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Gorecki A, Ostapczuk P, Dziewit L. Diversity of antibiotic resistance gene variants at subsequent stages of the wastewater treatment process revealed by a metagenomic analysis of PCR amplicons. Front Genet 2024; 14:1334646. [PMID: 38274111 PMCID: PMC10808613 DOI: 10.3389/fgene.2023.1334646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Wastewater treatment plants have been recognised as point sources of various antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG) which are considered recently emerging biological contaminants. So far, culture-based and molecular-based methods have been successfully applied to monitor antimicrobial resistance (AMR) in WWTPs. However, the methods applied do not permit the comprehensive identification of the true diversity of ARGs. In this study we applied next-generation sequencing for a metagenomic analysis of PCR amplicons of ARGs from the subsequent stages of the analysed WWTP. The presence of 14 genes conferring resistance to different antibiotic families was screened by PCR. In the next step, three genes were selected for detailed analysis of changes of the profile of ARG variants along the process. A relative abundance of 79 variants was analysed. The highest diversity was revealed in the ermF gene, with 52 variants. The relative abundance of some variants changed along the purification process, and some ARG variants might be present in novel hosts for which they were currently unassigned. Additionally, we identified a pool of novel ARG variants present in the studied WWTP. Overall, the results obtained indicated that the applied method is sufficient for analysing ARG variant diversity.
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Affiliation(s)
- Adrian Gorecki
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Piotr Ostapczuk
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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2
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Ajijah N, Fiodor A, Dziurzynski M, Stasiuk R, Pawlowska J, Dziewit L, Pranaw K. Biocontrol potential of Pseudomonas protegens ML15 against Botrytis cinerea causing gray mold on postharvest tomato ( Solanum lycopersicum var. cerasiforme). Front Plant Sci 2023; 14:1288408. [PMID: 38143572 PMCID: PMC10748600 DOI: 10.3389/fpls.2023.1288408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023]
Abstract
Gray mold, caused by Botrytis cinerea is a major cause of post-harvest rot of fresh fruits and vegetables. The utilization of selected microorganisms as biocontrol agents is a promising alternative to effectively control gray mold on tomatoes. The current study was conducted to explore potential biocontrol mechanisms of the Pseudomonas strain to control infections on post-harvest tomatoes. Among the 8 tested bacterial isolates, Pseudomonas protegens ML15 demonstrated antagonistic activity to Botrytis cinerea. Moreover, P. protegens ML15 exhibited the production of siderophores, hydrogen cyanide, ammonia, exopolysaccharides, lipase, biosurfactant, 2,4-diacetylphloroglucinol, and several other antifungal compounds, such as 1-tetradecanol, cyclododecane, 2,4-di-tert-butylphenol, and 2-methyl-1-hexadecanol. A comprehensive genomic analysis of P. protegens ML15 unravels 18 distinct genetic regions with the potential for biosynthesizing secondary metabolites, known for their pivotal role in biocontrol responses against plant pathogens. In vivo, experiments showed that both culture suspension and cell-free supernatant of P. protegens ML15 significantly reduced fungal growth (53.0 ± 0.63%) and mitigated disease development (52.8 ± 1.5%) in cherry tomatoes at four days post-B. cinerea inoculation. During the infection, the application of P. protegens ML15 resulted in the augmentation of total antioxidant, phenolic content, and ascorbic acids content. Thus, our results suggested that P. protegens ML15's role as a biocontrol agent against B. cinerea-induced postharvest tomato decay achieved through the secretion of antifungal substances, induction of tomato defense responses, and inhibition of mycelial growth of B. cinerea. These findings provide a significant contribution to the ongoing search for alternative, eco-friendly methods of controlling gray mold in fresh products. The utilization of P. protegens ML15 as a biocontrol agent could help to reduce the reliance on chemical fungicides and promote sustainable agriculture practices.
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Affiliation(s)
- Nur Ajijah
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Angelika Fiodor
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Mikolaj Dziurzynski
- Department of Biology (DBIO), University of Florence, Sesto Fiorentino, Florence, Italy
| | - Robert Stasiuk
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Julia Pawlowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Center, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Kumar Pranaw
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Decewicz P, Romaniuk K, Gorecki A, Radlinska M, Dabrowska M, Wyszynska A, Dziewit L. Structure and functions of a multireplicon genome of Antarctic Psychrobacter sp. ANT_H3: characterization of the genetic modules suitable for the construction of the plasmid-vectors for cold-active bacteria. J Appl Genet 2023; 64:545-557. [PMID: 37145222 PMCID: PMC10457243 DOI: 10.1007/s13353-023-00759-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/01/2023] [Accepted: 04/22/2023] [Indexed: 05/06/2023]
Abstract
Among Psychrobacter spp., there are several multireplicon strains, carrying more than two plasmids. Psychrobacter sp. ANT_H3 carries as many as 11 extrachromosomal replicons, which is the highest number in Psychrobacter spp. Plasmids of this strain were subjected to detailed genomic analysis, which enables an insight into the structure and functioning of this multireplicon genome. The replication and conjugal transfer modules of ANT_H3 plasmids were analyzed functionally to discover their potential for being used as building blocks for the construction of novel plasmid-vectors for cold-active bacteria. It was shown that two plasmids have a narrow host range as they were not able to replicate in species other than Psychrobacter, while remaining plasmids had a wider host range and were functional in various Alpha- and Gammaproteobacteria. Moreover, it was confirmed that mobilization modules of seven plasmids were functional, i.e., could be mobilized for conjugal transfer by the RK2 conjugation system. Auxiliary genes were also distinguished in ANT_H3 plasmids, including these encoding putative DNA-protecting protein DprA, multidrug efflux SMR transporter of EmrE family, glycine cleavage system T protein, MscS small-conductance mechanosensitive channel protein, and two type II restriction-modification systems. Finally, all genome-retrieved plasmids of Psychrobacter spp. were subjected to complex genome- and proteome-based comparative analyses showing that Antarctic replicons are significantly different from plasmids from other locations.
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Affiliation(s)
- Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Krzysztof Romaniuk
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Adrian Gorecki
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Monika Radlinska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Maria Dabrowska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agnieszka Wyszynska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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Dziurzynski M, Gorecki A, Pawlowska J, Istel L, Decewicz P, Golec P, Styczynski M, Poszytek K, Rokowska A, Gorniak D, Dziewit L. Revealing the diversity of bacteria and fungi in the active layer of permafrost at Spitsbergen island (Arctic) - Combining classical microbiology and metabarcoding for ecological and bioprospecting exploration. Sci Total Environ 2023; 856:159072. [PMID: 36179845 DOI: 10.1016/j.scitotenv.2022.159072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Arctic soils are constantly subjected to extreme environmental conditions such as low humidity, strong winds, high salinity, freeze-thaw cycles, UV exposition, and low nutrient availability, therefore, they have developed unique microbial ecosystems. These environments provide excellent opportunities to study microbial ecology and evolution within pristine (i.e. with limited anthropogenic influence) regions since the High Arctic is still considered one of the wildest and least explored environments on the planet. This environment is also of interest for the screening and recovery of unique microbial strains suitable for various biotechnological applications. In this study, a combination of culture-depended and culture-independent approaches was used to determine the cultivation bias in studies of the diversity of cold-active microorganisms. Cultivation bias is a reduction in recovered diversity, introduced when applying a classical culturing technique. Six different soil types, collected in the vicinity of the Polish Polar Station Hornsund (Spitsbergen, Norway), were tested. It was revealed that the used media allowed recovery of only 6.37 % of bacterial and 20 % of fungal genera when compared with a culture-independent approach. Moreover, it was shown that a combination of R2A and Marine Broth media recovered as much as 93.6 % of all cultivable bacterial genera detected in this study. Based on these results, a novel protocol for genome-guided bioprospecting, combining a culture-dependent approach, metabarcoding, next-generation sequencing, and genomic data reuse was developed. With this methodology, 14 psychrotolerant, multi-metal-resistant strains, including the highly promising Rhodococcus spp., were obtained. These strains, besides increased metal tolerance, have a petroleum hydrocarbon utilization capacity, and thus may be good candidates for future bioremediation technologies, also suited to permanently cold regions.
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Affiliation(s)
- Mikolaj Dziurzynski
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Adrian Gorecki
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Julia Pawlowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-89 Warsaw, Poland
| | - Lukasz Istel
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-89 Warsaw, Poland
| | - Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Piotr Golec
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Michal Styczynski
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Krzysztof Poszytek
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Anna Rokowska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Dorota Gorniak
- Department of Microbiology and Mycology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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Fiodor A, Ajijah N, Dziewit L, Pranaw K. Biopriming of seed with plant growth-promoting bacteria for improved germination and seedling growth. Front Microbiol 2023; 14:1142966. [PMID: 36925481 PMCID: PMC10011460 DOI: 10.3389/fmicb.2023.1142966] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/06/2023] [Indexed: 03/08/2023] Open
Abstract
Several seed priming methods can be used to improve seed germination, seedling vigor, and to overcome abiotic stress. In addition to these benefits, only the biopriming method provides the additional benefit of biotic stress management, earning it special attention. Seed biopriming is useful in almost all crops around the world and is an environmentally friendly alternative to chemical fungicides. Biopriming usually refers to use of beneficial microorganisms, in particular plant growth-promoting bacteria (PGPB) able to survive under various harsh environmental conditions. In this study, various bacterial strains were isolated from samples of different origins, i.e., rhizospheric soil, desert sand, and sea mud. Preliminary screening of 156 bacterial isolates was conducted on the basis of their potassium (K), phosphorus (P) solubilization ability, and production of plant growth hormone, i.e., indole acetic acid (IAA). The most efficient bacteria were identified by 16S rRNA gene nucleotide sequences and further examined for their ACC deaminase activity, ammonia production, and biocontrol activity (defined via chitinolytic activity, HCN, and siderophores production). Finally, carrot seed germination assay was conducted with 10 shortlisted most potent isolates. 68.6, 58.3, and 66.7% of tested bacterial isolates were capable of P, K, and Zn solubilization, respectively. Klebsiella aerogenes AF3II1 showed the highest P and K solubilization, while isolate AF4II5, AF7II3, and PC3 showed the highest IAA synthesis ability. Serratia plymuthica EDC15 and Pseudomonas putida AF1I1 showed the strongest chitinolytic and siderophore production activity, respectively. Seven isolates demonstrated strong HCN production ability. Five isolates improved carrot seed germination. Only selected isolates with plant growth-promoting properties can improve carrot germination. The results of this study demonstrate that mainly auxins are involved in seed germination. Furthermore, the data suggest that phosphate solubilization ability may play an additional role in seed germination.
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Affiliation(s)
- Angelika Fiodor
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Nur Ajijah
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Kumar Pranaw
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Styczynski M, Rogowska A, Nyabayo C, Decewicz P, Romaniuk F, Pączkowski C, Szakiel A, Suessmuth R, Dziewit L. Heterologous production and characterization of a pyomelanin of Antarctic Pseudomonas sp. ANT_H4: a metabolite protecting against UV and free radicals, interacting with iron from minerals and exhibiting priming properties toward plant hairy roots. Microb Cell Fact 2022; 21:261. [PMID: 36527127 PMCID: PMC9756463 DOI: 10.1186/s12934-022-01990-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Antarctica has one of the most extreme environments in the world. This region is inhabited by specifically adapted microorganisms that produce various unique secondary metabolites (e.g. pigments) enabling their survival under the harsh environmental conditions. It was already shown that these natural, biologically active molecules may find application in various fields of biotechnology. RESULTS In this study, a cold-active brown-pigment-producing Pseudomonas sp. ANT_H4 strain was characterized. In-depth genomic analysis combined with the application of a fosmid expression system revealed two different pathways of melanin-like compounds biosynthesis by the ANT_H4 strain. The chromatographic behavior and Fourier-transform infrared spectroscopic analyses allowed for the identification of the extracted melanin-like compound as a pyomelanin. Furthermore, optimization of the production and thorough functional analyses of the pyomelanin were performed to test its usability in biotechnology. It was confirmed that ANT_H4-derived pyomelanin increases the sun protection factor, enables scavenging of free radicals, and interacts with the iron from minerals. Moreover, it was shown for the first time that pyomelanin exhibits priming properties toward Calendula officinalis hairy roots in in vitro cultures. CONCLUSIONS Results of the study indicate the significant biotechnological potential of ANT_H4-derived pyomelanin and open opportunities for future applications. Taking into account protective features of analyzed pyomelanin it may be potentially used in medical biotechnology and cosmetology. Especially interesting was showing that pyomelanin exhibits priming properties toward hairy roots, which creates a perspective for its usage for the development of novel and sustainable agrotechnical solutions.
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Affiliation(s)
- Michal Styczynski
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agata Rogowska
- grid.12847.380000 0004 1937 1290Department of Plant Biochemistry, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Christine Nyabayo
- grid.6734.60000 0001 2292 8254Institute of Chemistry, Technical University of Berlin, Berlin, Germany
| | - Przemyslaw Decewicz
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Filip Romaniuk
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Cezary Pączkowski
- grid.12847.380000 0004 1937 1290Department of Plant Biochemistry, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Szakiel
- grid.12847.380000 0004 1937 1290Department of Plant Biochemistry, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Roderich Suessmuth
- grid.6734.60000 0001 2292 8254Institute of Chemistry, Technical University of Berlin, Berlin, Germany
| | - Lukasz Dziewit
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Okrasińska A, Decewicz P, Majchrowska M, Dziewit L, Muszewska A, Dolatabadi S, Kruszewski Ł, Błocka Z, Pawłowska J. Marginal lands and fungi - linking the type of soil contamination with fungal community composition. Environ Microbiol 2022; 24:3809-3825. [PMID: 35415861 PMCID: PMC9544152 DOI: 10.1111/1462-2920.16007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 11/27/2022]
Abstract
Fungi can be found in almost all ecosystems. Some of them can even survive in harsh, anthropogenically transformed environments, such as post-industrial soils. In order to verify how the soil fungal diversity may be changed by pollution, two soil samples from each of the 28 post-industrial sites were collected. Each soil sample was characterized in terms of concentration of heavy metals and petroleum derivatives. To identify soil fungal communities, fungal ITS2 amplicon was sequenced for each sample using Illumina MiSeq platform. There were significant differences in the community structure and taxonomic diversity among the analyzed samples. The highest taxon richness and evenness were observed in the non-polluted sites, and lower numbers of taxa were identified in multi-polluted soils. The presence of monocyclic aromatic hydrocarbons, gasoline, and mineral oil were determined as the factors driving the differences in the mycobiome. Further, in the culture-based selection experiment, two main groups of fungi growing on polluted media were identified - generalists able to live in the presence of pollution, and specialists adapted to the usage of BTEX as a sole source of energy. Our selection experiment proved that it is long-term soil contamination that shapes the community, rather than temporary addition of pollutant. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Alicja Okrasińska
- Institute of Evolutionary Biology, Centre of Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw
| | - Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Maria Majchrowska
- Institute of Evolutionary Biology, Centre of Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Łukasz Kruszewski
- Institute of Geological Sciences, Polish Academy of Sciences, Warsaw, Poland
| | - Zuzanna Błocka
- Institute of Evolutionary Biology, Centre of Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw
| | - Julia Pawłowska
- Institute of Evolutionary Biology, Centre of Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw
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Gorecki A, Musialowski M, Wolacewicz M, Decewicz P, Ferreira C, Vejmelkova D, Grzesiuk M, Manaia CM, Bartacek J, Dziewit L. Development and validation of novel PCR primers for identification of plasmid-mediated colistin resistance (mcr) genes in various environmental settings. J Hazard Mater 2022; 425:127936. [PMID: 34883371 DOI: 10.1016/j.jhazmat.2021.127936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/31/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance is considered one of the biggest threats to public health and has become a major concern for governments and international organizations. Combating this problem starts with improving global surveillance of antibiotic resistance genes (ARGs) and applying standardized protocols, both in a clinical and environmental context, in agreement with the One Health approach. Exceptional efforts should be directed to controlling ARGs conferring resistance to Critically Important Antimicrobials (CIA). In this study, a systematic literature review to synthesize data on the identification of mcr genes using a PCR technique was performed. Additionally, a novel set of PCR primers for mcr-1 - mcr-9 genes detection was proposed. The developed primers were in silico and experimentally validated by comparison with mcr-specific PCR primers reported in the literature. This validation, besides being a proof-of-concept for primers' usefulness, provided insight into the distribution of mcr genes in municipal wastewater, clay and river sediments, glacier moraine, manure, seagulls and auks feces and daphnids from four countries. This analysis proved that commonly used primers may deliver false results, and some mcr genes may be overlooked in tested samples. Newly-developed PCR primers turned out to be relevant for the screening of mcr genes in various environments.
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Affiliation(s)
- Adrian Gorecki
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Marcin Musialowski
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Mikolaj Wolacewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Catarina Ferreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, Porto 4169-005, Portugal
| | - Dana Vejmelkova
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Malgorzata Grzesiuk
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Celia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, Porto 4169-005, Portugal
| | - Jan Bartacek
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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Styczynski M, Biegniewski G, Decewicz P, Rewerski B, Debiec-Andrzejewska K, Dziewit L. Application of Psychrotolerant Antarctic Bacteria and Their Metabolites as Efficient Plant Growth Promoting Agents. Front Bioeng Biotechnol 2022; 10:772891. [PMID: 35284420 PMCID: PMC8907978 DOI: 10.3389/fbioe.2022.772891] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
Iron is the fourth most abundant element on earth. However, its low bioavailability is a key plant-growth limiting factor. Bacteria play an important role in plant growth promotion since they produce specific secondary metabolites that may increase macro- and micronutrient accessibility in soil. Therefore, bacterial-derived iron chelators, as well as surface-active compounds, are recognised as essential to plant welfare. In this study, three cold-active Antarctic bacterial strains, i.e. Pseudomonas sp. ANT_H12B, Psychrobacter sp. ANT_H59 and Bacillus sp. ANT_WA51, were analysed. The physiological and genomic characterisation of these strains revealed their potential for plant growth promotion, reflected in the production of various biomolecules, including biosurfactants (that may lower the medium surface tension of even up to 53%) and siderophores (including ANT_H12B-produced mixed-type siderophore that demonstrated the highest production, reaching the concentration of up to 1.065 mM), increasing the availability of nutrients in the environment and neutralising fungal pathogens. Tested bacteria demonstrated an ability to promote the growth of a model plant, alfalfa, increasing shoots’ length and fresh biomass even up to 26 and 46% respectively; while their metabolites increased the bioavailability of iron in soil up to 40%. It was also revealed that the introduced strains did not disrupt physicochemical conditions and indigenous soil microbial composition, which suggests that they are promising amendments preserving the natural biodiversity of soil and increasing its fertility.
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Affiliation(s)
- Michal Styczynski
- Institute of Microbiology, Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Gabriel Biegniewski
- Institute of Microbiology, Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Przemyslaw Decewicz
- Institute of Microbiology, Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bartosz Rewerski
- Institute of Microbiology, Department of Geomicrobiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Klaudia Debiec-Andrzejewska
- Institute of Microbiology, Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Institute of Microbiology, Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- *Correspondence: Lukasz Dziewit,
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10
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Miłobedzka A, Ferreira C, Vaz-Moreira I, Calderón-Franco D, Gorecki A, Purkrtova S, Dziewit L, Singleton CM, Nielsen PH, Weissbrodt DG, Manaia CM. Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle. J Hazard Mater 2022; 424:127407. [PMID: 34629195 DOI: 10.1016/j.jhazmat.2021.127407] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 05/10/2023]
Abstract
Antibiotic resistance (AR) is a global problem requiring international cooperation and coordinated action. Global monitoring must rely on methods available and comparable across nations to quantify AR occurrence and identify sources and reservoirs, as well as paths of AR dissemination. Numerous analytical tools that are gaining relevance in microbiology, have the potential to be applied to AR research. This review summarizes the state of the art of AR monitoring methods, considering distinct needs, objectives and available resources. Based on the overview of distinct approaches that are used or can be adapted to monitor AR, it is discussed the potential to establish reliable and useful monitoring schemes that can be implemented in distinct contexts. This discussion places the environmental monitoring within the One-Health approach, where two types of risk, dissemination across distinct environmental compartments, and transmission to humans, must be considered. The plethora of methodological approaches to monitor AR and the variable features of the monitored sites challenge the capacity of the scientific community and policy makers to reach a common understanding. However, the dialogue between different methods and the production of action-oriented data is a priority. The review aims to warm up this discussion.
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Affiliation(s)
- Aleksandra Miłobedzka
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic; Institute of Evolutionary Biology, University of Warsaw, Warsaw, Poland.
| | - Catarina Ferreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | | | - Adrian Gorecki
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Sabina Purkrtova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Caitlin M Singleton
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | | | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal.
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11
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Krucon T, Dziewit L, Drewniak L. Insight Into Ecology, Metabolic Potential, and the Taxonomic Composition of Bacterial Communities in the Periodic Water Pond on King George Island (Antarctica). Front Microbiol 2021; 12:708607. [PMID: 34690951 PMCID: PMC8531505 DOI: 10.3389/fmicb.2021.708607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022] Open
Abstract
Polar regions contain a wide variety of lentic ecosystems. These include periodic ponds that have a significant impact on carbon and nitrogen cycling in polar environments. This study was conducted to assess the taxonomic and metabolic diversity of bacteria found in Antarctic pond affected by penguins and sea elephants and to define their role in ongoing processes. Metabolic assays showed that of the 168 tested heterotrophic bacteria present in the Antarctic periodic pond, 96% are able to degrade lipids, 30% cellulose, 26% proteins, and 26% starch. The taxonomic classification of the obtained isolates differs from that based on the composition of the 16S rRNA relative abundances in the studied pond. The dominant Actinobacteria constituting 45% of isolates represents a low proportion of the community, around 4%. With the addition of run-off, the proportions of inhabiting bacteria changed, including a significant decrease in the abundance of Cyanobacteria, from 2.38 to 0.33%, increase of Firmicutes from 9.32 to 19.18%, and a decreasing richness (Chao1 index from 1299 to 889) and diversity (Shannon index from 4.73 to 4.20). Comparative studies of communities found in different Antarctic environments indicate a great role for penguins in shaping bacterial populations.
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Affiliation(s)
- Tomasz Krucon
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Drewniak
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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12
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Pyzik A, Ciuchcinski K, Dziurzynski M, Dziewit L. The Bad and the Good-Microorganisms in Cultural Heritage Environments-An Update on Biodeterioration and Biotreatment Approaches. Materials (Basel) 2021; 14:E177. [PMID: 33401448 PMCID: PMC7795576 DOI: 10.3390/ma14010177] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022]
Abstract
Cultural heritage objects constitute a very diverse environment, inhabited by various bacteria and fungi. The impact of these microorganisms on the degradation of artworks is undeniable, but at the same time, some of them may be applied for the efficient biotreatment of cultural heritage assets. Interventions with microorganisms have been proven to be useful in restoration of artworks, when classical chemical and mechanical methods fail or produce poor or short-term effects. The path to understanding the impact of microbes on historical objects relies mostly on multidisciplinary approaches, combining novel meta-omic technologies with classical cultivation experiments, and physico-chemical characterization of artworks. In particular, the development of metabolomic- and metatranscriptomic-based analyses associated with metagenomic studies may significantly increase our understanding of the microbial processes occurring on different materials and under various environmental conditions. Moreover, the progress in environmental microbiology and biotechnology may enable more effective application of microorganisms in the biotreatment of historical objects, creating an alternative to highly invasive chemical and mechanical methods.
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Affiliation(s)
- Adam Pyzik
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (K.C.); (M.D.); (L.D.)
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13
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Ciezkowska M, Bajda T, Decewicz P, Dziewit L, Drewniak L. Effect of Clinoptilolite and Halloysite Addition on Biogas Production and Microbial Community Structure during Anaerobic Digestion. Materials (Basel) 2020; 13:E4127. [PMID: 32957462 PMCID: PMC7560405 DOI: 10.3390/ma13184127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 01/22/2023]
Abstract
The study presents a comparison of the influence of a clinoptilolite-rich rock-zeolite (commonly used for improving anaerobic digestion processes)-and a highly porous clay mineral, halloysite (mainly used for gas purification), on the biogas production process. Batch experiments showed that the addition of each mineral increased the efficiency of mesophilic anaerobic digestion of both sewage sludge and maize silage. However, halloysite generated 15% higher biogas production during maize silage transformation. Halloysite also contributed to a much higher reduction of chemical oxygen demand for both substrates (by ~8% for maize silage and ~14% for sewage sludge) and a higher reduction of volatile solids and total ammonia for maize silage (by ~8% and ~4%, respectively). Metagenomic analysis of the microbial community structure showed that the addition of both mineral sorbents influenced the presence of key members of archaea and bacteria occurring in a well-operated biogas reactor. The significant difference between zeolite and halloysite is that the latter promoted the immobilization of key methanogenic archaea Methanolinea (belong to Methanomicrobia class). Based on this result, we postulate that halloysite could be useful not only as a sorbent for (bio)gas treatment methodologies but also as an agent for improving biogas production.
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Affiliation(s)
- Martyna Ciezkowska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (M.C.); (P.D.); (L.D.)
| | - Tomasz Bajda
- Department of Mineralogy, Petrography and Geochemistry, Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland;
| | - Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (M.C.); (P.D.); (L.D.)
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (M.C.); (P.D.); (L.D.)
| | - Lukasz Drewniak
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (M.C.); (P.D.); (L.D.)
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14
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Piotrowska M, Dziewit L, Ostrowski R, Chmielowska C, Popowska M. Molecular Characterization and Comparative Genomics of IncQ-3 Plasmids Conferring Resistance to Various Antibiotics Isolated from a Wastewater Treatment Plant in Warsaw (Poland). Antibiotics (Basel) 2020; 9:antibiotics9090613. [PMID: 32957637 PMCID: PMC7557826 DOI: 10.3390/antibiotics9090613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022] Open
Abstract
As small, mobilizable replicons with a broad host range, IncQ plasmids are widely distributed among clinical and environmental bacteria. They carry antibiotic resistance genes, and it has been shown that they confer resistance to β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, sulphonamides, and tetracycline. The previously proposed classification system divides the plasmid group into four subgroups, i.e., IncQ-1, IncQ-2, IncQ-3, and IncQ-4. The last two subgroups have been poorly described so far. The aim of this study was to analyze five newly identified IncQ-3 plasmids isolated from a wastewater treatment plant in Poland and to compare them with all known plasmids belonging to the IncQ-3 subgroup whose sequences were retrieved from the NCBI database. The complete nucleotide sequences of the novel plasmids were annotated and bioinformatic analyses were performed, including identification of core genes and auxiliary genetic load. Furthermore, functional experiments testing plasmid mobility were carried out. Phylogenetic analysis based on three core genes (repA, mobA/repB, and mobC) revealed the presence of three main clusters of IncQ-3 replicons. Apart from having a highly conserved core, the analyzed IncQ-3 plasmids were vectors of antibiotic resistance genes, including (I) the qnrS2 gene that encodes fluoroquinolone resistance and (II) β-lactam, trimethoprim, and aminoglycoside resistance genes within integron cassettes.
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Affiliation(s)
- Marta Piotrowska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Rafał Ostrowski
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Cora Chmielowska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Magdalena Popowska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
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15
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Maj A, Dziewit L, Drewniak L, Garstka M, Krucon T, Piatkowska K, Gieczewska K, Czarnecki J, Furmanczyk E, Lasek R, Baj J, Bartosik D. In vivo creation of plasmid pCRT01 and its use for the construction of carotenoid-producing Paracoccus spp. strains that grow efficiently on industrial wastes. Microb Cell Fact 2020; 19:141. [PMID: 32660485 PMCID: PMC7359593 DOI: 10.1186/s12934-020-01396-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022] Open
Abstract
Background Carotenoids are natural tetraterpene pigments widely utilized in the food, pharmaceutical and cosmetic industries. Currently, chemical synthesis of these compounds outperforms their production in Escherichia coli or yeast due to the limited efficiency of the latter. The use of natural microbial carotenoid producers, such as bacteria of the genus Paracoccus (Alphaproteobacteria), may help to optimize this process. In order to couple the ability to synthesize these pigments with the metabolic versatility of this genus, we explored the possibility of introducing carotenoid synthesis genes into strains capable of efficient growth on simple low-cost media. Results We constructed two carotenoid-producing strains of Paracoccus carrying a new plasmid, pCRT01, which contains the carotenoid synthesis gene locus crt from Paracoccus marcusii OS22. The plasmid was created in vivo via illegitimate recombination between crt-carrying vector pABW1 and a natural “paracoccal” plasmid pAMI2. Consequently, the obtained fusion replicon is stably maintained in the bacterial population without the need for antibiotic selection. The introduction of pCRT01 into fast-growing “colorless” strains of Paracoccus aminophilus and Paracoccus kondratievae converted them into efficient producers of a range of both carotenes and xanthophylls. The exact profile of the produced pigments was dependent on the strain genetic background. To reduce the cost of carotenoid production in this system, we tested the growth and pigment synthesis efficiency of the two strains on various simple media, including raw industrial effluent (coal-fired power plant flue gas desulfurization wastewater) supplemented with molasses, an industrial by-product rich in sucrose. Conclusions We demonstrated a new approach for the construction of carotenoid-producing bacterial strains which relies on a single plasmid-mediated transfer of a pigment synthesis gene locus between Paracoccus strains. This strategy facilitates screening for producer strains in terms of synthesis efficiency, pigment profile and ability to grow on low-cost industrial waste-based media, which should increase the cost-effectiveness of microbial production of carotenoids.
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Affiliation(s)
- Anna Maj
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Lukasz Drewniak
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Maciej Garstka
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Krucon
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Katarzyna Piatkowska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Katarzyna Gieczewska
- Department of Plant Anatomy and Cytology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Jakub Czarnecki
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.,Bacterial Genome Plasticity, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Ewa Furmanczyk
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.,Department of Plant Protection from Pests, Research Institute of Horticulture, Skierniewice, Poland
| | - Robert Lasek
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Jadwiga Baj
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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Bilinski J, Dziurzynski M, Grzesiowski P, Podsiadly E, Stelmaszczyk-Emmel A, Dzieciatkowski T, Dziewit L, Basak GW. Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods. J Clin Med 2020; 9:E2036. [PMID: 32610522 PMCID: PMC7409046 DOI: 10.3390/jcm9072036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 01/27/2023] Open
Abstract
Methods of stool assessment are mostly focused on next-generation sequencing (NGS) or classical culturing, but only rarely both. We conducted a series of experiments using a multi-method approach to trace the stability of gut microbiota in various donors over time, to find the best method for the proper selection of fecal donors and to find "super-donor" indicators. Ten consecutive stools donated by each of three donors were used for the experiments (30 stools in total). The experiments assessed bacterial viability measured by flow cytometry, stool culturing on different media and in various conditions, and NGS (90 samples in total). There were no statistically significant differences between live and dead cell numbers; however, we found a group of cells classified as not-dead-not-alive, which may be possibly important in selection of "good" donors. Donor C, being a regular stool donor, was characterized by the largest number of cultivable species (64). Cultivable core microbiota (shared by all donors) was composed of only 16 species. ANCOM analysis of NGS data highlighted particular genera to be more abundant in one donor vs. the others. There was a correlation between the not-dead-not-alive group found in flow cytometry and Anaeroplasma found by NGS, and we could distinguish a regular stool donor from the others. In this work, we showed that combining various methods of microbiota assessment gives more information than each method separately.
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Affiliation(s)
- Jaroslaw Bilinski
- Department of Hematology, Oncology and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Mikolaj Dziurzynski
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Pawel Grzesiowski
- Foundation for the Infection Prevention Institute, 02-991 Warsaw, Poland;
| | - Edyta Podsiadly
- Department of Microbiology, Institute of Medical Sciences, University of Rzeszów, 35-310 Rzeszów, Poland;
| | - Anna Stelmaszczyk-Emmel
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Tomasz Dzieciatkowski
- Department of Medical Microbiology, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Grzegorz W. Basak
- Department of Hematology, Oncology and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland;
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Decewicz P, Golec P, Szymczak M, Radlinska M, Dziewit L. Identification and Characterization of the First Virulent Phages, Including a Novel Jumbo Virus, Infecting Ochrobactrum spp. Int J Mol Sci 2020; 21:ijms21062096. [PMID: 32197547 PMCID: PMC7139368 DOI: 10.3390/ijms21062096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 12/26/2022] Open
Abstract
The Ochrobactrum genus consists of an extensive repertoire of biotechnologically valuable bacterial strains but also opportunistic pathogens. In our previous study, a novel strain, Ochrobactrum sp. POC9, which enhances biogas production in wastewater treatment plants (WWTPs) was identified and thoroughly characterized. Despite an insightful analysis of that bacterium, its susceptibility to bacteriophages present in WWTPs has not been evaluated. Using raw sewage sample from WWTP and applying the enrichment method, two virulent phages, vB_OspM_OC and vB_OspP_OH, which infect the POC9 strain, were isolated. These are the first virulent phages infecting Ochrobactrum spp. identified so far. Both phages were subjected to thorough functional and genomic analyses, which allowed classification of the vB_OspM_OC virus as a novel jumbo phage, with a genome size of over 227 kb. This phage encodes DNA methyltransferase, which mimics the specificity of cell cycle regulated CcrM methylase, a component of the epigenetic regulatory circuits in Alphaproteobacteria. In this study, an analysis of the overall diversity of Ochrobactrum-specific (pro)phages retrieved from databases and extracted in silico from bacterial genomes was also performed. Complex genome mining allowed us to build similarity networks to compare 281 Ochrobactrum-specific viruses. Analyses of the obtained networks revealed a high diversity of Ochrobactrum phages and their dissimilarity to the viruses infecting other bacteria.
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Affiliation(s)
- Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.D.); (M.R.)
| | - Piotr Golec
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.G.); (M.S.)
| | - Mateusz Szymczak
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.G.); (M.S.)
| | - Monika Radlinska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.D.); (M.R.)
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.D.); (M.R.)
- Correspondence: ; Tel.: +48-225-541-406
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18
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019. [PMID: 31285584 DOI: 10.1038/s41564-019-04904-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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19
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019; 4:1727-1736. [PMID: 31285584 DOI: 10.1101/527796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 05/22/2019] [Indexed: 05/26/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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20
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Gorecki A, Decewicz P, Dziurzynski M, Janeczko A, Drewniak L, Dziewit L. Literature-based, manually-curated database of PCR primers for the detection of antibiotic resistance genes in various environments. Water Res 2019; 161:211-221. [PMID: 31200218 DOI: 10.1016/j.watres.2019.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/31/2019] [Accepted: 06/04/2019] [Indexed: 06/09/2023]
Abstract
A literature-based, manually-curated database of PCR primers for the detection of antibiotic resistance genes in various environments was constructed (LCPDb-ARG; lcpdb.ddg.biol.uw.edu.pl and lcpdb.ddlemb.com). Currently, this database is comprised of 607 PCR primer pairs designed for the amplification of various genes conferring resistance to antibiotics representing 10 classes of antimicrobial agents. Three parameters were assigned for each primer pair: specificity, efficacy and taxonomic efficacy. These parameters were evaluated using a novel bioinformatic tool, UniPriVal, developed for this study. UniPriVal was used to validate each primer pair against various databases, including the Bacterial Antimicrobial Resistance Reference Gene Database (BARRGDB) and those of the National Center of Biotechnology Information (NCBI). Primer pairs specific for each antibiotic resistance gene were ranked based on their model success metric value. To validate the utility and correctness of the information collected in the LCPDb-ARG, selected primer pairs were tested in bioinformatic and experimental PCR surveys. To our knowledge, this is the first database designed to facilitate PCR monitoring of the occurrence and diversity of antibiotic resistance genes in environmental and clinical samples. The internal validation system of this user-friendly application enables the quantified ranking of PCR primer pairs, which assists selection of the best primers for each application.
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Affiliation(s)
- Adrian Gorecki
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Przemyslaw Decewicz
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Mikolaj Dziurzynski
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Anna Janeczko
- Municipal and Industrial Wastewater Treatment Plant, Nadwislanska 46, 32-600, Oswiecim, Poland
| | - Lukasz Drewniak
- University of Warsaw, Faculty of Biology, Laboratory of Environmental Pollution Analysis, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Lukasz Dziewit
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096, Warsaw, Poland.
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21
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Poszytek K, Karczewska-Golec J, Dziurzynski M, Stepkowska-Kowalska O, Gorecki A, Decewicz P, Dziewit L, Drewniak L. Genome-Wide and Functional View of Proteolytic and Lipolytic Bacteria for Efficient Biogas Production through Enhanced Sewage Sludge Hydrolysis. Molecules 2019; 24:molecules24142624. [PMID: 31323902 PMCID: PMC6680700 DOI: 10.3390/molecules24142624] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/17/2019] [Accepted: 07/17/2019] [Indexed: 11/23/2022] Open
Abstract
In this study, we used a multifaceted approach to select robust bioaugmentation candidates for enhancing biogas production and to demonstrate the usefulness of a genome-centric approach for strain selection for specific bioaugmentation purposes. We also investigated the influence of the isolation source of bacterial strains on their metabolic potential and their efficiency in enhancing anaerobic digestion. Whole genome sequencing, metabolic pathway reconstruction, and physiological analyses, including phenomics, of phylogenetically diverse strains, Rummeliibacillus sp. POC4, Ochrobactrum sp. POC9 (both isolated from sewage sludge) and Brevundimonas sp. LPMIX5 (isolated from an agricultural biogas plant) showed their diverse enzymatic activities, metabolic versatility and ability to survive under varied growth conditions. All tested strains display proteolytic, lipolytic, cellulolytic, amylolytic, and xylanolytic activities and are able to utilize a wide array of single carbon and energy sources, as well as more complex industrial by-products, such as dairy waste and molasses. The specific enzymatic activity expressed by the three strains studied was related to the type of substrate present in the original isolation source. Bioaugmentation with sewage sludge isolates–POC4 and POC9–was more effective for enhancing biogas production from sewage sludge (22% and 28%, respectively) than an approach based on LPMIX5 strain (biogas production boosted by 7%) that had been isolated from an agricultural biogas plant, where other type of substrate is used.
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Affiliation(s)
- Krzysztof Poszytek
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Joanna Karczewska-Golec
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Mikolaj Dziurzynski
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Olga Stepkowska-Kowalska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Adrian Gorecki
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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22
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Decewicz P, Dziewit L, Golec P, Kozlowska P, Bartosik D, Radlinska M. Characterization of the virome of Paracoccus spp. (Alphaproteobacteria) by combined in silico and in vivo approaches. Sci Rep 2019; 9:7899. [PMID: 31133656 PMCID: PMC6536676 DOI: 10.1038/s41598-019-44460-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/17/2019] [Indexed: 12/19/2022] Open
Abstract
Bacteria of the genus Paracoccus inhabit various pristine and anthropologically-shaped environments. Many Paracoccus spp. have biotechnological value and several are opportunistic human pathogens. Despite extensive knowledge of their metabolic potential and genome architecture, little is known about viruses of Paracoccus spp. So far, only three active phages infecting these bacteria have been identified. In this study, 16 Paracoccus strains were screened for the presence of active temperate phages, which resulted in the identification of five novel viruses. Mitomycin C-induced prophages were isolated, visualized and their genomes sequenced and thoroughly analyzed, including functional validation of their toxin-antitoxin systems. This led to the identification of the first active Myoviridae phage in Paracoccus spp. and four novel Siphoviridae phages. In addition, another 53 prophages were distinguished in silico within genomic sequences of Paracoccus spp. available in public databases. Thus, the Paracoccus virome was defined as being composed of 66 (pro)phages. Comparative analyses revealed the diversity and mosaicism of the (pro)phage genomes. Moreover, similarity networking analysis highlighted the uniqueness of Paracoccus (pro)phages among known bacterial viruses.
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Affiliation(s)
- Przemyslaw Decewicz
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Lukasz Dziewit
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096, Warsaw, Poland.
| | - Piotr Golec
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Patrycja Kozlowska
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Virology, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Dariusz Bartosik
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Monika Radlinska
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Virology, Miecznikowa 1, 02-096, Warsaw, Poland
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23
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Romaniuk K, Golec P, Dziewit L. Insight Into the Diversity and Possible Role of Plasmids in the Adaptation of Psychrotolerant and Metalotolerant Arthrobacter spp. to Extreme Antarctic Environments. Front Microbiol 2018; 9:3144. [PMID: 30619210 PMCID: PMC6305408 DOI: 10.3389/fmicb.2018.03144] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/04/2018] [Indexed: 11/13/2022] Open
Abstract
Arthrobacter spp. are coryneform Gram-positive aerobic bacteria, belonging to the class Actinobacteria. Representatives of this genus have mainly been isolated from soil, mud, sludge or sewage, and are usually mesophiles. In recent years, the presence of Arthrobacter spp. was also confirmed in various extreme, including permanently cold, environments. In this study, 36 psychrotolerant and metalotolerant Arthrobacter strains isolated from petroleum-contaminated soil from the King George Island (Antarctica), were screened for the presence of plasmids. The identified replicons were thoroughly characterized in order to assess their diversity and role in the adaptation of Arthrobacter spp. to harsh Antarctic conditions. The screening process identified 11 different plasmids, ranging in size from 8.4 to 90.6 kb. A thorough genomic analysis of these replicons detected the presence of numerous genes encoding proteins that potentially perform roles in adaptive processes such as (i) protection against ultraviolet (UV) radiation, (ii) resistance to heavy metals, (iii) transport and metabolism of organic compounds, (iv) sulfur metabolism, and (v) protection against exogenous DNA. Moreover, 10 of the plasmids carry genetic modules enabling conjugal transfer, which may facilitate their spread among bacteria in Antarctic soil. In addition, transposable elements were identified within the analyzed plasmids. Some of these elements carry passenger genes, which suggests that these replicons may be actively changing, and novel genetic modules of adaptive value could be acquired by transposition events. A comparative genomic analysis of plasmids identified in this study and other available Arthrobacter plasmids was performed. This showed only limited similarities between plasmids of Antarctic Arthrobacter strains and replicons of other, mostly mesophilic, isolates. This indicates that the plasmids identified in this study are novel and unique replicons. In addition, a thorough meta-analysis of 247 plasmids of psychrotolerant bacteria was performed, revealing the important role of these replicons in the adaptation of their hosts to extreme environments.
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Affiliation(s)
- Krzysztof Romaniuk
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Piotr Golec
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
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24
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Ciok A, Dziewit L. Exploring the genome of Arctic Psychrobacter sp. DAB_AL32B and construction of novel Psychrobacter-specific cloning vectors of an increased carrying capacity. Arch Microbiol 2018; 201:559-569. [PMID: 30448872 PMCID: PMC6579772 DOI: 10.1007/s00203-018-1595-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/27/2018] [Accepted: 11/09/2018] [Indexed: 01/03/2023]
Abstract
Cold-active bacteria are currently of great interest in biotechnology, and their genomic and physiological features have been extensively studied. One of the model psychrotolerant bacteria are Psychrobacter spp. Analysis of Arctic psychrophilic Psychrobacter sp. DAB_AL32B genome content provided an insight into its overall stress response, and genes conferring protection against various life-limiting factors (i.e., low temperature, increased ultraviolet radiation, oxidative stress and osmotic pressure) were recognized and described. Moreover, it was revealed that the strain carries a large plasmid pP32BP2. Its replication system was used for the construction of two novel shuttle vectors (pPS-NR-Psychrobacter-Escherichia coli-specific plasmid and pPS-BR-Psychrobacter-various Proteobacteria-specific plasmid) of an increased carrying capacity, which may be used for genetic engineering of Psychrobacter spp.
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Affiliation(s)
- Anna Ciok
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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25
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Fagorzi C, Checcucci A, diCenzo GC, Debiec-Andrzejewska K, Dziewit L, Pini F, Mengoni A. Harnessing Rhizobia to Improve Heavy-Metal Phytoremediation by Legumes. Genes (Basel) 2018; 9:genes9110542. [PMID: 30413093 PMCID: PMC6266702 DOI: 10.3390/genes9110542] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 12/15/2022] Open
Abstract
Rhizobia are bacteria that can form symbiotic associations with plants of the Fabaceae family, during which they reduce atmospheric di-nitrogen to ammonia. The symbiosis between rhizobia and leguminous plants is a fundamental contributor to nitrogen cycling in natural and agricultural ecosystems. Rhizobial microsymbionts are a major reason why legumes can colonize marginal lands and nitrogen-deficient soils. Several leguminous species have been found in metal-contaminated areas, and they often harbor metal-tolerant rhizobia. In recent years, there have been numerous efforts and discoveries related to the genetic determinants of metal resistance by rhizobia, and on the effectiveness of such rhizobia to increase the metal tolerance of host plants. Here, we review the main findings on the metal resistance of rhizobia: the physiological role, evolution, and genetic determinants, and the potential to use native and genetically-manipulated rhizobia as inoculants for legumes in phytoremediation practices.
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Affiliation(s)
- Camilla Fagorzi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Alice Checcucci
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - George C diCenzo
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Klaudia Debiec-Andrzejewska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Francesco Pini
- Department of Agri-food Production and Environmental Science, University of Florence, 50144 Florence, Italy.
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
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26
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diCenzo GC, Debiec K, Krzysztoforski J, Uhrynowski W, Mengoni A, Fagorzi C, Gorecki A, Dziewit L, Bajda T, Rzepa G, Drewniak L. Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. Genes (Basel) 2018; 9:E379. [PMID: 30060533 PMCID: PMC6115938 DOI: 10.3390/genes9080379] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/22/2018] [Accepted: 07/25/2018] [Indexed: 12/23/2022] Open
Abstract
Ensifer (Sinorhizobium) sp. M14 is an efficient arsenic-oxidizing bacterium (AOB) that displays high resistance to numerous metals and various stressors. Here, we report the draft genome sequence and genome-guided characterization of Ensifer sp. M14, and we describe a pilot-scale installation applying the M14 strain for remediation of arsenic-contaminated waters. The M14 genome contains 6874 protein coding sequences, including hundreds not found in related strains. Nearly all unique genes that are associated with metal resistance and arsenic oxidation are localized within the pSinA and pSinB megaplasmids. Comparative genomics revealed that multiple copies of high-affinity phosphate transport systems are common in AOBs, possibly as an As-resistance mechanism. Genome and antibiotic sensitivity analyses further suggested that the use of Ensifer sp. M14 in biotechnology does not pose serious biosafety risks. Therefore, a novel two-stage installation for remediation of arsenic-contaminated waters was developed. It consists of a microbiological module, where M14 oxidizes As(III) to As(V) ion, followed by an adsorption module for As(V) removal using granulated bog iron ores. During a 40-day pilot-scale test in an abandoned gold mine in Zloty Stok (Poland), water leaving the microbiological module generally contained trace amounts of As(III), and dramatic decreases in total arsenic concentrations were observed after passage through the adsorption module. These results demonstrate the usefulness of Ensifer sp. M14 in arsenic removal performed in environmental settings.
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Affiliation(s)
- George C diCenzo
- Laboratory of Microbial Genetics, Department of Biology, University of Florence, via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Klaudia Debiec
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Jan Krzysztoforski
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Warynskiego 1, 00-645 Warsaw, Poland.
| | - Witold Uhrynowski
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Alessio Mengoni
- Laboratory of Microbial Genetics, Department of Biology, University of Florence, via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Camilla Fagorzi
- Laboratory of Microbial Genetics, Department of Biology, University of Florence, via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Adrian Gorecki
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Tomasz Bajda
- Department of Mineralogy, Petrography and Geochemistry, Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland.
| | - Grzegorz Rzepa
- Department of Mineralogy, Petrography and Geochemistry, Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland.
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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27
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Ciok A, Budzik K, Zdanowski MK, Gawor J, Grzesiak J, Decewicz P, Gromadka R, Bartosik D, Dziewit L. Plasmids of Psychrotolerant Polaromonas spp. Isolated From Arctic and Antarctic Glaciers - Diversity and Role in Adaptation to Polar Environments. Front Microbiol 2018; 9:1285. [PMID: 29967598 PMCID: PMC6015842 DOI: 10.3389/fmicb.2018.01285] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/25/2018] [Indexed: 12/23/2022] Open
Abstract
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.
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Affiliation(s)
- Anna Ciok
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Karol Budzik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Marek K. Zdanowski
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jan Gawor
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jakub Grzesiak
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Robert Gromadka
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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28
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Burczynska A, Dziewit L, Decewicz P, Struzycka I, Wroblewska M. Application of Metagenomic Analyses in Dentistry as a Novel Strategy Enabling Complex Insight into Microbial Diversity of the Oral Cavity. Pol J Microbiol 2018; 66:9-15. [PMID: 29359689 DOI: 10.5604/17331331.1234988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The composition of the oral microbiome in healthy individuals is complex and dynamic, and depends on many factors, such as anatomical location in the oral cavity, diet, oral hygiene habits or host immune responses. It is estimated at present that worldwide about 2 billion people suffer from diseases of the oral cavity, mainly periodontal disease and dental caries. Importantly, the oral microflora involved in local infections may spread and cause systemic, even life-threatening infections. In search for etiological agents of infections in dentistry, traditional approaches are not sufficient, as about 50% of oral bacteria are not cultivable. Instead, metagenomic analyses are particularly useful for studies of the complex oral microbiome - both in healthy individuals, and in patients with oral and dental diseases. In this paper we review the current and future applications of metagenomic studies in evaluation of both the composition of the oral microbiome as well as its potential pathogenic role in infections in dentistry.
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Affiliation(s)
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland
| | - Przemysław Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland; Research and Development for Life Sciences Ltd., Poland
| | - Izabela Struzycka
- Department of Comprehensive Dental Care, Medical University of Warsaw, Poland
| | - Marta Wroblewska
- Department of Dental Microbiology, Medical University of Warsaw, Poland; Department of Microbiology, Central Clinical Hospital in Warsaw, Poland
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29
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Czarnecki J, Dziewit L, Puzyna M, Prochwicz E, Tudek A, Wibberg D, Schlüter A, Pühler A, Bartosik D. Lifestyle-determining extrachromosomal replicon pAMV1 and its contribution to the carbon metabolism of the methylotrophic bacterium Paracoccus aminovorans JCM 7685. Environ Microbiol 2017; 19:4536-4550. [PMID: 28856785 DOI: 10.1111/1462-2920.13901] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/11/2017] [Accepted: 08/24/2017] [Indexed: 11/29/2022]
Abstract
Plasmids play an important role in the adaptation of bacteria to changeable environmental conditions. As the main vectors of horizontal gene transfer, they can spread genetic information among bacteria, sometimes even across taxonomic boundaries. Some plasmids carry genes involved in the utilization of particular carbon compounds, which can provide a competitive advantage to their hosts in particular ecological niches. Analysis of the multireplicon genome of the soil bacterium P. aminovorans JCM 7685 revealed the presence of an extrachromosomal replicon pAMV1 (185 kb) with a unique structure and properties. This lifestyle-determining plasmid carries genes facilitating the metabolism of many different carbon compounds including sugars, short-chain organic acids and C1 compounds. Plasmid pAMV1 contains a large methylotrophy island (MEI) that is essential not only for the utilization of particular C1 compounds but also for the central methylotrophic metabolism required for the assimilation of C1 units (serine cycle). We demonstrate that the expression of the main serine cycle genes is induced in the presence of C1 compounds by the transcriptional regulator ScyR. The extrachromosomal localization of the MEI and the distribution of related genes in Paracoccus spp. indicate that it could have been acquired by HGT by an ancestor of P. aminovorans.
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Affiliation(s)
- Jakub Czarnecki
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw 02-096, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw 02-096, Poland
| | - Maria Puzyna
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw 02-096, Poland
| | - Emilia Prochwicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw 02-096, Poland
| | - Agnieszka Tudek
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw 02-096, Poland
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Senior Research Group: Genome Research of Industrial Microorganisms, Universitätsstrasse 27, Bielefeld University, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Senior Research Group: Genome Research of Industrial Microorganisms, Universitätsstrasse 27, Bielefeld University, 33615 Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Senior Research Group: Genome Research of Industrial Microorganisms, Universitätsstrasse 27, Bielefeld University, 33615 Bielefeld, Germany
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw 02-096, Poland
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Wojcieszak M, Dziewit L, Drewniak L. Biostimulation and bioaugmentation of microbial community involved in the biogas production of sewage sludge. J Biotechnol 2017. [DOI: 10.1016/j.jbiotec.2017.06.688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Uhrynowski W, Decewicz P, Dziewit L, Radlinska M, Krawczyk PS, Lipinski L, Adamska D, Drewniak L. Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism. Front Microbiol 2017; 8:936. [PMID: 28611742 PMCID: PMC5446998 DOI: 10.3389/fmicb.2017.00936] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/09/2017] [Indexed: 12/28/2022] Open
Abstract
Aeromonas spp. are among the most ubiquitous microorganisms, as they have been isolated from different environmental niches including waters, soil, as well as wounds and digestive tracts of poikilothermic animals and humans. Although much attention has been paid to the pathogenicity of Aeromonads, the role of these bacteria in environmentally important processes, such as transformation of heavy metals, remains to be discovered. Therefore, the aim of this study was a detailed genomic characterization of Aeromonas sp. O23A, the first representative of this genus capable of dissimilatory arsenate reduction. The strain was isolated from microbial mats from the Zloty Stok mine (SW Poland), an environment strongly contaminated with arsenic. Previous physiological studies indicated that O23A may be involved in both mobilization and immobilization of this metalloid in the environment. To discover the molecular basis of the mechanisms behind the observed abilities, the genome of O23A (∼5.0 Mbp) was sequenced and annotated, and genes for arsenic respiration, heavy metal resistance (hmr) and other phenotypic traits, including siderophore production, were identified. The functionality of the indicated gene modules was assessed in a series of minimal inhibitory concentration analyses for various metals and metalloids, as well as mineral dissolution experiments. Interestingly, comparative analyses revealed that O23A is related to a fish pathogen Aeromonas salmonicida subsp. salmonicida A449 which, however, does not carry genes for arsenic respiration. This indicates that the dissimilatory arsenate reduction ability may have been lost during genome reduction in pathogenic strains, or acquired through horizontal gene transfer. Therefore, particular emphasis was placed upon the mobilome of O23A, consisting of four plasmids, a phage, and numerous transposable elements, which may play a role in the dissemination of hmr and arsenic metabolism genes in the environment. The obtained results indicate that Aeromonas sp. O23A is well-adapted to the extreme environmental conditions occurring in the Zloty Stok mine. The analysis of genome encoded traits allowed for a better understanding of the mechanisms of adaptation of the strain, also with respect to its presumable role in colonization and remediation of arsenic-contaminated waters, which may never have been discovered based on physiological analyses alone.
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Affiliation(s)
- Witold Uhrynowski
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of WarsawWarsaw, Poland
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of WarsawWarsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of WarsawWarsaw, Poland
| | - Monika Radlinska
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of WarsawWarsaw, Poland
| | - Pawel S Krawczyk
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | - Leszek Lipinski
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | - Dorota Adamska
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of WarsawWarsaw, Poland
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Alsarraf M, Mohallal EME, Mierzejewska EJ, Behnke-Borowczyk J, Welc-Falęciak R, Bednarska M, Dziewit L, Zalat S, Gilbert F, Behnke JM, Bajer A. Description of Candidatus Bartonella fadhilae n. sp. and Candidatus Bartonella sanaae n. sp. (Bartonellaceae) from Dipodillus dasyurus and Sekeetamys calurus (Gerbillinae) from the Sinai Massif (Egypt). Vector Borne Zoonotic Dis 2017; 17:483-494. [PMID: 28541836 PMCID: PMC5512320 DOI: 10.1089/vbz.2016.2093] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Bartonella spp. are parasites of mammalian erythrocytes and endothelial cells, transmitted by blood-feeding arthropod ectoparasites. Different species of rodents may constitute the main hosts of Bartonella, including several zoonotic species of Bartonella. The aim of this study was to identify and compare Bartonella species and genotypes isolated from rodent hosts from the South Sinai, Egypt. Prevalence of Bartonella infection was assessed in rodents (837 Acomys dimidiatus, 73 Acomys russatus, 111 Dipodillus dasyurus, and 65 Sekeetamys calurus) trapped in 2000, 2004, 2008, and 2012 in four dry montane wadis around St. Katherine town in the Sinai Mountains. Total DNA was extracted from blood samples, and PCR amplification and sequencing of the Bartonella-specific 860-bp gene fragment of rpoB and the 810-bp gene fragment of gltA were used for molecular and phylogenetic analyses. The overall prevalence of Bartonella in rodents was 7.2%. Prevalence differed between host species, being 30.6%, 10.8%, 9.6%, and 3.6% in D. dasyurus, S. calurus, A. russatus, and A. dimidiatus, respectively. The phylogenetic analyses of six samples of Bartonella (five from D. dasyurus and one from S. calurus) based on a fragment of the rpoB gene, revealed the existence of two distinct genetic groups (with 95–96% reciprocal sequence identity), clustering with several unidentified isolates obtained earlier from the same rodent species, and distant from species that have already been described (90–92% of sequence identity to the closest match from the GenBank reference database). Thus, molecular and phylogenetic analyses led to the description of two species: Candidatus Bartonella fadhilae n. sp. and Candidatus Bartonella sanaae n. sp. The identification of their vectors and the medical significance of these species need further investigation.
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Affiliation(s)
- Mohammed Alsarraf
- 1 Department of Parasitology, Faculty of Biology, Institute of Zoology, University of Warsaw , Warsaw, Poland
| | | | - Ewa J Mierzejewska
- 1 Department of Parasitology, Faculty of Biology, Institute of Zoology, University of Warsaw , Warsaw, Poland
| | - Jolanta Behnke-Borowczyk
- 3 Department of Forest Phytopathology, Faculty of Forestry, Poznań University of Life Sciences , Poznań, Poland
| | - Renata Welc-Falęciak
- 1 Department of Parasitology, Faculty of Biology, Institute of Zoology, University of Warsaw , Warsaw, Poland
| | - Małgorzata Bednarska
- 1 Department of Parasitology, Faculty of Biology, Institute of Zoology, University of Warsaw , Warsaw, Poland
| | - Lukasz Dziewit
- 4 Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw , Warsaw, Poland
| | - Samy Zalat
- 5 Department of Zoology, Suez Canal University , Ismailia, Egypt
| | - Francis Gilbert
- 6 School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham , Nottingham, United Kingdom
| | - Jerzy M Behnke
- 6 School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham , Nottingham, United Kingdom
| | - Anna Bajer
- 1 Department of Parasitology, Faculty of Biology, Institute of Zoology, University of Warsaw , Warsaw, Poland
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Romaniuk K, Dziewit L, Decewicz P, Mielnicki S, Radlinska M, Drewniak L. Molecular characterization of the pSinB plasmid of the arsenite oxidizing, metallotolerant Sinorhizobium sp. M14 - insight into the heavy metal resistome of sinorhizobial extrachromosomal replicons. FEMS Microbiol Ecol 2017; 93:fiw215. [PMID: 27797963 DOI: 10.1093/femsec/fiw215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2016] [Indexed: 11/13/2022] Open
Abstract
Sinorhizobium sp. M14 is an As(III)-oxidizing, psychrotolerant strain, capable of growth in the presence of extremely high concentrations of arsenic and many other heavy metals. Metallotolerant abilities of the M14 strain depend upon the presence of two extrachromosomal replicons: pSinA (∼ 109 kb) and pSinB (∼ 300 kb). The latter was subjected to complex analysis. The performed analysis demonstrated that the plasmid pSinB is a narrow-host-range repABC-type replicon, which is fully stabilized by the phd-vapC-like toxin-antitoxin stabilizing system. In silico analysis showed that among the phenotypic gene clusters of the plasmid pSinB, eight modules are potentially involved in heavy metals resistance (HMR). These modules carry genes encoding efflux pumps, permeases, transporters and copper oxidases, which provide resistance to arsenic, cadmium, cobalt, copper, iron, mercury, nickel, silver and zinc. The functional analysis revealed that the HMR modules are active and have an effect on the minimal inhibitory concentration (MIC) values observed for the heterological host cells. The phenotype was manifested by an increase or decrease of the MICs of heavy metals and it was strain specific. The analysis of distribution of the heavy metal resistance genes, i.e. resistome, in Sinorhizobium spp. plasmids, revealed that the HMR modules are common in these replicons.
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Affiliation(s)
- Krzysztof Romaniuk
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Sebastian Mielnicki
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Monika Radlinska
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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Ciok A, Adamczuk M, Bartosik D, Dziewit L. Identification and Characterization of Putative Integron-Like Elements of the Heavy-Metal-Hypertolerant Strains of Pseudomonas spp. J Microbiol Biotechnol 2016; 26:1983-1992. [PMID: 27470282 DOI: 10.4014/jmb.1605.05068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Pseudomonas strains isolated from the heavily contaminated Lubin copper mine and Zelazny Most post-flotation waste reservoir in Poland were screened for the presence of integrons. This analysis revealed that two strains carried homologous DNA regions composed of a gene encoding a DNA_BRE_C domain-containing tyrosine recombinase (with no significant sequence similarity to other integrases of integrons) plus a three-component array of putative integron gene cassettes. The predicted gene cassettes encode three putative polypeptides with homology to (i) transmembrane proteins, (ii) GCN5 family acetyltransferases, and (iii) hypothetical proteins of unknown function (homologous proteins are encoded by the gene cassettes of several class 1 integrons). Comparative sequence analyses identified three structural variants of these novel integron-like elements within the sequenced bacterial genomes. Analysis of their distribution revealed that they are found exclusively in strains of the genus Pseudomonas.
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Affiliation(s)
- Anna Ciok
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland
| | - Marcin Adamczuk
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland
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35
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diCenzo GC, Checcucci A, Bazzicalupo M, Mengoni A, Viti C, Dziewit L, Finan TM, Galardini M, Fondi M. Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti. Nat Commun 2016; 7:12219. [PMID: 27447951 PMCID: PMC4961836 DOI: 10.1038/ncomms12219] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 06/10/2016] [Indexed: 12/14/2022] Open
Abstract
The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental adaptations and/or niche switching) remains unclear. Here we report a genome-scale metabolic model of the legume symbiont Sinorhizobium meliloti that is integrated with carbon utilization data for 1,500 genes with 192 carbon substrates. Growth of S. meliloti is modelled in three ecological niches (bulk soil, rhizosphere and nodule) with a focus on the role of each of its three replicons. We observe clear metabolic differences during growth in the tested ecological niches and an overall reprogramming following niche switching. In silico examination of the inferred fitness of gene deletion mutants suggests that secondary replicons evolved to fulfil a specialized function, particularly host-associated niche adaptation. Thus, genes on secondary replicons might potentially be manipulated to promote or suppress host interactions for biotechnological purposes. The genome of some bacteria consists of two or more chromosomes or replicons. Here, diCenzo et al. integrate genome-scale metabolic modelling and growth data from a collection of mutants of the plant symbiont Sinorhizobium meliloti to estimate the fitness contribution of each replicon in three environments.
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Affiliation(s)
- George C diCenzo
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 1A1
| | - Alice Checcucci
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Marco Bazzicalupo
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Carlo Viti
- Department of Agri-food Production and Environmental Sciences, University of Florence, 50144 Sesto Fiorentino, Italy
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Turlough M Finan
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 1A1
| | - Marco Galardini
- EMBL-EBI, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Marco Fondi
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
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Dziewit L, Radlinska M. Two novel temperate bacteriophages co-existing in Aeromonas sp. ARM81 - characterization of their genomes, proteomes and DNA methyltransferases. J Gen Virol 2016; 97:2008-2022. [PMID: 27184451 DOI: 10.1099/jgv.0.000504] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Aeromonas species are causative agents of a wide spectrum of diseases in animals and humans. Although these bacteria are commonly found in various environments, little is known about their phages. Thus far, only one temperate Aeromonas phage has been characterized. Whole-genome sequencing of an Aeromonas sp. strain ARM81 revealed the presence of two prophage clusters. One of them is integrated into the chromosome and the other was maintained as an extrachromosomal, linear plasmid-like prophage encoding a protelomerase. Both prophages were artificially and spontaneously inducible. We separately isolated both phages and compared their genomes with other known viruses. The novel phages show no similarity to the previously characterized Aeromonas phages and might represent new evolutionary lineages of viruses infecting Aeromonadaceae. Apart from the comparative genomic analyses of these phages, complemented with their structural and molecular characterization, a functional analysis of four DNA methyltransferases encoded by these viruses was conducted. One of the investigated N6-adenine-modifying enzymes shares sequence specificity with a Dam-like methyltransferase of its bacterial host, while another one is non-specific, as it catalyzes adenine methylation in various sequence contexts. The presented results shed new light on the diversity of Aeromonas temperate phages.
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Affiliation(s)
- Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Monika Radlinska
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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37
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Ciok A, Dziewit L, Grzesiak J, Budzik K, Gorniak D, Zdanowski MK, Bartosik D. Identification of miniature plasmids in psychrophilic Arctic bacteria of the genus Variovorax. FEMS Microbiol Ecol 2016; 92:fiw043. [PMID: 26917781 DOI: 10.1093/femsec/fiw043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2016] [Indexed: 11/13/2022] Open
Abstract
The Svalbard archipelago (Spitsbergen Island) is the northernmost landmass in the European Arctic and has a variety of small- and medium-sized glaciers. The plasmidome of eleven psychrophilic strains of Variovorax spp. isolated from the ice surface of Hans and Werenskiold Glaciers of Spitsbergen Island, was defined. This analysis revealed the presence of six plasmids whose nucleotide sequences have been determined. Four of them, exhibiting high reciprocal sequence similarity, possess unique structures, since their genomes lack any recognized genes. These miniature replicons, not exceeding 1 kb in size, include pHW69V1 (746 bp), which is the smallest autonomous replicon so far identified in free-living bacteria. The miniature plasmids share no similarity with known sequences present in the databases. In silico and experimental analyses identified conserved DNA regions essential for the initiation of replication of these replicons.
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Affiliation(s)
- Anna Ciok
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Jakub Grzesiak
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Karol Budzik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Dorota Gorniak
- Department of Microbiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Marek K Zdanowski
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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Dziewit L, Czarnecki J, Prochwicz E, Wibberg D, Schlüter A, Pühler A, Bartosik D. Genome-guided insight into the methylotrophy of Paracoccus aminophilus JCM 7686. Front Microbiol 2015; 6:852. [PMID: 26347732 PMCID: PMC4543880 DOI: 10.3389/fmicb.2015.00852] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/04/2015] [Indexed: 11/13/2022] Open
Abstract
Paracoccus aminophilus JCM 7686 (Alphaproteobacteria) is a facultative, heterotrophic methylotroph capable of utilizing a wide range of C1 compounds as sole carbon and energy sources. Analysis of the JCM 7686 genome revealed the presence of genes involved in the oxidation of methanol, methylamine, dimethylamine, trimethylamine, N,N-dimethylformamide, and formamide, as well as the serine cycle, which appears to be the only C1 assimilatory pathway in this strain. Many of these genes are located in different extrachromosomal replicons and are not present in the genomes of most members of the genus Paracoccus, which strongly suggests that they have been horizontally acquired. When compared with Paracoccus denitrificans Pd1222 (type strain of the genus Paracoccus), P. aminophilus JCM 7686 has many additional methylotrophic capabilities (oxidation of dimethylamine, trimethylamine, N,N-dimethylformamide, the serine cycle), which are determined by the presence of three separate gene clusters. Interestingly, related clusters form compact methylotrophy islands within the genomes of Paracoccus sp. N5 and many marine bacteria of the Roseobacter clade.
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Affiliation(s)
- Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Jakub Czarnecki
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Emilia Prochwicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Daniel Wibberg
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University Bielefeld, Germany
| | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University Bielefeld, Germany
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University Bielefeld, Germany
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
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Dziewit L, Pyzik A, Romaniuk K, Sobczak A, Szczesny P, Lipinski L, Bartosik D, Drewniak L. Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities. Front Microbiol 2015. [PMID: 26217325 PMCID: PMC4493836 DOI: 10.3389/fmicb.2015.00694] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Methanogenic Archaea produce approximately one billion tons of methane annually, but their biology remains largely unknown. This is partially due to the large phylogenetic and phenotypic diversity of this group of organisms, which inhabit various anoxic environments including peatlands, freshwater sediments, landfills, anaerobic digesters and the intestinal tracts of ruminants. Research is also hampered by the inability to cultivate methanogenic Archaea. Therefore, biodiversity studies have relied on the use of 16S rRNA and mcrA [encoding the α subunit of the methyl coenzyme M (methyl-CoM) reductase] genes as molecular markers for the detection and phylogenetic analysis of methanogens. Here, we describe four novel molecular markers that should prove useful in the detailed analysis of methanogenic consortia, with a special focus on methylotrophic methanogens. We have developed and validated sets of degenerate PCR primers for the amplification of genes encoding key enzymes involved in methanogenesis: mcrB and mcrG (encoding β and γ subunits of the methyl-CoM reductase, involved in the conversion of methyl-CoM to methane), mtaB (encoding methanol-5-hydroxybenzimidazolylcobamide Co-methyltransferase, catalyzing the conversion of methanol to methyl-CoM) and mtbA (encoding methylated [methylamine-specific corrinoid protein]:coenzyme M methyltransferase, involved in the conversion of mono-, di- and trimethylamine into methyl-CoM). The sensitivity of these primers was verified by high-throughput sequencing of PCR products amplified from DNA isolated from microorganisms present in anaerobic digesters. The selectivity of the markers was analyzed using phylogenetic methods. Our results indicate that the selected markers and the PCR primer sets can be used as specific tools for in-depth diversity analyses of methanogenic consortia.
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Affiliation(s)
- Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Adam Pyzik
- Laboratory of RNA Metabolism and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences Warsaw, Poland
| | - Krzysztof Romaniuk
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Adam Sobczak
- Laboratory of RNA Metabolism and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences Warsaw, Poland ; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Pawel Szczesny
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences Warsaw, Poland ; Department of Systems Biology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Leszek Lipinski
- Laboratory of RNA Metabolism and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
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Bocian-Ostrzycka KM, Grzeszczuk MJ, Dziewit L, Jagusztyn-Krynicka EK. Diversity of the Epsilonproteobacteria Dsb (disulfide bond) systems. Front Microbiol 2015; 6:570. [PMID: 26106374 PMCID: PMC4460558 DOI: 10.3389/fmicb.2015.00570] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/24/2015] [Indexed: 12/20/2022] Open
Abstract
The bacterial proteins of the Dsb family—important components of the post-translational protein modification system—catalyze the formation of disulfide bridges, a process that is crucial for protein structure stabilization and activity. Dsb systems play an essential role in the assembly of many virulence factors. Recent rapid advances in global analysis of bacteria have thrown light on the enormous diversity among bacterial Dsb systems. While the Escherichia coli disulfide bond-forming system is quite well understood, the mechanisms of action of Dsb systems in other bacteria, including members of class Epsilonproteobacteria that contain pathogenic and non-pathogenic bacteria colonizing extremely diverse ecological niches, are poorly characterized. Here we present a review of current knowledge on Epsilonproteobacteria Dsb systems. We have focused on the Dsb systems of Campylobacter spp. and Helicobacter spp. because our knowledge about Dsb proteins of Wolinella and Arcobacter spp. is still scarce and comes mainly from bioinformatic studies. Helicobacter pylori is a common human pathogen that colonizes the gastric epithelium of humans with severe consequences. Campylobacter spp. is a leading cause of zoonotic enteric bacterial infections in most developed and developing nations. We focus on various aspects of the diversity of the Dsb systems and their influence on pathogenicity, particularly because Dsb proteins are considered as potential targets for a new class of anti-virulence drugs to treat human infections by Campylobacter or Helicobacter spp.
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Affiliation(s)
- Katarzyna M Bocian-Ostrzycka
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Magdalena J Grzeszczuk
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Elżbieta K Jagusztyn-Krynicka
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
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Czarnecki J, Dziewit L, Kowalski L, Ochnio M, Bartosik D. Maintenance and genetic load of plasmid pKON1 of Paracoccus kondratievae, containing a highly efficient toxin-antitoxin module of the hipAB family. Plasmid 2015; 80:45-53. [PMID: 25752994 DOI: 10.1016/j.plasmid.2015.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 02/20/2015] [Accepted: 02/23/2015] [Indexed: 11/30/2022]
Abstract
Paracoccus kondratievae NCIMB 13773(T), isolated from the maize rhizosphere, carries a large (95,049 bp) plasmid pKON1, whose structure has been significantly influenced by transposition. Almost 30% of the plasmid genome is composed of complete or truncated insertion sequences (ISs), representing seven IS families. The ISs are accompanied by numerous genes and gene clusters commonly found in bacterial chromosomes, encoding, among others, (i) a putative type III secretion system of the Rhizobiales-T3SS family, (ii) a type I restriction-modification system associated with the anti-codon nuclease (ACNase) gene prrC and (iii) OstA and OstB proteins involved in trehalose synthesis. The backbone of pKON1 is composed of replication and partitioning modules conserved in several large alphaproteobacterial replicons, including secondary chromid pAMI6 of Paracoccus aminophilus JCM 7686 and chromosome 2 (chromid) of Rhodobacter sphaeroides 2.4.1. pKON1 also contains a toxin-antitoxin system of the hipAB family, whose presence precludes removal of the plasmid from bacterial cells. This system, unlike two other related hipAB-family loci originating from plasmid pAMI8 and the chromosome of Paracoccus aminophilus JCM 7686, is highly efficient and permits very stable maintenance of a heterologous replicon in various hosts.
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Affiliation(s)
- Jakub Czarnecki
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Lukasz Kowalski
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Magdalena Ochnio
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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Dziewit L, Pyzik A, Szuplewska M, Matlakowska R, Mielnicki S, Wibberg D, Schlüter A, Pühler A, Bartosik D. Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals. Front Microbiol 2015; 6:152. [PMID: 26074880 PMCID: PMC4447125 DOI: 10.3389/fmicb.2015.00152] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/09/2015] [Indexed: 12/31/2022] Open
Abstract
The Lubin underground mine, is one of three mining divisions in the Lubin-Glogow Copper District in Lower Silesia province (Poland). It is the source of polymetallic ore that is rich in copper, silver and several heavy metals. Black shale is also significantly enriched in fossil organic matter in the form of long-chain hydrocarbons, polycyclic aromatic hydrocarbons, organic acids, esters, thiophenes and metalloporphyrins. Biological analyses have revealed that this environment is inhabited by extremophilic bacteria and fungi. Kupfershiefer black shale and samples of water, bottom and mineral sediments from the underground (below 600 m) Lubin mine were taken and 20 bacterial strains were isolated and characterized. All exhibited multi-resistant and hypertolerant phenotypes to heavy metals. We analyzed the plasmidome of these strains in order to evaluate the diversity and role of mobile DNA in adaptation to the harsh conditions of the mine environment. Experimental and bioinformatic analyses of 11 extrachromosomal replicons were performed. Three plasmids, including a broad-host-range replicon containing a Tn3 family transposon, carried genes conferring resistance to arsenic, cadmium, cobalt, mercury and zinc. Functional analysis revealed that the resistance modules exhibit host specificity, i.e., they may increase or decrease tolerance to toxic ions depending on the host strain. The other identified replicons showed diverse features. Among them we identified a catabolic plasmid encoding enzymes involved in the utilization of histidine and vanillate, a putative plasmid-like prophage carrying genes responsible for NAD biosynthesis, and two repABC-type plasmids containing virulence-associated genes. These findings provide an unique molecular insight into the pool of extrachromosomal replicons and highlight their role in the biology and adaptation of extremophilic bacteria inhabiting terrestrial deep subsurface.
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Affiliation(s)
- Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Adam Pyzik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Magdalena Szuplewska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Renata Matlakowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Sebastian Mielnicki
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Daniel Wibberg
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University Bielefeld, Germany
| | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University Bielefeld, Germany
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University Bielefeld, Germany
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
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Dziewit L, Bartosik D. Comparative analyses of extrachromosomal bacterial replicons, identification of chromids, and experimental evaluation of their indispensability. Methods Mol Biol 2015; 1231:15-29. [PMID: 25343856 DOI: 10.1007/978-1-4939-1720-4_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Bacterial genomic information can be divided between various replicons, including chromosomes, plasmids, and chromids (essential plasmid-like replicons with properties of both chromosomes and plasmids). Comparative analyses of bacterial plasmids, including homology searches, phylogenetic and phylogenomic analyses, as well as network construction for the characterization of their relationships, are good starting points for the identification of chromids. Chromids possess several chromosome-like genetic features (e.g., codon usage, GC content), but most significantly, they carry housekeeping genes, which make them indispensable for cell viability. However, it is important to confirm in silico predictions experimentally. The essential nature of a predicted chromid is usually verified by the application of a target-oriented replicon curing technique, based on the incompatibility phenomenon. Further tests examining growth in various media are used to distinguish secondary chromids from plasmids, and mutational analysis (e.g., using the yeast FLP/FRT recombination system) is employed to identify essential genes carried by particular chromids.
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Affiliation(s)
- Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland,
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Dziewit L, Bartosik D. Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. Front Microbiol 2014; 5:596. [PMID: 25426110 PMCID: PMC4224046 DOI: 10.3389/fmicb.2014.00596] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/21/2014] [Indexed: 11/24/2022] Open
Abstract
Extremely cold environments are a challenge for all organisms. They are mostly inhabited by psychrophilic and psychrotolerant bacteria, which employ various strategies to cope with the cold. Such harsh environments are often highly vulnerable to the influence of external factors and may undergo frequent dynamic changes. The rapid adjustment of bacteria to changing environmental conditions is crucial for their survival. Such “short-term” evolution is often enabled by plasmids—extrachromosomal replicons that represent major players in horizontal gene transfer. The genomic sequences of thousands of microorganisms, including those of many cold-active bacteria have been obtained over the last decade, but the collected data have yet to be thoroughly analyzed. This report describes the results of a meta-analysis of the NCBI sequence databases to identify and characterize plasmids of psychrophilic and psychrotolerant bacteria. We have performed in-depth analyses of 66 plasmids, almost half of which are cryptic replicons not exceeding 10 kb in size. Our analyses of the larger plasmids revealed the presence of numerous genes, which may increase the phenotypic flexibility of their host strains. These genes encode enzymes possibly involved in (i) protection against cold and ultraviolet radiation, (ii) scavenging of reactive oxygen species, (iii) metabolism of amino acids, carbohydrates, nucleotides and lipids, (iv) energy production and conversion, (v) utilization of toxic organic compounds (e.g., naphthalene), and (vi) resistance to heavy metals, metalloids and antibiotics. Some of the plasmids also contain type II restriction-modification systems, which are involved in both plasmid stabilization and protection against foreign DNA. Moreover, approx. 50% of the analyzed plasmids carry genetic modules responsible for conjugal transfer or mobilization for transfer, which may facilitate the spread of these replicons among various bacteria, including across species boundaries.
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Affiliation(s)
- Lukasz Dziewit
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
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Dziewit L, Czarnecki J, Wibberg D, Radlinska M, Mrozek P, Szymczak M, Schlüter A, Pühler A, Bartosik D. Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids. BMC Genomics 2014; 15:124. [PMID: 24517536 PMCID: PMC3925955 DOI: 10.1186/1471-2164-15-124] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 02/07/2014] [Indexed: 11/10/2022] Open
Abstract
Background Paracoccus aminophilus JCM 7686 is a methylotrophic α-Proteobacterium capable of utilizing reduced one-carbon compounds as sole carbon and energy source for growth, including toxic N,N-dimethylformamide, formamide, methanol, and methylamines, which are widely used in the industry. P. aminophilus JCM 7686, as many other Paracoccus spp., possesses a genome representing a multipartite structure, in which the genomic information is split between various replicons, including chromids, essential plasmid-like replicons, with properties of both chromosomes and plasmids. In this study, whole-genome sequencing and functional genomics approaches were applied to investigate P. aminophilus genome information. Results The P. aminophilus JCM 7686 genome has a multipartite structure, composed of a single circular chromosome and eight additional replicons ranging in size between 5.6 and 438.1 kb. Functional analyses revealed that two of the replicons, pAMI5 and pAMI6, are essential for host viability, therefore they should be considered as chromids. Both replicons carry housekeeping genes, e.g. responsible for de novo NAD biosynthesis and ammonium transport. Other mobile genetic elements have also been identified, including 20 insertion sequences, 4 transposons and 10 prophage regions, one of which represents a novel, functional serine recombinase-encoding bacteriophage, ϕPam-6. Moreover, in silico analyses allowed us to predict the transcription regulatory network of the JCM 7686 strain, as well as components of the stress response, recombination, repair and methylation machineries. Finally, comparative genomic analyses revealed that P. aminophilus JCM 7686 has a relatively distant relationship to other representatives of the genus Paracoccus. Conclusions P. aminophilus genome exploration provided insights into the overall structure and functions of the genome, with a special focus on the chromids. Based on the obtained results we propose the classification of bacterial chromids into two types: “primary” chromids, which are indispensable for host viability and “secondary” chromids, which are essential, but only under some environmental conditions and which were probably formed quite recently in the course of evolution. Detailed genome investigation and its functional analysis, makes P. aminophilus JCM 7686 a suitable reference strain for the genus Paracoccus. Moreover, this study has increased knowledge on overall genome structure and composition of members within the class Alphaproteobacteria.
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Affiliation(s)
- Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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Maj A, Dziewit L, Czarnecki J, Wlodarczyk M, Baj J, Skrzypczyk G, Giersz D, Bartosik D. Plasmids of carotenoid-producing Paracoccus spp. (Alphaproteobacteria) - structure, diversity and evolution. PLoS One 2013; 8:e80258. [PMID: 24260361 PMCID: PMC3832669 DOI: 10.1371/journal.pone.0080258] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 10/11/2013] [Indexed: 11/25/2022] Open
Abstract
Plasmids are components of many bacterial genomes. They enable the spread of a large pool of genetic information via lateral gene transfer. Many bacterial strains contain mega-sized replicons and these are particularly common in Alphaproteobacteria. Considerably less is known about smaller alphaproteobacterial plasmids. We analyzed the genomes of 14 such plasmids residing in 4 multireplicon carotenoid-producing strains of the genus Paracoccus (Alphaproteobacteria): P. aestuarii DSM 19484, P. haeundaensis LG P-21903, P. marcusii DSM 11574 and P. marcusii OS22. Comparative analyses revealed mosaic structures of the plasmids and recombinational shuffling of diverse genetic modules involved in (i) plasmid replication, (ii) stabilization (including toxin-antitoxin systems of the relBE/parDE, tad-ata, higBA, mazEF and toxBA families) and (iii) mobilization for conjugal transfer (encoding relaxases of the MobQ, MobP or MobV families). A common feature of the majority of the plasmids is the presence of AT-rich sequence islets (located downstream of exc1-like genes) containing genes, whose homologs are conserved in the chromosomes of many bacteria (encoding e.g. RelA/SpoT, SMC-like proteins and a retron-type reverse transcriptase). The results of this study have provided insight into the diversity and plasticity of plasmids of Paracoccus spp., and of the entire Alphaproteobacteria. Some of the identified plasmids contain replication systems not described previously in this class of bacteria. The composition of the plasmid genomes revealed frequent transfer of chromosomal genes into plasmids, which significantly enriches the pool of mobile DNA that can participate in lateral transfer. Many strains of Paracoccus spp. have great biotechnological potential, and the plasmid vectors constructed in this study will facilitate genetic studies of these bacteria.
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Affiliation(s)
- Anna Maj
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Dziewit L, Grzesiak J, Ciok A, Nieckarz M, Zdanowski MK, Bartosik D. Sequence determination and analysis of three plasmids of Pseudomonas sp. GLE121, a psychrophile isolated from surface ice of Ecology Glacier (Antarctica). Plasmid 2013; 70:254-62. [PMID: 23721858 DOI: 10.1016/j.plasmid.2013.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/12/2013] [Accepted: 05/17/2013] [Indexed: 11/24/2022]
Abstract
Pseudomonas sp. GLE121 (a psychrophilic Antarctic strain) carries three plasmids: pGLE121P1 (6899 bp), pGLE121P2 (8330 bp) and pGLE121P3 (39,583 bp). Plasmids pGLE121P1 and pGLE121P2 show significant sequence similarity to members of the IncP-9 and IncP-7 incompatibility groups, respectively, while the largest replicon, pGLE121P3, is highly related to plasmid pNCPPB880-40 of Pseudomonas syringae pathovar tomato NCPPB880. All three plasmids have a narrow host range, limited to members of the genus Pseudomonas. Plasmid pGLE121P3 encodes a conjugal transfer system, while pGLE121P1 carries only a putative MOB module, conserved in many mobilizable plasmids. Plasmid pGLE121P3 contains an additional load of genetic information, including a pair of genes with homology to the rulAB operon, responsible for ultraviolet radiation (UVR) tolerance. Given the increasing UV exposure in Antarctic regions, the expression of these genes is likely to be an important adaptive response.
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Affiliation(s)
- Lukasz Dziewit
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096 Warsaw, Poland.
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Dziewit L, Pyzik A, Matlakowska R, Baj J, Szuplewska M, Bartosik D. Characterization of Halomonas sp. ZM3 isolated from the Zelazny Most post-flotation waste reservoir, with a special focus on its mobile DNA. BMC Microbiol 2013; 13:59. [PMID: 23497212 PMCID: PMC3606827 DOI: 10.1186/1471-2180-13-59] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 03/08/2013] [Indexed: 11/10/2022] Open
Abstract
Background Halomonas sp. ZM3 was isolated from Zelazny Most post-flotation mineral waste repository (Poland), which is highly contaminated with heavy metals and various organic compounds. Mobile DNA of the strain (i.e. plasmids and transposons) were analyzed in order to identify genetic information enabling adaptation of the bacterium to the harsh environmental conditions. Results The analysis revealed that ZM3 carries plasmid pZM3H1 (31,370 bp), whose replication system may be considered as an archetype of a novel subgroup of IncU-like replicons. pZM3H1 is a narrow host range, mobilizable plasmid (encodes a relaxase of the MOBV family) containing mercury resistance operon (mer) and czcD genes (mediate resistance to zinc and cobalt), which are part of a large truncated Tn3 family transposon. Further analysis demonstrated that the phenotypes determined by the pZM3H1 resistance cassette are highly dependent on the host strain. In another strand of the study, the trap plasmid pMAT1 was employed to identify functional transposable elements of Halomonas sp. ZM3. Using the sacB positive selection strategy two insertion sequences were identified: ISHsp1 - representing IS5 group of IS5 family and ISHsp2 - a distinct member of the IS630 family. Conclusions This study provides the first detailed description of mobile DNA in a member of the family Halomonadaceae. The identified IncU plasmid pZM3H1 confers resistance phenotypes enabling adaptation of the host strain to the Zelazny Most environment. The extended comparative analysis has shed light on the distribution of related IncU plasmids among bacteria, which, in many cases, reflects the frequency and direction of horizontal gene transfer events. Our results also identify plasmid-encoded modules, which may form the basis of novel shuttle vectors, specific for this group of halophilic bacteria.
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Affiliation(s)
- Lukasz Dziewit
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, Warsaw, 02-096, Poland
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Dziewit L, Cegielski A, Romaniuk K, Uhrynowski W, Szych A, Niesiobedzki P, Zmuda-Baranowska MJ, Zdanowski MK, Bartosik D. Plasmid diversity in arctic strains of Psychrobacter spp. Extremophiles 2013; 17:433-44. [PMID: 23479249 PMCID: PMC3632715 DOI: 10.1007/s00792-013-0521-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 02/14/2013] [Indexed: 12/05/2022]
Abstract
Six strains of Psychrobacter spp. isolated from guano of little auks collected on Spitsbergen island (Arctic) carried nine plasmids that were fully sequenced. These replicons (ranging in size from 2917 to 14924 bp) contained either repA (ColE2-type) or repB (iteron-type) replication systems of a relatively narrow host range, limited to Psychrobacter spp. All but one of the plasmids carried predicted mobilization for conjugal transfer systems, encoding relaxases of the MOBQ, MOBV or MOBP families. The plasmids also contained diverse additional genetic load, including a type II restriction-modification system and a gene encoding a putative subunit C of alkyl hydroperoxide reductase (AhpC)—an antioxidant enzyme and major scavenger of reactive oxygen species. Detailed comparative sequence analyses, extended to all plasmids identified so far in psychrophilic bacteria, distinguished groups of the most ubiquitous replicons, which play a key role in horizontal gene transfer in cold environments.
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Affiliation(s)
- Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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Drewniak L, Dziewit L, Ciezkowska M, Gawor J, Gromadka R, Sklodowska A. Structural and functional genomics of plasmid pSinA of Sinorhizobium sp. M14 encoding genes for the arsenite oxidation and arsenic resistance. J Biotechnol 2013; 164:479-88. [PMID: 23454063 DOI: 10.1016/j.jbiotec.2013.01.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 01/15/2013] [Accepted: 01/16/2013] [Indexed: 11/19/2022]
Abstract
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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Affiliation(s)
- Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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