Reflections on the introduction of the Digital Protologue Database – a partial success? [Editorial]

Modern science revolves around databases, be they the massive (e.g. NCBI) or the bespoke (e.g. EzBioCloud). There are enormous databases covering the sequence world and the protein world but what of the organisms from which they are derived? With this is mind, we have argued (Sutcliffe et al. 2012; Rosselló-Móra 2012; Rosselló-Móra and Amann 2015; Sutcliffe 2015; Rossello-Mora and Whitman 2019) that microbial systematics needs to become a database driven science. After all, if it has taken more than a century to characterise  10 m prokaryotic species (< 0.2%), then a flexible repository will be needed if we are to complete a timely systematic census of the microbial world. An ideal database would integrate information on the characteristics of a taxon with nomenclatural information and links out to other databases, particularly for sequence data, and back to the original data source (primary publication). Entries would range from the minimal information needed to delineate a novel taxon through to maximal descriptions of well characterised taxa

Addressing the sublime scale of the microbial world: reconciling an appreciation of microbial diversity with the need to describe species

There are fewer than 20,000 prokaryotic species with validly published names, meaning >99% of a reasonable estimate of microbial diversity remains formally unnamed. Here we explore the damaging consequences of the current practice in which each new species is described in a standardized publication, most typically a 'single strain species description'. This approach is both an impediment to scaling up progress in naming the microbial world and also a significant factor in the poor reputation of the discipline of microbial taxonomy. We conclude that significant changes in author habits are needed and make constructive suggestions as to how author practice should adapt

Diversity of extremely halophilic cultivable prokaryotes in Mediterranean, Atlantic and Pacific solar salterns: Evidence that unexplored sites constitute sources of cultivable novelty

The culturable fraction of aerobic, heterotrophic and extremely halophilic microbiota retrieved from sediment and brine samples of eight sampling sites in the Mediterranean, Canary Islands and Chile was studied by means of a tandem approach combining large-scale cultivation, MALDI-TOF MS targeting whole cell biomass, and phylogenetic reconstruction based on 16S rRNA gene analysis. The approach allowed the identification of more than 4200 strains and a comparison between different sampling sites. The results indicated that the method constituted an excellent tool for the discovery of taxonomic novelty. Four new genera and nine new species could be identified within the archaeal family Halobacteriaceae, as well as one new bacterial species, and a representative of Salinibacter ruber phylotype II, a group that had been refractory to isolation for the last fifteen years. Altogether, the results indicated that in order to provide better yields for the retrieval of novel taxa from the environment, performance of non-redundant environment sampling is recommended together with the screening of large sets of strains.The current study was funded with the scientific support given by the Spanish Ministry of Economy through the projectsCGL2012-39627-C03-01 and CGL2012-39627-C03-03, which were also supported with European Regional Development Fund (FEDER) funds, and the preparatory phase of the Microbial Resource Research Infrastructure (MIRRI) funded by the EU (grant number 312251). In addition, the funding from competitive research groups (Microbiology) of the Government of the Balearic Islands (also co-supported with FEDER funds), is also acknowledged. TVP acknowledges the predoctoral fellowship of the Ministerio de Economía y Competitividad of the Spanish Government for the FPI fellowship (Nr BES-2013-064420) supporting his research activities

Public discussion on a proposed revision of the International Code of Nomenclature of Prokaryotes

The Editorial Board for the International Code of Nomenclature of Prokaryotes (ICNP) has compiled proposed revisions of the ICNP. As outlined previously (Oren et al., Int J Syst Evol Microbiol 2021;71:004598; https://doi.org/10.1099/ijsem.0.004598) and to comply with Articles 13(b)(4) and 4(d) of the statutes of the International Committee on Systematics of Prokaryotes, a public discussion of the document will start on 1 July 2021, to last for 6 months. Here, we present the procedure for this discussion

Emendation of Rules 5b, 8, 15 and 22 of the International Code of Nomenclature of Prokaryotes to include the rank of phylum

Following the International Committee on Systematics of Prokaryotes electronic discussion and vote on proposals to include the rank of phylum in the rules of the International Code of Nomenclature of Prokaryotes, we here announce the results of the ballot. We also present draft versions of the emended Rules 5b, 8, 15 and 22, based on the outcome of the ballot, to be included in the proposal for the preparation of a new revision of the International Code of Nomenclature of Prokaryotes

Ancient saltern metagenomics: tracking changes in microbes and their viruses from the underground to the surface

Microbial communities in hypersaline underground waters derive from ancient organisms trapped within the evaporitic salt crystals and are part of the poorly known subterranean biosphere. Here, we characterized the viral and prokaryotic assemblages present in the hypersaline springs that dissolve Triassic-Keuper evaporite rocks and feed the Anana Salt Valley (Araba/Alava, Basque Country, Spain). Four underground water samples (around 23% total salinity) with different levels of exposure to the open air were analysed by means of microscopy and metagenomics. Cells and viruses in the spring water had lower concentrations than what are normally found in hypersaline environments and seemed to be mostly inactive. Upon exposure to the open air, there was an increase in activity of both cells and viruses as well as a selection of phylotypes. The underground water was inhabited by a rich community harbouring a diverse set of genes coding for retinal binding proteins. A total of 35 viral contigs from 15 to 104 kb, representing partial or total viral genomes, were assembled and their evolutionary changes through the spring system were followed by SNP analysis and metagenomic island tracking. Overall, both the viral and the prokaryotic assemblages changed quickly upon exposure to the open air conditions.We would like to thank Anana Salt Valley Foundation, and Andoni Erkiaga Agirre, its director at the time of sampling, for their kind help. Thanks to Leire Arana, Edorta Loma and Kika Colom for their help with sampling and to Eduardo Gonzalez-Pastor for telling us about the Anana Salt Valley. We thank Heather Maughan for the professional English editing and the critical reading of the manuscript and Esther Rubio-Portillo for her help with statistical analyses. This work was funded by the Spanish Ministry of Science, Innovation and Universities grant MICROMATES (PGC2018-096956-B-C41 and C44, to J.A./F.S. and R.R.-M.), which was also supported with European Regional Development Fund (FEDER) funds, and by the Generalitat Valenciana grant PROMETEO/2017/129. Documen

Effects of the 2015 heat wave on benthic invertebrates in the Tabarca Marine Protected Area (southeast Spain)

In the late summer of 2015, extensive mortality of scleratinian corals, gorgonians, and sponges was observed in the Marine Protected Area of Tabarca (southeast Spain). Quantitative data indicated that at 25 m depth the sea fan Eunicella singularis was the most affected species (50% of colonies affected by partial mortality); while in shallow waters more than 40% of the endemic scleractinian coral Cladocora caespitosa population showed tissue lesions that affected more than 10% of their surfaces. Other affected species were the scleractinian corals Oculina patagonica and Phyllangia mouchezii, the sea fan Leptogorgia sarmentosa and the sponge Sarcotragus fasciculatus. This mortality event coincided with an abnormal rise in seawater temperature in this region. Microbiological analysis showed a higher abundance of culturable Vibrio species in invertebrates exhibiting tissue lesions, which indicated that these opportunistic pathogens could be a key factor in the process

Novel Genes Involved in Resistance to Both Ultraviolet Radiation and Perchlorate From the Metagenomes of Hypersaline Environments

Microorganisms that thrive in hypersaline environments on the surface of our planet are exposed to the harmful effects of ultraviolet radiation. Therefore, for their protection, they have sunscreen pigments and highly efficient DNA repair and protection systems. The present study aimed to identify new genes involved in UV radiation resistance from these microorganisms, many of which cannot be cultured in the laboratory. Thus, a functional metagenomic approach was used and for this, small-insert libraries were constructed with DNA isolated from microorganisms of high-altitude Andean hypersaline lakes in Argentina (Diamante and Ojo Seco lakes, 4,589 and 3,200 m, respectively) and from the Es Trenc solar saltern in Spain. The libraries were hosted in a UV radiation-sensitive strain of Escherichia coli (recA mutant) and they were exposed to UVB. The resistant colonies were analyzed and as a result, four clones were identified with environmental DNA fragments containing five genes that conferred resistance to UV radiation in E. coli. One gene encoded a RecA-like protein, complementing the mutation in recA that makes the E. coli host strain more sensitive to UV radiation. Two other genes from the same DNA fragment encoded a TATA-box binding protein and an unknown protein, both responsible for UV resistance. Interestingly, two other genes from different and remote environments, the Ojo Seco Andean lake and the Es Trenc saltern, encoded two hypothetical proteins that can be considered homologous based on their significant amino acid similarity (49%). All of these genes also conferred resistance to 4-nitroquinoline 1-oxide (4-NQO), a compound that mimics the effect of UV radiation on DNA, and also to perchlorate, a powerful oxidant that can induce DNA damage. Furthermore, the hypothetical protein from the Es Trenc salterns was localized as discrete foci possibly associated with damaged sites in the DNA in cells treated with 4-NQO, so it could be involved in the repair of damaged DNA. In summary, novel genes involved in resistance to UV radiation, 4-NQO and perchlorate have been identified in this work and two of them encoding hypothetical proteins that could be involved in DNA damage repair activities not previously described.Fil: Lamprecht Grandío, María. Consejo Superior de Investigaciones Cientificas. Centro de Astrobiologia.; EspañaFil: Cortesão, Marta. Consejo Superior de Investigaciones Cientificas. Centro de Astrobiologia.; EspañaFil: Mirete, Salvador. Consejo Superior de Investigaciones Cientificas. Centro de Astrobiologia.; EspañaFil: Benguigui de la Cámara, Macarena. Consejo Superior de Investigaciones Cientificas. Centro de Astrobiologia.; EspañaFil: de Figueras, Carolina G.. Consejo Superior de Investigaciones Cientificas. Centro de Astrobiologia.; EspañaFil: Pérez Pantoja, Danilo. Universidad Tecnológica Metropolitana; EspañaFil: White, Joseph John. Consejo Superior de Investigaciones Cientificas. Centro de Astrobiologia.; EspañaFil: Farias, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Rosselló Móra, Ramon. Instituto Mediterráneo Estudios Avanzados; EspañaFil: González Pastor, José Eduardo. Consejo Superior de Investigaciones Cientificas. Centro de Astrobiologia.; Españ

Characterization of Adherent-Invasive Escherichia coli (AIEC) Outer Membrane Proteins Provides Potential Molecular Markers to Screen Putative AIEC Strains

Adherent-invasive E. coli (AIEC) is a pathotype associated with the etiopathogenesis of Crohn's disease (CD), albeit with an as-yet unclear role. The main pathogenic mechanisms described for AIEC are adherence to epithelial cells, invasion of epithelial cells, and survival and replication within macrophages. A few virulence factors have been described as participating directly in these phenotypes, most of which have been evaluated only in AIEC reference strains. To date, no molecular markers have been identified that can differentiate AIEC from other E. coli pathotypes, so these strains are currently identified based on the phenotypic characterization of their pathogenic mechanisms. The identification of putative AIEC molecular markers could be beneficial not only from the diagnostic point of view but could also help in better understanding the determinants of AIEC pathogenicity. The objective of this study was to identify molecular markers that contribute to the screening of AIEC strains. For this, we characterized outer membrane protein (OMP) profiles in a group of AIEC strains and compared them with the commensal E. coli HS strain. Notably, we found a set of OMPs that were present in the AIEC strains but absent in the HS strain. Moreover, we developed a PCR assay and performed phylogenomic analyses to determine the frequency and distribution of the genes coding for these OMPs in a larger collection of AIEC and other E. coli strains. As result, it was found that three genes (chuA, eefC, and fitA) are widely distributed and significantly correlated with AIEC strains, whereas they are infrequent in commensal and diarrheagenic E. coli strains (DEC). Additional studies are needed to validate these markers in diverse strain collections from different geographical regions, as well as investigate their possible role in AIEC pathogenicity