Draft Genome Sequences of Facultative Methylotrophs, Gemmobacter sp. Strain LW1 and Mesorhizobium sp. Strain 1M-11, Isolated from Movile Cave, Romania

Facultative methylotrophs belonging to the genera Gemmobacter and Mesorhizobium were isolated from microbial mat and cave water samples obtained from the Movile Cave ecosystem. Both bacteria can utilize methylated amines as their sole carbon and nitrogen source. Here, we report the draft genome sequences of Gemmobacter sp. strain LW1 and Mesorhizobium sp. strain IM1

Occurrence of methane oxidizing bacteria and methanogenic archaea in Earth’s cave systems : a metagenomic analysis

Funding This study received funding from NERC DTP studentship to AA (NE/S007377/1-2429402), Department for Economy NI studentship to MC and QUB for funding to DK. RD and DK were supported by DfE US-Ireland R&D partnership project 154. AH-V was supported by CNCS-UEFISCDI project PN-IIIP4-ID-PCCF-2016-0016, PCCF 16/2018 (DARKFOOD, PI Dr. O. T. Moldovan). Acknowledgments The authors thank the funders of this study for their support.Peer reviewedPublisher PD

Microbial eukaryotes in the suboxic chemosynthetic ecosystem of Movile Cave, Romania

International audienceMovile Cave is a small system of partially inundated galleries in limestone settings close to the Black Sea in Southeast Romania. Isolated from the surface for 6 million years, its sulfidic, methane and ammoniarich waters harbour unique chemosynthetic prokaryotic communities that include sulphur and ammonium-metabolizing chemolithotrophs, methanogens, methanotrophs and methylotrophs. The cave also harbours cave-dwelling invertebrates and fungi, but the diversity of other microbial eukaryotes remained completely unknown. Here, we apply an 18S rRNA gene-based metabarcoding approach to study the composition of protist communities in floating microbial mats and plankton from a wellpreserved oxygen-depleted cave chamber. Our results reveal a wide protist diversity with, as dominant groups, ciliates (Alveolata), Stramenopiles, especially bicosoecids, and jakobids (Excavata). Ciliate sequences dominated both, microbial mats and plankton, followed by either Stramenopiles or excavates. Stramenopiles were more prominent in microbial mats, whereas jakobids dominated the plankton fraction of the oxygen-depleted water column. Mats cultured in the laboratory were enriched in Cercozoa. Consistent with local low oxygen levels, Movile Cave protists are most likely anaerobic or microaerophilic. Several newly detected OTU clades were very divergent from cultured species or environmental sequences in databases and represent phylogenetic novelty, notably within jakobids. Movile Cave protists likely cover a variety of ecological roles in this ecosystem including predation, parasitism, saprotrophy and possibly diverse prokaryote-protist syntrophies

Searching for cold-adapted microorganisms in the underground glacier of Scarisoara Ice Cave, Romania

Scarisoara Ice Cave (Romania) hosts one of world’s largest and oldest underground glacier. While no studies were carried out on the existence of microorganisms in this cave’s ice block, our interest is to investigate the presence of microorganisms and their chronological distribution in the cave’s subterranean ice in relationship with past climatic changes. Samples were collected from ice layers of different age (from present to ~900 cal. yrs. BP), and the diversity of embedded microbial communities was assessed by classical cultivation and molecular techniques. The microorganisms from icesediments were cultivated at 4 °C and 15 °C, in the presence and absence of light. Epifluorescence microscopy analysis indicates the presence of autotrophic prokaryotes and eukaryotes in sunlightexposed ice and water samples. Total DNA was isolated from each ice sample and the bacterial and eukaryotic SSU-rRNA genes were amplified by PCR. The chemical composition and organic content of both deeply buried (>10 m inside the ice block) and surface (supra- glacial pond water) habitats were analyzed in relation to their age and organic composition. This study is the first to report on the presence of both prokaryotic and eukaryotic microorganisms in the subterranean ice block of Scarisoara Ice Cave, thriving in both organic-rich ice and clear ice layers. Phototrophic prokaryotes and eukaryotes were identified in sun-exposed recent ice. The composition of cold-adapted ice embedded microbiota varied with the habitat age and organic content, as resulting from dissimilarities in growth curve profiles at two different temperatures. The presence of bacteria and eukaryotes in all the analyzed samples was asserted by PCR amplification of SSU-rRNA gene fragments. These findings can be further used to reconstruct changes in the microbial diversity over the past approximately 5000 years, in correlation with climatic and environmental changes recorded by the ice block

The Evolutionary and Phylogeographic History of Woolly Mammoths: A Comprehensive Mitogenomic Analysis

Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ∼1.0-2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths

К проблеме социальной эффективности инноваций в профессиональном образовании

Movile Cave, Romania, is an unusual underground ecosystem that has been sealed off from the outside world for several million years and is sustained by non-phototrophic carbon fixation. Methane and sulfur-oxidising bacteria are the main primary producers, supporting a complex food web that includes bacteria, fungi and cave-adapted invertebrates. A range of methylotrophic bacteria in Movile Cave grow on one-carbon compounds including methylated amines, which are produced via decomposition of organic-rich microbial mats. The role of methylated amines as a carbon and nitrogen source for bacteria in Movile Cave was investigated using a combination of cultivation studies and DNA stable isotope probing (DNA-SIP) using 13C-monomethylamine (MMA). Two newly developed primer sets targeting the gene for gamma-glutamylmethylamide synthetase (gmaS), the first enzyme of the recently-discovered indirect MMA-oxidation pathway, were applied in functional gene probing. SIP experiments revealed that the obligate methylotroph Methylotenera mobilis is one of the dominant MMA utilisers in the cave. DNA-SIP experiments also showed that a new facultative methylotroph isolated in this study, Catellibacterium sp. LW-1 is probably one of the most active MMA utilisers in Movile Cave. Methylated amines were also used as a nitrogen source by a wide range of non-methylotrophic bacteria in Movile Cave. PCR-based screening of bacterial isolates suggested that the indirect MMA-oxidation pathway involving GMA and N-methylglutamate is widespread among both methylotrophic and non-methylotrophic MMA utilisers from the cave

Preliminary data on the bacterial diversity of Dobšinská and Demänovská ice caves (Slovakia)

Our work brings preliminary data on the diversity of microorganisms in Dobšinská and Demänovská ice caves (Slovakia). The caves are located at about 80 km from each other. Demänovská Ice Cave is part of the Demänovské caves system, located in the Demänovská Valley in the Low Tatras National Park. Dobšinská Ice Cave (969m asl), is part of the Stratená Cave System, located on the south-western edge of the Slovak Paradise National Park in the Spiš-Gemer karst. Both caves have been opened for the public during the last decades of the 19th century and are presently intensively visited by tourists [in 2014 alone, Demänovská ice cave was visited by 70,769 tourists (Nudziková 2018)].There are few reports on the biocenosis of these two caves, the available data referring mainly to the invertebrate fauna (Papáč et al. 2019). In what concerns the microorganisms, up to our investigation, in focus have been only the fungi. Thus, in Dobšinská Ice Cave was reported the presence of species such as Botrytis cinerea and Aspergillus fumigatus isolated from bat guano (Nováková 2006) and the abundance of fungi outside and inside the cave was compared while from Demänovská Ice Cave, based on ITS sequences, Ogórek et al. (2018) reports on the phenotypic and genotypic diversity of airborne fungal spores.Our work complements these two studies adding data on the bacterial diversity from different parts of the two caves and depending on the substrate types (ice blocks and/or sediments).Using Sanger sequencing of the 16S amplicons from DNA isolated from pure bacterial cultures obtained from ice and/or sediments of Demänovská and Dobšinská Ice Caves, we identified 7 and respectively 12 species of bacteria. Surprisingly, only two species where common to both caves. In both Demänovská Ice Cave and Dobšinská Ice Cave the bacterial communities were dominated by Acinetobacter and Bacillus. Beside the identification of the main bacterial groups present in the underground habitats, Illumina sequencing enabled us to build genus heatmaps for the caves, allowing for comparision between various segments of each cave in relation with the specific climate features. When compared, the different types of samples (water, sediment, ice) showed different abundance of bacteria, ice diversity being greater than sediment/water diversity in both Dobšinska and Demänovská ice caves. The chemical composition of the samples (ice and water) is also discussed.This work is the first to bring insights on the bacterial diversity of Demänovská and Dobšinská Ice Caves and we appreciate what it opens new directions of research not only on the evolution of the microbial communities in relation to the climate changes occurred in past times, but also on how intense visiting affects the structures of the microorganisms communities

Methanobacterium movilense sp. nov., a hydrogenotrophic, secondary alcohol utilizing methanogen from the anoxic sediment of the subsurface lake in Movile Cave, Romania

A novel strain of methanogenic archaea, designated MC-20T, was isolated from the anoxic sediment of a subsurface lake in Movile Cave, Mangalia, Romania. Cells were non-motile, Gram-stain-negative rods 3.5–4.0 µm in length and 0.6–0.7 µm in width, and occurred either singly or in short chains. Strain MC-20T was able to utilize H2/CO2, formate, 2-propanol and 2-butanol as substrate, but not acetate, methanol, ethanol, dimethyl sulfide, monomethylamine, dimethylamine or trimethylamine. Neither trypticase peptone nor yeast extract was required for growth. The major membrane lipids of strain MC-20T were archaeol phosphatidylethanolamine and diglycosyl archaeol, while archaeol phosphatidylinositol and glycosyl archaeol were present only in minor amounts. Optimal growth was observed at 33 °C, pH 7.4 and 0.08 M NaCl. Based on phylogenetic analysis of 16S rRNA gene sequences, strain MC-20T was closely affiliated with Methanobacterium oryzae FPiT (similarity 97.1 %) and Methanobacterium lacus 17A1T (97.0 %). The G+C content of the genomic DNA was 33.0 mol%. Based on phenotypic and genotypic differences, strain MC-20T was assigned to a novel species of the genus Methanobacterium for which the name Methanobacterium movilense sp. nov. is proposed. The type strain is MC-20T ( = DSM 26032T = JCM 18470T).</jats:p

Occurrence of methane-oxidizing bacteria and methanogenic archaea in earth’s cave systems—A metagenomic analysis

Funding This study received funding from NERC DTP studentship to AA (NE/S007377/1-2429402), Department for Economy NI studentship to MC and QUB for funding to DK. RD and DK were supported by DfE US-Ireland R&D partnership project 154. AH-V was supported by CNCS-UEFISCDI project PN-IIIP4-ID-PCCF-2016-0016, PCCF 16/2018 (DARKFOOD, PI Dr. O. T. Moldovan). Acknowledgments The authors thank the funders of this study for their support.Peer reviewedPublisher PD

Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake

A novel methanogenic archaeon, strain MC-15T, was isolated from a floating biofilm on a sulphurous subsurface lake in Movile Cave (Mangalia, Romania). Cells were non-motile sarcina-like cocci with a diameter of 2–4 µm, occurring in aggregates. The strain was able to grow autotrophically on H2/CO2. Additionally, acetate, methanol, monomethylamine, dimethylamine and trimethylamine were utilized, but not formate or dimethyl sulfide. Trypticase peptone and yeast extract were not required for growth. Optimal growth was observed at 33 °C, pH 6.5 and a salt concentration of 0.05 M NaCl. The predominant membrane lipids of MC-15T were archaeol and hydroxyarchaeol phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol as well as hydroxyarchaeol phosphatidylserine and archaeol glycosaminyl phosphatidylinositol. The closely related species, Methanosarcina vacuolata and Methanosarcina horonobensis, had a similar composition of major membrane lipids to strain MC-15T. The 16S rRNA gene sequence of strain MC-15T was similar to those of Methanosarcina vacuolata DSM 1232T (sequence similarity 99.3 %), Methanosarcina horonobensis HB-1T (98.8 %), Methanosarcina barkeri DSM 800T (98.7 %) and Methanosarcina siciliae T4/MT (98.4 %). DNA–DNA hybridization revealed 43.3 % relatedness between strain MC-15T and Methanosarcina vacuolata DSM 1232T. The G+C content of the genomic DNA was 39.0 mol%. Based on physiological, phenotypic and genotypic differences, strain MC-15T represents a novel species of the genus Methanosarcina , for which the name Methanosarcina spelaei sp. nov. is proposed. The type strain is MC-15T ( = DSM 26047T = JCM 18469T).</jats:p