TY  - JOUR
AU  - Pantelić, Brana
AU  - Siaperas, Romanos
AU  - Budin, Clémence
AU  - de Boer, Tjalf
AU  - Topakas, Evangelos
AU  - Nikodinović-Runić, Jasmina
PY  - 2024
UR  - https://onlinelibrary.wiley.com/doi/abs/10.1111/1751-7915.14445
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2337
AB  - Global plastic waste accumulation has become omnipresent in public discourse and the focus of scientific research. Ranking as the sixth most produced polymer globally, polyurethanes (PU) significantly contribute to plastic waste and environmental pollution due to the toxicity of their building blocks, such as diisocyanates. In this study, the effects of PU on soil microbial communities over 18 months were monitored revealing that it had marginal effects on microbial diversity. However, Streptomyces sp. PU10, isolated from this PU-contaminated soil, proved exceptional in the degradation of a soluble polyester-PU (Impranil) across a range of temperatures with over 96% degradation of 10 g/L in 48 h. Proteins involved in PU degradation and metabolic changes occurring in this strain with Impranil as the sole carbon source were further investigated employing quantitative proteomics. The proposed degradation mechanism implicated the action of three enzymes: a polyester-degrading esterase, a urethane bond-degrading amidase and an oxidoreductase. Furthermore, proteome data revealed that PU degradation intermediates were incorporated into Streptomyces sp. PU10 metabolism via the fatty acid degradation pathway and subsequently channelled to polyketide biosynthesis. Most notably, the production of the tri-pyrrole undecylprodigiosin was confirmed paving the way for establishing PU upcycling strategies to bioactive metabolites using Streptomyces strains.
PB  - Wiley
T2  - Microbial Biotechnology
T2  - Microbial Biotechnology
T1  - Proteomic examination of polyester-polyurethane degradation by Streptomyces sp. PU10: Diverting polyurethane intermediates to secondary metabolite production
IS  - 3
SP  - e14445
VL  - 17
DO  - 10.1111/1751-7915.14445
ER  - 

@article{
author = "Pantelić, Brana and Siaperas, Romanos and Budin, Clémence and de Boer, Tjalf and Topakas, Evangelos and Nikodinović-Runić, Jasmina",
year = "2024",
abstract = "Global plastic waste accumulation has become omnipresent in public discourse and the focus of scientific research. Ranking as the sixth most produced polymer globally, polyurethanes (PU) significantly contribute to plastic waste and environmental pollution due to the toxicity of their building blocks, such as diisocyanates. In this study, the effects of PU on soil microbial communities over 18 months were monitored revealing that it had marginal effects on microbial diversity. However, Streptomyces sp. PU10, isolated from this PU-contaminated soil, proved exceptional in the degradation of a soluble polyester-PU (Impranil) across a range of temperatures with over 96% degradation of 10 g/L in 48 h. Proteins involved in PU degradation and metabolic changes occurring in this strain with Impranil as the sole carbon source were further investigated employing quantitative proteomics. The proposed degradation mechanism implicated the action of three enzymes: a polyester-degrading esterase, a urethane bond-degrading amidase and an oxidoreductase. Furthermore, proteome data revealed that PU degradation intermediates were incorporated into Streptomyces sp. PU10 metabolism via the fatty acid degradation pathway and subsequently channelled to polyketide biosynthesis. Most notably, the production of the tri-pyrrole undecylprodigiosin was confirmed paving the way for establishing PU upcycling strategies to bioactive metabolites using Streptomyces strains.",
publisher = "Wiley",
journal = "Microbial Biotechnology, Microbial Biotechnology",
title = "Proteomic examination of polyester-polyurethane degradation by Streptomyces sp. PU10: Diverting polyurethane intermediates to secondary metabolite production",
number = "3",
pages = "e14445",
volume = "17",
doi = "10.1111/1751-7915.14445"
}

Pantelić, B., Siaperas, R., Budin, C., de Boer, T., Topakas, E.,& Nikodinović-Runić, J.. (2024). Proteomic examination of polyester-polyurethane degradation by Streptomyces sp. PU10: Diverting polyurethane intermediates to secondary metabolite production. in Microbial Biotechnology
Wiley., 17(3), e14445.
https://doi.org/10.1111/1751-7915.14445

Pantelić B, Siaperas R, Budin C, de Boer T, Topakas E, Nikodinović-Runić J. Proteomic examination of polyester-polyurethane degradation by Streptomyces sp. PU10: Diverting polyurethane intermediates to secondary metabolite production. in Microbial Biotechnology. 2024;17(3):e14445.
doi:10.1111/1751-7915.14445 .

Pantelić, Brana, Siaperas, Romanos, Budin, Clémence, de Boer, Tjalf, Topakas, Evangelos, Nikodinović-Runić, Jasmina, "Proteomic examination of polyester-polyurethane degradation by Streptomyces sp. PU10: Diverting polyurethane intermediates to secondary metabolite production" in Microbial Biotechnology, 17, no. 3 (2024):e14445,
https://doi.org/10.1111/1751-7915.14445 . .

TY  - CONF
AU  - Ćirić, Milica
AU  - Šaraba, Vladimir
AU  - Budin, Clémence
AU  - Boer de, Tjalf
AU  - Milovanović, Jelena
AU  - Nikodinović-Runić, Jasmina
PY  - 2023
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2105
AB  - Three mineral water occurrences, captured by wells with a depth of 6.5-442.5 m and used for drinking
and bathing purposes, were sampled and cultivated under conditions favouring the growth of anaerobic,
microaerophilic or CO2 bacteria, in order to capture predominantly anaerobic portion of the bacteriome, which is
dominant in water and soils. Cultivated bacteria were identified by next-generation 16S sequencing and their
biotechnological potential in plastics and lignocellulose degradation was explored. Most abundant genera
detected in examined samples mainly belong to facultative anaerobes that are common representatives of water
and soil environments. In total, 17 genera were detected with a relative abundance over 1% in all three samples,
including Aeromonas, Exiguobacterium, Comamonas and Acinetobacter. Half of the screened isolates demonstrated
growth on at least one plastic or lignocellulosic polymer, with one isolate demonstrating growth on all tested
substrates, one demonstrating carboxymethyl cellulose- and one arabinoxylan-degrading ability. Some of the
representatives of genera identified with high relative abundance in mineral water samples, such as Aeromonas,
Klebsiella, Escherichia, Salmonella, Enterobacter, Pseudomonas and Staphylococcus, have been previously documented
to have pathogenic potential. Due to the use of investigated mineral waters for drinking and bathing, the health
risk from such bacteria in these occurrences needs to be continuously monitored, while, on the other hand,
mineral waters deserve special attention in the future from the aspect of screening for biotechnologically
relevant enzymes.
PB  - Kragujevac : Institute for Information Technologies
C3  - 2nd International Conference on Chemo and Bioinformatics
T1  - Bacteria in drinking and bathing mineral waters of Serbia with polymer-degrading potential
EP  - 195
SP  - 191
DO  - 10.46793/ICCBI23.091C
ER  - 

@conference{
author = "Ćirić, Milica and Šaraba, Vladimir and Budin, Clémence and Boer de, Tjalf and Milovanović, Jelena and Nikodinović-Runić, Jasmina",
year = "2023",
abstract = "Three mineral water occurrences, captured by wells with a depth of 6.5-442.5 m and used for drinking
and bathing purposes, were sampled and cultivated under conditions favouring the growth of anaerobic,
microaerophilic or CO2 bacteria, in order to capture predominantly anaerobic portion of the bacteriome, which is
dominant in water and soils. Cultivated bacteria were identified by next-generation 16S sequencing and their
biotechnological potential in plastics and lignocellulose degradation was explored. Most abundant genera
detected in examined samples mainly belong to facultative anaerobes that are common representatives of water
and soil environments. In total, 17 genera were detected with a relative abundance over 1% in all three samples,
including Aeromonas, Exiguobacterium, Comamonas and Acinetobacter. Half of the screened isolates demonstrated
growth on at least one plastic or lignocellulosic polymer, with one isolate demonstrating growth on all tested
substrates, one demonstrating carboxymethyl cellulose- and one arabinoxylan-degrading ability. Some of the
representatives of genera identified with high relative abundance in mineral water samples, such as Aeromonas,
Klebsiella, Escherichia, Salmonella, Enterobacter, Pseudomonas and Staphylococcus, have been previously documented
to have pathogenic potential. Due to the use of investigated mineral waters for drinking and bathing, the health
risk from such bacteria in these occurrences needs to be continuously monitored, while, on the other hand,
mineral waters deserve special attention in the future from the aspect of screening for biotechnologically
relevant enzymes.",
publisher = "Kragujevac : Institute for Information Technologies",
journal = "2nd International Conference on Chemo and Bioinformatics",
title = "Bacteria in drinking and bathing mineral waters of Serbia with polymer-degrading potential",
pages = "195-191",
doi = "10.46793/ICCBI23.091C"
}

Ćirić, M., Šaraba, V., Budin, C., Boer de, T., Milovanović, J.,& Nikodinović-Runić, J.. (2023). Bacteria in drinking and bathing mineral waters of Serbia with polymer-degrading potential. in 2nd International Conference on Chemo and Bioinformatics
Kragujevac : Institute for Information Technologies., 191-195.
https://doi.org/10.46793/ICCBI23.091C

Ćirić M, Šaraba V, Budin C, Boer de T, Milovanović J, Nikodinović-Runić J. Bacteria in drinking and bathing mineral waters of Serbia with polymer-degrading potential. in 2nd International Conference on Chemo and Bioinformatics. 2023;:191-195.
doi:10.46793/ICCBI23.091C .

Ćirić, Milica, Šaraba, Vladimir, Budin, Clémence, Boer de, Tjalf, Milovanović, Jelena, Nikodinović-Runić, Jasmina, "Bacteria in drinking and bathing mineral waters of Serbia with polymer-degrading potential" in 2nd International Conference on Chemo and Bioinformatics (2023):191-195,
https://doi.org/10.46793/ICCBI23.091C . .

TY  - JOUR
AU  - Šaraba, Vladimir
AU  - Milovanović, Jelena
AU  - Nikodinović-Runić, Jasmina
AU  - Budin, Clémence
AU  - de Boer, Tjalf
AU  - Ćirić, Milica
PY  - 2023
UR  - https://doi.org/10.1007/s00248-023-02278-8
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2062
AB  - The selected brackish groundwater occurrences in the geotectonic regions of Inner Dinarides of western Serbia (Obrenovačka Banja) and Serbian crystalline core (Lomnički Kiseljak and Velika Vrbnica) were sampled for isolation and identification of plastic- and lignocellulose-degrading bacteria, as well as for the assessment of their enzymatic potential. The examined occurrences belong to the cold and warm (subthermal), weakly alkaline, neutral, and weakly acidic groundwater, and their genetic types are HCO3–Na + K and HCO3–Ca, Mg. The most abundant genera identified by next-generation 16S sequencing of cultivated groundwater samples belong to Aeromonas and Exiguobacterium. Of isolates screened on plastic and lignocellulosic substrates, 85.3% demonstrated growth and/or degrading activity on at least one tested substrate, with 27.8% isolates degrading plastic substrate Impranil® DLN-SD (SD), 1.9% plastic substrate bis(2-hydroxyethyl)terephthalate, and 5.6% carboxymethyl cellulose (CMC). Isolates degrading SD that were identified by 16S rDNA sequencing belonged to genera Stenotrophomonas, Flavobacterium, Pantoea, Enterobacter, Pseudomonas, Serratia, Acinetobacter, and Proteus, while isolates degrading CMC belonged to genera Rhizobium and Shewanella. All investigated brackish groundwaters harbor bacteria with potential in degradation of plastics or cellulose. Taking into account that microplastics contamination of groundwater resources is becoming a significant problem, the finding of plastic-degrading bacteria may have potential in bioremediation treatments of polluted groundwater. Subterranean ecosystems, which are largely untapped resources of biotechnologically relevant enzymes, are not traditionally considered the environment of choice for screening for plastic- and cellulose-degrading bacteria and therefore deserve a special attention from this aspect.
T2  - Microbial Ecology
T2  - Microbial EcologyMicrob Ecol
T1  - Brackish Groundwaters Contain Plastic- and Cellulose-Degrading Bacteria
DO  - 10.1007/s00248-023-02278-8
ER  - 

@article{
author = "Šaraba, Vladimir and Milovanović, Jelena and Nikodinović-Runić, Jasmina and Budin, Clémence and de Boer, Tjalf and Ćirić, Milica",
year = "2023",
abstract = "The selected brackish groundwater occurrences in the geotectonic regions of Inner Dinarides of western Serbia (Obrenovačka Banja) and Serbian crystalline core (Lomnički Kiseljak and Velika Vrbnica) were sampled for isolation and identification of plastic- and lignocellulose-degrading bacteria, as well as for the assessment of their enzymatic potential. The examined occurrences belong to the cold and warm (subthermal), weakly alkaline, neutral, and weakly acidic groundwater, and their genetic types are HCO3–Na + K and HCO3–Ca, Mg. The most abundant genera identified by next-generation 16S sequencing of cultivated groundwater samples belong to Aeromonas and Exiguobacterium. Of isolates screened on plastic and lignocellulosic substrates, 85.3% demonstrated growth and/or degrading activity on at least one tested substrate, with 27.8% isolates degrading plastic substrate Impranil® DLN-SD (SD), 1.9% plastic substrate bis(2-hydroxyethyl)terephthalate, and 5.6% carboxymethyl cellulose (CMC). Isolates degrading SD that were identified by 16S rDNA sequencing belonged to genera Stenotrophomonas, Flavobacterium, Pantoea, Enterobacter, Pseudomonas, Serratia, Acinetobacter, and Proteus, while isolates degrading CMC belonged to genera Rhizobium and Shewanella. All investigated brackish groundwaters harbor bacteria with potential in degradation of plastics or cellulose. Taking into account that microplastics contamination of groundwater resources is becoming a significant problem, the finding of plastic-degrading bacteria may have potential in bioremediation treatments of polluted groundwater. Subterranean ecosystems, which are largely untapped resources of biotechnologically relevant enzymes, are not traditionally considered the environment of choice for screening for plastic- and cellulose-degrading bacteria and therefore deserve a special attention from this aspect.",
journal = "Microbial Ecology, Microbial EcologyMicrob Ecol",
title = "Brackish Groundwaters Contain Plastic- and Cellulose-Degrading Bacteria",
doi = "10.1007/s00248-023-02278-8"
}

Šaraba, V., Milovanović, J., Nikodinović-Runić, J., Budin, C., de Boer, T.,& Ćirić, M.. (2023). Brackish Groundwaters Contain Plastic- and Cellulose-Degrading Bacteria. in Microbial Ecology.
https://doi.org/10.1007/s00248-023-02278-8

Šaraba V, Milovanović J, Nikodinović-Runić J, Budin C, de Boer T, Ćirić M. Brackish Groundwaters Contain Plastic- and Cellulose-Degrading Bacteria. in Microbial Ecology. 2023;.
doi:10.1007/s00248-023-02278-8 .

Šaraba, Vladimir, Milovanović, Jelena, Nikodinović-Runić, Jasmina, Budin, Clémence, de Boer, Tjalf, Ćirić, Milica, "Brackish Groundwaters Contain Plastic- and Cellulose-Degrading Bacteria" in Microbial Ecology (2023),
https://doi.org/10.1007/s00248-023-02278-8 . .

TY  - JOUR
AU  - Ćirić, Milica
AU  - Šaraba, Vladimir
AU  - Budin, Clémence
AU  - de Boer, Tjalf
AU  - Nikodinović-Runić, Jasmina
PY  - 2023
UR  - https://doi.org/10.1007/s00248-023-02338-z
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2304
AB  - Plastic waste is a global environmental burden and long-lasting plastic polymers, including ubiquitous and toxic polyurethanes (PUs), rapidly accumulate in the water environments. In this study, samples were collected from the three alkaline groundwater occurrences in the geotectonic regions of the Pannonian basin of northern Serbia (Torda and Slankamen Banja) and Inner Dinarides of western Serbia (Mokra Gora) with aim to isolate and identify bacteria with plastic- and lignocellulose-degrading potential, that could be applied to reduce the burden of environmental plastic pollution. The investigated occurrences belong to cold, mildly alkaline (pH: 7.6–7.9) brackish and hyperalkaline (pH: 11.5) fresh groundwaters of the SO4 – Na + K, Cl – Na + K and OH, Cl – Ca, Na + K genetic type. Full-length 16S rDNA sequencing, using Oxford Nanopore sequencing device, was performed with DNA extracted from colonies obtained by cultivation of all groundwater samples, as well as with DNA extracted directly from one groundwater sample. The most abundant genera belong to Pseudomonas, Acidovorax, Kocuria and Methylotenera. All screened isolates (100%) had the ability to grow on at least 3 of the tested plastic and lignocellulosic substrates, with 53.9% isolates degrading plastic substrate Impranil® DLN-SD (SD), a model compound for PUs degradation. Isolates degrading SD that were identified by partial 16S rDNA sequencing belong to the Stenotrophomonas, Pseudomonas, Paraburkholderia, Aeromonas, Vibrio and Acidovorax genera. Taking into account that plastics, including commonly produced PUs, are widespread in groundwater, identification of PUs-degrading bacteria may have potential applications in bioremediation of groundwater polluted with this polymer.
PB  - Springer Nature
T2  - Microbial Ecology
T1  - Polyurethane-Degrading Potential of Alkaline Groundwater Bacteria
IS  - 1
SP  - 21
VL  - 87
DO  - 10.1007/s00248-023-02338-z
ER  - 

@article{
author = "Ćirić, Milica and Šaraba, Vladimir and Budin, Clémence and de Boer, Tjalf and Nikodinović-Runić, Jasmina",
year = "2023",
abstract = "Plastic waste is a global environmental burden and long-lasting plastic polymers, including ubiquitous and toxic polyurethanes (PUs), rapidly accumulate in the water environments. In this study, samples were collected from the three alkaline groundwater occurrences in the geotectonic regions of the Pannonian basin of northern Serbia (Torda and Slankamen Banja) and Inner Dinarides of western Serbia (Mokra Gora) with aim to isolate and identify bacteria with plastic- and lignocellulose-degrading potential, that could be applied to reduce the burden of environmental plastic pollution. The investigated occurrences belong to cold, mildly alkaline (pH: 7.6–7.9) brackish and hyperalkaline (pH: 11.5) fresh groundwaters of the SO4 – Na + K, Cl – Na + K and OH, Cl – Ca, Na + K genetic type. Full-length 16S rDNA sequencing, using Oxford Nanopore sequencing device, was performed with DNA extracted from colonies obtained by cultivation of all groundwater samples, as well as with DNA extracted directly from one groundwater sample. The most abundant genera belong to Pseudomonas, Acidovorax, Kocuria and Methylotenera. All screened isolates (100%) had the ability to grow on at least 3 of the tested plastic and lignocellulosic substrates, with 53.9% isolates degrading plastic substrate Impranil® DLN-SD (SD), a model compound for PUs degradation. Isolates degrading SD that were identified by partial 16S rDNA sequencing belong to the Stenotrophomonas, Pseudomonas, Paraburkholderia, Aeromonas, Vibrio and Acidovorax genera. Taking into account that plastics, including commonly produced PUs, are widespread in groundwater, identification of PUs-degrading bacteria may have potential applications in bioremediation of groundwater polluted with this polymer.",
publisher = "Springer Nature",
journal = "Microbial Ecology",
title = "Polyurethane-Degrading Potential of Alkaline Groundwater Bacteria",
number = "1",
pages = "21",
volume = "87",
doi = "10.1007/s00248-023-02338-z"
}

Ćirić, M., Šaraba, V., Budin, C., de Boer, T.,& Nikodinović-Runić, J.. (2023). Polyurethane-Degrading Potential of Alkaline Groundwater Bacteria. in Microbial Ecology
Springer Nature., 87(1), 21.
https://doi.org/10.1007/s00248-023-02338-z

Ćirić M, Šaraba V, Budin C, de Boer T, Nikodinović-Runić J. Polyurethane-Degrading Potential of Alkaline Groundwater Bacteria. in Microbial Ecology. 2023;87(1):21.
doi:10.1007/s00248-023-02338-z .

Ćirić, Milica, Šaraba, Vladimir, Budin, Clémence, de Boer, Tjalf, Nikodinović-Runić, Jasmina, "Polyurethane-Degrading Potential of Alkaline Groundwater Bacteria" in Microbial Ecology, 87, no. 1 (2023):21,
https://doi.org/10.1007/s00248-023-02338-z . .