Publications

@article{Musiałowski2025,

title = {A novel two-step metabarcoding approach improves soil microbiome biodiversity assessment},

author = {Marcin Musiałowski and Monika Mierzwa-Hersztek and Krzysztof Gondek and Klaudia Dębiec-Andrzejewska},

doi = {10.1038/s41598-025-18936-5},

issn = {2045-2322},

year  = {2025},

date = {2025-12-00},

urldate = {2025-12-00},

journal = {Sci Rep},

volume = {15},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jarosz2025,

title = {Effect of innovative mineral-organic mixtures on enzymatic activity, ecotoxicity, and microbial communities in contaminated soil},

author = {Renata Jarosz and Agnieszka Klimkowicz-Pawlas and Karolina Biel and Jakub Mokrzycki and Marcin Musiałowski and Klaudia Dębiec-Andrzejewska and Monika Mierzwa-Hersztek},

doi = {10.1016/j.still.2025.106655},

issn = {0167-1987},

year  = {2025},

date = {2025-11-00},

journal = {Soil and Tillage Research},

volume = {253},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Salinitro2025c,

title = {From waste to value: agromining of nickel, cobalt, and selenium from mine waste amended with sewage sludge},

author = {Mirko Salinitro and Michela Schiavon and Marcin Musiałowski and Klaudia Dębiec-Andrzejewska and Mark G. M. Aarts and Elio Padoan and Benedetta Montanarini and Annalisa Tassoni and Antony van der Ent},

doi = {10.1007/s11104-025-07924-3},

issn = {1573-5036},

year  = {2025},

date = {2025-10-17},

journal = {Plant Soil},

publisher = {Springer Science and Business Media LLC},

abstract = {Abstract

          

            Background and aims

            The global demand for critical elements such as nickel, cobalt, and selenium is projected to increase significantly, driven by the transition to renewable energy. Mine wastes and sewage sludge, often enriched with these elements, represent untapped secondary resources. Agromining, an emerging phytotechnology that employs hyperaccumulator plants to extract metals from contaminated or enriched soils, offers a sustainable recovery method. The aim of this study is to provide a crucial proof-of-concept for the recovery of the critical elements nickel, cobalt, and selenium from these alternative resources through agromining.

          

          

            Methods

            Mine wastes from three Italian mining sites were amended with sewage sludge at rates of 0, 15, and 30 kg m−2. Three hyperaccumulator species targeting cobalt, (Berkheya coddii), selenium (Astragalus bisulcatus) and nickel (Odontarrhena chalcidica) were grown on these wastes. Biogeochemical characterization of the substrate was performed before and after agromining. In addition, plant biomass and metal accumulation were monitored.

          

          

            Results

            Sewage sludge increased biomass across all species, especially in A. bisulcatus, but metal accumulation decreased by 33–60% for nickel, 0–41% for cobalt, and 67–74% for selenium. Furthermore, sewage sludge and agromining enhanced mine waste fertility and microbial diversity.

          

          

            Conclusions

            Agromining of sewage sludge-amended mine wastes shows potential for sustainable recovery of selenium and cobalt. However, high sewage sludge application increased plant biomass, but concurrently reduced plant tissue metal concentrations. This study underscores the importance of optimizing sewage sludge / mine waste ratios for successful agromining. 

          },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Potenza2025.09.20.677519,

title = {Droplet microfluidic PicoSorter for high throughput and active selection of cellulolytic microorganisms},

author = {Luca Potenza and Łukasz Kozon and Lukasz Drewniak and Tomasz S. Kaminski},

url = {https://www.biorxiv.org/content/early/2025/09/21/2025.09.20.677519},

doi = {10.1101/2025.09.20.677519},

year  = {2025},

date = {2025-01-01},

urldate = {2025-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Classical enrichment methods for microorganisms rely on growth in selective media, but such practices are relatively expensive, low-throughput, and may result in a biased representation of taxa. Alternatively, microorganisms can be cultivated in thousands of picoliter droplets of equal volume, with the most efficient strains selected through quantitative assays at unprecedented ultrahigh throughput. Here, we present a novel high-throughput microfluidic technology for the characterization of cellulolytic microbial communities at the single-cell level. Individual microbial cells are encapsulated in picoliter droplets for clonal cultivation, after which a colorimetric assay using Congo red is applied to identify positive droplets containing cellulose-degrading strains. These positive droplets are then actively sorted at high throughput using absorbance-activated droplet sorting. The critical component of the enrichment assay we propose is the PicoSorter module, which expands the range of available droplet-based enrichment methods. The platform introduces a new design that enables buffer picoinjection required for the assay, followed by droplet sorting on a millisecond timescale.Highlights- Development of a novel device (PicoSorter) capable of performing multiple microfluidic operations simultaneously.- Implementation of a colorimetric droplet-based assay for the detection of cellulose.- The proposed absorbance-based HTS enables active and efficient enrichment of cellulolytic bacteria.Competing Interest StatementThe authors have declared no competing interest.TEAM-NET programme of the Foundation for Polish Science, POIR.04.04.00-00-14E6/18-00National Science Centre, sonata bis, 2023/50/E/ST4/00545},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WILCZYNSKI2025118366b,

title = {Chronic toxicity of triphenylarsine to Danio rerio},

author = {Wojciech Wilczynski and Tomasz Brzeziński and Jakub Nawała and Daniel Dziedzic and Stanisław Popiel and Marcin Lukasz Zebrowski and Michał Czub and Jacek Bełdowski and Monika Radlinska},

url = {https://www.sciencedirect.com/science/article/pii/S014765132500702X},

doi = {https://doi.org/10.1016/j.ecoenv.2025.118366},

issn = {0147-6513},

year  = {2025},

date = {2025-01-01},

journal = {Ecotoxicology and Environmental Safety},

volume = {299},

pages = {118366},

abstract = {Triphenylarsine (TPA) is a persistent organoarsenical that has emerged as a major environmental concern due to the extensive marine disposal of chemical munitions throughout the 20th century. The waterborne toxicity of TPA in aquatic organisms remains poorly understood, with limited and often inconclusive data, and its chronic effects are entirely unexplored. To address this gap, a 28-day exposure study was conducted, focusing on assessing the long-term toxicity of TPA in the model fish species Danio rerio. The results indicate that chronic exposure to trace concentrations of TPA significantly reduces body length, weight, and growth rate in fish. Furthermore, TPA and its primary degradation product, triphenylarsine oxide (TPAO), accumulate in the muscle tissues of fish. The accumulation rates are 0.61 μg × g⁻¹ (dry weight) for TPA and 9.1 μg × g⁻¹ (dry weight) for TPAO, for every microgram of TPA per litre of water over 28 days of exposure. Additionally, chronic exposure induced oxidative stress in the gills, as evidenced by altered mRNA expression and elevated enzymatic activity of detoxification-related proteins. Therefore, TPA exposure represents a significant threat to fish. This compound should be recognized as a high-priority environmental contaminant, and its concentrations should be routinely monitored in bottom waters, particularly near chemical munitions dumping sites. Expanding research to predict and assess the toxicity of other persistent organoarsenicals co-disposed with TPA is essential for understanding their cumulative ecological and health impacts.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Goszcz2025b,

title = {Bacterial osmoprotectants—a way to survive in saline conditions and potential crop allies},

author = {Aleksandra Goszcz and Karolina Furtak and Robert Stasiuk and Joanna Wójtowicz and Marcin Musiałowski and Michela Schiavon and Klaudia Dębiec-Andrzejewska},

doi = {10.1093/femsre/fuaf020},

issn = {1574-6976},

year  = {2025},

date = {2025-00-00},

volume = {49},

publisher = {Oxford University Press (OUP)},

abstract = {Abstract

               Soil salinization, affecting 6.5% of arable land, deteriorates soil properties, reduces microbiota activity, hinders plant growth, and accelerates soil erosion. Excessive salt induces physiological drought and toxicity stress in plants, causing chlorosis, ion imbalances, and enzyme disruptions. This paper discusses microorganisms’ resistance mechanisms, plant responses to salt stress, and summarizes current knowledge on bacterial osmoprotectants and their functions. It also reviews emerging agrobiotechnological strategies using microbial osmoprotectants to remediate salinized soils and enhance plant growth and productivity under salt stress. Osmoprotectants stabilize proteins, buffer redox potential, and retain water, thus alleviating osmotic stress and promoting bacteria and plants growth. Their application improves soil properties by enhancing aggregate formation, water permeability, moisture content, cation exchange capacity, and ion availability. Despite extensive literature on the function of osmoprotectants, the knowledge about their role in soil environments and agrobiotechnology applications remains limited. This paper indicates proposed research perspectives, including discovering new osmoprotectants, their correlation with soil fertilization, interactions with the soil microbiome, and plant responses. It also identifies significant knowledge gaps in these areas, highlighting the need for further studies to consolidate existing data and assess the potential of this approach to enhance soil health and crop productivity in saline environments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vaccaro2024c,

title = {Genotype-by-genotype interkingdom cross-talk between symbiotic nitrogen fixing Sinorhizobium meliloti strains and Trichoderma species},

author = {Francesca Vaccaro and Iacopo Passeri and Nur Ajijah and Priscilla Bettini and Pierre Emmanuel Courty and Klaudia Dębiec-Andrzejewska and Namrata Joshi and Łucja Kowalewska and Robert Stasiuk and Marcin Musiałowski and Kumar Pranaw and Alessio Mengoni},

doi = {10.1016/j.micres.2024.127768},

issn = {0944-5013},

year  = {2024},

date = {2024-08-00},

journal = {Microbiological Research},

volume = {285},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Joshi2024b,

title = {Unveiling the secretome of Penicillium fuscoglaucum JAM-1 for efficient dual substrate degradation and waste valorization},

author = {Namrata Joshi and Jasneet Grewal and Robert Stasiuk and Lukasz Drewniak and Kumar Pranaw},

url = {https://link.springer.com/article/10.1007/s13399-024-05809-6},

doi = {10.1007/S13399-024-05809-6/FIGURES/6},

issn = {21906823},

year  = {2024},

date = {2024-01-01},

journal = {Biomass Conversion and Biorefinery},

pages = {1-12},

publisher = {Springer Science and Business Media Deutschland GmbH},

abstract = {In the pursuit of cost-effective and superior enzymes crucial for the efficient hydrolysis of diverse lignocellulosic biomasses, filamentous fungi have emerged as key candidates for bioprospecting endeavors. In our exploration for potent lignocellulosic biomass degraders, we have identified a strain of Penicillium fuscoglaucum JAM-1, showcasing multipurpose hydrolase capabilities in its secretome. During fermentation, P. fuscoglaucum JAM-1 effectively utilized rapeseed cake (RSC), resulting in improved enzymatic activities, including xylanase (612 U/gds), β-glucosidase (264 U/gds), endoglucanase (102 U/gds), FPase (21.3 U/gds), and exo-polygalacturonase (49.17 U/gds), as compared to pine sawdust (PSD). Secretome profiling revealed a protein abundance totaling 435 and 120 proteins during RSC and PSD utilization, respectively. The major component of carbohydrate-active enzymes (CAZymes) consists of cellulose-degrading proteins, including endoglucanases (GH5, GH7), β-glucosidases (GH1, GH3, GH17), and cellobiohydrolases (GH6, GH7). Correspondingly, hemicellulose-degrading enzymes were present, encompassing endo-1,4-xylanase (GH10), α/β-galactosidase (GH27, GH35, GH36), α/β-mannosidases (GH38, GH2, GH47, GH5), and α-l-arabinofuranosidase (GH43, GH62, GH51, GH54) and carbohydrate-active auxiliary activities enzymes, such as AA9 (formerly known as GH61) lytic polysaccharide monooxygenase (LPMO). Upon application to fruit waste, the crude enzyme demonstrated higher saccharification potential compared to commercial cellulase (Cellic CTec2). Specifically, the crude enzyme yielded 565 mg/g of reducing sugar within 72 h, outperforming Cellic CTec2, which yielded 352 mg/g under identical conditions. A comprehensive comparative analysis of enzyme workings, activities, and secretome profiling underscores P. fuscoglaucum JAM-1 as a potent cellulase producer, showcasing its potential to boost lignocellulose biodegradation. These findings highlight the practical applications of the P. fuscoglaucum JAM-1 in various industrial processes, suggesting its role as a valuable candidate for further exploration and exploitation in biotechnological applications. Graphical abstract: (Figure presented.)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Joshi2024c,

title = {Bioprospecting CAZymes repertoire of Aspergillus fumigatus for eco-friendly value-added transformations of agro-forest biomass},

author = {Namrata Joshi and Jasneet Grewal and Lukasz Drewniak and Kumar Pranaw},

url = {https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-023-02453-6 http://creativecommons.org/publicdomain/zero/1.0/},

doi = {10.1186/S13068-023-02453-6/TABLES/3},

issn = {27313654},

year  = {2024},

date = {2024-01-01},

journal = {Biotechnology for Biofuels and Bioproducts},

volume = {17},

issue = {1},

pages = {1-13},

publisher = {BioMed Central Ltd},

abstract = {Background: Valorizing waste residues is crucial to reaching sustainable development goals and shifting from a linear fossil-based economy to a circular economy. Fungal cell factories, due to their versatility and robustness, are instrumental in driving the bio-transformation of waste residues. The present work isolated a potent strain, i.e., Aspergillus fumigatus (ZS_AF), from an ancient Złoty Stok gold mine, which showcased distinctive capabilities for efficient hydrolytic enzyme production from lignocellulosic wastes. Results: The present study optimized hydrolytic enzyme production (cellulases, xylanases, and β-glucosidases) from pine sawdust (PSD) via solid-state fermentation using Aspergillus fumigatus (ZS_AF). The optimization, using response surface methodology (RSM), produced a twofold increase with maximal yields of 119.41 IU/gds for CMCase, 1232.23 IU/gds for xylanase, 63.19 IU/gds for β-glucosidase, and 31.08 IU/gds for FPase. The secretome profiling validated the pivotal role of carbohydrate-active enzymes (CAZymes) and auxiliary enzymes in biomass valorization. A total of 77% of carbohydrate-active enzymes (CAZymes) were constituted by glycoside hydrolases (66%), carbohydrate esterases (9%), auxiliary activities (3%), and polysaccharide lyases (3%). The saccharification of pretreated wheat straw and PSD generated high reducing sugar yields of 675.36 mg/g and 410.15 mg/g, respectively. Conclusion: These findings highlight the significance of an efficient, synergistic, and cost-effective arsenal of fungal enzymes for lignocellulosic waste valorization and their potential to contribute to waste-to-wealth creation through solid-waste management. The utilization of Aspergillus fumigatus (ZS_AF) from an unconventional origin and optimization strategies embodies an innovative approach that holds the potential to propel current waste valorization methods forward, directing the paradigm toward improved efficiency and sustainability.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{D3LC00656E,

title = {Droplet microfluidic system for high throughput and passive selection of bacteria producing biosurfactants},

author = {Klaudia Staskiewicz and Maria Dabrowska-Zawada and Lukasz Kozon and Zofia Olszewska and Lukasz Drewniak and Tomasz S. Kaminski},

url = {http://dx.doi.org/10.1039/D3LC00656E},

doi = {10.1039/D3LC00656E},

year  = {2024},

date = {2024-01-01},

journal = {Lab Chip},

volume = {24},

issue = {7},

pages = {1947-1956},

publisher = {The Royal Society of Chemistry},

abstract = {Traditional methods for the enrichment of microorganisms rely on growth in a selective liquid medium or on an agar plate, followed by tedious characterization. Droplet microfluidic techniques have been recently used to cultivate microorganisms and preserve enriched bacterial taxonomic diversity. However, new methods are needed to select droplets comprising not only growing microorganisms but also those exhibiting specific properties, such as the production of value-added compounds. We describe here a droplet microfluidic screening technique for the functional selection of biosurfactant-producing microorganisms, which are of great interest in the bioremediation and biotechnology industries. Single bacterial cells are first encapsulated into picoliter droplets for clonal cultivation and then passively sorted at high throughput based on changes in interfacial tension in individual droplets. Our method expands droplet-based microbial enrichment with a novel approach that reduces the time and resources needed for the selection of surfactant-producing bacteria.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{KRUCON2024177501,

title = {Application of xylene-degrading bacteria in the treatment of soil contaminated with petroleum hydrocarbons – A comprehensive laboratory to pilot-scale analysis},

author = {Tomasz Krucon and Witold Uhrynowski and Katarzyna Piatkowska and Michal Styczynski and Robert Stasiuk and Lukasz Dziewit and Lukasz Drewniak},

url = {https://www.sciencedirect.com/science/article/pii/S0048969724076587},

doi = {https://doi.org/10.1016/j.scitotenv.2024.177501},

issn = {0048-9697},

year  = {2024},

date = {2024-01-01},

journal = {Science of The Total Environment},

volume = {957},

pages = {177501},

abstract = {Petroleum hydrocarbons, including both aliphatic (gasoline, mineral oil) and aromatic compounds (BTEX), are known for their harmful effects on ecosystems and human health. Despite many studies, large-scale treatment of contaminated soils continues to be challenging, especially at lower temperatures. The use of metabolically-versatile, psychrotolerant, cold-active microorganisms, seems a promising, cost-effective and eco-friendly solution to boost remediation rates. In this study, a suitable microbial consortium was prepared and tested both in lab- and pilot-scale. To achieve the best bioremediation results, bacterial strains were isolated from BTEX-contaminated soil and then tested for the desired traits over a wide range of conditions. Of 5 preselected strains, 3 Pseudomonas strains capable of denitrification and aerobic/anaerobic degradation of hydrocarbons (up to 41.53±7.39 %), further characterized by a broad temperature (4–37 °C), pH (3–4 to 11) and salinity (0–8 %) tolerance, as well as resistance to freezing, were selected. Physiological studies were supported by genetic analyses, which indicated the presence of both alkB and xylM genes, and excluded similarity of the strains to the known opportunistic pathogens. To further confirm the applicability of the consortium, lab-scale analyses were followed by comprehensive pilot-scale tests on ~5 m3 biopile/biocell, at different conditions. The results revealed increased efficacy of the consortium in bioremediation, when compared to biostimulated indigenous strains, for volatile hydrocarbons (93 % vs 88 %) and mineral oil (23 % vs 15 %), as well as 175 % and 136 % acceleration of remediation for the respective compounds in terms of time needed to complete the process. Moreover, the high survivability and metabolic activity of the consortium at different temperatures indicate the possibility of its year-round use for bioremediation of soil contaminated with petroleum hydrocarbons. The study proves the potential of specialized bacteria in the removal of pollutants, and emphasizes the role of bio-based strategies in addressing complex environmental challenges and remediation of contaminated sites.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1021/acs.analchem.4c02979,

title = {Passive Droplet Microfluidic Platform for High-Throughput Screening of Microbial Proteolytic Activity},

author = {Luca Potenza and Lukasz Kozon and Lukasz Drewniak and Tomasz S. Kaminski},

url = {https://doi.org/10.1021/acs.analchem.4c02979},

doi = {10.1021/acs.analchem.4c02979},

year  = {2024},

date = {2024-01-01},

journal = {Analytical Chemistry},

volume = {96},

number = {40},

pages = {15931-15940},

note = {PMID: 39320273},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WILCZYNSKI2024143478b,

title = {Multi-biomarker assessment of chronic toxicity induced by the chemical warfare agent adamsite in Danio rerio},

author = {Wojciech Wilczynski and Monika Radlinska and Marcin Lukasz Zebrowski and Jakub Nawała and Daniel Dziedzic and Michał Czub and Piotr Maszczyk and Jacek Bełdowski and Stanisław Popiel and Tomasz Brzeziński},

url = {https://www.sciencedirect.com/science/article/pii/S0045653524023786},

doi = {https://doi.org/10.1016/j.chemosphere.2024.143478},

issn = {0045-6535},

year  = {2024},

date = {2024-01-01},

journal = {Chemosphere},

volume = {366},

pages = {143478},

abstract = {Several hundred thousand tons of chemical warfare agents (CWAs) were disposed of at sea, leading to environmental contamination. Among the most toxic and persistent CWAs is adamsite; however, the ecotoxicological data on this compound is limited. Presented research focuses on the long-term effects of adamsite on fish. A 28-day exposure study was conducted, evaluating the impact of adamsite on life history parameters (body length, body mass, growth rate), tissue accumulation, and the expression/activity of detoxification-related enzymes in the model fish species, Danio rerio. Results indicate that chronic adamsite exposure significantly reduces body length, weight, and growth rate of fish at trace concentrations (0.20 and 0.25 μg × L−1). Adamsite-related compounds accumulate in fish muscle tissues, increasing by approximately 4 μg per gram (dry weight) for every microgram of adamsite per litre of water during chronic exposure. The mRNA expression and activity of detoxification-related enzymes were elevated in the gills of fish, indicating oxidative stress. This study highlights the severe chronic toxicity of adamsite, which could not be anticipated based on acute toxicity. It underscores the need for comprehensive long-term toxicity assays for CWAs and emphasizes the potential ecological and health risks posed by adamsite, necessitating more stringent risk assessments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Musialowski2023c,

title = {Metabolically versatile psychrotolerant Antarctic bacterium Pseudomonas sp. ANT_H12B is an efficient producer of siderophores and accompanying metabolites (SAM) useful for agricultural purposes},

author = {M. Musialowski and Ł. Kowalewska and R. Stasiuk and T. Krucoń and K. Debiec-Andrzejewska},

doi = {10.1186/s12934-023-02105-2},

issn = {1475-2859},

year  = {2023},

date = {2023-12-00},

journal = {Microb Cell Fact},

volume = {22},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {Abstract

                Background

                Bacterial siderophores are chelating compounds with the potential of application in agriculture, due to their plant growth-promoting (PGP) properties, however, high production and purification costs are limiting factors for their wider application. Cost-efficiency of the production could be increased by omitting purification processes, especially since siderophores accompanying metabolites (SAM) often also possess PGP traits. In this study, the metabolism versatility of Pseudomonas sp. ANT_H12B was used for the optimization of siderophores production and the potential of these metabolites and SAM was characterized in the context of PGP properties.

              

                Results

                The metabolic diversity of ANT_H12B was examined through genomic analysis and phenotype microarrays. The strain was found to be able to use numerous C, N, P, and S sources, which allowed for the design of novel media suitable for efficient production of siderophores in the form of pyoverdine (223.50–512.60 μM). Moreover, depending on the culture medium, the pH of the siderophores and SAM solutions varied from acidic (pH < 5) to alkaline (pH > 8). In a germination test, siderophores and SAM were shown to have a positive effect on plants, with a significant increase in germination percentage observed in beetroot, pea, and tobacco. The PGP potential of SAM was further elucidated through GC/MS analysis, which revealed other compounds with PGP potential, such as indolic acetic acids, organic acids, fatty acids, sugars and alcohols. These compounds not only improved seed germination but could also potentially be beneficial for plant fitness and soil quality.

              

                Conclusions

                Pseudomonas sp. ANT_H12B was presented as an efficient producer of siderophores and SAM which exhibit PGP potential. It was also shown that omitting downstream processes could not only limit the costs of siderophores production but also improve their agricultural potential.

              },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Decewicz2023,

title = {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},

author = {Przemyslaw Decewicz and Krzysztof Romaniuk and Adrian Gorecki and Monika Radlinska and Maria Dabrowska and Agnieszka Wyszynska and Lukasz Dziewit},

doi = {10.1007/s13353-023-00759-7},

issn = {2190-3883},

year  = {2023},

date = {2023-09-00},

journal = {J Appl Genetics},

volume = {64},

number = {3},

pages = {545--557},

publisher = {Springer Science and Business Media LLC},

abstract = {AbstractAmong 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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zakrzewska2023b,

title = {Reduction of bioavailability and phytotoxicity effect of cadmium in soil by microbial-induced carbonate precipitation using metabolites of ureolytic bacterium Ochrobactrum sp. POC9},

author = {Marta Zakrzewska and Grzegorz Rzepa and Marcin Musialowski and Aleksandra Goszcz and Robert Stasiuk and Klaudia Debiec-Andrzejewska},

doi = {10.3389/fpls.2023.1109467},

issn = {1664-462X},

year  = {2023},

date = {2023-06-21},

journal = {Front. Plant Sci.},

volume = {14},

publisher = {Frontiers Media SA},

abstract = {The application of ureolytic bacteria for bioremediation of soil contaminated with heavy metals, including cadmium (Cd), allows for the efficient immobilization of heavy metals by precipitation or coprecipitation with carbonates. Microbially-induced carbonate precipitation process may be useful also in the case of the cultivation of crop plants in various agricultural soils with trace but legally permissible Cd concentrations, which may be still uptaken by plants. This study aimed to investigate the influence of soil supplementation with metabolites containing carbonates (MCC) produced by the ureolytic bacterium Ochrobactrum sp. POC9 on the Cd mobility in the soil as well as on the Cd uptake efficiency and general condition of crop plants (Petroselinum crispum). In the frame of the conducted studies (i) carbonate productivity of the POC9 strain, (ii) the efficiency of Cd immobilization in soil supplemented with MCC, (iii) crystallization of cadmium carbonate in the soil enriched with MCC, (iv) the effect of MCC on the physico-chemical and microbiological properties of soil, and (v) the effect of changes in soil properties on the morphology, growth rate, and Cd-uptake efficiency of crop plants were investigated. The experiments were conducted in soil contaminated with a low concentration of Cd to simulate the natural environmental conditions. Soil supplementation with MCC significantly reduced the bioavailability of Cd in soil with regard to control variants by about 27-65% (depending on the volume of MCC) and reduced the Cd uptake by plants by about 86% and 74% in shoots and roots, respectively. Furthermore, due to the decrease in soil toxicity and improvement of soil nutrition with other metabolites produced during the urea degradation (MCC), some microbiological properties of soil (quantity and activity of soil microorganisms), as well as the general condition of plants, were also significantly improved. Soil supplementation with MCC enabled efficient Cd stabilization and significantly reduced its toxicity for soil microbiota and plants. Thus, MCC produced by POC9 strain may be used not only as an effective Cd immobilizer in soil but also as a microbe and plant stimulators.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{JOSHI2023109017,

title = {Faujasite Na-X zeolite as a novel carrier for cellulase immobilization and application in biomass saccharification},

author = {Namrata Joshi and Jasneet Grewal and Jakub Matusik and Lukasz Drewniak and Kumar Pranaw},

url = {https://www.sciencedirect.com/science/article/pii/S1369703X23002127},

doi = {https://doi.org/10.1016/j.bej.2023.109017},

issn = {1369-703X},

year  = {2023},

date = {2023-01-01},

journal = {Biochemical Engineering Journal},

volume = {198},

pages = {109017},

abstract = {As a sustainable and eco-friendly alternative to conventional chemical catalysis, the immobilization of enzymes has been advocated as an attractive strategy to offset the limitations of single-use and rapid loss of activity. The present study aimed to investigate an inert inorganic material, i.e. Na-X zeolite derived from fly ash as a solid carrier for the immobilization of cellulase, a pivotal enzyme for biomass valorization. The cellulase enzyme (Cellic CTec2) was covalently immobilized over Na-X zeolite using glutaraldehyde as a cross-linking agent with immobilization efficiency and yield of 73% and 77%, respectively. The immobilized cellulase exhibited better pH stability (5.0–9.0), temperature optima of 60 °C, and a three-fold half-life (t1/2) enhancement at 60 °C than its free counterpart. The immobilized preparation retained > 80% residual activity after 5 repeated cycles of usage and had enhanced shelf life, as reflected by good storage stability at both 4 °C and 22 °C after 4 weeks of incubation. The immobilized formulation was utilized to saccharify alkaline pretreated wheat straw to demonstrate its potential for biorefinery applications, and structural deconstruction was validated by SEM, XRD, and FTIR analysis. The high reducing sugar yield for two consecutive cycles confirms its suitability for continuous operation in hydrolyzing lignocellulosic substrates.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{IWAN2023138358,

title = {Biotransformation of coal fly ash with high carbon content; behavior and release patterns of coal fly ash constituents under the influence of allochtonic Pseudomonas stutzer MT1},

author = {Mikołaj A. Iwan and Marco Günthel and Tomasz S. Kaminski and Wojciech Franus and Łukasz Drewniak},

url = {https://www.sciencedirect.com/science/article/pii/S0959652623025167},

doi = {https://doi.org/10.1016/j.jclepro.2023.138358},

issn = {0959-6526},

year  = {2023},

date = {2023-01-01},

journal = {Journal of Cleaner Production},

volume = {420},

pages = {138358},

abstract = {The aim of this study was to analyze the influence of Pseudomonas stutzeri MT1 on the weathering of CFA, with particular emphasis on the transformation of unburnt carbon. Batch experiment with two common types of coal fly ash (one with high carbon content) showed that microbial transformation leads to metal (loid)s and organic compounds release. The concentrations of metal (loid)s leached from CFA were the highest for As and Al, reaching 951 μg/L and 1353 μg/L respectively, in the presence of bacteria. It was shown that some metal (loid)s (Al, Fe, Cr, As) leached in higher quantities when bacteria used CFA as a sole carbon source as compared to variants where external carbon source was provided. Anthracene or phenanthrene were present in every leachate variant. The addition of bacteria resulted in a higher presence of short-chain carboxylic acids as well as 9,10-anthracenedione, which is assumed to be a product of the bacterial oxidation of anthracene. Based on the performed experiments we noticed that the microbial consumption of carbon contained within CFA was crucial to increasing the leaching rate of metal (loid)s, which may have consequences for the long-term storage of CFA.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{KRUCON2023115785,

title = {Bioprospecting of the Antarctic Bacillus subtilis strain for potential application in leaching hydrocarbons and trace elements from contaminated environments based on functional and genomic analysis},

author = {Tomasz Krucoń and Zuzanna Ruszkowska and Weronika Pilecka and Anna Szych and Łukasz Drewniak},

url = {https://www.sciencedirect.com/science/article/pii/S0013935123005777},

doi = {https://doi.org/10.1016/j.envres.2023.115785},

issn = {0013-9351},

year  = {2023},

date = {2023-01-01},

journal = {Environmental Research},

volume = {227},

pages = {115785},

abstract = {The production of secondary metabolites including biosurfactants by the Bacillus subtilis ANT_WA51 and the evaluation of its ability to leach metals and petroleum derivatives from the soil, using post-culture medium was investigated. The ANT_WA51 strain isolated from a pristine, harsh Antarctic environment produces the biosurfactants surfactin and fengycin, which reduce the surface tension of molasses-based post-culture medium to 26.6 mN m-1 at a critical micellization concentration (CMC) of 50 mg L-1 and a critical micelle dilution (CMD) of 1:19. The presence of biosurfactants and other secondary metabolites in the post-culture medium contributed to significant removal of xenobiotics from contaminated soils in the batch washing experiment - 70% hydrocarbons and 10–23% metals (Zn, Ni and Cu). The isolate's tolerance to different abiotic stresses, including freezing, freeze-thaw cycles, salinity (up to 10%), the presence of metals - Cr(VI), Pb(II), Mn(II), As(V) (up to 10 mM) and Mo(VI) (above 500 mM) and petroleum hydrocarbons (up to 20.000 mg kg-1) as well as the confirmed metabolic activity of these bacteria in toxic environments in the OxiTop® system indicate that they can be used directly in bioremediation. Comparative genomic analysis of this bacteria revealed a high similarity of its genome to the associated plant strains from America and Europe indicating the wide applicability of plant growth-promoting Bacillus subtilis and that the data can be extrapolated to a wide range of environmental strains. An important aspect of the study was to present the absence of inherent features which would indicate its clear pathogenicity enables its safe use in the environment. Based on the obtained results, we also conclude that the use of post-culture medium, obtained on low-cost byproducts like molasses, for leaching contaminants, especially hydrocarbons, is a promising bioremediation method that can be a replacement for the use of synthetic surfactants and provides a base for further large-scale research but the selection of an appropriate leaching may be dependent on the concentration of contaminants.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{YANG2023138662,

title = {Decreasing lactate input for cost-effective sulfidogenic metal removal in sulfate-rich effluents: Mechanistic insights from (bio)chemical kinetics to microbiome response},

author = {Zhendong Yang and Ne Ji and Jin Huang and Jing Wang and Lukasz Drewniak and Huaqun Yin and Cheng Hu and Yazhi Zhan and Zhaoyue Yang and Li Zeng and Zhenghua Liu},

url = {https://www.sciencedirect.com/science/article/pii/S0045653523009293},

doi = {https://doi.org/10.1016/j.chemosphere.2023.138662},

issn = {0045-6535},

year  = {2023},

date = {2023-01-01},

journal = {Chemosphere},

volume = {330},

pages = {138662},

abstract = {High material cost is the biggest barrier for the industrial use of low-molecular-weight organics (i.e. lactate) as external carbon and electron source for sulfidogenic metal removal in sulfate-rich effluents. This study aims to provide mechanistic evidence from kinetics to microbiome analysis by batch modeling to support the possibility of decreasing the lactate input to achieve cost-effective application. The results showed that gradient COD/SO42− ratios at a low level had promising treatment performance, reaching neutralized pH with nearly total elimination of COD (91%–99%), SO42− (85%–99%), metals (80%–99%) including Cu, Zn, and Mn. First-order kinetics exhibited the best fit (R2 = 0.81–0.98) to (bio)chemical reactions, and the simulation results revealed that higher COD/SO42− accelerated the reaction rate of SO42− and COD but not suitable to that of metals. On the other hand, we found that the decreasing COD/SO42− ratio increased average path distance but decreased clustering coefficient and heterogeneity in microbial interaction network. Genetic prediction found that the sulfate-reduction-related functions were significantly correlated with the reaction kinetics changed with COD/SO42− ratios. Our study, combining reaction kinetics with microbiome analysis, demonstrates that the use of lactate as a carbon source under low COD/SO42− ratios entails significant efficiency of metal removal in sulfate-rich effluent using SRB-based technology. However, further studies should be carried out, including parameter-driven optimization and life cycle assessments are necessary, for its practical application.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WILCZYNSKI2023115116,

title = {Acute toxicity of organoarsenic chemical warfare agents to Danio rerio embryos},

author = {Wojciech Wilczynski and Tomasz Brzeziński and Piotr Maszczyk and Antoni Ludew and Michał J. Czub and Daniel Dziedzic and Jakub Nawala and Stanislaw Popiel and Jacek Beldowski and Hans Sanderson and Monika Radlinska},

url = {https://www.sciencedirect.com/science/article/pii/S0147651323006206},

doi = {https://doi.org/10.1016/j.ecoenv.2023.115116},

issn = {0147-6513},

year  = {2023},

date = {2023-01-01},

journal = {Ecotoxicology and Environmental Safety},

volume = {262},

pages = {115116},

abstract = {During the 20th century, thousands of tons of munitions containing organoarsenic chemical warfare agents (CWAs) were dumped into oceans, seas and inland waters around the world. As a result, organoarsenic CWAs continue to leak from corroding munitions into sediments and their environmental concentrations are expected to peak over the next few decades. There remains, however, a lack of knowledge about their potential toxicity to aquatic vertebrates, such as fish. The aim of this study was to fill in this gap in research, by investigating the acute toxicity of organoarsenic CWAs on fish embryos, using the model species, Danio rerio. To estimate the acute toxicity thresholds of organoarsenic CWAs (Clark I, Adamsite, PDCA), a CWA-related compound (TPA), as well as four organoarsenic CWA degradation products (Clark I[ox], Adamsite[ox], PDCA[ox], TPA[ox]), standardized tests were performed following the OECD no. 236 Fish Embryo Acute Toxicity Test guidelines. Additionally, the detoxification response in D. rerio embryos was investigated by analysing the mRNA expression of five genes encoding antioxidant enzymes (CAT, SOD, GPx, GR and GST). During the 96 h of exposure, organoarsenic CWAs induced lethal effects in D. rerio embryos at very low concentrations (classified as 1st category pollutants according to GHS categorization), and were therefore deemed to be serious environmental hazards. Although TPA and the four CWA degradation products caused no acute toxicity even at their maximum solubility, the transcription of antioxidant-related genes was altered upon exposure to these compounds, indicating the need for further testing for chronic toxicity. Incorporating the results of this study into ecological risk assessments will provide a more accurate prediction of the environmental hazards posed by CWA-related organoarsenicals.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zebrowski2022,

title = {The effect of microplastics on the interspecific competition of Daphnia},

author = {Marcin Lukasz Zebrowski and Ewa Babkiewicz and Aleksandra Błażejewska and Szymon Pukos and Julia Wawrzeńczak and Wojciech Wilczynski and Jacek Zebrowski and Mirosław Ślusarczyk and Piotr Maszczyk},

doi = {10.1016/j.envpol.2022.120121},

issn = {0269-7491},

year  = {2022},

date = {2022-11-00},

journal = {Environmental Pollution},

volume = {313},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Poria2022b,

title = {Plant Growth-Promoting Bacteria (PGPB) integrated phytotechnology: A sustainable approach for remediation of marginal lands},

author = {Vikram Poria and Klaudia Dębiec-Andrzejewska and Angelika Fiodor and Marharyta Lyzohub and Nur Ajijah and Surender Singh and Kumar Pranaw},

doi = {10.3389/fpls.2022.999866},

issn = {1664-462X},

year  = {2022},

date = {2022-10-21},

journal = {Front. Plant Sci.},

volume = {13},

publisher = {Frontiers Media SA},

abstract = {Land that has little to no utility for agriculture or industry is considered marginal land. This kind of terrain is frequently found on the edge of deserts or other arid regions. The amount of land that can be used for agriculture continues to be constrained by increasing desertification, which is being caused by climate change and the deterioration of agriculturally marginal areas. Plants and associated microorganisms are used to remediate and enhance the soil quality of marginal land. They represent a low-cost and usually long-term solution for restoring soil fertility. Among various phytoremediation processes (viz., phytodegradation, phytoextraction, phytostabilization, phytovolatilization, phytofiltration, phytostimulation, and phytodesalination), the employment of a specific mechanism is determined by the state of the soil, the presence and concentration of contaminants, and the plant species involved. This review focuses on the key economically important plants used for phytoremediation, as well as the challenges to plant growth and phytoremediation capability with emphasis on the advantages and limits of plant growth in marginal land soil. Plant growth-promoting bacteria (PGPB) boost plant development and promote soil bioremediation by secreting a variety of metabolites and hormones, through nitrogen fixation, and by increasing other nutrients’ bioavailability through mineral solubilization. This review also emphasizes the role of PGPB under different abiotic stresses, including heavy-metal-contaminated land, high salinity environments, and organic contaminants. In our opinion, the improved soil fertility of marginal lands using PGPB with economically significant plants (e.g., Miscanthus) in dual precession technology will result in the reclamation of general agriculture as well as the restoration of native vegetation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bujak2022,

title = {Characterization of Three Novel Virulent Aeromonas Phages Provides Insights into the Diversity of the Autographiviridae Family},

author = {Katarzyna Bujak and Przemyslaw Decewicz and Michal Kitowicz and Monika Radlinska},

doi = {10.3390/v14051016},

issn = {1999-4915},

year  = {2022},

date = {2022-05-00},

journal = {Viruses},

volume = {14},

number = {5},

publisher = {MDPI AG},

abstract = {In this study, we isolated and characterized three novel virulent Autographiviridae bacteriophages, vB_AspA_Bolek, vB_AspA_Lolek, and vB_AspA_Tola, which infect different Aeromonas strains. These three host–pathogen pairs were derived from the same sampling location—the arsenic-containing microbial mats of the Zloty Stok gold mine. Functional analysis showed they are psychrotolerant (4–25 °C), albeit with a much wider temperature range of propagation for the hosts (≤37 °C). Comparative genomic analyses revealed a high nucleotide and amino acid sequence similarity of vB_AspA_Bolek and vB_AspA_Lolek, with significant differences exclusively in the C-terminal region of their tail fibers, which might explain their host range discrimination. The protein-based phage network, together with a phylogenetic analysis of the marker proteins, allowed us to assign vB_AspA_Bolek and vB_AspA_Lolek to the Beijerinckvirinae and vB_AspA_Tola to the Colwellvirinae subfamilies, but as three novel species, due to their low nucleotide sequence coverage and identity with other known phage genomes. Global comparative analysis showed that the studied phages are also markedly different from most of the 24 Aeromonas autographiviruses known so far. Finally, this study provides in-depth insight into the diversity of the Autographiviridae phages and reveals genomic similarities between selected groups of this family as well as between autographiviruses and their relatives of other Caudoviricetes families.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Styczynski2022,

title = {Application of Psychrotolerant Antarctic Bacteria and Their Metabolites as Efficient Plant Growth Promoting Agents},

author = {Michal Styczynski and Gabriel Biegniewski and Przemyslaw Decewicz and Bartosz Rewerski and Klaudia Debiec-Andrzejewska and Lukasz Dziewit},

doi = {10.3389/fbioe.2022.772891},

issn = {2296-4185},

year  = {2022},

date = {2022-02-24},

journal = {Front. Bioeng. Biotechnol.},

volume = {10},

publisher = {Frontiers Media SA},

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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DABROWSKA2022115967,

title = {Use of lignocellulosic waste materials in the passive treatment of highly alkaline wastewater contaminated with sulfates and metals – From a laboratory study to pilot scale},

author = {Maria Dabrowska and Jacek Retka and Witold Uhrynowski and Lukasz Drewniak},

url = {https://www.sciencedirect.com/science/article/pii/S0301479722015407},

doi = {https://doi.org/10.1016/j.jenvman.2022.115967},

issn = {0301-4797},

year  = {2022},

date = {2022-01-01},

journal = {Journal of Environmental Management},

volume = {321},

pages = {115967},

abstract = {Passive wastewater treatment systems are an alternative to costly and ineffective chemical wastewater treatment methods. Lignocellulosic waste materials (LWM) are often used in passive wastewater treatment systems as a cheap and accessible source of nutrients. LWM, such as spent mushroom compost and woodchips, have been implemented for the successful management of mildly alkaline effluents, which constitute a large fraction of industrial wastewater. The objective of the study was to provide an extensive study of the parameters in four types of commonly used LWM (raw and composted sawdust, spent mushroom compost and woodchips), which can be used in the planning of a passive wastewater treatment plant. LWM were shown to remove up to 90% Zn2+ and Pb2+ from a model solution and neutralize wastewater. Moreover, the LWM were inhabited by a physiologically diverse microbial consortium containing sulfate-reducing and cellulolytic microbes, which can influence the treatment process. Another purpose of this study was to construct a pilot wastewater treatment plant based on the use of LWM and gravel and to present its ability to effectively treat extremely alkaline flotation wastewater (pH = 12) originating from a lead and zinc mine located in Montenegro. The treated wastewater had a unique, but challenging chemical composition for passive treatment, as it was heavily contaminated with sulfates (∼1200 mg/L) and lead (∼1 g/L). The removal within the developed installation reached a rate of 66%, while the treated effluent, after initial neutralization, was maintained at a pH of approximately 7. Lead and zinc concentrations after treatment were also kept at levels required by Montenegrin law for wastewater disposal.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fermentation8090440,

title = {Pigment Production by Paracoccus spp. Strains through Submerged Fermentation of Valorized Lignocellulosic Wastes},

author = {Weronika Pyter and Jasneet Grewal and Dariusz Bartosik and Lukasz Drewniak and Kumar Pranaw},

url = {https://www.mdpi.com/2311-5637/8/9/440},

doi = {10.3390/fermentation8090440},

issn = {2311-5637},

year  = {2022},

date = {2022-01-01},

journal = {Fermentation},

volume = {8},

number = {9},

abstract = {Due to the increasing emphasis on the circular economy, research in recent years has focused on the feasibility of using biomass as an alternative energy source. Plant biomass is a potential substitute for countering the dependence on depleting fossil-derived energy sources and chemicals. However, in particular, lignocellulosic waste materials are complex and recalcitrant structures that require effective pretreatment and enzymatic saccharification to release the desired saccharides, which can be further fermented into a plethora of value-added products. In this context, pigment production from waste hydrolysates is a viable ecological approach to producing safe and natural colorings, which are otherwise produced via chemical synthesis and raise health concerns. The present study aims to evaluate two such abundant lignocellulosic wastes, i.e., wheat straw and pinewood sawdust as low-cost feedstocks for carotenoid production with Paracoccus strains. An alkali pretreatment approach, followed by enzymatic saccharification using an indigenous lab-isolated fungal hydrolase, was found to be effective for the release of fermentable sugars from both substrates. The fermentation of the pretreated sawdust hydrolysate by Paracoccus aminophilus CRT1 and Paracoccus kondratievae CRT2 resulted in the highest carotenoid production, 631.33 and 758.82 μg/g dry mass, respectively. Thus, the preliminary but informative research findings of the present work exhibit the potential for sustainable and economically feasible pigment production from lignocellulosic feedstocks after optimal process development on the pilot scale.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{GREWAL2022119796,

title = {Recent perspectives on microbial and ionic liquid interactions with implications for biorefineries},

author = {Jasneet Grewal and Sunil Kumar Khare and Lukasz Drewniak and Kumar Pranaw},

url = {https://www.sciencedirect.com/science/article/pii/S0167732222013344},

doi = {https://doi.org/10.1016/j.molliq.2022.119796},

issn = {0167-7322},

year  = {2022},

date = {2022-01-01},

journal = {Journal of Molecular Liquids},

volume = {362},

pages = {119796},

abstract = {In recent years, in pursuit of sustainable and green chemistry, a plethora of ionic liquids (ILs) have been formulated to serve as safe alternatives to toxic solvents for numerous applications in electrochemistry, organic synthesis, inorganic/organic transformations, catalysis etc. Nonetheless, the unique and easily tunable physico-chemical properties of these ILs have progressed their usage as reaction media in biocatalysis. Especially in the context of lignocellulosic biomass valorization, ILs have emerged as a promising choice for dissolution of biomass leading to better enzymatic digestibility due to efficient pretreatment. The present review highlights the potency of IL mediated valorization of waste feedstocks for the development of sustainable circular biorefineries. However, the usage of IL mediated biocatalysis at bench scale has been hampered by enzyme denaturation and viability loss of fermenting microbes in IL laden environments, which prevents the realization of the ultimate aim of consolidated biomass processing in one-pot. Though enzyme stabilization in ILs has witnessed significant improvement with various approaches, the studies for a comprehensive understanding of microbial interactions with ILs are still in an exploratory phase. The present review intends to provide elaborative insights into toxicological issues of ILs to microbial cells and their mechanism of growth inhibition, which can potentiate their pharmaceutical applications as anti-microbial agents as well as provide insights for designing biocompatible catalytic systems. Further, the adaptive mechanisms exhibited by IL-resilient microbes have been elaborately discussed. A comprehensive elucidation of the current and future directions of designing compatible IL-microbe biocatalytic systems has been encompassed, which will facilitate advancements in IL-assisted biocatalysis for sustainable production of value-added products via waste-derived biorefineries.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.3389/fmicb.2022.832918,

title = {Colorful Treasure From Agro-Industrial Wastes: A Sustainable Chassis for Microbial Pigment Production},

author = {Jasneet Grewal and Mikołaj Woła̧cewicz and Weronika Pyter and Namrata Joshi and Lukasz Drewniak and Kumar Pranaw},

url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.832918},

doi = {10.3389/fmicb.2022.832918},

issn = {1664-302X},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Microbiology},

volume = {Volume 13 - 2022},

abstract = {Colors with their attractive appeal have been an integral part of human lives and the easy cascade of chemical catalysis enables fast, bulk production of these synthetic colorants with low costs. However, the resulting hazardous impacts on the environment and human health has stimulated an interest in natural pigments as a safe and ecologically clean alternative. Amidst sources of natural producers, the microbes with their diversity, ease of all-season production and peculiar bioactivities are attractive entities for industrial production of these marketable natural colorants. Further, in line with circular bioeconomy and environmentally clean technologies, the use of agro-industrial wastes as feedstocks for carrying out the microbial transformations paves way for sustainable and cost-effective production of these valuable secondary metabolites with simultaneous waste management. The present review aims to comprehensively cover the current green workflow of microbial colorant production by encompassing the potency of waste feedstocks and fermentation technologies. The commercially important pigments viz. astaxanthin, prodigiosin, canthaxanthin, lycopene and β-carotene produced by native and engineered bacterial, fungal or yeast strains have been elaborately discussed with their versatile applications in food, pharmaceuticals, textiles, cosmetics etc. The limitations and their economic viability to meet the future market demands have been envisaged. The most recent advances in various molecular approaches to develop engineered microbiological systems for enhanced pigment production have been included to provide new perspectives to this burgeoning field of research.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{YANG2022114689,

title = {Life cycle assessment and cost analysis for copper hydrometallurgy industry in China},

author = {Zhaoyue Yang and Zhendong Yang and Sheng Yang and Ziliang Liu and Zhenghua Liu and Yongjun Liu and Lukasz Drewniak and Chengying Jiang and Qian Li and Wen Li and Huaqun Yin},

url = {https://www.sciencedirect.com/science/article/pii/S0301479722002626},

doi = {https://doi.org/10.1016/j.jenvman.2022.114689},

issn = {0301-4797},

year  = {2022},

date = {2022-01-01},

journal = {Journal of Environmental Management},

volume = {309},

pages = {114689},

abstract = {Understanding the environmental and economic impacts of copper hydrometallurgy throughout the whole life cycle is necessary for sustainable development of the copper industry. In this study, the environmental impacts and economic costs throughout the two major copper hydrometallurgical routes in China, including heap leaching and heap-agitation leaching, are analyzed and compared using the life cycle assessment (LCA) and life cycle cost (LCC) technique. The life cycle inventory compiled from the annual statistics of the Muliashi Copper Mine, and the data regarding energy and materials process are based on the GaBi databases. The environmental impacts are quantified into 12 indicators. The results show that compared with heap leaching route, heap-agitation leaching route reduces 36.8% of abiotic depletion potential (ADP elements), but increases over half of cumulative energy demand (CED), marine aquatic ecotoxicity potential (MAETP) and human toxicity potential (HTP). Furthermore, the stage of electrowinning and agitation leaching contributes the largest environmental impact to heap leaching and heap-agitation leaching route, respectively. This is mainly due to huge consumption of electricity and sulfuric acid. The analysis of economic cost reveals that heap leaching route needs internal cost of $3225/t Cu and external cost of $426/t Cu. Compared with heap leaching route, heap-agitation leaching route increased the internal and external cost by 18.9% and 54.2%, respectively. But the economic return from heap-agitation leaching is double that from heap leaching. Together, these results indicate heap-agitation leaching has a larger environmental impact and higher economic benefit than heap leaching, which is helpful for the government to design ecological compensation policies in the balance between ecological environment and economic development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ijms232113539,

title = {Characteristics and Comparative Genomic Analysis of a Novel Virus, VarioGold, the First Bacteriophage of Variovorax},

author = {Przemyslaw Decewicz and Michal Kitowicz and Monika Radlinska},

url = {https://www.mdpi.com/1422-0067/23/21/13539},

doi = {10.3390/ijms232113539},

issn = {1422-0067},

year  = {2022},

date = {2022-01-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

number = {21},

abstract = {Variovorax represents a widespread and ecologically significant genus of soil bacteria. Despite the ecological importance of these bacteria, our knowledge about the viruses infecting Variovorax spp. is quite poor. This study describes the isolation and characterization of the mitomycin-induced phage, named VarioGold. To the best of our knowledge, VarioGold represents the first characterized virus for this genus. Comparative genomic analyses suggested that VarioGold is distinct from currently known bacteriophages at both the nucleotide and protein levels; thus, it could be considered a new virus genus. In addition, another 37 prophages were distinguished in silico within the complete genomic sequences of Variovorax spp. that are available in public databases. The similarity networking analysis highlighted their general high diversity, which, despite clustering with previously described phages, shows their unique genetic load. Therefore, the novelty of Variovorax phages warrants the great enrichment of databases, which could, in turn, improve bioinformatic strategies for finding (pro)phages.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{toxics10050206,

title = {Metagenomic Analysis of the Gastrointestinal Microbiota of Gadus morhua callarias L. Originating from a Chemical Munition Dump Site},

author = {Wojciech Wilczynski and Monika Radlinska and Klaus Wysujack and Michał Czub and Tomasz Brzeziński and Grzegorz Kowalczyk and Jacek Bełdowski and Pedro Nogueira and Piotr Maszczyk},

url = {https://www.mdpi.com/2305-6304/10/5/206},

doi = {10.3390/toxics10050206},

issn = {2305-6304},

year  = {2022},

date = {2022-01-01},

journal = {Toxics},

volume = {10},

number = {5},

abstract = {Several hundred thousand tonnes of munitions containing chemical warfare agents (CWAs) are lying on the seafloor worldwide. CWAs have started leaking from corroded munitions, and their presence in the environment and in organisms inhabiting dump sites has been detected. The presence of CWAs in the water negatively affects fish, macrobenthos and free-living bacteria. It can be expected that the presence of CWAs would also affect the gut-associated bacteria in fish, which are vital for their condition. The main aim of this study was to test if the microbiota of cod collected in the Baltic Bornholm Deep (highly polluted with CWAs) is dysregulated. To investigate this, we conducted metagenomic studies based on 16S rRNA gene sequencing. We found that the microbiota of cod inhabiting the dump site was significantly less taxonomically diverse compared to those from a non-polluted reference site. Moreover, taxa associated with fish diseases (e.g., Vibrionaceae, Aeromonadaceae) were more prevalent, and probiotic taxa (e.g., Actinobacteriota, Rhodobacteraceae) were less frequent in the guts of individuals from the dump site, than those from the reference site. The differences in vulnerability of various bacterial taxa inhabiting cod gastrointestinal tracts to CWAs were hypothesised to be responsible for the observed microbiota dysregulation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mroczek2021,

title = {Determination of Saponins in Leaves of Four Swiss Chard (\textit{Beta vulgaris} L.) Cultivars by UHPLC-CAD/QTOF-MS/MS},

author = {Agnieszka Mroczek and Urszula Klimczak and Mariusz Kowalczyk},

doi = {10.31883/pjfns/134623},

issn = {2083-6007},

year  = {2021},

date = {2021-04-20},

journal = {Pol. J. Food Nutr. Sci.},

pages = {147--159},

publisher = {Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ijms222011070,

title = {Genome Study of a Novel Virulent Phage vB_SspS_KASIA and Mu-like Prophages of Shewanella sp. M16 Provides Insights into the Genetic Diversity of the Shewanella Virome},

author = {Katarzyna Bujak and Przemyslaw Decewicz and Joanna M. Rosinska and Monika Radlinska},

url = {https://www.mdpi.com/1422-0067/22/20/11070},

doi = {10.3390/ijms222011070},

issn = {1422-0067},

year  = {2021},

date = {2021-01-01},

journal = {International Journal of Molecular Sciences},

volume = {22},

number = {20},

abstract = {Shewanella is a ubiquitous bacterial genus of aquatic ecosystems, and its bacteriophages are also isolated from aquatic environments (oceans, lakes, ice, and wastewater). In this study, the isolation and characterization of a novel virulent Shewanella phage vB_SspS_KASIA and the identification of three prophages of its host, Shewanella sp. M16, including a mitomycin-inducible Mu-like siphovirus, vB_SspS_MuM16-1, became the starting point for comparative analyses of phages infecting Shewanella spp. and the determination of their position among the known bacterial viruses. A similarity networking analysis revealed the high diversity of Shewanella phages in general, with vB_SspS_KASIA clustering exclusively with Colwellia phage 9A, with which it forms a single viral cluster composed of two separate viral subclusters. Furthermore, vB_SspS_MuM16-1 presented itself as being significantly different from the phages deposited in public databases, expanding the diversity of the known Mu-like phages and giving potential molecular markers for the identification of Mu-like prophages in bacterial genomes. Moreover, the functional analysis performed for vB_SspS_KASIA suggested that, despite the KASIA host, the M16 strain grows better in a rich medium and at 30 °C the phage replication cycle seems to be optimal in restrictive culture conditions mimicking their natural environment, the Zloty Stok gold and arsenic mine.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ijms21186709,

title = {Identification, Characterization, and Genomic Analysis of Novel Serratia Temperate Phages from a Gold Mine},

author = {Katarzyna Bujak and Przemyslaw Decewicz and Jerzy Kaminski and Monika Radlinska},

url = {https://www.mdpi.com/1422-0067/21/18/6709},

doi = {10.3390/ijms21186709},

issn = {1422-0067},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {18},

abstract = {Bacteria of the genus Serratia inhabit a variety of ecological niches like water, soil, and the bodies of animals, and have a wide range of lifestyles. Currently, the complete genome sequences of 25 Serratia phages are available in the NCBI database. All of them were isolated from nutrient-rich environments like sewage, with the use of clinical Serratia strains as hosts. In this study, we identified a novel Serratia myovirus named vB_SspM_BZS1. Both the phage and its host Serratia sp. OS31 were isolated from the same oligotrophic environment, namely, an abandoned gold mine (Zloty Stok, Poland). The BZS1 phage was thoroughly characterized here in terms of its genomics, morphology, and infection kinetics. We also demonstrated that Serratia sp. OS31 was lysogenized by mitomycin-inducible siphovirus vB_SspS_OS31. Comparative analyses revealed that vB_SspM_BZS1 and vB_SspS_OS31 were remote from the known Serratia phages. Moreover, vB_SspM_BZS1 was only distantly related to other viruses. However, we discovered similar prophage sequences in genomes of various bacteria here. Additionally, a protein-based similarity network showed a high diversity of Serratia phages in general, as they were scattered across nineteen different clusters. In summary, this work broadened our knowledge on the diverse relationships of Serratia phages.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ijms21062096,

title = {Identification and Characterization of the First Virulent Phages, Including a Novel Jumbo Virus, Infecting Ochrobactrum spp.},

author = {Przemyslaw Decewicz and Piotr Golec and Mateusz Szymczak and Monika Radlinska and Lukasz Dziewit},

url = {https://www.mdpi.com/1422-0067/21/6/2096},

doi = {10.3390/ijms21062096},

issn = {1422-0067},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {6},

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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Decewicz2019,

title = {Characterization of the virome of Paracoccus spp. (Alphaproteobacteria) by combined in silico and in vivo approaches},

author = {Przemyslaw Decewicz and Lukasz Dziewit and Piotr Golec and Patrycja Kozlowska and Dariusz Bartosik and Monika Radlinska},

doi = {10.1038/s41598-019-44460-4},

issn = {2045-2322},

year  = {2019},

date = {2019-12-00},

journal = {Sci Rep},

volume = {9},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {AbstractBacteria 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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Maszczyk2019,

title = {Combined effects of elevated epilimnetic temperature and metalimnetic hypoxia on the predation rate of planktivorous fish},

author = {Piotr Maszczyk and Ewa Babkiewicz and Krzysztof Ciszewski and Kamil Dabrowski and Przemysław Dynak and Karol Krajewski and Paulina Urban and Marcin Żebrowski and Wojciech Wilczynski},

doi = {10.1093/plankt/fbz048},

issn = {1464-3774},

year  = {2019},

date = {2019-09-27},

volume = {41},

number = {5},

pages = {709--722},

publisher = {Oxford University Press (OUP)},

abstract = {AbstractIncreased temperature in the epilimnion and hypoxia in the metalimnion of a lake would result in an increase of positive-size-selective fish predation on zooplankton and in turn in a decrease of mean body size in zooplankton populations and communities. We tested this hypothesis in four types of experiments with juvenile rudd (Scardinius erythrophthalmus) foraging on Daphnia longispina in an indoor twin column tank system. In each experiment of the first three types, one column contained one of three types of experimental treatments differing from the control treatment (in the other column) by the following: (i) elevated temperature in the epilimnion, (ii) hypoxia in the metalimnion and (iii) simultaneous elevated temperature in the epilimnion and hypoxia in the metalimnion. In the fourth type of experiment, the gradients of temperature and oxygen concentration in both columns were the same, but prior to the experiments, Daphnia and fish in the control treatment were acclimated to normoxia and, in the experimental treatment, to hypoxia. The results confirmed our hypothesis, since the predation rate of fish was greater in each of the first three experimental treatments than in the control. We did not detect an effect of the acclimation to hypoxia on the predation rate of the fish.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mroczek2019,

title = {MS/MS and UPLC-MS profiling of triterpenoid saponins from leaves and roots of four red beet (Beta vulgaris L.) cultivars},

author = {Agnieszka Mroczek and Ireneusz Kapusta and Anna Stochmal and Wirginia Janiszowska},

doi = {10.1016/j.phytol.2019.02.015},

issn = {1874-3900},

year  = {2019},

date = {2019-04-00},

journal = {Phytochemistry Letters},

volume = {30},

pages = {333--337},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ijms20051018,

title = {Genomic Analysis of Shewanella sp. O23S—The Natural Host of the pSheB Plasmid Carrying Genes for Arsenic Resistance and Dissimilatory Reduction},

author = {Witold Uhrynowski and Monika Radlinska and Lukasz Drewniak},

url = {https://www.mdpi.com/1422-0067/20/5/1018},

doi = {10.3390/ijms20051018},

issn = {1422-0067},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {5},

abstract = {Shewanella sp. O23S is a dissimilatory arsenate reducing bacterial strain involved in arsenic transformations within the abandoned gold mine in Zloty Stok (SW Poland). Previous physiological studies revealed that O23S may not only release arsenic from minerals, but also facilitate its immobilization through co-precipitation with reduced sulfur species. Given these uncommon, complementary characteristics and the application potential of the strain in arsenic-removal technologies, its genome (~5.3 Mbp), consisting of a single chromosome, two large plasmids (pSheA and pSheB) and three small plasmid-like phages (pSheC-E) was sequenced and annotated. Genes encoding putative proteins involved in heavy metal transformations, antibiotic resistance and other phenotypic traits were identified. An in-depth comparative analysis of arsenic respiration (arr) and resistance (ars) genes and their genetic context was also performed, revealing that pSheB carries the only copy of the arr genes, and a complete ars operon. The plasmid pSheB is therefore a unique natural vector of these genes, providing the host cells arsenic respiration and resistance abilities. The functionality of the identified genes was determined based on the results of the previous and additional physiological studies, including: the assessment of heavy metal and antibiotic resistance under various conditions, adhesion-biofilm formation assay and BiologTM metabolic preferences test. This combined genetic and physiological approach shed a new light on the capabilities of O23S and their molecular basis, and helped to confirm the biosafety of the strain in relation to its application in bioremediation technologies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{v9070161,

title = {Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome},

author = {Przemyslaw Decewicz and Monika Radlinska and Lukasz Dziewit},

url = {https://www.mdpi.com/1999-4915/9/7/161},

doi = {10.3390/v9070161},

issn = {1999-4915},

year  = {2017},

date = {2017-01-01},

journal = {Viruses},

volume = {9},

number = {7},

abstract = {The genus Sinorhizobium/Ensifer mostly groups nitrogen-fixing bacteria that create root or stem nodules on leguminous plants and transform atmospheric nitrogen into ammonia, which improves the productivity of the plants. Although these biotechnologically-important bacteria are commonly found in various soil environments, little is known about their phages. In this study, the genome of Sinorhizobium sp. LM21 isolated from a heavy-metal-contaminated copper mine in Poland was investigated for the presence of prophages and DNA methyltransferase-encoding genes. In addition to the previously identified temperate phage, ΦLM21, and the phage-plasmid, pLM21S1, the analysis revealed the presence of three prophage regions. Moreover, four novel phage-encoded DNA methyltransferase (MTase) genes were identified and the enzymes were characterized. It was shown that two of the identified viral MTases methylated the same target sequence (GANTC) as cell cycle-regulated methyltransferase (CcrM) of the bacterial host strain, LM21. This discovery was recognized as an example of the evolutionary convergence between enzymes of sinorhizobial viruses and their host, which may play an important role in virus cycle. In the last part of the study, thorough comparative analyses of 31 sinorhizobial (pro)phages (including active sinorhizobial phages and novel putative prophages retrieved and manually re-annotated from Sinorhizobium spp. genomes) were performed. The networking analysis revealed the presence of highly conserved proteins (e.g., holins and endolysins) and a high diversity of viral integrases. The analysis also revealed a large number of viral DNA MTases, whose genes were frequently located within the predicted replication modules of analyzed prophages, which may suggest their important regulatory role. Summarizing, complex analysis of the phage protein similarity network enabled a new insight into overall sinorhizobial virome diversity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.3389/fmicb.2017.00936,

title = {Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism},

author = {Witold Uhrynowski and Przemyslaw Decewicz and Lukasz Dziewit and Monika Radlinska and Pawel S. Krawczyk and Leszek Lipinski and Dorota Adamska and Lukasz Drewniak},

url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.00936},

doi = {10.3389/fmicb.2017.00936},

issn = {1664-302X},

year  = {2017},

date = {2017-01-01},

journal = {Frontiers in Microbiology},

volume = {Volume 8 - 2017},

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 4 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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Dziewit2016b,

title = {Two novel temperate bacteriophages co-existing in Aeromonas sp. ARM81 – characterization of their genomes, proteomes and DNA methyltransferases},

author = {Lukasz Dziewit and Monika Radlinska},

doi = {10.1099/jgv.0.000504},

issn = {1465-2099},

year  = {2016},

date = {2016-08-01},

volume = {97},

number = {8},

pages = {2008--2022},

publisher = {Microbiology Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Dziewit2016,

title = {Two Inducible Prophages of an Antarctic Pseudomonas sp. ANT_H14 Use the Same Capsid for Packaging Their Genomes – Characterization of a Novel Phage Helper-Satellite System},

author = {Lukasz Dziewit and Monika Radlinska},

editor = {Mark J van Raaij},

doi = {10.1371/journal.pone.0158889},

issn = {1932-6203},

year  = {2016},

date = {2016-07-07},

journal = {PLoS ONE},

volume = {11},

number = {7},

publisher = {Public Library of Science (PLoS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1093/femsec/fiw215,

title = {Molecular characterization of the pSinB plasmid of the arsenite oxidizing, metallotolerant Sinorhizobium sp. M14 – insight into the heavy metal resistome of sinorhizobial extrachromosomal replicons},

author = {Krzysztof Romaniuk and Lukasz Dziewit and Przemyslaw Decewicz and Sebastian Mielnicki and Monika Radlinska and Lukasz Drewniak},

url = {https://doi.org/10.1093/femsec/fiw215},

doi = {10.1093/femsec/fiw215},

issn = {0168-6496},

year  = {2016},

date = {2016-01-01},

journal = {FEMS Microbiology Ecology},

volume = {93},

number = {1},

pages = {fiw215},

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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mroczek2015,

title = {Phytochemistry and bioactivity of triterpene saponins from Amaranthaceae family},

author = {Agnieszka Mroczek},

doi = {10.1007/s11101-015-9394-4},

issn = {1572-980X},

year  = {2015},

date = {2015-08-00},

journal = {Phytochem Rev},

volume = {14},

number = {4},

pages = {577--605},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DREWNIAK201542,

title = {Construction of the recombinant broad-host-range plasmids providing their bacterial hosts arsenic resistance and arsenite oxidation ability},

author = {Lukasz Drewniak and Martyna Ciezkowska and Monika Radlinska and Aleksandra Sklodowska},

url = {https://www.sciencedirect.com/science/article/pii/S016816561500022X},

doi = {https://doi.org/10.1016/j.jbiotec.2015.01.013},

issn = {0168-1656},

year  = {2015},

date = {2015-01-01},

journal = {Journal of Biotechnology},

volume = {196-197},

pages = {42-51},

abstract = {The plasmid pSinA of Sinorhizobium sp. M14 was used as a source of functional phenotypic modules, encoding proteins involved in arsenite oxidation and arsenic resistance, to obtain recombinant broad-host-range plasmids providing their bacterial hosts arsenic resistance and arsenite oxidative ability. An arsenite oxidation module was cloned into pBBR1MCS-2 vector yielding plasmid vector pAIO1, while an arsenic resistance module was cloned into pCM62 vector yielding plasmid pARS1. Both plasmid constructs were introduced (separately and together) into the cells of phylogenetically distant (representing Alpha-, Beta-, and Gammaproteobacteria) and physiologically diversified (unable to oxidize arsenite and susceptible/resistant to arsenite and arsenate) bacteria. Functional analysis of the modified strains showed that: (i) the plasmid pARS1 can be used for the construction of strains with an increased resistance to arsenite [up to 20mM of As(III), (ii) the presence of the plasmid pAIO1 in bacteria previously unable to oxidize As(III) to As(V), contributes to the acquisition of arsenite oxidation abilities by these cells, (iii) the highest arsenite utilization rate are observed in the culture of strains harbouring both the plasmids pAIO1 and pARS1, (iv) the strains harbouring the plasmid pAIO1 were able to grow on arsenic-contaminated mine waters (∼3.0mgAsL−1) without any supplementation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}