pH 7.0, and 3 % NaCl, whereas strain KJ40-1T showed optimal growth at 25 °C, pH 7.0, and 2 % NaCl. The respiratory quinones of strain KJ10-1T were ubiquinone-8, ubiquinone-7, menaquinone-7, and methylated menaquinone-7, while the respiratory quinone of strain KJ40-1T was only ubiquinone-8. As major fatty acids, strain KJ10-1T contained C16 : 0, C17 : 1 ω8c, iso-C15 : 0, and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and strain KJ40-1T contained C16 : 0 and summed features 3 and 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids in strain KJ10-1T were phosphatidylethanolamine, phosphatidylglycerol, and an unidentified aminolipid, whereas those in strain KJ40-1T were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The DNA G+C contents of strains KJ10-1T and KJ40-1T were 42.1 and 40.8 mol%, respectively. Based on 16S rRNA gene sequences, strains KJ10-1T and KJ40-1T exhibited the closest relatedness to Shewanella saliphila MMS16-UL250T (98.6 %) and Vibrio rumoiensis S-1T (95.4 %), respectively. Phylogenetic analyses, based on both 16S rRNA and 92 housekeeping genes, showed that the strains formed distinct phylogenic lineages within the genera Shewanella and Vibrio. Digital DNA-DNA hybridization and orthologous average nucleotide identity values between strain KJ10-1T and other Shewanella species, as well as between strain KJ40-1T and other Vibrio species, were below the thresholds commonly accepted for prokaryotic species delineation. Based on the phenotypic, chemotaxonomic, and phylogenetic data, strains KJ10-1T and KJ40-1T represent novel species of the genera Shewanella and Vibrio, respectively, for which the names Shewanella phaeophyticola sp. nov. and Vibrio algarum sp. nov. are proposed, respectively. The type strains of S. phaeophyticola and V. algarum are KJ10-1T (=KACC 22589T=JCM 35409T) and KJ40-1T (=KACC 22588T=JCM 35410T), respectively.