Phylogenetic Lineages Research Articles

Resolving the Sticta fuliginosa Morphodeme (Lichenized Ascomycota: Peltigeraceae) in Northwestern North America

Sticta is a subcosmopolitan, predominantly epiphytic lichenizing fungal genus characteristic of open sites in humid late-successional ecosystems. Recent molecular analysis has shown that the laminally isidiate species S. fuliginosa, long assumed to be well delimited, encompasses >20 phylospecies which, taken together, constitute the S. fuliginosa morphodeme. Here we elucidate the northwestern North American members of this morphodeme based on a rich sampling from throughout the Pacific Northwest regions of the U.S.A. and Canada: Alaska, British Columbia, California, Oregon and Washington. Our results support recognition of five species, three of which – S. arenosella sp. nov., S. fasciculata sp. nov. and S. torii – appear to be endemic. Of the remainder, S. globulifuliginosa was described from Colombia, while S. gretae sp. nov. occurs also in the Canary Islands and China. Two of our new species – S. fasciculata and S. gretae comprise a new phylogenetic lineage and is referred to as the S. gretae clade. New taxonomically informative thallus characters are introduced and a key to the genus Sticta in northwest North America is provided.

Timescale for the Kasimovian Stage

Abstract The Kasimovian Stage is the lower stage of the Upper Pennsylvanian Subsystem, in which a series of considerable biotic and abiotic events happened and changed the Earth. The Variscan orogeny and the Late Paleozoic Glaciation are two major events that caused geographical isolation of marine faunas and difficulties for a global correlation of biostratigraphy. Regional timescales of the Kasimovian across major continents are reviewed here. A global correlation of the Kasimovian is tentatively established based on a detailed review of major fossil groups such as conodonts, fusulines and some macrofossils. The index taxon for the base of the Kasimovian Stage has not been selected. The conodont species Swadelina subexcelsa , Idiognathodus heckeli , I. turbatus and I. sagittalis have good potential. Among them, I . heckeli is considered the best marker for the base of the Kasimovian Stage because it can mark a bioevent in a wide geographical range, and more importantly, it has a clear taxonomic definition within a phylogenetic lineage. The fusuline Montiparus might be regarded as an auxiliary marker to define the base of the Kasimovian based on its wider distribution. Other proxies, i.e. isotopic dating and strontium, carbon and oxygen isotopic stratigraphy throughout the Kasimovian, are also reviewed. The Global Boundary Stratotype Section and Point (GSSP) candidates for the Kasimovian Stage include the Naqing section, South China, the Usolka section, South Urals and the Afanasievo section, Moscow Basin. The Naqing section is regarded as the most appropriate GSSP candidate in terms of its complete sedimentary succession, well-recorded conodont lineages and well-studied bio-, chemo- and cyclo-stratigraphy.

Physicochemical determinants and mechanisms of the hard‐to‐cook problem of Senegalia seeds, overlooked wild legumes in the arid tropics

SummaryThis study was carried out to elucidate the factors responsible for the hard‐to‐cook problem of Senegalia seeds, overlooked wild legumes in the arid tropics. Accordingly, they were identified as medium size (diameter = 7–9 mm and weight = 60–100 mg), flattened (thickness = 1.5–2.5 mm), and wax‐coated seeds, demonstrating high and variable coat fractions (25–41), mucilage (15–39), lignin (2.2–4.9), cellulose (6.7–13), and hemicellulose (1.9–5.6) contents (g/100 g dry weight), cooking times (3–5 h), and hydration properties. The hard‐to‐cook problem was primarily associated with the seed coats' microstructures and chemical compositions (i.e., cellular layers and fibre compositions). Besides, sodium bicarbonate (common cooking aid) helped half the cooking times but failed to overcome the toughness of the seed coats. Furthermore, unfortunately, there was no clear association between the seeds' cooking properties and phylogenetic lineages, indicating that each species should be assessed individually. This work provides unprecedented insights that will considerably assist in selecting, formulating, and promoting food products from Senegalia seeds.

Comprehensive Comparative Analysis Sheds Light on the Patterns of Microsatellite Distribution across Birds Based on the Chromosome-Level Genomes.

Microsatellites (SSRs) are widely distributed in the genomes of organisms and are an important genetic basis for genome evolution and phenotypic adaptation. Although the distribution patterns of microsatellites have been investigated in many phylogenetic lineages, they remain unclear within the morphologically and physiologically diverse avian clades. Here, based on high-quality chromosome-level genomes, we examined the microsatellite distribution patterns for 53 birds from 16 orders. The results demonstrated that each type of SSR had the same ratio between taxa. For example, the frequency of imperfect SSRs (I-SSRs) was 69.90-84.61%, while perfect SSRs (P-SSRs) were 14.86-28.13% and compound SSRs (C-SSRs) were 0.39-2.24%. Mononucleotide SSRs were dominant for perfect SSRs (32.66-76.48%) in most bird species (98.11%), and A(n) was the most abundant repeat motifs of P-SSRs in all birds (5.42-68.22%). Our study further confirmed that the abundance and diversity of microsatellites were less effected by evolutionary history but its length. The number of P-SSRs decreased with increasing repeat times, and longer P-SSRs motifs had a higher variability coefficient of the repeat copy number and lower diversity, indicating that longer motifs tended to have more stable preferences in avian genomes. We also found that P-SSRs were mainly distributed at the gene ends, and the functional annotation for these genes demonstrated that they were related to signal transduction and cellular process. In conclusion, our research provided avian SSR distribution patterns, which will help to explore the genetic basis for phenotypic diversity in birds.

Long-Term Persistence of <i>Yersinia pestis</i> in Association with Acanthamoeba castellanii in Experiment

The aim of the study was to test the feasibility of long-term survival and preservation of the properties of Yersinia pestis in association with soil amoeba Acanthamoeba castellanii. Materials and methods. Y. pestis strains and acanthamoeba isolated in the common area of the Gorno-Altai high-mountain plague focus were used for the study. The systematic affiliation of protozoa was determined through analyzing the 18S rRNA gene fragment sequencing data, followed by alignment with amoeba sequences from the NCBI GenBank database. A fluorescent Y. pestis strain was obtained by electroporation using the pTurboGFP-B plasmid. Co-cultivation was carried out in saline buffer in the absence of nutrients for the cells of plague pathogen. The influence of co-culturing with protozoa on Y. pestis properties was determined using microbiological, biological, and molecular-genetic methods. Results and discussion. The cell viability preservation for 22 months of the experiment in Y. pestis strain belonging to the main subspecies of the antique biovar, the 4.ANT phylogenetic line in co-culture with amoeba cells in the absence of additional nutrients has been established. Co-cultivation with amoebae did not lead to a change in the cultural, morphological, genetic and virulent properties of the plague pathogen strain. The data obtained confirm the possibility of using Acanthamoeba castellanii by the plague microbe to persist in soil biocenoses and open up the prospect of studying the mechanisms of plague pathogen surviving during extended inter-epizootic periods.

Variability of <i>pgm</i>‑Region Genes in <i>Yersinia pestis</i> Strains from the Caspian Sandy and Adjacent Plague Foci

The aim of the study was to compare the nucleotide sequences of pgm‑region genes in Yersinia pestis strains isolated on the territory of the Caspian sandy and adjacent plague foci in 1925–2015. Materials and methods. 65 Y. pestis strains from the Caspian sandy and adjacent plague foci were used in the work. DNA isolation was performed using the PureLink Genomic DNA Mini Kit. Whole genome sequencing was conducted in Ion S5 XL System (Thermo Fischer Scientific). Data processing was carried out using Ion Torrent Suite software package 3.4.2 and NewblerGS Assembler 2.6. To compare the obtained sequences with the NCBI GenBank database, the Blast algorithm was used. The phylogenetic analysis was performed according to the data of whole genome SNP analysis based on 1183 identified SNPs. The search for marker SNPs was performed using the Snippy 4.6 program. The phylogenetic tree was constructed using the Maximum Likelihood algorithm, the GTR nucleotide substitution model. Results and discussion. The nucleotide sequences of pgm‑region genes of 65 Y. pestis strains from the Caspian sandy and adjacent plague foci have been assessed. Single nucleotide substitutions have been identified in Y. pestis strains from the Caspian sandy and Kobystan plain-foothill foci in the hmsR, astB, ybtS, ypo1944, ypo1943, ypo1936 genes, as well as a deletion of 5 bp in the ypo1945 gene, which is characteristic of strains of one of the phylogenetic lines of Y. pestis from the foci of Caucasus and Transcaucasia, isolated in 1968–2001. The data obtained can be used to differentiate Y. pestis strains from the Caspian sandy focus, as well as to establish the directions of microevolution of the plague pathogen in this region and adjacent foci.

Standing genetic variation as a potential mechanism of novel cave phenotype evolution in the freshwater isopod, Asellus aquaticus.

Novel phenotypes can come about through a variety of mechanisms including standing genetic variation from a founding population. Cave animals are an excellent system in which to study the evolution of novel phenotypes such as loss of pigmentation and eyes. Asellus aquaticus is a freshwater isopod crustacean found in Europe and has both a surface and a cave ecomorph which vary in multiple phenotypic traits. An orange eye phenotype was previously revealed by F2 crosses and backcrosses to the cave parent within two examined Slovenian cave populations. Complete loss of pigmentation, both in eye and body, is epistatic to the orange eye phenotype and therefore the orange eye phenotype is hidden within the cave populations. Our goal was to investigate the origin of the orange eye alleles within the Slovenian cave populations by examining A. aquaticus individuals from Slovenian and Romanian surface populations and Asellus aquaticus infernus individuals from a Romanian cave population. We found orange eye individuals present in lab raised surface populations of A. aquaticus from both Slovenia and Romania. Using a mapping approach with crosses between individuals of two surface populations, we found that the region known to be responsible for the orange eye phenotype within the two previously examined Slovenian cave populations was also responsible within both the Slovenian and the Romanian surface populations. Complementation crosses between orange eye Slovenian and orange eye Romanian surface individuals suggest that the same gene is responsible for the orange eye phenotype in both surface populations. Additionally, we observed a low frequency phenotype of eye loss in crosses generated between the two surface populations and also in the Romanian surface population. Finally, in a cave population from Romania, A. aquaticus infernus, we found that the same region is also responsible for the orange eye phenotype as the Slovenian cave populations and the Slovenian and Romanian surface populations. Therefore, we present evidence that variation present in the cave populations could originate from standing variation present in the surface populations and/or transgressive hybridization of different surface phylogenetic lineages rather than de novo mutations.

Evolutionary Dynamics of Avian Influenza Viruses Isolated from Wild Birds in Moscow.

Forty-five strains of AIVs were isolated from wild aquatic birds during their autumn migration through Moscow (Russia). The aim of this work is to study the dynamics of AIV genomes in their natural habitat. Viruses were isolated from fecal sample in embryonated chicken eggs; their complete genomes were sequenced, and a phylogenetic analysis was performed. The gene segments of the same lineage persisted over the years in the absence of persistence of complete viral genomes. The genes for internal proteins of the same lineage were often maintained by the viruses over few years; however, they were typically associated with the genes of novel HA and NA subtypes. Although frequent reassortment events were observed for any pair of internal genes, there was no reassortment between HA and NA segments. The differences in the persistence of phylogenetic lineages of surface and internal proteins and the different evolutionary strategy for these two types of genes of AIVs in primary hosts are discussed.

Modulation of Mechanical Properties of Short Bioinspired Peptide Materials by Single Amino-Acid Mutations.

The occurrence of modular peptide repeats in load-bearing (structural) proteins is common in nature, with distinctive peptide sequences that often remain conserved across different phylogenetic lineages. These highly conserved peptide sequences endow specific mechanical properties to the material, such as toughness or elasticity. Here, using bioinformatic tools and phylogenetic analysis, we have identified the GX8 peptide with the sequence GLYGGYGX (where X can be any residue) in a wide range of organisms. By simple mutation of the X residue, we demonstrate that GX8 can be self-assembled into various supramolecular structures, exhibiting vastly different physicochemical and viscoelastic properties, from liquid-like coacervate microdroplets to hydrogels to stiff solid materials. A combination of spectroscopic, electron microscopy, mechanical, and molecular dynamics studies is employed to obtain insights into molecular scale interactions driving self-assembly of GX8 peptides, underscoring that π-π stacking and hydrophobic interactions are the drivers of peptide self-assembly, whereas the X residue determines the extent of hydrogen bonding that regulates the macroscopic mechanical response. This study highlights the ability of single amino-acid polymorphism to tune the supramolecular assembly and bulk material properties of GX8 peptides, enabling us to cover a broad range of potential biomedical applications such as hydrogels for tissue engineering or coacervates for drug delivery.

A Revision of the Rhinolophus hipposideros group (Chiroptera: Rhinolophidae) with Definition of an Additional Species from the Middle East

Initially, the Rhinolophus hipposideros group was defined by two morphological traits, the structure of the nose-leaf and the shape of basioccipital bone of the skull. Originally, it consisted of two species, R. hipposideros and R. midas, whereas currently it is considered to contain a single species, R. hipposideros, under whose rank both original species have been joined. The interpretation of geographic variability within the group has traditionally been based on variation in body and skull size, nose-leaf shape, and several selected skull and tooth characters. This approach resulted in delimitations of up to seven subspecies, mostly in the Mediterranean area, a conception introduced more than a hundred years ago and accepted by many authors till today. We investigated the phylogenetic relationships among populations of R. hipposideros with the help of molecular genetic, morphological, and acoustic examinations. Our analysis uncovered the existence of an unexpected diversity within the R. hipposideros group, challenging its current phylogenetic and taxonomic arrangements. The molecular genetic analysis of almost 100 samples and morphological examinations of about 300 specimens showed two main, geographically exclusive, phylogenetic lineages within the group, well delimited by molecular characteristics and possessing two distinct morphotypes and two distinct echotypes. These two lineages are isolated deep enough to be considered separate species. One of them, R. hipposideros s.str., is widespread over the south-western Eurasia and north-western and north-eastern Africa, and the other, R. midas, is distributed in a small range around the Strait of Hormuz and Gulf of Oman. The extensive range of R. hipposideros s.str. is inhabited at least by two subspecies, separated mainly by the genetic characters, whereas the morphological and echolocation traits do not distinguish the populations sufficiently. The western R. h. hipposideros occurs in the Maghreb and Europe west of the Dnieper River, Bosporus, and the Strait of Karpathos, and the eastern R. h. minimus lives east of this boundary, including the populations of Crimea, Caucasus, the Middle East, and north-eastern Africa (Sudan to Djibouti). The two subspecies also differ in karyotype, with 2n = 58 in R. h. minimus and 2n = 54–56 in R. h. hipposideros. The taxonomic position of the easternmost populations of R. hipposideros s.str. (West Turkestan, Afghanistan, Kashmir) remains unresolved and has to be investigated more elaborately and using a more extensive sample set.

Diversity and molecular mechanisms of channelrhodopsins.

Channelrhodopsins (ChRs) are light-gated channels that guide phototaxis in eukaryotic microorganisms and are widely used as molecular tools to control cell membrane potential with light (optogenetics). Expression of ChR genes in neurons and cardiomyocytes enables photoactivation or photoinhibition of these cells’ activity with submillisecond precision. Recent advances in polynucleotide sequencing have led to identification of hundreds of ChR homologs in many phylogenetic lineages, but only a few have been characterized functionally. ChRs differ in their ionic selectivity, spectral sensitivity, and photocurrent kinetics and thus provide an exceptional platform for the study of structure-function relationships in membrane proteins. Current evidence suggests that ion channel function has evolved within the superfamily of microbial rhodopsins by several convergent routes. Our laboratory has discovered natural ChR variant families with major different biophysical properties, and we are studying their photochemical mechanisms by atomic structure determination, electrophysiology, kinetic spectroscopy, and structure/function analysis by mutagenesis. Also, we apply molecular engineering to improve their biophysical properties to suit practical needs of optogenetics. Recently we identified potassium-selective ChRs in non-photosynthetic stramenopile and alveolate microbes and demonstrated the utility of these molecules as inhibitory optogenetic tools. These proteins are promising for research and potentially for treatment of potassium channelopathies such as epilepsy, Parkinson's disease, and cardiac arrhythmias.

Keeping alert to the hypervirulent K1, K2, K3, K5, K54 and K57 strains of Klebsiella pneumoniae within dairy production process

Klebsiella pneumoniae (Kp) is now recognized as an urgent threat to public health since the emergence of multidrug-resistant and hypervirulent isolates. We identified a hypervirulent K2 isolate from the milk samples possibly associated with an infection incident in children, which raised the alarm to the zoonotic potential of bovine mastitis Kp as a foodborne pathogen. Subsequently, numerous K1, K2, K3, K5, K54 and K57 strains were identified from mastitis milk samples, and showed high pathogenicity in infected mouse. Further analysis based on complete genomes found that these isolates showed closely evolutionary relationships with the human hypervirulent strains in diverse phylogenetic lineages, suggesting their potential risk to public health.

Combination of growth conditions and InlB-specific dot-immunoassay for rapid detection of Listeria monocytogenes in raw milk

The gram-positive bacterium Listeria monocytogenes is an important foodborne pathogen contaminating dairy products. Closely related to L. monocytogenes saprophytic Listeria spp. are also frequent contaminators of food and, particularly, dairy products. To distinguish L. monocytogenes from nonpathogenic Listeria spp. and other bacteria, a dot-immunoassay was developed. The immunoassay is based on the polyclonal antibody to the secreted form of the surface virulence-associated L. monocytogenes-specific InlB protein. To increase InlB production, bacteria were grown on the brain-heart infusion agar supplemented with 0.2% activated charcoal (BHIC agar). Direct plating of artificially contaminated raw milk samples on the BHIC agar followed by the dot-immunoassay allowed a rapid identification of L. monocytogenes in concentrations as little as 10 cfu/mL. Using the developed approach, preliminary results were obtained within 14 h, and the final results were obtained after 26 h. The dot-immunoassay was tested on L. monocytogenes strains belonging to different clonal complexes and phylogenetic lineages, Listeria spp., and other bacterial species. Results showed the exceptional specificity of the developed dot-immunoassay for the rapid identification of L. monocytogenes.

Emergence of Antifungal Resistant Subclades in the Global Predominant Phylogenetic Population of Candida albicans.

Candida albicans remains the most common species causing invasive candidiasis. In this study, we present the population structure of 551 global C. albicans strains. Of these, the antifungal susceptibilities of 370 strains were tested. Specifically, 66.6% of the azole-nonsusceptible (NS)/non-wild-type (NWT) strains that were tested belonged to Clade 1. A phylogenetic analysis, a principal components analysis, the population structure, and a loss of heterozygosity events revealed two nested subclades in Clade 1, namely, Clade 1-R and Clade 1-R-α, that exhibited higher azole-NS/NWT rates (75.0% and 100%, respectively). In contrast, 6.4% (21/326) of the non-Clade 1-R isolates were NS/NWT to at least 1 of 4 azoles. Notably, all of the Clade 1-R-α isolates were pan-azole-NS/NWT that carried unique A114S and Y257H double substitutions in Erg11p and had the overexpression of ABC-type efflux pumps introduced by the substitution A736V in transcript factor Tac1p. It is worth noting that the Clade 1-R and Clade 1-R-α isolates were from different cities that are distributed over a large geographic span. Our study demonstrated the presence of specific phylogenetic subclades that are associated with antifungal resistance among C. albicans Clade 1, which calls for public attention on the monitoring of the future spread of these clones. IMPORTANCE Invasive candidiasis is the most common human fungal disease among hospitalized patients, and Candida albicans is the predominant pathogen. Considering the large number of infected cases and the limited alternative therapies, the azole-resistance of C. albicans brings a huge clinical threat. Here, our study suggested that antifungal resistance in C. albicans could also be associated with phylogenetic lineages. Specifically, it was revealed that more than half of the azole-resistant C. albicans strains belonged to the same clade. Furthermore, two nested subclades of the clade exhibited extremely high azole-resistance. It is worth noting that the isolates of two subclades were from different cities that are distributed over a large geographic span in China. This indicates that the azole-resistant C. albicans subclades may develop into serious public health concerns.

The Contact Zone of Phylogenetic Lineages of Freshwater Fish in Arctic Eurasia: Genetic Polymorphism of Coregonid Populations

The reconstruction of regional fauna history is very important in the context of recent climate change and anthropogenic transformation. We analyzed the mitochondrial nd1 gene polymorphism in populations of whitefish Coregonus lavaretus and certain widespread Eurasian ciscoes species: vendace Coregonus albula and least cisco Coregonus sardinella, inhabiting waterbodies from the Anadyr River in the east (the Pacific Ocean basin) to Loch Lomond in the west (the Atlantic Ocean basin). Distinct phylogenetic lineages and secondary contact zones have been found in these species. Most of these are species-specific with the exception of the zone from the Pechora River basin to at least the western part of the Taymyr Peninsula, in which whitefish, vendace, and least cisco share with each other and with various cold-water hydrobionts. We associate differences in the geographical position and propagation of the secondary contact regions with the species-specific morpho-ecological features, in particular, with the ability for long-term migrations. Based on the data obtained, we also discuss certain limitations of the phylogeography and phylogeny of the considered coregonid species and the correctness of the taxonomic status of certain populations or their groups.

Genomic analysis of an ultrasmall freshwater green alga, Medakamo hakoo

Ultrasmall algae have attracted the attention of biologists investigating the basic mechanisms underlying living systems. Their potential as effective organisms for producing useful substances is also of interest in bioindustry. Although genomic information is indispensable for elucidating metabolism and promoting molecular breeding, many ultrasmall algae remain genetically uncharacterized. Here, we present the nuclear genome sequence of an ultrasmall green alga of freshwater habitats, Medakamo hakoo. Evolutionary analyses suggest that this species belongs to a new genus within the class Trebouxiophyceae. Sequencing analyses revealed that its genome, comprising 15.8 Mbp and 7629 genes, is among the smallest known genomes in the Viridiplantae. Its genome has relatively few genes associated with genetic information processing, basal transcription factors, and RNA transport. Comparative analyses revealed that 1263 orthogroups were shared among 15 ultrasmall algae from distinct phylogenetic lineages. The shared gene sets will enable identification of genes essential for algal metabolism and cellular functions.

Comparative analysis of allergenicity and predicted linear epitopes in α and β parvalbumin from turbot (Scophthalmus maximus).

Parvalbumin (PV) can be subdivided into two phylogenetic lineages, αPV and βPV. The bony fish βPV is considered a major fish allergen. However, there is no available report on the immunological property and epitope mapping of bony fish αPV. To characterize the allergenic property of bony fish αPV and investigate the difference in allergenic property of bony fish αPV and βPV, turbot (Scophthalmus maximus) αPV and βPV were identified by mass spectrometry and were expressed in Escherichia coli system in this study. Spectra analysis and three-dimensional (3D) modeling showed the similar structure between αPV and βPV. However, αPV exhibited lower immunoglobulin E/immunoglobulin G (IgE/IgG) binding capacity than βPV. Three identified βPV epitopes possessed higher IgE reactivity and more hydrophobic residues than three identified αPV epitopes. In addition, less similarity in sequence homology of αPV epitopes was observed with allergen sequences in database. These finding expanded information on fish PV epitopes and substantiated the difference in allergenicity and epitope mapping between fish αPV and βPV, which will improve the epitope-based detection tools of PV and diagnostic of PV induced fish allergy. © 2023 Society of Chemical Industry.

Genomic epidemiology of Campylobacter fetus subsp. venerealis from Germany.

Campylobacter fetus subsp. venerealis (Cfv) causes bovine genital campylobacteriosis (BGC), a World Organization for Animal Health (WOAH)-listed trade-relevant disease characterized by severe reproductive losses, such as infertility, early embryonic death and abortion in cattle. BGC has significant economic implications that have prompted several countries to adopt stringent eradication and surveillance measures to contain the disease. In Germany, there has been a low incidence of BGC cases over the past 28 years. This study aimed to illustrate the genomic diversity of German Cfv strains isolated from different federal states in Germany. This study analyzed 63 Cfv strains, collected between 1985 and 2015, by whole-genome sequencing and compared them with genome data of 91 international Cfv isolates. The phylogenetic analysis showed that the Cfv population is genetically conserved and has geographic clusters. In Germany, one phylogenetic lineage comprising all strains was identified. This German lineage was part of a subclade that probably emerged in the nineteenth century and diversified over time. The results of this study point to a non-recurrent cross-border introduction of Cfv in Germany. The BGC control interventions in Germany can be considered successful as no outbreaks were reported since 2015.

Flavihumibacter fluminis sp. nov., a novel thermotolerant bacterium isolated from river silt.

A yellow, Gram-stain-positive, strictly aerobic, thermotolerant, non-motile and rod-shaped bacterial strain, designated RY-1T, was isolated from a silt sample of Fuyang River, Wuqiang County, Hengshui City, Hebei Province, PR China. Cells showed oxidase- and catalase-positive activities. Growth occurred at 20-45 °C (optimum, 37 °C) and pH 6.0-8.0 (optimum, pH 7.0), and in the presence of 0-1.5 % (w/v) NaCl (optimum, 0%). A phylogenetic tree based on 16S rRNA gene sequences revealed that strain RY-1T formed a phylogenetic lineage with Flavihumibacter members within the family Chitinophagaceae. A comparison of 16S rRNA gene sequences showed that strain RY-1T was most closely related to Flavihumibacter cheonanensis WS16T (98.6 %), Flavihumibacter sediminis CJ663T (97.7 %) and Flavihumibacter solisilvae 3-3T (97.6 %). The genome size of strain RY-1T was 4.71 Mb, and the DNA G+C content was 44.3 %. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between strain RY-1T and reference strains were all lower than the threshold values for species delineation. Strain RY-1T contained menaquinone-7 and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1G as the sole respiratory isoprenoid quinone and major cellular fatty acids (≥5 %), respectively. The major polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids and four unidentified lipids. According to the results of phenotypic, phylogenetic and chemotaxonomic characteristics, strain RY-1T represents a novel species of the genus Flavihumibacter, for which the name Flavihumibacter fluminis sp. nov. is proposed. The type strain is RY-1T (=GDMCC 1.2775T=JCM 34870T).

Heterogeneity in diagnostic characters across ecoregions: A case study with Botrynema (Hydrozoa: Trachylina: Halicreatidae)

IntroductionBotrynema, a genus of medusozoans in the trachyline family Halicreatidae, currently contains two species: B. brucei and B. ellinorae, distinguished by the presence or absence, respectively, of an apical knob as a diagnostic character. However, no study has corroborated if these taxonomic diagnoses have a biological and evolutionary basis. Therefore, in this study we attempted to address the question “do the two nominal species in the genus Botrynema represent independent phylogenetic lineages, or two phenotypic variants of a single species?MethodsIn this study we took advantage of legacy collections from different research expeditions across the globe from 2000 to 2021 to study the phylogenetics and taxonomy of the genus Botrynema.ResultsB. brucei and B. ellinorae present partially overlapping vertical distributions in the Arctic and as a whole in the Arctic the genus seems to be limited to the Atlantic water masses. The phylogenetic reconstruction based on the concatenated alignment corroborates the validity of the family Halicreatidae and of genus Botrynema as monophyletic groups. However no clear differentiation was found between the two presently accepted species, B. ellinorae and B. brucei.DiscussionBased on the evidence we gathered, we conclude that while the genus Botrynema does contain at least two species lineages, these lineages are not concordant with current species definitions. The species B. ellinorae is reassigned as a subspecies of B. brucei and diagnostic characters are provided.