Methylation of the Selected TP53 Introns in Advanced-Stage Ovarian Carcinomas.

Objective: Advanced-stage ovarian cancer (OC) is among the most fatal female genital tract neoplasms worldwide. Although different genetic mechanisms have been shown to be involved in ovarian carcinogenesis, the role of TP53 introns methylation is still unresolved. We performed methylation analysis of introns 1, 3, and 4 of the TP53 to identify patterns in primary stage III OCs, corresponding metastases, and healthy tissues. Methods: The study involved samples of paraffin-embedded tissues obtained from 80 patients with stage III OCs, who underwent surgery at the Department of Gynecology and Gynecologic Oncology of the Military Institute of Medicine in Warsaw, Poland. Altogether, 40 serous-type G2/3 OCs and 40 endometrioid-type G2/3 OCs were included. From the same patient, metastatic and normal tissues were simultaneously analyzed. As a control group, 80 tissue samples were collected from patients after bariatric operations. Human ovarian cancer A2780 cell line was also investigated. Total genomic DNA was isolated from paraffin-embedded tissue blocks and the methylation analysis was performed by bisulfite DNA conversion, DNA amplification with specific primers, cloning, and DNA sequencing. Results: All of the samples of intron 1 of TP53 were un-methylated in OCs, metastatic tissues, and in healthy tissues from the same patient. Also, no methylation of TP53 intron 1 was detected in cells from the human A2780 ovarian cancer cell line and in all samples from control group. In all samples, introns 3 and 4 of the TP53 were methylated in primary tumors, metastatic tissue, and in healthy tissue from the same patient, in human A2780 ovarian cell line, and in DNA samples from healthy patients. None of the clinicopatholocal features was related to the TP53 introns methylation status. Conclusions: Our data on TP53 introns methylation sheds new light on the mechanism of p53 activity for a better understanding of cancer biology. The study suggests the existence of an additional regulation rule of TP53 activity that involves demethylation-methylation mechanisms. Methylation at introns 3 and 4 may also overall help in protecting TP53 against damage by viral restrictases or viral DNA integration.

Does Salmonella diarizonae 58:r:z53 Isolated from a Mallard Duck Pose a Threat to Human Health?

Salmonella diarizonae (IIIb) is frequently isolated from reptiles and less frequently from birds and mammals. However, its isolation from invasive human infections has not been widely reported. Migratory mallard ducks are excellent bioindicators of pathogen presence and pathogen antibiotic resistance (AMR). We present the first isolation from a mallard duck in central Europe of the antibiotic-resistant Salmonella enterica subsp. diarizonae with the unique antigenic pattern 58:r:z53 and report its whole-genome sequencing, serosequencing, and genotyping, which enabled the prediction of its pathogenicity and comparison with phenotypic AMR. The isolated strain was highly similar to S. diarizonae isolated from humans and food. Twenty-four AMR genes were detected, including those encoding aminoglycoside, fluoroquinolone, macrolide, carbapenem, tetracycline, cephalosporin, nitroimidazole, peptide antibiotic, and disinfecting agent/antiseptic resistance. Six Salmonella pathogenicity islands were found (SPI-1, SPI-2, SPI-3, SPI-5, SPI-9, and SPI-13). An iron transport system was detected in SPI-1 centisome C63PI. Plasmid profile analyses showed three to be present. Sequence mutations in the invA and invF genes were noted, which truncated and elongated the proteins, respectively. The strain also harbored genes encoding type-III secretion-system effector proteins and many virulence factors found in S. diarizonae associated with human infections. This study aims to elucidate the AMR and virulence genes in S. enterica subsp. diarizonae that may most seriously threaten human health.

Interaction of bacteriophage P1 with an epiphytic Pantoea agglomerans strain-the role of the interplay between various mobilome elements.

P1 is a model, temperate bacteriophage of the 94 kb genome. It can lysogenize representatives of the Enterobacterales order. In lysogens, it is maintained as a plasmid. We tested P1 interactions with the biocontrol P. agglomerans L15 strain to explore the utility of P1 in P. agglomerans genome engineering. A P1 derivative carrying the Tn9 (cmR) transposon could transfer a plasmid from Escherichia coli to the L15 cells. The L15 cells infected with this derivative formed chloramphenicol-resistant colonies. They could grow in a liquid medium with chloramphenicol after adaptation and did not contain prophage P1 but the chromosomally inserted cmR marker of P1 Tn9 (cat). The insertions were accompanied by various rearrangements upstream of the Tn9 cat gene promoter and the loss of IS1 (IS1L) from the corresponding region. Sequence analysis of the L15 strain genome revealed a chromosome and three plasmids of 0.58, 0.18, and 0.07 Mb. The largest and the smallest plasmid appeared to encode partition and replication incompatibility determinants similar to those of prophage P1, respectively. In the L15 derivatives cured of the largest plasmid, P1 with Tn9 could not replace the smallest plasmid even if selected. However, it could replace the smallest and the largest plasmid of L15 if its Tn9 IS1L sequence driving the Tn9 mobility was inactivated or if it was enriched with an immobile kanamycin resistance marker. Moreover, it could develop lytically in the L15 derivatives cured of both these plasmids. Clearly, under conditions of selection for P1, the mobility of the P1 selective marker determines whether or not the incoming P1 can outcompete the incompatible L15 resident plasmids. Our results demonstrate that P. agglomerans can serve as a host for bacteriophage P1 and can be engineered with the help of this phage. They also provide an example of how antibiotics can modify the outcome of horizontal gene transfer in natural environments. Numerous plasmids of Pantoea strains appear to contain determinants of replication or partition incompatibility with P1. Therefore, P1 with an immobile selective marker may be a tool of choice in curing these strains from the respective plasmids to facilitate their functional analysis.

Highly Resistant Serotype 19A Streptococcus pneumoniae of the GPSC1/CC320 Clone from Invasive Infections in Poland Prior to Antipneumococcal Vaccination of Children.

INTRODUCTION: The introduction of pneumococcal conjugate vaccines (PCV) into the national immunization programs (NIPs) has significantly reduced the number of pneumococcal infections. However, infections caused by isolates of non-vaccine serotypes (NVT) started spreading shortly thereafter and strains of NVT 19A have become the main cause of invasive pneumococcal disease burden worldwide. The aim of the study was to characterize serotype 19A invasive pneumococci of GPSC1/CC320 circulating in Poland before the introduction of PCV into the Polish NIP in 2017 and to compare them to isolates from other countries where PCVs were implemented much earlier than in Poland. METHODS: All the GPSC1/CC320 isolates were analyzed by serotyping, susceptibility testing, and whole genome sequencing followed by analyses of resistome, virulome, and core genome multilocus sequence typing (cgMLST), including comparative analysis with isolates with publicly accessible genomic sequences (PubMLST). RESULTS: During continuous surveillance the NRCBM collected 4237 invasive Streptococcus pneumoniae isolates between 1997 and 2016, including 200 isolates (4.7%) of serotype 19A. The most prevalent among 19A pneumococci were highly resistant representatives of Global Pneumococcal Sequence Cluster 1/Clonal Complex 320, GPSC1/CC320 (n = 97, 48.5%). Isolates of GPSC1/CC320 belonged to three sequence types (STs): ST320 (75.2%) ST4768 (23.7%), and ST15047 (1.0%), which all represented the 19A-III cps subtype and had complete loci for both PI-1 and PI-2 pili types. On the basis of the cgMLST analysis the majority of Polish GPSC1/CC320 isolates formed a group clearly distinct from pneumococci of this clone observed in other countries. CONCLUSION: Before introduction of PCV in the Polish NIP we noticed an unexpected increase of serotype 19A in invasive pneumococcal infections, with the most common being representatives of highly drug-resistant GPSC1/CC320 clone, rarely identified in Europe both before and even after PCV introduction.

Comparative genomic analysis of two ST320 Streptococcus pneumoniae isolates, representing serotypes 19A and 19F.

BACKGROUND: Streptococcus pneumoniae (pneumococcus) represents an important human pathogen, responsible for respiratory and invasive infections in the community. The efficacy of polysaccharide conjugate vaccines formulated against pneumococci is reduced by the phenomenon of serotype replacement in population of this pathogen. The aim of the current study was to obtain and compare complete genomic sequences of two pneumococcal isolates, both belonging to ST320 but differing by the serotype. RESULTS: Here, we report genomic sequences of two isolates of important human pathogen, S. pneumoniae. Genomic sequencing resulted in complete sequences of chromosomes of both isolates, 2,069,241 bp and 2,103,144 bp in size, and confirmed the presence of cps loci specific for serotypes 19A and 19F. The comparative analysis of these genomes revealed several instances of recombination, which involved not only S. pneumoniae but also presumably other streptococci as donors. CONCLUSIONS: We report the complete genomic sequences of two S. pneumoniae isolates of ST320 and serotypes 19A and 19F. The detailed comparative analysis of these genomes revealed the history of several recombination events, clustered in the region including the cps locus.

Functional Characterization of TetR-like Transcriptional Regulator PA3973 from Pseudomonas aeruginosa.

Pseudomonas aeruginosa, a human opportunistic pathogen, is a common cause of nosocomial infections. Its ability to survive under different conditions relies on a complex regulatory network engaging transcriptional regulators controlling metabolic pathways and capabilities to efficiently use the available resources. P. aeruginosa PA3973 encodes an uncharacterized TetR family transcriptional regulator. In this study, we applied a transcriptome profiling (RNA-seq), genome-wide identification of binding sites using ChIP-seq, as well as the phenotype analyses to unravel the biological role of PA3973. Transcriptional profiling of P. aeruginosa PAO1161 overexpressing PA3973 showed changes in the mRNA level of 648 genes. Concomitantly, ChIP-seq analysis identified more than 300 PA3973 binding sites in the P. aeruginosa genome. A 13 bp sequence motif was indicated as the binding site of PA3973. The PA3973 regulon encompasses the PA3972-PA3971 genes encoding a probable acyl-CoA dehydrogenase and a thioesterase. In vitro analysis showed PA3973 binding to PA3973p. Accordingly, the lack of PA3973 triggered increased expression of PA3972 and PA3971. The ∆PA3972-71 PAO1161 strain demonstrated impaired growth in the presence of stress-inducing agents hydroxylamine or hydroxyurea, thus suggesting the role of PA3972-71 in pathogen survival upon stress. Overall our results showed that TetR-type transcriptional regulator PA3973 has multiple binding sites in the P. aeruginosa genome and influences the expression of diverse genes, including PA3972-PA3971, encoding proteins with a proposed role in stress response.

Root-Associated Bacteria Community Characteristics of Antarctic Plants: Deschampsia antarctica and Colobanthus quitensis-a Comparison.

Colobanthus quitensis (Kunth) Bartl. and Deschampsia antarctica Desv. are the only Magnoliophyta to naturally colonize the Antarctic region. The reason for their sole presence in Antarctica is still debated as there is no definitive consensus on how only two unrelated flowering plants managed to establish breeding populations in this part of the world. In this study, we have explored and compared the rhizosphere and root-endosphere dwelling microbial community of C. quitensis and D. antarctica specimens sampled in maritime Antarctica from sites displaying contrasting edaphic characteristics. Bacterial phylogenetic diversity (high-throughput 16S rRNA gene fragment targeted sequencing) and microbial metabolic activity (Biolog EcoPlates) with a geochemical soil background were assessed. Gathered data showed that the microbiome of C. quitensis root system was mostly site-dependent, displaying different characteristics in each of the examined locations. This plant tolerated an active bacterial community only in severe conditions (salt stress and nutrient deprivation), while in other more favorable circumstances, it restricted microbial activity, with a possibility of microbivory-based nutrient acquisition. The microbial communities of D. antarctica showed a high degree of similarity between samples within a particular rhizocompartment. The grass' endosphere was significantly enriched in plant beneficial taxa of the family Rhizobiaceae, which displayed obligatory endophyte characteristics, suggesting that at least part of this community is transmitted vertically. Ultimately, the ecological success of C. quitensis and D. antarctica in Antarctica might be largely attributed to their associations and management of root-associated microbiota.

Case Report of COVID-19 after Full Vaccination: Viral Loads and Anti-SARS-CoV-2 Antibodies.

The introduction of effective vaccines against SARS-CoV-2 is expected to prevent COVID-19. However, sporadic cases of infection in vaccinated persons have been reported. We describe a case of a double-dose vaccinated woman with COVID-19. All stages of infection were observed, from no identification of virus, then the start of the infection, a high viral load, coming out of viraemia, and finally no detection of the virus. Despite the high viral load, the woman demonstrated mild COVID-19 symptoms, manifested only by a sore throat. The antibody results showed that she produced both post-infectious and post-vaccination immune responses. Phylogenetic analysis of the obtained viral genome sequence indicated that the virus belonged to the UK SARS-CoV-2 lineage B.1.1.7 (GR 501Y.V1; 20I/S:501Y.V1; Alpha variant).

Evaluation of acidogenesis products' effect on biogas production performed with metagenomics and isotopic approaches.

BACKGROUND: During the acetogenic step of anaerobic digestion, the products of acidogenesis are oxidized to substrates for methanogenesis: hydrogen, carbon dioxide and acetate. Acetogenesis and methanogenesis are highly interconnected processes due to the syntrophic associations between acetogenic bacteria and hydrogenotrophic methanogens, allowing the whole process to become thermodynamically favorable. The aim of this study is to determine the influence of the dominant acidic products on the metabolic pathways of methane formation and to find a core microbiome and substrate-specific species in a mixed biogas-producing system. RESULTS: Four methane-producing microbial communities were fed with artificial media having one dominant component, respectively, lactate, butyrate, propionate and acetate, for 896 days in 3.5-L Up-flow Anaerobic Sludge Blanket (UASB) bioreactors. All the microbial communities showed moderately different methane production and utilization of the substrates. Analyses of stable carbon isotope composition of the fermentation gas and the substrates showed differences in average values of δ13C(CH4) and δ13C(CO2) revealing that acetate and lactate strongly favored the acetotrophic pathway, while butyrate and propionate favored the hydrogenotrophic pathway of methane formation. Genome-centric metagenomic analysis recovered 234 Metagenome Assembled Genomes (MAGs), including 31 archaeal and 203 bacterial species, mostly unknown and uncultivable. MAGs accounted for 54%-67% of the entire microbial community (depending on the bioreactor) and evidenced that the microbiome is extremely complex in terms of the number of species. The core microbiome was composed of Methanothrix soehngenii (the most abundant), Methanoculleus sp., unknown Bacteroidales and Spirochaetaceae. Relative abundance analysis of all the samples revealed microbes having substrate preferences. Substrate-specific species were mostly unknown and not predominant in the microbial communities. CONCLUSIONS: In this experimental system, the dominant fermentation products subjected to methanogenesis moderately modified the final effect of bioreactor performance. At the molecular level, a different contribution of acetotrophic and hydrogenotrophic pathways for methane production, a very high level of new species recovered, and a moderate variability in microbial composition depending on substrate availability were evidenced. Propionate was not a factor ceasing methane production. All these findings are relevant because lactate, acetate, propionate and butyrate are the universal products of acidogenesis, regardless of feedstock.

Bacterial Communities Associated with Poa annua Roots in Central European (Poland) and Antarctic Settings (King George Island).

Poa annua (annual bluegrass) is one of the most ubiquitous grass species in the world. In isolated regions of maritime Antarctica, it has become an invasive organism threatening native tundra communities. In this study, we have explored and compared the rhizosphere and root-endosphere dwelling microbial community of P. annua specimens of maritime Antarctic and Central European origin in terms of bacterial phylogenetic diversity and microbial metabolic activity with a geochemical soil background. Our results show that the rhizospheric bacterial community was unique for each sampling site, yet the endosphere communities were similar to each other. However, key plant-associated bacterial taxa such as the Rhizobiaceae family were poorly represented in Antarctic samples, probably due to high salinity and heavy metal concentrations in the soil. Metabolic activity in the Antarctic material was considerably lower than in Central European samples. Antarctic root endosphere showed unusually high numbers of certain opportunistic bacterial groups, which proliferated due to low competition conditions. Thirteen bacterial families were recognized in this study to form a core microbiome of the P. annua root endosphere. The most numerous were the Flavobacteriaceae, suspected to be major contributors to the ecological success of annual bluegrass, especially in harsh, Antarctic conditions.

A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis.

BACKGROUND: Colourless microalgae of the Prototheca genus are the only known plants that have consistently been implicated in a range of clinically relevant opportunistic infections in both animals and humans. The Prototheca algae are emerging pathogens, whose incidence has increased importantly over the past two decades. Prototheca wickerhamii is a major human pathogen, responsible for at least 115 cases worldwide. Although the algae are receiving more attention nowadays, there is still a substantial knowledge gap regarding their biology, and pathogenicity in particular. Here we report, for the first time, the complete nuclear genome, organelle genomes, and transcriptome of the P. wickerhamii type strain ATCC 16529. RESULTS: The assembled genome size was of 16.7 Mbp, making it the smallest and most compact genome sequenced so far among the protothecans. Key features of the genome included a high overall GC content (64.5%), a high number (6081) and proportion (45.9%) of protein-coding genes, and a low repetitive sequence content (2.2%). The vast majority (90.6%) of the predicted genes were confirmed with the corresponding transcripts upon RNA-sequencing analysis. Most (93.2%) of the genes had their putative function assigned when searched against the InterProScan database. A fourth (23.3%) of the genes were annotated with an enzymatic activity possibly associated with the adaptation to the human host environment. The P. wickerhamii genome encoded a wide array of possible virulence factors, including those already identified in two model opportunistic fungal pathogens, i.e. Candida albicans and Trichophyton rubrum, and thought to be involved in invasion of the host or elicitation of the adaptive stress response. Approximately 6% of the P. wickerhamii genes matched a Pathogen-Host Interaction Database entry and had a previously experimentally proven role in the disease development. Furthermore, genes coding for proteins (e.g. ATPase, malate dehydrogenase) hitherto considered as potential virulence factors of Prototheca spp. were demonstrated in the P. wickerhamii genome. CONCLUSIONS: Overall, this study is the first to describe the genetic make-up of P. wickerhamii and discovers proteins possibly involved in the development of protothecosis.

Sequencing and Analysis of the Complete Organellar Genomes of Prototheca wickerhamii.

Of the Prototheca genus, Prototheca wickerhamii has the highest clinical significance in humans. However, neither nuclear nor organellar genomes of this species were sequenced until now. The hitherto determined and analyzed mitochondrial and plastid genomes of the alleged P. wickerhamii species belong in fact to another species, recently named Prototheca xanthoriae. This study provides a first insight into the organellar genomes of a true P. wickerhamii (type strain ATCC 16529). The P. wickerhamii mitochondrion had a 53.8-kb genome, which was considerably larger than that of Prototheca ciferrii (formerly Prototheca zopfii gen. 1) and Prototheca bovis (formerly Prototheca zopfii gen. 2), yet similarly functional, with the differences in size attributable to a higher number of introns and the presence of extra unique putative genes. The 48-kb plastid genome of P. wickerhamii, compared to autotrophic Trebouxiophyceae, was highly reduced due to the elimination of the photosynthesis-related genes. The gene content of the plastid genome of P. wickerhamii was, however, very similar to other colorless Prototheca species. Plastid genome-based phylogeny reinforced the polyphyly of the genus Prototheca, with Helicosporidium and Auxenochlorella branching within clades of Prototheca species. Phylogenetic reconstruction also confirmed the close relationship of P. wickerhamii and P. xanthoriae, which is reflected in the synteny of their organellar genomes. Interestingly, the entire set of atp genes was lost in P. wickerhamii plastid genome while being preserved in P. xanthoriae.

Biodiversity and Habitats of Polar Region Polyhydroxyalkanoic Acid-Producing Bacteria: Bioprospection by Popular Screening Methods.

Polyhydroxyalkanoates (PHAs), the intracellular polymers produced by various microorganisms as carbon and energy storage, are of great technological potential as biodegradable versions of common plastics. PHA-producing microbes are therefore in great demand and a plethora of different environments, especially extreme habitats, have been probed for the presence of PHA-accumulators. However, the polar region has been neglected in this regard, probably due to the low accessibility of the sampling material and unusual cultivation regime. Here, we present the results of a screening procedure involving 200 bacterial strains isolated from 25 habitats of both polar regions. Agar-based tests, microscopy, and genetic methods were conducted to elucidate the biodiversity and potential of polar-region PHA-accumulators. Microscopic observation of Nile Red stained cells proved to be the most reliable screening method as it allowed to confirm the characteristic bright orange glow of the Nile Red-PHA complex as well as the typical morphology of the PHA inclusions. Psychrophilic PHA-producers belonged mostly to the Comamonadaceae family (Betaproteobacteria) although actinobacterial PHA synthesizers of the families, Microbacteriaceae and Micrococcaceae also featured prominently. Glacial and postglacial habitats as well as developed polar region soils, were evaluated as promising for PHA-producer bioprospection. This study highlights the importance of psychrophiles as biodiverse and potent polyhydroxyalkanoate sources for scientific and application-aimed research.

Nostoc edaphicum CCNP1411 from the Baltic Sea-A New Producer of Nostocyclopeptides.

Nostocyclopeptides (Ncps) constitute a small class of nonribosomal peptides, exclusively produced by cyanobacteria of the genus Nostoc. The peptides inhibit the organic anion transporters, OATP1B3 and OATP1B1, and prevent the transport of the toxic microcystins and nodularin into hepatocytes. So far, only three structural analogues, Ncp-A1, Ncp-A2 and Ncp-M1, and their linear forms were identified in Nostoc strains as naturally produced cyanometabolites. In the current work, the whole genome sequence of the new Ncps producer, N. edaphicum CCNP1411 from the Baltic Sea, has been determined. The genome consists of the circular chromosome (7,733,505 bps) and five circular plasmids (from 44.5 kb to 264.8 kb). The nostocyclopeptide biosynthetic gene cluster (located between positions 7,609,981-7,643,289 bps of the chromosome) has been identified and characterized in silico. The LC-MS/MS analyzes of N. edaphicum CCNP1411 cell extracts prepared in aqueous methanol revealed several products of the genes. Besides the known peptides, Ncp-A1 and Ncp-A2, six other compounds putatively characterized as new noctocyclopeptide analogues were detected. This includes Ncp-E1 and E2 and their linear forms (Ncp-E1-L and E2-L), a cyclic Ncp-E3 and a linear Ncp-E4-L. Regardless of the extraction conditions, the cell contents of the linear nostocyclopeptides were found to be higher than the cyclic ones, suggesting a slow rate of the macrocyclization process.

Molecular identification of Trichocera maculipennis, an invasive fly species in the Maritime Antarctic.

Trichocera maculipennis, an invasive Diptera, was described for the first time in Antarctica in 2006 in a sewage system of one of the scientific stations on King George Island, South Shetland Islands, and started to increase its distribution within the island. To date, only taxonomical description of this species, based on morphological data has been available, as there were no molecular data recorded. In the present study, we present two methods of molecular identification of this species-based on partial cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S) genes. An appropriate and easy-to-use assay for proper and fast identification of invasive species is a key requirement for further management decisions, especially in such a fragile environment as found in terrestrial Antarctica.

Bacterial community dynamics in spontaneous sourdoughs made from wheat, spelt, and rye wholemeal flour.

Sourdough fermentation is a traditional process that is used to improve bread quality. A spontaneous sourdough ecosystem consists of a mixture of flour and water that is fermented by endogenous lactic acid bacteria (LAB) and yeasts. The aim of this study was to identify bacterial diversity during backslopping of spontaneous sourdoughs prepared from wheat, spelt, or rye wholemeal flour. Culture-dependent analyses showed that the number of LAB (109  CFU/ml) was higher by three orders of magnitude than the number of yeasts (106  CFU/ml), irrespective of the flour type. These results were complemented by next-generation sequencing of the 16S rDNA V3 and V4 variable regions. The dominant phylum in all sourdough samples was Firmicutes, which was represented exclusively by the Lactobacillales order. The two remaining and less abundant phyla were Proteobacteria and Bacteroidetes. The culture-independent approach allowed us to detect changes in microbial ecology during the 72-hr fermentation period. Weissella sp. was the most abundant genus after 24 hr of fermentation of the rye sourdough, but as the process progressed, its abundance decreased in favor of the Lactobacillus genus similarly as in wheat and spelt sourdoughs. The Lactobacillus genus was dominant in all sourdoughs after 72 hr, which was consistent with our results obtained using culture-dependent analyses. This work was carried out to determine the microbial biodiversity of sourdoughs that are made from wheat, spelt, and rye wholemeal flour and can be used as a source of strains for specific starter cultures to produce functional bread.

A smelly business: Microbiology of Adélie penguin guano (Point Thomas rookery, Antarctica).

Adélie penguins (Pygoscelis adeliae) are the most numerous flightless bird group breeding in coastal areas of Maritime and Continental Antarctica. Their activity leaves a mark on the land in the form of large guano deposits. This guano is an important nutrient source for terrestrial habitats of ice-free Antarctic areas, most notably by being the source of ammonia vapors which feed the surrounding grass, lichen and algae communities. Although investigated by researchers, the fate of the guano-associated microbial community and its role in decomposition processes remain vague. Therefore, by employing several direct community assessment methods combined with a broad culture-based approach we provide data on bacterial numbers, their activity and taxonomic affiliation in recently deposited and decayed Adélie penguin guano sampled at the Point Thomas rookery in Maritime Antarctica (King George Island). Our research indicates that recently deposited guano harbored mostly bacteria of penguin gut origin, presumably inactive in cold rookery settings. This material was rich in mesophilic enzymes active also at low temperatures, likely mediating early stage decomposition. Fresh guano colonization by environmental bacteria was minor, accomplished mostly by ammonia scavenging Jeotgalibaca sp. cells. Decayed guano contained 10-fold higher bacterial numbers with cold-active enzymes dominating the samples. Guano was colonized by uric-acid degrading and lipolytic Psychrobacter spp. and proteolytic Chryseobacterium sp. among others. Several spore-forming bacteria of penguin gut origin persisted in highly decomposed material, most notably uric-acid fermenting members of the Gottschalkiaceae family.

High-throughput sequencing approach in analysis of microbial communities colonizing natural gas pipelines.

This study provides a deep modern insight into the phylogenetic diversity among bacterial consortia found in working and nonworking high-methane natural gas pipelines located in Poland. The working pipeline was characterized by lower biodiversity (140-154 bacterial genera from 22 to 23 classes, depending on the source of the debris) in comparison to the off-gas pipeline (169 bacterial genera from 23 classes). The sediment recovered from the working pipeline contained mostly DNA identified as belonging to the phylum Firmicutes (66.4%-45.9% operational taxonomic units [OTUs]), predominantly Bacillus (41.4%-31.1% OTUs) followed by Lysinibacillus (2.6%-1.5% OTUs) and Clostridium (2.4%-1.8% OTUs). In the nonworking pipeline, Proteobacteria (46.8% OTUs) and Cyanobacteria (27.8% OTUs) were dominant. Over 30% of the Proteobacteria sequences showed homologies to Gammaproteobacteria, with Pseudomonas (7.1%), Enhydrobacter (2.1%), Stenotrophomonas (0.5%), and Haempohilus (0.4%) among the others. Differences were noted in terms of the chemical compositions of deposits originating from the working and nonworking gas pipelines. The deposits from the nonworking gas pipeline contained iron, as well as carbon (42.58%), sulphur (15.27%), and oxygen (15.32%). This composition can be linked to both the quantity and type of the resident microorganisms. The presence of a considerable amount of silicon (17.42%), and of aluminum, potassium, calcium, and magnesium at detectable levels, may likewise affect the metabolic activity of the resident consortia in the working gas pipeline. All the analyzed sediments included both bacteria known for causing and intensifying corrosion (e.g., Pseudomonas, Desulfovibrio, Shewanella, Serratia) and bacteria that can protect the surface of pipelines against deterioration (e.g., Bacillus). Biocorrosion is not related to a single mechanism or one species of microorganism, but results from the multidirectional activity of multiple microbial communities. The analysis presented here of the state of the microbiome in a gas pipeline during the real gas transport is a particularly valuable element of this work.

Draft Genome Sequences of the Highly Halotolerant Strain Zygosaccharomyces rouxii ATCC 42981 and the Novel Allodiploid Strain Zygosaccharomyces sapae ATB301T Obtained Using the MinION Platform.

Here, we report draft genome sequences of the halotolerant and allodiploid strains Zygosaccharomyces rouxii ATCC 42981 and Zygosaccharomyces sapae ABT301T. Illumina and Oxford Nanopore MinION sequencing revealed genome sizes of 20.9 and 24.7 Mb, respectively. This information will be useful for deciphering the genetics of hybrid adaptation to high salt and sugar concentrations in nonconventional yeasts.

Plasmids of Psychrotolerant Polaromonas spp. Isolated From Arctic and Antarctic Glaciers - Diversity and Role in Adaptation to Polar Environments.

Cold-active bacteria of the genus Polaromonas (class Betaproteobacteria) are important components of glacial microbiomes. In this study, extrachromosomal replicons of 26 psychrotolerant Polaromonas strains, isolated from Arctic and Antarctic glaciers, were identified, sequenced, and characterized. The plasmidome of these strains consists of 13 replicons, ranging in size from 3,378 to 101,077 bp. In silico sequence analyses identified the conserved backbones of these plasmids, composed of genes required for plasmid replication, stable maintenance, and conjugal transfer. Host range analysis revealed that all of the identified plasmids are narrow-host-range replicons, only able to replicate in bacteria of closely related genera (Polaromonas and Variovorax) of the Comamonadaceae family. Special attention was paid to the identification of plasmid auxiliary genetic information, which may contribute to the adaptation of bacteria to environmental conditions occurring in glaciers. Detailed analysis revealed the presence of genes encoding proteins potentially involved in (i) protection against reactive oxygen species, ultraviolet radiation, and low temperatures; (ii) transport and metabolism of organic compounds; (iii) transport of metal ions; and (iv) resistance to heavy metals. Some of the plasmids also carry genes required for the molecular assembly of iron-sulfur [Fe-S] clusters. Functional analysis of the predicted heavy metal resistance determinants demonstrated that their activity varies, depending on the host strain. This study provides the first molecular insight into the mobile DNA of Polaromonas spp. inhabiting polar glaciers. It has generated valuable data on the structure and properties of a pool of plasmids and highlighted their role in the biology of psychrotolerant Polaromonas strains and their adaptation to the environmental conditions of Arctic and Antarctic glaciers.