Publications by authors named "Jan Gawor"

25 Publications

  • Page 1 of 1

Sequencing and Analysis of the Complete Organellar Genomes of .

Front Plant Sci 2020 1;11:1296. Epub 2020 Sep 1.

Department of Medical Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland.

Of the genus, 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 species belong in fact to another species, recently named e. This study provides a first insight into the organellar genomes of a true (type strain ATCC 16529). The mitochondrion had a 53.8-kb genome, which was considerably larger than that of (formerly gen. 1) and (formerly 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 , compared to autotrophic Trebouxiophyceae, was highly reduced due to the elimination of the photosynthesis-related genes. The gene content of the plastid genome of was, however, very similar to other colorless species. Plastid genome-based phylogeny reinforced the polyphyly of the genus , with and branching within clades of species. Phylogenetic reconstruction also confirmed the close relationship of and , which is reflected in the synteny of their organellar genomes. Interestingly, the entire set of genes was lost in plastid genome while being preserved in .
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http://dx.doi.org/10.3389/fpls.2020.01296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7492744PMC
September 2020

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

Mar Drugs 2020 Aug 26;18(9). Epub 2020 Aug 26.

Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Piłsudskiego 46, PL-81378 Gdynia, Poland.

Nostocyclopeptides (Ncps) constitute a small class of nonribosomal peptides, exclusively produced by cyanobacteria of the genus . 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 strains as naturally produced cyanometabolites. In the current work, the whole genome sequence of the new Ncps producer, . 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 . The LC-MS/MS analyzes of . 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.
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http://dx.doi.org/10.3390/md18090442DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551626PMC
August 2020

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

Genes (Basel) 2020 07 31;11(8). Epub 2020 Jul 31.

Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences Pawińskiego 5A, 02-106 Warszawa, Poland.

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 family (Betaproteobacteria) although actinobacterial PHA synthesizers of the families, and 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.
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http://dx.doi.org/10.3390/genes11080873DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7464897PMC
July 2020

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

Mol Biol Rep 2020 Aug 10;47(8):6379-6384. Epub 2020 Jun 10.

Institute of Biology, University of Opole, Oleska 22, 45-052, Opole, Poland.

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.
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http://dx.doi.org/10.1007/s11033-020-05566-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7455578PMC
August 2020

Plasmidome of an environmental Acinetobacter lwoffii strain originating from a former gold and arsenic mine.

Plasmid 2020 07 4;110:102505. Epub 2020 May 4.

Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland. Electronic address:

Emerging important Acinetobacter strains commonly accommodate a plethora of mobile elements including plasmids of different size. Plasmids, apart from encoding modules enabling their self-replication and/or transmission, can carry a diverse number of genes, allowing the host cell to survive in an environment that would otherwise be lethal or restrictive for growth. The present study characterizes the plasmidome generated from an arsenic-resistant strain named ZS207, classified as Acinetobacter lwoffii. Sequencing effort revealed the presence of nine plasmids in the size between 4.3 and 38.4 kb as well as one 186.6 kb megaplasmid. All plasmids, except the megaplasmid, do apparently not confer distinguishing phenotypic features. In contrast, the megaplasmid carries arsenic and heavy metals resistance regions similar to those found in permafrost A. lwoffii strains. In-depth in silico analyses have shown a significant similarity between the regions from these plasmids, especially concerning multiple transposable elements, transfer and mobilization genes, and toxin-antitoxin systems. Since ars genes encode proteins of major significance in terms of potential use in bioremediation, arsenic resistance level of ZS207 was determined and the functionality of selected ars genes was examined. Additionally, we checked the functionality of plasmid-encoded toxin-antitoxin systems and their impact on the formation of persister cells.
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http://dx.doi.org/10.1016/j.plasmid.2020.102505DOI Listing
July 2020

A Tailspike with Exopolysaccharide Depolymerase Activity from a New Providencia stuartii Phage Makes Multidrug-Resistant Bacteria Susceptible to Serum-Mediated Killing.

Appl Environ Microbiol 2020 06 17;86(13). Epub 2020 Jun 17.

CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal

is emerging as a significant drug-resistant nosocomial pathogen, which encourages the search for alternative therapies. Here, we have isolated phage Stuart, a novel podovirus infecting multidrug-resistant hospital isolates of this bacterium. Phage Stuart is a proposed member of a new subfamily genus, with a 41,218-bp genome, direct 345-bp repeats at virion DNA ends, and limited sequence similarity of proteins to proteins in databases. Twelve out of the 52 predicted Stuart proteins are virion components. We found one to be a tailspike with depolymerase activity. The tailspike could form a highly thermostable oligomeric β-structure migrating close to the expected trimer in a nondenaturing gel. It appeared to be essential for the infection of three out of four hosts infected by phage Stuart. Moreover, it degraded the exopolysaccharide of relevant phage Stuart hosts, making the bacteria susceptible to serum killing. Prolonged exposure of a sensitive host to the tailspike did not cause the emergence of bacteria resistant to the phage or to serum killing, opposite to the prolonged exposure to the phage. This indicates that phage tail-associated depolymerases are attractive antivirulence agents that could complement the immune system in the fight with The pace at which multidrug-resistant strains emerge has been alarming. is an infrequent but relevant drug-resistant nosocomial pathogen causing local to systemic life-threatening infections. We propose an alternative approach to fight this bacterium based on the properties of phage tailspikes with depolymerase activity that degrade the surface bacterial polymers, making the bacteria susceptible to the immune system. Unlike antibiotics, phage tailspikes have narrow and specific substrate spectra, and by acting as antivirulent but not bactericidal agents they do not cause the selection of resistant bacteria.
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http://dx.doi.org/10.1128/AEM.00073-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7301845PMC
June 2020

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

Microbiologyopen 2020 04 11;9(4):e1009. Epub 2020 Feb 11.

Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.

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 (10  CFU/ml) was higher by three orders of magnitude than the number of yeasts (10  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.
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http://dx.doi.org/10.1002/mbo3.1009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142371PMC
April 2020

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

Sci Total Environ 2020 Apr 16;714:136714. Epub 2020 Jan 16.

Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland.

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.
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http://dx.doi.org/10.1016/j.scitotenv.2020.136714DOI Listing
April 2020

Genome sequence of Pseudomonas aeruginosa PAO1161, a PAO1 derivative with the ICEPae1161 integrative and conjugative element.

BMC Genomics 2020 Jan 6;21(1):14. Epub 2020 Jan 6.

Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Microbial Biochemistry, Warsaw, Poland.

Background: Pseudomonas aeruginosa is a cause of nosocomial infections, especially in patients with cystic fibrosis and burn wounds. PAO1 strain and its derivatives are widely used to study the biology of this bacterium, however recent studies demonstrated differences in the genomes and phenotypes of derivatives from different laboratories.

Results: Here we report the genome sequence of P. aeruginosa PAO1161 laboratory strain, a leu-, Rif, restriction-modification defective PAO1 derivative, described as the host of IncP-8 plasmid FP2, conferring the resistance to mercury. Comparison of PAO1161 genome with PAO1-UW sequence revealed lack of an inversion of a large genome segment between rRNA operons and 100 nucleotide polymorphisms, short insertions and deletions. These included a change in leuA, resulting in E108K substitution, which caused leucine auxotrophy and a mutation in rpoB, likely responsible for the rifampicin resistance. Nonsense mutations were detected in PA2735 and PA1939 encoding a DNA methyltransferase and a putative OLD family endonuclease, respectively. Analysis of revertants in these two genes showed that PA2735 is a component of a restriction-modification system, independent of PA1939. Moreover, a 12 kb RPG42 prophage and a novel 108 kb PAPI-1 like integrative conjugative element (ICE) encompassing a mercury resistance operon were identified. The ICEPae1161 was transferred to Pseudomonas putida cells, where it integrated in the genome and conferred the mercury resistance.

Conclusions: The high-quality P. aeruginosa PAO1161 genome sequence provides a reference for further research including e.g. investigation of horizontal gene transfer or comparative genomics. The strain was found to carry ICEPae1161, a functional PAPI-1 family integrative conjugative element, containing loci conferring mercury resistance, in the past attributed to the FP2 plasmid of IncP-8 incompatibility group. This indicates that the only known member of IncP-8 is in fact an ICE.
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http://dx.doi.org/10.1186/s12864-019-6378-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6945700PMC
January 2020

Comparative genomics and functional analysis of a highly adhesive dairy Lactobacillus paracasei subsp. paracasei IBB3423 strain.

Appl Microbiol Biotechnol 2019 Sep 29;103(18):7617-7634. Epub 2019 Jul 29.

Institute of Biochemistry and Biophysics, Polish Academy of Sciences (IBB PAS), Pawińskiego 5a, 02-106, Warsaw, Poland.

Various Lactobacillus paracasei strains are found in diverse environments, including dairy and plant materials and the intestinal tract of humans and animals, and are also used in the food industry or as probiotics. In this study, we have isolated a new strain L. paracasei subsp. paracasei IBB3423 from samples of raw cow milk collected in a citizen science project. IBB3423 showed some desired probiotic features such as high adhesion capacity and ability to metabolize inulin. Its complete genome sequence comprising the chromosome of 3,183,386 bp and two plasmids of 5986 bp and 51,211 bp was determined. In silico analysis revealed numerous genes encoding proteins involved in carbohydrate metabolism and of extracellular localization likely supporting interaction with host tissues. In vitro tests confirmed the high adhesion capacity of IBB3423 and showed that it even exceeds that of the highly adhesive L. rhamnosus GG. Curing of the larger plasmid indicated that the adhesive properties depend on the plasmid and thus could be determined by its pilus-encoding spaCBA genes.
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http://dx.doi.org/10.1007/s00253-019-10010-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6717177PMC
September 2019

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

Microbiologyopen 2019 08 6;8(8):e00806. Epub 2019 Feb 6.

Faculty of Biotechnology and Food Sciences, Institute of Fermentation Technology and Microbiology, Lodz University of Technology, Lodz, Poland.

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.
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http://dx.doi.org/10.1002/mbo3.806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6692550PMC
August 2019

The Ability of Lytic Staphylococcal Podovirus vB_SauP_phiAGO1.3 to Coexist in Equilibrium With Its Host Facilitates the Selection of Host Mutants of Attenuated Virulence but Does Not Preclude the Phage Antistaphylococcal Activity in a Nematode Infection Model.

Front Microbiol 2018 18;9:3227. Epub 2019 Jan 18.

Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.

Phage vB_SauP_phiAGO1.3 (phiAGO1.3) is a polyvalent lytic podovirus with a 17.6-kb genome (Gozdek et al., 2018). It can infect most of the human isolates of dominant clonal complexes. We show that a major factor contributing to the wide host range of phiAGO1.3 is a lack or sparcity of target sites for certain restriction-modification systems of types I and II in its genome. Phage phiAGO1.3 requires for adsorption β--GlcNAcylated cell wall teichoic acid, which is also essential for the expression of methicillin resistance. Under certain conditions an exposure of to phiAGO1.3 can lead to the establishment of a mixed population in which the bacteria and phages remain in equilibrium over multiple generations. This is reminiscent of the so called phage carrier state enabling the co-existence of phage-resistant and phage-sensitive cells supporting a continuous growth of the bacterial and phage populations. The stable co-existence of bacteria and phage favors the emergence of phage-resistant variants of the bacterium. All phiAGO1.3-resistant cells isolated from the phage-carrier-state cultures contained a mutation inactivating the two-component regulatory system ArlRS, essential for efficient expression of numerous virulence-associated traits. Moreover, the mutants were unaffected in their susceptibility to infection with an unrelated, polyvalent phage of the genus . The ability of phiAGO1.3 to establish phage-carrier-state cultures did not preclude its antistaphylococcal activity in an nematode infection model. Taken together our results suggest that phiAGO1.3 could be suitable for the therapeutic application in humans and animals, alone or in cocktails with phages. It might be especially useful in the treatment of infections with the majority of methicillin-resistant strains.
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http://dx.doi.org/10.3389/fmicb.2018.03227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346686PMC
January 2019

Draft Genome Sequences of the Highly Halotolerant Strain Zygosaccharomyces rouxii ATCC 42981 and the Novel Allodiploid Strain Zygosaccharomyces sapae ATB301 Obtained Using the MinION Platform.

Microbiol Resour Announc 2018 Aug 2;7(4). Epub 2018 Aug 2.

Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy.

Here, we report draft genome sequences of the halotolerant and allodiploid strains Zygosaccharomyces rouxii ATCC 42981 and Zygosaccharomyces sapae ABT301. 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.
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http://dx.doi.org/10.1128/MRA.00874-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256427PMC
August 2018

as a New Genetic Marker for Differentiation of Prototheca Species.

J Clin Microbiol 2018 10 25;56(10). Epub 2018 Sep 25.

Department of Molecular Phylogenetics and Evolution, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland.

Achlorophyllous unicellular microalgae of the genus (, ) are the only known plants that cause infections in both humans and animals, collectively referred to as protothecosis. Human protothecosis, most commonly manifested as cutaneous, articular, and disseminated disease, is primarily caused by , followed by and, sporadically, by and In veterinary medicine, however, is a major pathogen responsible for bovine mastitis, which is a predominant form of protothecal disease in animals. Historically, identification of spp. has relied upon phenotypic criteria; these were later replaced by molecular typing schemes, including DNA sequencing. However, the molecular markers interrogated so far, mostly located in the ribosomal DNA (rDNA) cluster, do not provide sufficient discriminatory power to distinguish among all spp. currently recognized. Our study is the first attempt to develop a fast, reliable, and specific molecular method allowing identification of all spp. We propose the mitochondrial gene as a new and robust marker for diagnostics and phylogenetic studies of the algae. The gene displayed important advantages over the rDNA markers. Not only did the gene have the highest discriminatory capacity for resolving all species, but it also performed best in terms of technical feasibility, understood as ease of amplification, sequencing, and multiple alignment analysis. Based on the species-specific polymorphisms in the partial gene, we developed a fast and straightforward PCR-restriction fragment length polymorphism (RFLP) assay for identification and differentiation of all species described so far. The newly proposed method is advocated to be a new gold standard in diagnostics of protothecal infections in human and animal populations.
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http://dx.doi.org/10.1128/JCM.00584-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156311PMC
October 2018

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

Front Microbiol 2018 18;9:1285. Epub 2018 Jun 18.

Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.

Cold-active bacteria of the genus (class ) are important components of glacial microbiomes. In this study, extrachromosomal replicons of 26 psychrotolerant 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. 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 ( and ) of the 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 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 strains and their adaptation to the environmental conditions of Arctic and Antarctic glaciers.
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http://dx.doi.org/10.3389/fmicb.2018.01285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015842PMC
June 2018

Complete Genome Sequences of Two Novel Staphylococcus aureus Podoviruses of Potential Therapeutic Use, vB_SauP_phiAGO1.3 and vB_SauP_phiAGO1.9.

Genome Announc 2018 Apr 26;6(17). Epub 2018 Apr 26.

Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences (IBB PAS), Warsaw, Poland

Here, we report the genome sequences of two phages belonging to the family and subfamily , vB_SauP_phiAGO1.3 and vB_SauP_phiAGO1.9, which were isolated from Warsaw sewage. Analysis of their genomes provides valuable information about the diversity of phages belonging to the genus and their genes that undergo evolutionary adaptation to cells of different host strains.
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http://dx.doi.org/10.1128/genomeA.00048-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920172PMC
April 2018

A modified method for molecular identification of Baylisascaris transfuga in European brown bears (Ursus arctos).

Parasitol Res 2017 Dec 27;116(12):3447-3452. Epub 2017 Oct 27.

Tatra National Park, Chałubińskiego 42a, 34-500, Zakopane, Poland.

Baylisascaris transfuga is a roundworm that has been reported worldwide in most bear species. In mammals and possibly humans, the larvae of B. transfuga can migrate in the tissues of aberrant hosts with larva migrans syndrome. The current study was performed to identify B. transfuga in faecal samples from free-ranging brown bears in the Tatra Mountains National Park in southern Poland. A commercial kit was used to extract genomic DNA directly from faecal samples. Additionally, a Chelex resin-based technique was successfully implemented to prepare a PCR template from eggs retrieved by flotation. Based on the flotation results of 32 collected faecal samples, the prevalence of B. transfuga was 15.6%. The parasite was confirmed in samples found to be positive during the initial flotation by a molecular assay using DNA isolated directly from faeces. The retrieved eggs were confirmed as B. transfuga after their DNA was extracted using the Chelex protocol. Based on PCR amplification and sequencing of a 413-bp segment of cytochrome c oxidase 1 (COI), the obtained sequence was 100% identical to the COI segment of B. transfuga after a BLAST comparison to the GenBank™ database. The current study includes the first molecular confirmation of B. transfuga in brown bears in the western part of the Carpathians. We show that direct extraction of parasite DNA from bear faeces is efficient for molecular assays. As an alternative, we present the effectiveness of a Chelex-based technique for fast and convenient DNA isolation from the difficult-to-disrupt eggs of B. transfuga for PCR. Molecular tests of parasite DNA extracted directly from faecal material have limits of detection related to the amount of eggs in the samples. Thus, using classical flotation to obtain eggs for PCR may increase the credibility of the results, particularly in cases with a low number of excreted eggs. The Chelex resin protocol has potential for application in studies of intestinal parasites in wildlife for which conventional flotation is routinely used for microscopy.
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http://dx.doi.org/10.1007/s00436-017-5660-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5691110PMC
December 2017

An optimized method for high quality DNA extraction from microalga for genome sequencing.

Plant Methods 2017 3;13:77. Epub 2017 Oct 3.

DNA Sequencing and Oligonucleotides Synthesis Laboratory at the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106 Warsaw, Poland.

Background: The complex cell wall structure of algae often precludes efficient extraction of their genetic material. The purpose of this study was to design a next-generation sequencing-suitable DNA isolation method for unicellular, achlorophyllous, yeast-like microalgae of the genus , the only known plant pathogens of both humans and animals. The effectiveness of the newly proposed scheme was compared with five other, previously described methods, commonly used for DNA isolation from plants and/or yeasts, available either as laboratory-developed, in-house assays, based on liquid nitrogen grinding or different enzymatic digestion, or as commercially manufactured kits.

Results: All five, previously described, isolation assays yielded DNA concentrations lower than those obtained with the new method, averaging 16.15 ± 25.39 vs 74.2 ± 0.56 ng/µL, respectively. The new method was also superior in terms of DNA purity, as measured by A260/A280 (-0.41 ± 4.26 vs 2.02 ± 0.03), and A260/A230 (1.20 ± 1.12 vs 1.97 ± 0.07) ratios. Only the liquid nitrogen-based method yielded DNA of comparable quantity (60.96 ± 0.16 ng/µL) and quality (A260/A280 = 2.08 ± 0.02; A260/A230 = 2.23 ± 0.26). Still, the new method showed higher integrity, which was best illustrated upon electrophoretic analysis. Genomic DNA of POL-1 strain isolated with the protocol herein proposed was successfully sequenced on the Illumina MiSeq platform.

Conclusions: A new method for DNA isolation from algae is described. The method, whose protocol involves glass beads pulverization and cesium chloride (CsCl) density gradient centrifugation, was demonstrated superior over the other common assays in terms of DNA quantity and quality. The method is also the first to offer the possibility of preparation of DNA template suitable for whole genome sequencing of spp.
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http://dx.doi.org/10.1186/s13007-017-0228-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627410PMC
October 2017

A Lytic Providencia rettgeri Virus of Potential Therapeutic Value Is a Deep-Branching Member of the Genus.

Appl Environ Microbiol 2017 Dec 16;83(23). Epub 2017 Nov 16.

Centre of Biological Engineering, Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Braga, Portugal

is emerging as a new opportunistic pathogen with high antibiotic resistance. The need to find alternative methods to control antibiotic-resistant bacteria and the recent advances in phage therapy motivate the search for new phages able to infect spp. This study describes the isolation and characterization of an obligatory lytic phage, vB_PreS_PR1 (PR1), with therapeutic potential against drug-resistant PR1 is a siphovirus. Its virion DNA size (118,537 bp), transcriptional organization, terminal repeats (10,461 bp), and nicks in the 3'-to-5' strand are similar to those of phage T5. However, sequence similarities of PR1 to phages of the genus at the DNA and protein levels are limited, suggesting that it belongs to a new species within the family. PR1 exhibits the ability to kill antibiotic-resistant strains, is highly specific to the species, and did not present known genomic markers indicating a temperate lifestyle. The lack of homologies between its proteins and proteins of the only other sequenced prophage, Redjac, suggests that these two phages evolved separately and may target different host proteins. The alarming increase in the number of bacteria resistant to antibiotics has been observed worldwide. This is particularly true for Gram-negative bacteria. For certain of their strains, no effective antibiotics are available. sp. has been a neglected pathogen but is emerging as a multidrug-resistant bacterium. This has revived interest in bacteriophages as alternative therapeutic agents against this bacterium. We describe the morphological, physiological, and genomic characterization of a novel lytic virus, PR1, which is able to kill drug-resistant clinical isolates. Genomic and phylogenetic analyses indicate that PR1 is a distant relative of genus representatives. The lack of known virulence- or temperate lifestyle-associated genes in the genome of PR1 makes this phage a potential candidate for therapeutic use. Analysis of its genome also improves our knowledge of the ecology and diversity of T5-like siphoviruses, providing a new link for evolutionary studies of this phage group.
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http://dx.doi.org/10.1128/AEM.01567-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5691406PMC
December 2017

Microsatellite Mutation Rate in Atlantic Sturgeon (Acipenser oxyrinchus).

J Hered 2017 Sep;108(6):686-692

Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland.

Understanding mutation rates can greatly extend the utility of population and conservation genetic analyses. Herein, we present an estimate of genome-wide microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus) based on parent-offspring transmission patterns. We screened 307 individuals for parentage and mutation-rate analysis applying 43 variable markers. Out of 13228 allele transfers, 11 mutations were detected, producing a mutation rate of 8.3 × 10-4 per locus per generation (95% confidence interval: 1.48 × 10-3, 4.15 × 10-4). Single-step mutations predominated and there were trends toward mutations in loci with greater polymorphism and allele length. Two of the detected mutations were most probably cluster mutations, being identified in 12 and 28 sibs, respectively. Finally, we observed evidences of polyploidy based on the sporadic presence of 3 or 4 alleles per locus in the genotyped individuals, supporting previous reports of incomplete diploidization in Atlantic sturgeon.
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http://dx.doi.org/10.1093/jhered/esx057DOI Listing
September 2017

Enrichment of Cryoconite Hole Anaerobes: Implications for the Subglacial Microbiome.

Microb Ecol 2017 04 7;73(3):532-538. Epub 2016 Nov 7.

Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.

Glaciers have recently been recognized as ecosystems comprised of several distinct habitats: a sunlit and oxygenated glacial surface, glacial ice, and a dark, mostly anoxic glacial bed. Surface meltwaters annually flood the subglacial sediments by means of drainage channels. Glacial surfaces host aquatic microhabitats called cryoconite holes, regarded as "hot spots" of microbial abundance and activity, largely contributing to the meltwaters' bacterial diversity. This study presents an investigation of cryoconite hole anaerobes and discusses their possible impact on subglacial microbial communities, combining 16S rRNA gene fragment amplicon sequencing and the traditional enrichment culture technique. Cryoconite hole sediment harbored bacteria belonging mainly to the Proteobacteria (21%), Bacteroidetes (16%), Actinobacteria (14%), and Planctomycetes (6%) phyla. An 8-week incubation of those sediments in Postgate C medium for sulfate reducers in airtight bottles, emulating subglacial conditions, eliminated a great majority of dominant taxa, leading to enrichment of the Firmicutes (62%), Proteobacteria (14%), and Bacteroidetes (13%), which consisted of anaerobic genera like Clostridium, Psychrosinus, Paludibacter, and Acetobacterium. Enrichment of Pseudomonas spp. also occurred, suggesting it played a role as a dominant oxygen scavenger, providing a possible scenario for anaerobic niche establishment in subglacial habitats. To our knowledge, this is the first paper to provide insight into the diversity of the anaerobic part of the cryoconite hole microbial community and its potential to contribute to matter turnover in anoxic, subglacial sites.
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http://dx.doi.org/10.1007/s00248-016-0886-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348551PMC
April 2017

Evidence of adaptation, niche separation and microevolution within the genus Polaromonas on Arctic and Antarctic glacial surfaces.

Extremophiles 2016 Jul 20;20(4):403-13. Epub 2016 Apr 20.

Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.

Polaromonas is one of the most abundant genera found on glacier surfaces, yet its ecology remains poorly described. Investigations made to date point towards a uniform distribution of Polaromonas phylotypes across the globe. We compared 43 Polaromonas isolates obtained from surfaces of Arctic and Antarctic glaciers to address this issue. 16S rRNA gene sequences, intergenic transcribed spacers (ITS) and metabolic fingerprinting showed great differences between hemispheres but also between neighboring glaciers. Phylogenetic distance between Arctic and Antarctic isolates indicated separate species. The Arctic group clustered similarly, when constructing dendrograms based on 16S rRNA gene and ITS sequences, as well as metabolic traits. The Antarctic strains, although almost identical considering 16S rRNA genes, diverged into 2 groups based on the ITS sequences and metabolic traits, suggesting recent niche separation. Certain phenotypic traits pointed towards cell adaptation to specific conditions on a particular glacier, like varying pH levels. Collected data suggest, that seeding of glacial surfaces with Polaromonas cells transported by various means, is of greater efficiency on local than global scales. Selection mechanisms present of glacial surfaces reduce the deposited Polaromonas diversity, causing subsequent adaptation to prevailing environmental conditions. Furthermore, interactions with other supraglacial microbiota, like algae cells may drive postselectional niche separation and microevolution within the Polaromonas genus.
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http://dx.doi.org/10.1007/s00792-016-0831-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4921121PMC
July 2016

Structural and functional genomics of plasmid pSinA of Sinorhizobium sp. M14 encoding genes for the arsenite oxidation and arsenic resistance.

J Biotechnol 2013 Apr 21;164(4):479-88. Epub 2013 Feb 21.

Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.

Plasmid pSinA of Sinorhizobium sp. M14 (Alphaproteobacteria) is the first described, natural, self-transferable plasmid harboring a complete set of genes for oxidation of arsenite. Removal of this plasmid from cells of the host strain caused the loss of resistance to arsenic and heavy metals (Cd, Co, Zn and Hg) and abolished the ability to grow on minimal salt medium supplemented with sodium arsenite as the sole energy source. Plasmid pSinA was introduced into other representatives of Alphaproteobacteria which resulted in acquisition of new abilities concerning arsenic resistance and oxidation, as well as heavy metals resistance. Microcosm experiments revealed that plasmid pSinA can also be transferred via conjugation into other indigenous bacteria from microbial community of As-contaminated soils, including representatives of Alpha- and Gammaproteobacteria. Analysis of "natural" transconjugants showed that pSinA is functional (expresses arsenite oxidase) and is stably maintained in their cells after approximately 60 generations of growth under nonselective conditions. This work clearly demonstrates that pSinA is a self-transferable, broad-host-range plasmid, which plays an important role in horizontal transfer of arsenic metabolism genes.
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http://dx.doi.org/10.1016/j.jbiotec.2013.01.017DOI Listing
April 2013

Genomics of staphylococcal Twort-like phages--potential therapeutics of the post-antibiotic era.

Adv Virus Res 2012 ;83:143-216

Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.

Polyvalent bacteriophages of the genus Twort-like that infect clinically relevant Staphylococcus strains may be among the most promising phages with potential therapeutic applications. They are obligatorily lytic, infect the majority of Staphylococcus strains in clinical strain collections, propagate efficiently and do not transfer foreign DNA by transduction. Comparative genomic analysis of 11 S. aureus/S. epidermidis Twort-like phages, as presented in this chapter, emphasizes their strikingly high similarity and clear divergence from phage Twort of the same genus, which might have evolved in hosts of a different species group. Genetically, these phages form a relatively isolated group, which minimizes the risk of acquiring potentially harmful genes. The order of genes in core parts of their 127 to 140-kb genomes is conserved and resembles that found in related representatives of the Spounavirinae subfamily of myoviruses. Functions of certain conserved genes can be predicted based on their homology to prototypical genes of model spounavirus SPO1. Deletions in the genomes of certain phages mark genes that are dispensable for phage development. Nearly half of the genes of these phages have no known homologues. Unique genes are mostly located near termini of the virion DNA molecule and are expressed early in phage development as implied by analysis of their potential transcriptional signals. Thus, many of them are likely to play a role in host takeover. Single genes encode homologues of bacterial virulence-associated proteins. They were apparently acquired by a common ancestor of these phages by horizontal gene transfer but presumably evolved towards gaining functions that increase phage infectivity for bacteria or facilitate mature phage release. Major differences between the genomes of S. aureus/S. epidermidis Twort-like phages consist of single nucleotide polymorphisms and insertions/deletions of short stretches of nucleotides, single genes, or introns of group I. Although the number and location of introns may vary between particular phages, intron shuffling is unlikely to be a major factor responsible for specificity differences.
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http://dx.doi.org/10.1016/B978-0-12-394438-2.00005-0DOI Listing
October 2012

Genome sequence and analysis of the tuber crop potato.

Nature 2011 Jul 10;475(7355):189-95. Epub 2011 Jul 10.

BGI-Shenzhen, Chinese Ministry of Agricultural, Key Lab of Genomics, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.
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http://dx.doi.org/10.1038/nature10158DOI Listing
July 2011