International initiatives aimed at generating genomic resources, and particularly reference genomes, have flourished in recent years. Some focus on specific taxa, such as the Vertebrate Genomes Project, Bird Genome 10K Project, Bat1K Project, Global Invertebrate Genomics Alliance, 10 000 Plant Genomes Project, and 1000 Fungal Genomes project. Others focus on geographic regions, such as the California Conservation Genomics Project, Darwin Tree of Life for Britain and Ireland, Catalan Initiative for the Earth BioGenome Project in the Catalan territories, Endemixit in Italy, Norwegian Earth Biogenome Project, and SciLifeLab in Sweden, on applications such as the LOEWE Translational Biodiversity Genomics in Germany, or on ecological systems such as the Aquatic Symbiosis Genomics project. Collectively part of the Earth BioGenome Project (EBP), in Europe these initiatives are organized under the umbrella of the European Reference Genome Atlas (ERGA). A genome atlas of European biodiversityERGA is a pan-European scientific response to the current threats to biodiversity. Approximately one fifth of the ~200 000 eukaryotic species present in Europe can be inferred to be at risk of extinction according to the International Union for Conservation of Nature (IUCN) Red List classification (this estimate only considers the assessed species; https://www.iucn.org/regions/europe/our-work/biodiversity-conservation/european-red-list-threatened-species).ERGA aims to generate reference genomes of European eukaryotic species across the tree of life, including threatened, endemic, and keystone species, as well as pests and species important to agriculture, fisheries, and ecosystem function and stability. ERGA builds upon current genomic consortia in EU member states, EU Associated Countries, representatives of other countries within the European bioregion, and international collaborators. These reference genomes will address fundamental and applied questions in conservation, biology, and health. ERGA seeks to alert the EU about the potential of conservation genomics, and particularly the role of reference genomes, in biodiversity assessment, conservation strategies, and restoration efforts.
A new genus and species of subaerophytic cyanobacteria with very thin purple-red trichomes are described. The seven strains included in this genus were isolated from phototrophic biofilms growing on calcareous substrata in ancient hypogea. Trichomes were 1-3 mm thick, with small constrictions at the cross-walls and colourless sheaths. The thylakoid arrangement was parietal. Autapomorphic characters include the purple-red colouration of cells and a photosensitive orange spot at the tip of the trichome containing a rhodopsin-like pigment. Molecular and phylogenetic analyses based on 16 S rRNA gene sequences, resulted in a new 16 S rRNA cluster that indicated a separate position at the generic level. All strains were closely related (99% or higher similarity) and distantly related to other established cyanobacterial taxa (92%). The 16 S-23 S rRNA internal transcribed spacer (ITS) sequence of five of the red strains was almost identical. The ITS secondary folding structure was also unique to these strains and different to the Leptolyngbya type species. These strains have only been isolated from subterranean environments so far, and considering also this unique biotope and their particular ecology, we propose the new genus and species Oculatella subterranea. The genus name Oculatella means 'provided with a small eye'. The new genus is described using combined molecular and cytomorphological criteria, in accordance with the nomenclatorial recommendations of both the Bacteriological Code and the Botanical Code of Nomenclature. The genus Oculatella is of common distribution in hypogea and has been isolated from all hypogean environments so far studied in Rome and Malta. The type strain is VRUC135.
The main objective of this work was the comparative analysis of a large number of bacterial strains isolated from biodeteriorated surfaces in three different sites, namely the catacombs of St. Callistus in Rome, Italy, the catacombs dedicated to St. Agatha in Rabat, Malta and the Cave of Bats in Zuheros, Spain. Our results showed that even considering only culturable chemoorganotrophic bacteria the variability is very high, reflecting the great variety of microhabitats present. Hence any strategies to prevent, control or eliminate the biofilm-embedded microbiota from an archeological surface should take into account a number of considerations as stipulated in our study.
Abstract:The present study focuses on a description of the biodiversity of subaerial phototrophic biofilms occurring on archaeological surfaces in Maltese hypogean environments, namely St Paul's, St Agatha's and Abbatija tad-Dejr Catacombs, all situated in Rabat and the ancient Ħal Saflieni Hypogeum at Paola, Malta. Direct observation of the biofilms, carried out using light (LM), epifluorescent and confocal laser scanning microscopy (CLSM), allowed the description of the major cyanobacterial and microalgal taxa, and also the associated heterotrophic microorganisms, mainly actinobacteria. Some biofilm microorganisms were able to grow in culture and this allowed the isolation of cyanobacterial, microalgal and chemoorganotrophic bacterial strains. Thylakoid arrangement and cell division were examined using transmission electron microscopy (TEM). The cytomorphology of isolated microorganisms was described. The undisputed phototrophic protagonists in these subaerial biofilms of Maltese hypogean environments were the non-heterocytous (Oscillatorialean) cyanobacteria. In order to increase the limited data available for Leptolyngbya spp. from aerophytic epilithic biofilms in catacombs, the 16S rRNA genes of isolated Leptolyngbya strains were sequenced and compared with those obtained for related strains. Phylogenetic trees of cyanobacterial 16S rRNA sequences were constructed using parsimony and Bayesian analyses. Microorganisms forming biofilms in Maltese hypogea were found to be similar, both cytomorphologically and genetically, to those colonising lithic surfaces of caves and catacombs in other Mediterranean countries.
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