Pseudomonas guryensis sp. nov. and Pseudomonas ullengensis sp. nov., isolated from soil

Two Gram-staining-negative, aerobic, rod-shaped bacteria designated strains SR9T and UL070T, were isolated from soil and subjected to taxonomic characterization. Strain SR9T grew at 10–37 °C (optimum 30 °C), at pH 4.0–10.0 (optimum pH 8.0) and in the presence of 0–1 % NaCl (optimum 0 %), and UL070T at 4–33 °C (optimum 30 °C), at pH 4.0–10.0 (optimum pH 7.0) and in the presence of 0–2 % NaCl (optimum 0 %), respectively. Strain UL070T was motile with flagella. Analysis of 16S rRNA gene sequences indicated that the two strains fell into phylogenetic clusters belonging to the genus Pseudomonas . Both strains SR9T and UL070T were mostly related to Pseudomonas campi S1-A32-2T with 99.70 and 99.01% sequence similarities, and the similarity between the two isolates was 98.90 %. The genome-based in silico analyses indicated that each of the strains SR9T and UL070T was clearly separated from other species of Pseudomonas , as the orthologous average nucleotide identity (OrthoANI) and the digital DNA–DNA hybridization (dDDH) values were no higher than 93.09 and 50.03% respectively with any related species, which were clearly below the cutoff for species distinction. The fatty acid profiles of the two strains mainly consisting of unsaturated components, the presence of ubiquinone 9 (Q-9) as the major respiratory quinone, and phosphatidylethanolamine (PE) and diphosphatidylglycerol (DPG) as the diagnostic polar lipids were consistent with their classification into Pseudomonas . The DNA G+C contents of strains SR9T and UL070T were 63.2 mol% and 63.6 mol% respectively. On the basis of both phenotypic and phylogenetic evidences, each of the isolated strains should be classified as a novel species, for which the names Pseudomonas guryensis sp. nov. (type strain=SR9T=KCTC 82228T=JCM 34509T) and Pseudomonas ullengensis sp. nov. (type strain=UL070T=KCTC 82229T=JCM 34510T) are proposed.

Polyphasic taxonomic characterization of nine Penicillium species from soil of different parts of India

Aim: Morpho-molecular analyses for taxonomic characterization of nine predominant Penicillium species present in the soil of different parts of India. Methodology: Fifteen Penicillium isolates were isolated from the soil samples collected from the experimental field of ICAR-Indian Agricultural Research Institute (IARI), New Delhi. Another twenty-six isolates were procured from Indian Type Culture Collection (ITCC), Division of Plant Pathology, ICAR-IARI, New Delhi which were isolated from the soil of different parts of India. Total 41 isolates were characterized following distinct macroscopic (colony texture, colony colour exudate production; soluble pigmentation; reverse coloration and mycelial growth) and microscopic observations (type of penicillus; shape of phialides; conidial shape, size and pigmentation). Molecular characterization was done using partial β-tubulin gene sequence which is considered an excellent marker in differentiating Penicillium species. Results: The morphological data in species description perfectly matched with molecular data generated using β-tubulin gene marker and nine different species viz., P. aethiopicum, P. chrysogenum, P. crustosum, P. janthinellum, P. mononematosum, P. oxalicum, P. polonicum, P. singorense and Talaromyces pinophilus (Syn. P. pinophilum) were confirmed. Interpretation: Above nine Penicillium species are found predominantly in the soil collected from different parts of India. The β-tubulin gene can be considered as an excellent marker to differentiate Penicillium species as confirmed from this study. The combined morpho- molecular analyses can be further utilized to delineate morphologically similar Penicillium species and also helpful to establish new species of Penicillium.

Revised taxonomy and early evolution of fasciculiths at the Danian–Selandian transition

We present a taxonomic revision of the family Fasciculithaceae focused on forms that characterize the early evolution of this family group, which are currently included within the genera Gomphiolithus, Diantholitha, Lithoptychius and Fasciculithus. The investigation approach is based on a combined light microscope (LM) and scanning electron microscope (SEM) analysis of specimens from well-preserved ODP–DSDP site material (ODP Site 1209; Site 1262; ODP Site 1267; DSDP Site 356; DSDP Site 119) and outcrops (Bottaccione and Contessa, Italy; Qreiya, Egypt) across the Danian–Selandian transition. The direct LM–SEM comparison of the same individual specimen provides clarification of several taxa that were previously described only with the LM. One new genus (Tectulithus), five new combinations (Tectulithus janii, Tectulithus merloti, Tectulithus pileatus, Tectulithus stegastos and Tectulithus stonehengei) and six new species are defined (Diantholitha pilula, Diantholitha toquea, Lithoptychius galeottii, Lithoptychius maioranoae, Tectulithus pagodiformis and Fasciculithus realeae). The main characteristics useful to identify fasciculiths with the LM are provided, together with a 3D–2D drawing showing the main structural features. The accurate taxonomic characterization grants the development of an evolutionary lineage that documents a great fasciculith diversification during the late Danian and early Selandian. Four different well-constrained events have been documented: the lowest occurrence (LO) of Gomphiolithus, the paracme of Fasciculithaceae at the top of Chron C27r (PTC27r), the radiation of Diantholitha (LO Diantholitha), the paracme of Fasciculithaceae at the base of Chron C26r (PBC26r), the radiation of Lithoptychius (LO Lithoptychius) and the radiation of Tectulithus (lowest common occurrence of Tectulithus) that shows the biostratigraphic relevance of this group across the Danian–Selandian transition.

Anatomical Characteristics of African Cherry (Prunus Africana) Medicinal Plant for its Accurate Taxonomic Identification

Background: The genus Prunus (Family Rosaceae) comprises over 400 plant species and exhibits vast biodiversity worldwide. Due to its wide distribution, its taxonomic classification is important. Anatomical characters are conserved and stable and thus can be used as an important tool in plant taxonomic characterization. Thus, this study aimed at examining and documenting P. africana leaf, stem, and seed anatomy using micrographs and photographs for possible use in identification, quality control, and phylogenetic studies of the species.Methods: P. africana leaves, stems, and seeds were fixed, dehydrated in ascending ethanol series (50–100 %), embedded in Technovit resin, and sectioned using a microtome for mounting histological slides for anatomical observation under a microscope and subsequent description.Results: The anatomical sections of a young stem revealed a cortex consisting of isodiametric parenchyma cells, druse crystals, primary vascular bundles, and pith. The mature stem bark consisted majorly of rhytidome with periderm densely arranged in multiple layers, a cluster of stone cells, and sclerenchyma. The sections of the leaf were hypostomatic with stomata size ranging between 18.90– (22.34)–26.90 × 15.41– (18.40)–21.22 μm. The leaf sections showed the presence of characteristic druse crystals, vascular bundles, and mesophyll layers. The pericarp showed the presence of epicarp, mesocarp, and endocarp with a thickness of approximately 350–400, 300–350, and 30–50 μm, respectively and a seed testa with a thickness of approximately 50–60 μm. Conclusion: The characteristic morphological and anatomical features observed in P. africana leaves, stems, and seeds in this study could provide useful data in taxonomical identification of this species.

Comparative analysis of freshwater phytoplankton communities in two lakes of Burabay National Park using morphological and molecular approaches

We analyzed phytoplankton assemblages’ variations in oligo-mesotrophic Shchuchie and Burabay lakes using traditional morphological and next-generation sequencing (NGS) approaches. The total phytoplankton biodiversity and abundance estimated by both microscopy and NGS were significantly higher in Lake Burabay than in Lake Shchuchie. NGS of 16S and 18S rRNA amplicons adequately identify phytoplankton taxa only on the genera level, while species composition obtained by microscopic examination was significantly larger. The limitations of NGS analysis could be related to insufficient coverage of freshwater lakes phytoplankton by existing databases, short algal sequences available from current instrumentation, and high homology of chloroplast genes in eukaryotic cells. However, utilization of NGS, together with microscopy allowed us to perform a complete taxonomic characterization of phytoplankton lake communities including picocyanobacteria, often overlooked by traditional microscopy. We demonstrate the high potential of an integrated morphological and molecular approach in understanding the processes of organization in aquatic ecosystem assemblages.

Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition

Coral research is being ushered into the genomic era. To fully capitalize on the potential discoveries from this genomic revolution, the rapidly increasing number of high-quality genomes requires effective pairing with rigorous taxonomic characterizations of specimens and the contextualization of their ecological relevance. However, to date there is no formal framework that genomicists, taxonomists, and coral scientists can collectively use to systematically acquire and link these data. Spurred by the recently announced “Coral symbiosis sensitivity to environmental change hub” under the “Aquatic Symbiosis Genomics Project” - a collaboration between the Wellcome Sanger Institute and the Gordon and Betty Moore Foundation to generate gold-standard genome sequences for coral animal hosts and their associated Symbiodiniaceae microalgae (among the sequencing of many other symbiotic aquatic species) - we outline consensus guidelines to reconcile different types of data. The metaorganism nature of the coral holobiont provides a particular challenge in this context and is a key factor to consider for developing a framework to consolidate genomic, taxonomic, and ecological (meta)data. Ideally, genomic data should be accompanied by taxonomic references, i.e., skeletal vouchers as formal morphological references for corals and strain specimens in the case of microalgal and bacterial symbionts (cultured isolates). However, exhaustive taxonomic characterization of all coral holobiont member species is currently not feasible simply because we do not have a comprehensive understanding of all the organisms that constitute the coral holobiont. Nevertheless, guidelines on minimal, recommended, and ideal-case descriptions for the major coral holobiont constituents (coral animal, Symbiodiniaceae microalgae, and prokaryotes) will undoubtedly help in future referencing and will facilitate comparative studies. We hope that the guidelines outlined here, which we will adhere to as part of the Aquatic Symbiosis Genomics Project sub-hub focused on coral symbioses, will be useful to a broader community and their implementation will facilitate cross- and meta-data comparisons and analyses.

Seven Complete Chloroplast Genomes from Symplocos: Genome Organization and Comparative Analysis

In the present study, chloroplast genome sequences of four species of Symplocos (S. chinensis for. pilosa, S. prunifolia, S. coreana, and S. tanakana) from South Korea were obtained by Ion Torrent sequencing and compared with the sequences of three previously reported Symplocos chloroplast genomes from different species. The length of the Symplocos chloroplast genome ranged from 156,961 to 157,365 bp. Overall, 132 genes including 87 functional genes, 37 tRNA genes, and eight rRNA genes were identified in all Symplocos chloroplast genomes. The gene order and contents were highly similar across the seven species. The coding regions were more conserved than the non-coding regions, and the large single-copy and small single-copy regions were less conserved than the inverted repeat regions. We identified five new hotspot regions (rbcL, ycf4, psaJ, rpl22, and ycf1) that can be used as barcodes or species-specific Symplocos molecular markers. These four novel chloroplast genomes provide basic information on the plastid genome of Symplocos and enable better taxonomic characterization of this genus.