The Diversity Patterns of Rare to Abundant Microbial Eukaryotes Across a Broad Range of Salinities in a Solar Saltern

Solar salterns are excellent artificial systems for examining species diversity and succession along salinity gradients. Here, the eukaryotic community in surface water of a Korean solar saltern (30 to 380 practical salinity units) was investigated from April 2019 to October 2020 using Illumina sequencing targeting the V4 and V9 regions of 18S rDNA. A total of 926 operational taxonomic units (OTUs) and 1,999 OTUs were obtained with the V4 and V9 regions, respectively. Notably, most of the OTUs were microbial eukaryotes, and the high-abundance groups (> 5% relative abundance (RA), Alveolata, Stramenopila, Archaeplastida, and Opisthokonta) usually accounted for > 90% of the total cumulative read counts and > 80% of all OTUs. Moreover, the high-abundance Alveolata (larger forms) and Stramenopila (smaller forms) groups displayed a significant inverse relationship, probably due to predator–prey interactions. Most of the low-abundance (0.1–5% RA) and rare (< 0.1% RA) groups remained small portion during the field surveys. Taxonomic novelty (at < 90% sequence identity) was high in the Amoebozoa, Cryptista, Haptista, Rhizaria, and Stramenopila groups (69.8% of all novel OTUs), suggesting the presence of a large number of hidden species in hypersaline environments. Remarkably, the high-abundance groups had little overlap with the other groups, implying the weakness of rare-to-prevalent community dynamics. The low-abundance Discoba group alone temporarily became the high-abundance group, suggesting that it is an opportunistic group. Overall, the composition and diversity of the eukaryotic community in hypersaline environments may be persistently stabilized, despite diverse disturbance events.

The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments

Marine microorganisms are immensely diverse and play fundamental roles in global geochemical cycling. Recent metagenome-assembled genome studies, with special attention to large-scale projects such as Tara Oceans, have expanded the genomic repertoire of marine microorganisms. However, published marine metagenome data has not been fully explored yet. Here, we collected 2,057 marine metagenomes (>29 Tera bps of sequences) covering various marine environments and developed a new genome reconstruction pipeline. We reconstructed 52,325 qualified genomes composed of 8,466 prokaryotic species-level clusters spanning 59 phyla, including genomes from deep-sea deeper than 1,000 m (n=3,337), low-oxygen zones of <90 μmol O2 per kg water (n=7,884), and polar regions (n=7,752). Novelty evaluation using a genome taxonomy database shows that 6,256 species (73.9%) are novel and include genomes of high taxonomic novelty such as new class candidates. These genomes collectively expanded the known phylogenetic diversity of marine prokaryotes by 34.2% and the species representatives cover 26.5 - 42.0% of prokaryote-enriched metagenomes. This genome resource, thoroughly leveraging accumulated metagenomic data, illuminates uncharacterized marine microbial dark matter lineages.

Streptomyces tardus sp. nov.: A Slow-Growing Actinobacterium Producing Candicidin, Isolated From Sediments of the Trondheim Fjord

Marine environments are home to an extensive number of microorganisms, many of which remain unexplored for taxonomic novelty and functional capabilities. In this study, a slow-growing Streptomyces strain expressing unique genomic and phenotypic characteristics, P38-E01T, was described using a polyphasic taxonomic approach. This strain is part of a collection of over 8,000 marine Actinobacteria isolates collected in the Trondheim fjord of Norway by SINTEF Industry (Trondheim, Norway) and the Norwegian University of Science and Technology (NTNU, Trondheim, Norway). Strain P38-E01T was isolated from the sediments of the Trondheim fjord, and phylogenetic analyses affiliated this strain with the genus Streptomyces, but it was not closely affiliated with other described species. The closest related type strains were Streptomyces daliensis YIM 31724T (98.6%), Streptomyces rimosus subsp. rimosus ATCC 10970T (98.4%), and Streptomyces sclerotialus NRRL ISP-5269T (98.3%). Predominant fatty acids were C16:0 iso, C16:0, and Summed Feature 3, and the predominant respiratory quinones were MK-10(H6), MK-10(H4), and MK9(H4). The main polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphoglycolipid. The whole-cell sugars were glucose, ribose, and in minor amounts, mannose. The cell wall peptidoglycan contained LL-diaminopimelic acid. The draft genome has a size of 6.16 Mb, with a %G + C content of 71.4% and is predicted to contain at least 19 biosynthetic gene clusters encoding diverse secondary metabolites. Strain P38-E01T was found to inhibit the growth of the pathogenic yeast Candida albicans ATCC 90028 and a number of Gram-positive bacterial human and plant pathogens. Metabolites extracted from cultures of P38-E01T were analyzed by mass spectrometry, and it was found that the isolate produced the antifungal compound candicidin. Phenotypic and chemotaxonomic signatures, along with phylogenetic analyses, distinguished isolate P38-E01T from its closest neighbors; thus, this isolate represents a novel species of the genus Streptomyces for which the name Streptomyces tardus sp. nov. (P38-E01T = CCM 9049T = DSM 111582T) is proposed.

Poseidonibacter parvus sp. nov., isolated from a squid

A Gram-stain-negative, aerobic, short rod-shaped, motile, brownish-coloured bacterium, termed strain LPB0137T, was isolated from a squid. Its cells could grow weakly on marine agar 2216 with 0.04 % 2,3,5-triphenyl tetrazolium chloride (TTC). Each cell of strain LPB0137T has a circular chromosome with a length of 2.87 Mb and 27.7 mol% DNA G+C content. The genome includes 2698 protein-coding genes and six rRNA operons. In 16S rRNA gene sequence trees, strain LPB0137T formed a robust monophyletic clade with Poseidonibacter antarcticus SM1702T with a sequence similarity of 98.3 %. However, the average nucleotide identity and in silico DNA–DNA hybridization values between the two type strains were low (83.9 and 28.1 %, respectively). The overall phenotypic and genomic features of strain LPB0137T supported its assignment to the genus Poseidonibacter . However, the relatively low gene and genome sequence similarity between this strain and other type strains of the genus Poseidonibacter and several enzymatic characteristics indicated the taxonomic novelty of the isolated strain as a new member of the genus Poseidonibacter . Therefore, based on the phylogenetic and phenotypic characteristics of LPB0137T, we proposed a novel species of the genus Poseidonibacter for it, with the name Poseidonibacter parvus sp. nov. The type strain of this new species is thus LPB0137T (=KACC 18888T=JCM 31548T).

Mucilaginibacter celer sp. nov. and Aquirhabdus parva gen. nov., sp. nov., isolated from freshwater

Two novel bacteria, designated HYN0043T and HYN0046T, were isolated from a freshwater lake in Korea. 16S rRNA gene sequence phylogeny indicated that strain HYN0043T belongs to the genus Mucilaginibacter of the family Sphingobacteriaceae because it showed highest sequence similarity to Mucilaginibacter oryzae (98.2 %). The average nucleotide identity between strain HYN0043T and M. oryzae was 83.5 %, which is clearly below the suggested threshold for species demarcation. Strain HYN0046T was found to belong to the family Moraxellaceae and shared highest sequence similarity with Agitococcus lubricus (93.8 %). The average amino acid identity values between strain HYN0046T and representative type strains of closely related genera (Alkanindiges, Agitococcus and Acinetobacter ) were 53.1–60.7 %, implying the novelty of the isolate at the genus level. Phenotypic characteristics (physiological, biochemical and chemotaxonomic) also supported the taxonomic novelty of the two isolates. Thus, we suggest the following names to accommodate strains HYN0043T and HYN0046T: Mucilaginibacter celer sp. nov. (type strain HYN0043T=KACC 19184T=NBRC 112738T) in the family Spingobacteriaceae and phylum Bacteroidetes and Aquirhabdus parva gen. nov., sp. nov. (type strain HYN0046T=KACC 19178T=NBRC 112739T) in the family Moraxellaceae and phylum Proteobacteria .

Biodiversity data and new species descriptions of polychaetes from offshore waters of the Falkland Islands, an area undergoing hydrocarbon exploration

Benthic environmental impact assessments and monitoring programs accompanying offshore hydrocarbon industry activities result in large collections of benthic organisms. Such collections offer great potential for systematics, biodiversity and biogeography research, but these opportunities are only rarely realised. In recent decades, the hydrocarbon industry has started exploration activities in offshore waters off the Falkland Islands. A large collection of ca. 25,000 polychaete (Annelida) specimens, representing some 233 morphological species was processed at the Natural History Museum, London. Taxonomic assessment led to recognition of many polychaete species that are new to science. The existing taxonomic literature for the region is outdated and many species in existing literature are likely misidentifications. Initially, an online taxonomic guide (http://falklands.myspecies.info) was created, to provide a single taxonomic source for 191 polychaete species to standardise identification across different environmental contractors working in Falkland Islands. Here, this effort is continued to make data available for 18,015 specimens through publication of raw biodiversity data, checklist with links to online taxonomic information and formal descriptions of five new species. New species were chosen across different families to highlight the taxonomic novelty of this area: Apistobranchus jasoni Neal &amp; Paterson, sp. nov. (Apistobranchidae), Leitoscoloplos olei Neal &amp; Paterson, sp. nov. (Orbiniidae), Prosphaerosyllis modinouae Neal &amp; Paterson, sp. nov. (Syllidae) and Aphelochaeta falklandica Paterson &amp; Neal, sp. nov., and Dodecaceria saeria Paterson &amp; Neal, sp. nov. (both Cirratulidae). The potential of the Falkland Islands material to provide up to date informationfor known species described in the literature is also highlighted by publishing images and redescription of Harmothoe anderssoni Bergström, 1916 and Aphelochaeta longisetosa (Hartmann-Schröder, 1965). Biodiversity and abundance data are made available through a DarwinCore database, including material collected from 83 stations at Sea Lion developmental oil field in North Falklands Basin and voucher specimens’ data collected from exploratory oil wells in East Falklands Basin.

Graptopetalum sinaloensis (Crassulaceae), una nueva especie de Sinaloa, México

RESUMEN:Antecedentes y Objetivos: El género Graptopetalum (Crassulaceae) incluye cerca de 20 especies de herbáceas rosetoides, con tallos ramificados o acaules, que se desarrollan en ambientes semiáridos y poco accesibles (montañas o barrancas) de México y Arizona. Como parte del trabajo continuo de los autores para documentar la flora de Sinaloa, en el presente artículo, se reporta una novedad taxonómica del género Graptopetalum.Métodos: En junio de 2013, en el municipio Culiacán, Sinaloa, México, se encontró una pequeña población de plantas del género Graptopetalum con inflorescencias secas, de la cual se colectaron algunos individuos para cultivar; florecieron en marzo. Especímenes con flor se colectaron en campo en la misma localidad en febrero de 2014. Al comparar el material de campo y el cultivado con material de herbario, literatura y cultivo de otras especies del género, se determinó que se trataba de una especie nueva para la ciencia.Resultados clave: Se describe el nuevo taxón Graptopetalum sinaloensis de la sección Graptopetalum, se discuten diferencias y similitudes con las especies más cercanas y se proporciona una clave dicotómica nueva y actualizada para las ocho especies de esta sección.Conclusiones: Graptopetalum sinaloensis es endémica del centro-sur de Sinaloa, México. Crece sobre paredes rocosas de arroyos y pies de cerros muy localizados, en poblaciones pequeñas y áreas reducidas de entre 5 y 10 m2. Se diferencia fácilmente de las otras especies de la sección Graptopetalum de Sinaloa por su flor pentámera, ya que G. rusbyi presenta 6-7 meros, y por su inflorescencia en panícula, porque G. occidentale presenta una cima. Además, la distribución geográfica no se traslapa con ninguna de ellas. Palabras clave: Byrnesia, flora de Sinaloa, Graptopetalum occidentale, Graptopetalum rusbyi, Sedum, selva baja caducifolia.ABSTRACT:Background and Aims: The genus Graptopetalum includes about 20 species of branched or acaulescent rosette herbs that grew in little accessible semiarid environments (mountains or ravines) of Mexico and Arizona. The authors have developed continuous work to document the flora of Sinaloa and the present article reports a taxonomic novelty in the genus Graptopetalum.Methods: In the municipality of Culiacán, Sinaloa, Mexico, a small population of plants of the genus Graptopetalum with dry inflorescences was found in June 2013, and some plants were collected and cultivated, they flowered in March. Plants with flowers were collected from the same location in February 2014. Morphological data of wild and cultivated material were compared with that of herbarium specimens, literature, and cultivated Graptopetalum species; and it was determined that collected material is a new species for science.Key results: The new taxon Graptopetalum sinaloensis, section Graptopetalum, is described. Its differences and similarities with the closest species are discussed. Moreover, a new and updated dichotomous key is provided for the eight species of this section.Conclusions: Graptopetalum sinaloensis is endemic to south-central Sinaloa, Mexico. It grows in very localized areas, on rocky walls of streams and at the foot of hills, forming small populations in reduced areas of 5 to 10 m2. Graptopetalum sinaloensis differs from other Graptopetalum species from Sinaloa by its 5-merous flowers vs. G. rusbyi with 6-7-merous ones, and by its paniculate inflorescence, vs. G. occidentale with cymose ones. Additionally, the geographical distribution of the three species does not overlap.Key words: Byrnesia, flora of Sinaloa,Graptopetalum rusbyi, Graptopetalum occidentale, Sedum, tropical deciduous forest.

A new species of Rhipidocladum (Poaceae: Bambusoideae: Arthrostylidiinae) from Mexico

Mexico has a rich woody bamboo flora with over 52 species, 66% of which are endemic. Mexico represents the northernmost extent for many Neotropical bamboo genera such as the widespread Rhipidocladum, a genus with characteristic fan-like branching and variable synflorescence morphologies. Only four species of Rhipidocladum are known from Mexico: R. bartlettii, R. martinezii, R. pittieri and R. racemiflorum. Remarkably, the ranges of all four species overlap in the Mexican state of Chiapas. During field work in Chiapas, a flowering population of Rhipidocladum was discovered that had two glumes and retrorsely scabrous abaxial leaf surfaces, and lacked foliage leaf fimbriae. This combination of characters is unlike that of any known species in the genus. We conducted a comprehensive morphological study of specimens from this population and confirmed the existence of a new species of Rhipidocladum. We describe and illustrate the new taxon, discuss its diagnostic characters and provide an updated key to the species of Rhipidocladum distributed in Mexico. This taxonomic novelty increases the richness of the genus to 20 species and adds a new endemic woody bamboo to the flora of Mexico. The new species inhabits montane cloud forest, an important yet threatened vegetation type in Mexico.

Taxonomic Gap Analysis: A method of evaluating the taxa represented in biodiversity databases

The Global Genome Initiative (GGI) endeavors to collect the Earth’s genomic biodiversity, preserve this biodiversity as high quality genetic resources in Global Genome Biodiversity Network (GGBN) affiliated biorepositories, increase knowledge of biodiversity through genetic sequencing, and make resources and knowledge accessible to researchers via the GGBN Data Portal, the Global Catalogue of Microorganisms (GCM), and the National Center for Biotechnology Information (NCBI) GenBank. In GGI's seven year timespan, it is attempting to collect samples from all 9,870 families and half of the 165,683 genera of life on Earth (Roskov et al. 2019). To accomplish this, GGI must synergistically consider the following questions: What life exists? What has already been preserved as physical resources? What is already known from genetic sequencing? How will novel or legacy collections fill the gaps in resources or knowledge? What life exists? What has already been preserved as physical resources? What is already known from genetic sequencing? How will novel or legacy collections fill the gaps in resources or knowledge? To answer the first question, GGI has explored the use of taxonomic authorities such as the Global Biodiversity Information Facility (GBIF) Backbone Taxonomy and the Catalogue of Life as taxonomic backbones to variously match taxonomic names and derive complete lists of extant taxa at each taxonomic rank. To answer the second question, GGI utilizes the GGBN Data Portal API and the GCM website to extract lists of taxonomic names, which are then standardized to a taxonomic backbone. To answer the third question, following the recommendations of Hanner 2009 for identifying high-quality DNA barcode records, GGI employs the NCBI Entrez Programming Utilities to download GenBank records, then standardizes the associated taxa to a taxonomic backbone. Finally, GGI compares lists of taxa found in specific geographic areas or specific legacy collections to determine the amount of taxonomic novelty a new collection may supply. GGI refers to this comparison of taxonomic databases as a taxonomic gap analysis, an assessment of how well a potential collection fills the taxonomic gaps in physical collections and genetic knowledge. A gap analysis performed by GGI in March 2019 shows that 49% of families and 78% of genera still have no representation as either physical samples or genetic information (Table 1). There are substantial gaps to fill in the endeavor to capture the Earth's biodiversity, and taxonomic gap analysis will continue to be a powerful tool to identify the most promising potential new collections.