prof. dr hab. Łukasz Drewniak

@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},

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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.)},

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pubstate = {published},

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}

@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.},

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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.},

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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{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.},

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tppubtype = {article}

}