From the Atlantic Coast to Lake Tanganyika: Gill-Infecting Flatworms of Freshwater Pellonuline Clupeid Fishes in West and Central Africa, with Description of Eleven New Species and Key to Kapentagyrus (Monogenea, Dactylogyridae)

Unlike their marine counterparts, tropical freshwater clupeids receive little scientific attention. However, they sustain important fisheries that may be of (inter)national commercial interest. Africa harbours over 20 freshwater clupeid species within Pellonulini. Recent research suggests their most abundant parasites are gill-infecting monogenean flatworms within Kapentagyrus. After inspecting specimens of 12 freshwater clupeids from West and Central Africa, mainly sourced in biodiversity collections, we propose 11 new species of Kapentagyrus, which we describe using their haptoral and genital morphology. Because of their high morphological similarity, species delineation relies mostly on the morphometrics of anchors and hooks. Specifically, earlier, molecular taxonomic work indicated that the proportion between the length of the anchor roots, and between the hook and anchor length, is diagnostic. On average, about one species of Kapentagyrus exists per pellonuline species, although Pellonula leonensis harbours four species and Microthrissa congica two, while Microthrissa moeruensis and Potamothrissa acutirostris share a gill monogenean species. This study more than quadruples the number of known species of Kapentagyrus, also almost quadrupling the number of pellonuline species of which monogeneans are known. Since members of Kapentagyrus are informative about their hosts’ ecology, evolutionary history, and introduction routes, this enables a parasitological perspective on several data-poor African fisheries.

Out with the old and in with the new: time to rethink twentieth century chemotaxonomic practices in bacterial taxonomy

Chemotaxonomic methods played an important role in the development of the polyphasic approach to classification of Archaea and Bacteria. However, we here argue that routine application of these methods is unnecessary in an era when genomic data are available and sufficient for species delineation. Thus, authors who choose not to utilize such methods should not be forced to do so during the peer review and editorial handling of manuscripts describing novel species. Instead, we argue that chemotaxonomy will thrive if improved analytical methods are introduced and deployed, primarily by specialist laboratories, in studies at taxonomic levels above the characterisation of novel species.

Comparative genomic study on the complete plastomes of four officinal Ardisia species in China

Ardisia Sw. (Primulaceae) is naturally distributed in tropical and subtropical areas. Most of them possess edible and medicinal values and are popular in clinical and daily use in China. However, ambiguous species delineation and genetic information limit the development and utilization of this genus. In this study, the chloroplast genomes of four Ardisia species, namely A. gigantifolia Stapf, A. crenata Sims, A. villosa Roxb. and A. mamillata Hance, were sequenced, annotated, and analyzed comparatively. All the four chloroplast genomes possess a typical quadripartite structure, and each of the genomes is about 156 Kb in size. The structure and gene content of the Ardisia plastomes were conservative and showed low sequence divergence. Furthermore, we identified five mutation hotspots as candidate DNA barcodes for Ardisia, namely, trnT-psbD, ndhF-rpl32, rpl32-ccsA, ccsA-ndhD and ycf1. Phylogenetic analysis based on the whole-chloroplast genomes data showed that Ardisia was sister to Tapeinosperma Hook. f. In addition, the results revealed a great topological profile of Ardisia’s with strong support values, which matches their geographical distribution patterns. Summarily, our results provide useful information for investigations on taxonomic differences, molecular identification, and phylogenetic relationships of Ardisia plants.

From the Atlantic Coast to Lake Tanganyika: Gill-Infecting Flatworms of Freshwater Pellonuline Clupeid Fishes in West and Central Africa, With Description of Eleven New Species and Key to Kapentagyrus (Monogenea, Dactylogyridae)

Unlike their marine counterparts, tropical freshwater clupeids receive little scientific attention. However, they sustain important fisheries that may be of (inter)national commercial interest. Africa harbours over 20 freshwater clupeid species within Pellonulini. Recent research suggests their most abundant parasites are gill-infecting monogenean flatworms within Kapentagyrus. After inspecting specimens of 12 freshwater clupeids from West and Central Africa, mainly sourced in biodiversity collections, we propose 11 new species of Kapentagyrus which we describe using their haptoral and genital morphology. Because of their high morphological similarity, species delineation relies mostly on morphometrics of anchors and hooks. Specifically, earlier, molecular taxonomic work indicated that the proportion between the length of the anchor roots, and between hook and anchor length, are diagnostic. On average, about one species of Kapentagyrus exists per pellonuline species, although Pellonula leonensis harbours four species and Microthrissa congica two, while Microthrissa moeruensis and Potamothrissa acutirostris share a gill monogenean species. This study more than quadruples the number of known species of Kapentagyrus, also almost quadrupling the number of pellonuline species of which monogeneans are known. Since members of Kapentagyrus are informative about their hosts’ ecology, evolutionary history, and introduction routes, this enables a parasitological perspective on several data-poor African fisheries.

Treponema peruense sp. nov., a commensal spirochaete isolated from human faeces

A Gram-stain-negative, obligatory anaerobic spirochaete (RCC2812T) was isolated from a faecal sample obtained from an individual residing in a remote Amazonian community in Peru. The bacterium showed highest 16S rRNA gene sequence similarity to the pig intestinal spirochete Treponema succinifaciens (89.48 %). Average nucleotide identity values between strain RCC2812T and all available Treponema genomes from validated type strains were all <73 %, thus clearly lower than the species delineation threshold. The DNA G+C content of RCC2812T was 41.24 mol%. Phenotypic characterization using the API-ZYM and API 20A systems confirmed the divergent position of this bacterium within the genus Treponema . Strain RCC2812T could be differentiated from the phylogenetically most closely related T. succinifaciens by the presence of alkaline phosphatase and α -glucosidase activities. Unlike T. succinifaciens , strain RCC2812T grew equally well with or without serum. Strain RCC2812T is the first commensal Treponema isolated from the human faecal microbiota of remote populations, and based on the collected data represents a novel Treponema species for which the name Treponema peruense sp. nov. is proposed. The type strain is RCC2812T (=LMG 31794T=CIP 111910T).

Genome-based reclassification of Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii as later heterotypic synonyms of Caldicellulosiruptor acetigenus

The present study was carried out to re-clarify the taxonomic relationship of Caldicellulosiruptor acetigenus , Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii . The 16S rRNA sequence similarities between these species of the genus Caldicellulosiruptor were above the threshold values (98.65%) for bacterial species delineation. Similarly, the digital DNA–DNA hybridization and average nucleotide and amino acid identity values were greater than the thresholds for bacterial species delineation. In phylogenetic (based on 16S rRNA gene sequences) and phylogenomic trees Caldicellulosiruptor acetigenus , Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii clade together. The results of our analysis indicated that these three taxa are conspecific. Therefore, Caldicellulosiruptor lactoaceticus Mladenovska et al. 1997 and Caldicellulosiruptor kristjanssonii Bredholt et al. 1999 should be reclassified as later heterotypic synonyms of Caldicellulosiruptor acetigenus (Nielsen et al. 1994) Onyenwoke et al. 2006.

Gemella massiliensis sp. nov., a new bacterium isolated from the human sputum

Thanks to its ability to isolate previously uncultured bacterial species, culturomics has dynamized the study of the human microbiota. A new bacterial species, Gemella massiliensis Marseille-P3249T, was isolated from a sputum sample of a healthy French man. Strain Marseille-P3249T is a facultative anaerobe, catalase-negative, Gram positive, coccus, and unable to sporulate. The major fatty acids were C16:0 (34%), C18:1n9 (28%), C18:0 (15%) and C18:2n6 (13%). Its 16S rRNA sequence exhibits a 98.3% sequence similarity with Gemella bergeri strain 617-93T, its phylogenetically closest species with standing in nomenclature. Its digital DNA–DNA hybridization (dDDH) and OrthoANI values with G. bergeri of only 59.7 ± 5.6% and 94.8%, respectively. These values are lower than the thresholds for species delineation (> 70% and > 95%, respectively). This strain grows optimally at 37 °C and its genome is 1.80 Mbp long with a 30.5 mol% G + C content. Based on these results, we propose the creation of the new species Gemella massilienis sp. nov., strain Marseille-P3249T (= CSUR P3249 = DSMZ 103940).

A Soft Spot for Chemistry–Current Taxonomic and Evolutionary Implications of Sponge Secondary Metabolite Distribution

Marine sponges are the most prolific marine sources for discovery of novel bioactive compounds. Sponge secondary metabolites are sought-after for their potential in pharmaceutical applications, and in the past, they were also used as taxonomic markers alongside the difficult and homoplasy-prone sponge morphology for species delineation (chemotaxonomy). The understanding of phylogenetic distribution and distinctiveness of metabolites to sponge lineages is pivotal to reveal pathways and evolution of compound production in sponges. This benefits the discovery rate and yield of bioprospecting for novel marine natural products by identifying lineages with high potential of being new sources of valuable sponge compounds. In this review, we summarize the current biochemical data on sponges and compare the metabolite distribution against a sponge phylogeny. We assess compound specificity to lineages, potential convergences, and suitability as diagnostic phylogenetic markers. Our study finds compound distribution corroborating current (molecular) phylogenetic hypotheses, which include yet unaccepted polyphyly of several demosponge orders and families. Likewise, several compounds and compound groups display a high degree of lineage specificity, which suggests homologous biosynthetic pathways among their taxa, which identifies yet unstudied species of this lineage as promising bioprospecting targets.

Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans

Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensi s DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA–DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans .