TY  - CONF
AU  - Ćirić, Milica
AU  - Pantelić, Brana
AU  - Šaraba, Vladimir
AU  - Nikodinović-Runić, Jasmina
PY  - 2023
UR  - https://belbi.bg.ac.rs/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2044
AB  - Plastic waste is a global environmental burden. Polyurethanes (PU), toxic and ubiquitous
synthetic polymers, do not biodegrade quickly, leading to their rapid accumulation in the
soil and water environments. Highly efficient PU-degrading microorganisms are rare in
nature and are of fundamental importance for achieving circular plastic economy. Bacterial
isolates from groundwater, originating from magmatogenic massif and Tertiary basin
within metamorphic area, as well as soil isolates collected from various pristine (PS) and
contaminated sites (CS), were screened using PU model compound Impranil® DLN-SD
(IMP) as sole C source to identify PU-degrading isolates. Phylogenetic analysis of 16S rRNA
gene sequences from IMP-degrading isolates was performed using the neighbor-joining
method to observe their clustering. Thirty one of 96 isolates (32.3 %) from groundwater and
18 of 220 isolates (8.2%) from soil produced prominent IMP-clearing zones. Thirteen IMPdegrading
isolates from each type of environment, belonging to 8 genera (Pseudomonas,
Proteus, Enterobacter, Flavobacterium, Serratia, Pantoea, Acinetobacter and Stenotrophomonas)
for groundwater and to 6 genera (Streptomyces, Pseudomonas, Rhodococcus, Achromobacter,
Bacillus and Paenibacillus) for soil environment, were included in phylogenetic analysis. No
clear grouping of groundwater and soil isolates was observed, indicating that isolates are
too distinct. Stronger clustering was observed for groundwater compared to soil isolates. For
groundwater, strongest clustering was observed for 2 isolates belonging to Proteus genus,
2 belonging to Flavobacterium and 2 to Pseudomonas. For soil samples, strongest clustering
was observed for 3 isolates belonging to genus Streptomyces. There was no clear grouping
within isolates from CS and PS. In the future, wider range of environmental niches should be
included in screening efforts for development of biocatalytic processes for management of
plastic waste. Subterranean ecosystems, which are not readily accessible for sampling and
represent largely unexplored reservoir of biotechnologically relevant enzymatic activities,
should also be more represented in such screenings.
PB  - Belgrade : Institute of molecular genetics and genetic engineering
C3  - 4th Belgrade Bioinformatics Conference
T1  - Groundwater and soil as a reservoir for polyurethane-degrading bacteria
EP  - 99
SP  - 99
VL  - 4
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2044
ER  - 

@conference{
author = "Ćirić, Milica and Pantelić, Brana and Šaraba, Vladimir and Nikodinović-Runić, Jasmina",
year = "2023",
abstract = "Plastic waste is a global environmental burden. Polyurethanes (PU), toxic and ubiquitous
synthetic polymers, do not biodegrade quickly, leading to their rapid accumulation in the
soil and water environments. Highly efficient PU-degrading microorganisms are rare in
nature and are of fundamental importance for achieving circular plastic economy. Bacterial
isolates from groundwater, originating from magmatogenic massif and Tertiary basin
within metamorphic area, as well as soil isolates collected from various pristine (PS) and
contaminated sites (CS), were screened using PU model compound Impranil® DLN-SD
(IMP) as sole C source to identify PU-degrading isolates. Phylogenetic analysis of 16S rRNA
gene sequences from IMP-degrading isolates was performed using the neighbor-joining
method to observe their clustering. Thirty one of 96 isolates (32.3 %) from groundwater and
18 of 220 isolates (8.2%) from soil produced prominent IMP-clearing zones. Thirteen IMPdegrading
isolates from each type of environment, belonging to 8 genera (Pseudomonas,
Proteus, Enterobacter, Flavobacterium, Serratia, Pantoea, Acinetobacter and Stenotrophomonas)
for groundwater and to 6 genera (Streptomyces, Pseudomonas, Rhodococcus, Achromobacter,
Bacillus and Paenibacillus) for soil environment, were included in phylogenetic analysis. No
clear grouping of groundwater and soil isolates was observed, indicating that isolates are
too distinct. Stronger clustering was observed for groundwater compared to soil isolates. For
groundwater, strongest clustering was observed for 2 isolates belonging to Proteus genus,
2 belonging to Flavobacterium and 2 to Pseudomonas. For soil samples, strongest clustering
was observed for 3 isolates belonging to genus Streptomyces. There was no clear grouping
within isolates from CS and PS. In the future, wider range of environmental niches should be
included in screening efforts for development of biocatalytic processes for management of
plastic waste. Subterranean ecosystems, which are not readily accessible for sampling and
represent largely unexplored reservoir of biotechnologically relevant enzymatic activities,
should also be more represented in such screenings.",
publisher = "Belgrade : Institute of molecular genetics and genetic engineering",
journal = "4th Belgrade Bioinformatics Conference",
title = "Groundwater and soil as a reservoir for polyurethane-degrading bacteria",
pages = "99-99",
volume = "4",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2044"
}

Ćirić, M., Pantelić, B., Šaraba, V.,& Nikodinović-Runić, J.. (2023). Groundwater and soil as a reservoir for polyurethane-degrading bacteria. in 4th Belgrade Bioinformatics Conference
Belgrade : Institute of molecular genetics and genetic engineering., 4, 99-99.
https://hdl.handle.net/21.15107/rcub_imagine_2044

Ćirić M, Pantelić B, Šaraba V, Nikodinović-Runić J. Groundwater and soil as a reservoir for polyurethane-degrading bacteria. in 4th Belgrade Bioinformatics Conference. 2023;4:99-99.
https://hdl.handle.net/21.15107/rcub_imagine_2044 .

Ćirić, Milica, Pantelić, Brana, Šaraba, Vladimir, Nikodinović-Runić, Jasmina, "Groundwater and soil as a reservoir for polyurethane-degrading bacteria" in 4th Belgrade Bioinformatics Conference, 4 (2023):99-99,
https://hdl.handle.net/21.15107/rcub_imagine_2044 .

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  - CONF
AU  - Šaraba, Vladimir
AU  - Nikodinović-Runić, Jasmina
AU  - Obradović, Vesna
AU  - Dimkić, Ivica
AU  - Janakiev, Tamara
AU  - Ćirić, Milica
PY  - 2023
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2104
AB  - Targeted physiological groups of bacteria were cultivated and identified in the brackish
groundwaters of Obrenovačka Banja (OB), Lomnički Kiseljak (LK) and Velika Vrbnica (VV) using biological
activity reaction tests (BARTs) to assess the biocorrosion, biofouling and health risks. The highest density of
iron-related, sulfate-reducing, slime-forming, facultatively anaerobic heterotrophic, denitrifying bacteria and
representatives of Pseudomonas spp. was recorded in the OB sample, while the lowest density of the same
physiological groups of bacteria was recorded in the LK sample. Facultatively anaerobic heterotrophic
bacteria were the most abundant in the OB and LK samples, while, in contrast, heterotrophic aerobic bacteria
were the most abundant in the VV sample. All tested samples were characterized by a high degree of
biochemical activity associated with iron-related, sulfate-reducing, slime-forming, heterotrophic aerobic and
facultatively anaerobic bacteria. Also, high biochemical activity of denitrifying bacteria was recorded in the
OB sample, and the same activity of Pseudomonas species was recorded in the OB and VV samples. For OB
and LK groundwaters, the highest degree of risk was estimated for biocorrosion process, while for the OB
and VV occurrences, the highest degree of risk was estimated for biofouling process. The health risk was
present for all examined groundwaters. Caution is warranted in further use of all investigated occurrences
due to the established public health risk and an immediate revitalization of the OB, LK and VV wells is
necessary.
PB  - Kragujevac : Institute for Information Technologies
C3  - 2nd International Conference on Chemo and Bioinformatics
T1  - Biocorrosion, biofouling and health risk: biological activity reaction tests of selected brackish groundwater occurrences in Serbia
EP  - 190
SP  - 186
DO  - 10.46793/ICCBI23.086S
ER  - 

@conference{
author = "Šaraba, Vladimir and Nikodinović-Runić, Jasmina and Obradović, Vesna and Dimkić, Ivica and Janakiev, Tamara and Ćirić, Milica",
year = "2023",
abstract = "Targeted physiological groups of bacteria were cultivated and identified in the brackish
groundwaters of Obrenovačka Banja (OB), Lomnički Kiseljak (LK) and Velika Vrbnica (VV) using biological
activity reaction tests (BARTs) to assess the biocorrosion, biofouling and health risks. The highest density of
iron-related, sulfate-reducing, slime-forming, facultatively anaerobic heterotrophic, denitrifying bacteria and
representatives of Pseudomonas spp. was recorded in the OB sample, while the lowest density of the same
physiological groups of bacteria was recorded in the LK sample. Facultatively anaerobic heterotrophic
bacteria were the most abundant in the OB and LK samples, while, in contrast, heterotrophic aerobic bacteria
were the most abundant in the VV sample. All tested samples were characterized by a high degree of
biochemical activity associated with iron-related, sulfate-reducing, slime-forming, heterotrophic aerobic and
facultatively anaerobic bacteria. Also, high biochemical activity of denitrifying bacteria was recorded in the
OB sample, and the same activity of Pseudomonas species was recorded in the OB and VV samples. For OB
and LK groundwaters, the highest degree of risk was estimated for biocorrosion process, while for the OB
and VV occurrences, the highest degree of risk was estimated for biofouling process. The health risk was
present for all examined groundwaters. Caution is warranted in further use of all investigated occurrences
due to the established public health risk and an immediate revitalization of the OB, LK and VV wells is
necessary.",
publisher = "Kragujevac : Institute for Information Technologies",
journal = "2nd International Conference on Chemo and Bioinformatics",
title = "Biocorrosion, biofouling and health risk: biological activity reaction tests of selected brackish groundwater occurrences in Serbia",
pages = "190-186",
doi = "10.46793/ICCBI23.086S"
}

Šaraba, V., Nikodinović-Runić, J., Obradović, V., Dimkić, I., Janakiev, T.,& Ćirić, M.. (2023). Biocorrosion, biofouling and health risk: biological activity reaction tests of selected brackish groundwater occurrences in Serbia. in 2nd International Conference on Chemo and Bioinformatics
Kragujevac : Institute for Information Technologies., 186-190.
https://doi.org/10.46793/ICCBI23.086S

Šaraba V, Nikodinović-Runić J, Obradović V, Dimkić I, Janakiev T, Ćirić M. Biocorrosion, biofouling and health risk: biological activity reaction tests of selected brackish groundwater occurrences in Serbia. in 2nd International Conference on Chemo and Bioinformatics. 2023;:186-190.
doi:10.46793/ICCBI23.086S .

Šaraba, Vladimir, Nikodinović-Runić, Jasmina, Obradović, Vesna, Dimkić, Ivica, Janakiev, Tamara, Ćirić, Milica, "Biocorrosion, biofouling and health risk: biological activity reaction tests of selected brackish groundwater occurrences in Serbia" in 2nd International Conference on Chemo and Bioinformatics (2023):186-190,
https://doi.org/10.46793/ICCBI23.086S . .

TY  - CONF
AU  - Šaraba, Vladimir
AU  - Nikodinović-Runić, Jasmina
AU  - Ćirić, Milica
PY  - 2023
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2203
AB  - The examined groundwaters, orginating from the fractured type of aquifer formed by Pre-
Middle Jurassic ultramafic rocks, i. e. harzburgites, dunites, lherzolites and serpentinites, belong to the

fresh hyperalkaline cold groundwaters of OH, Cl – Ca, Na + K genetic type. Studied occurrence was
characterized by the presence of aerobic cultivable bacteria with ability to grow in a pH range of 7-12.
Bacterial isolates were screened using plastic,cellulosic and hemicellulosic polymeric substrates as
predominantcarbon source to assess their biotechnological potential. All 16 screened isolates (100%)
demonstrated growth and/or activity on at least one tested substrate. One isolate belonging to genus
Flavobacterium, produced prominent zone of clearing on Impranil® DLN-SD, a model substrate for
polyurethanes (PU). Plastic-degrading potential has been previously documented for members of
genus Flavobacterium. However, this is the first report of their PU-degrading activity. Accumulation of
PU in the environment is of special concern, due to its toxicity, high production rates and lack of
efficient recycling strategies. In the future, biotechnological potential of alkalophilic bacteria from
groundwater environments should be explored more intensly, especially from the aspect of their
application in the management of plastic waste and bioremediation treatments of plastic-polluted
groundwater resources.
PB  - Zrenjanin : Technical Faculty "Mihajlo Pupin",
C3  - XIII International Conference - Industrial Engineering and Environmental Protection
T1  - Fresh hyperalkaline groundwaters contain polyurethane-degrading Flavobacterium
EP  - 361
SP  - 357
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2203
ER  - 

@conference{
author = "Šaraba, Vladimir and Nikodinović-Runić, Jasmina and Ćirić, Milica",
year = "2023",
abstract = "The examined groundwaters, orginating from the fractured type of aquifer formed by Pre-
Middle Jurassic ultramafic rocks, i. e. harzburgites, dunites, lherzolites and serpentinites, belong to the

fresh hyperalkaline cold groundwaters of OH, Cl – Ca, Na + K genetic type. Studied occurrence was
characterized by the presence of aerobic cultivable bacteria with ability to grow in a pH range of 7-12.
Bacterial isolates were screened using plastic,cellulosic and hemicellulosic polymeric substrates as
predominantcarbon source to assess their biotechnological potential. All 16 screened isolates (100%)
demonstrated growth and/or activity on at least one tested substrate. One isolate belonging to genus
Flavobacterium, produced prominent zone of clearing on Impranil® DLN-SD, a model substrate for
polyurethanes (PU). Plastic-degrading potential has been previously documented for members of
genus Flavobacterium. However, this is the first report of their PU-degrading activity. Accumulation of
PU in the environment is of special concern, due to its toxicity, high production rates and lack of
efficient recycling strategies. In the future, biotechnological potential of alkalophilic bacteria from
groundwater environments should be explored more intensly, especially from the aspect of their
application in the management of plastic waste and bioremediation treatments of plastic-polluted
groundwater resources.",
publisher = "Zrenjanin : Technical Faculty "Mihajlo Pupin",",
journal = "XIII International Conference - Industrial Engineering and Environmental Protection",
title = "Fresh hyperalkaline groundwaters contain polyurethane-degrading Flavobacterium",
pages = "361-357",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2203"
}

Šaraba, V., Nikodinović-Runić, J.,& Ćirić, M.. (2023). Fresh hyperalkaline groundwaters contain polyurethane-degrading Flavobacterium. in XIII International Conference - Industrial Engineering and Environmental Protection
Zrenjanin : Technical Faculty "Mihajlo Pupin",., 357-361.
https://hdl.handle.net/21.15107/rcub_imagine_2203

Šaraba V, Nikodinović-Runić J, Ćirić M. Fresh hyperalkaline groundwaters contain polyurethane-degrading Flavobacterium. in XIII International Conference - Industrial Engineering and Environmental Protection. 2023;:357-361.
https://hdl.handle.net/21.15107/rcub_imagine_2203 .

Šaraba, Vladimir, Nikodinović-Runić, Jasmina, Ćirić, Milica, "Fresh hyperalkaline groundwaters contain polyurethane-degrading Flavobacterium" in XIII International Conference - Industrial Engineering and Environmental Protection (2023):357-361,
https://hdl.handle.net/21.15107/rcub_imagine_2203 .

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 . .

TY  - JOUR
AU  - Ćirić, Milica
AU  - Waite, David
AU  - Draper, Jenny
AU  - Jones, John Brian
PY  - 2019
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1238
AB  - With the growing importance of aquaculture worldwide, characterization of the microbiota of high-value aquaculture species and identification of their shifts induced by changes in fish physiology or nutrition is of special interest. Here we report the first 16S rRNA gene metabarcoding survey of the mid-intestinal bacteria of Chinook salmon (Oncorhynchus tshawytscha), an economically important aquacultured species. The microbiota of 30 farmed Chinook salmon from a single cohort was surveyed using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Seawater, feed and mid-intestinal samples and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles. Over 1000 operational taxonomic units were identified within the cohort, providing a first glimpse into the mid-intestinal microbiota of farmed Chinook salmon. The taxonomic distribution of the salmon microbiota was reasonably stable, with around two thirds of individuals dominated by members of the family Vibrionaceae. We anticipate that the workflow presented in this paper could be applied in other aquacultured fish species to capture variation or dysbiosis occurring as a result of changes in feed, health or environmental conditions.
PB  - Srpsko biološko društvo, Beograd, i dr.
T2  - Archives of Biological Sciences
T1  - Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding
EP  - 587
IS  - 4
SP  - 577
VL  - 71
DO  - 10.2298/ABS190402040C
ER  - 

@article{
author = "Ćirić, Milica and Waite, David and Draper, Jenny and Jones, John Brian",
year = "2019",
abstract = "With the growing importance of aquaculture worldwide, characterization of the microbiota of high-value aquaculture species and identification of their shifts induced by changes in fish physiology or nutrition is of special interest. Here we report the first 16S rRNA gene metabarcoding survey of the mid-intestinal bacteria of Chinook salmon (Oncorhynchus tshawytscha), an economically important aquacultured species. The microbiota of 30 farmed Chinook salmon from a single cohort was surveyed using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Seawater, feed and mid-intestinal samples and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles. Over 1000 operational taxonomic units were identified within the cohort, providing a first glimpse into the mid-intestinal microbiota of farmed Chinook salmon. The taxonomic distribution of the salmon microbiota was reasonably stable, with around two thirds of individuals dominated by members of the family Vibrionaceae. We anticipate that the workflow presented in this paper could be applied in other aquacultured fish species to capture variation or dysbiosis occurring as a result of changes in feed, health or environmental conditions.",
publisher = "Srpsko biološko društvo, Beograd, i dr.",
journal = "Archives of Biological Sciences",
title = "Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding",
pages = "587-577",
number = "4",
volume = "71",
doi = "10.2298/ABS190402040C"
}

Ćirić, M., Waite, D., Draper, J.,& Jones, J. B.. (2019). Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding. in Archives of Biological Sciences
Srpsko biološko društvo, Beograd, i dr.., 71(4), 577-587.
https://doi.org/10.2298/ABS190402040C

Ćirić M, Waite D, Draper J, Jones JB. Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding. in Archives of Biological Sciences. 2019;71(4):577-587.
doi:10.2298/ABS190402040C .

Ćirić, Milica, Waite, David, Draper, Jenny, Jones, John Brian, "Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding" in Archives of Biological Sciences, 71, no. 4 (2019):577-587,
https://doi.org/10.2298/ABS190402040C . .

TY  - JOUR
AU  - Gagić, Dragana
AU  - Ćirić, Milica
AU  - Wen, Wesley X.
AU  - Ng, Filomena
AU  - Rakonjac, Jasna
PY  - 2016
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/993
AB  - Microbial surface and secreted proteins (the secretome) contain a large number of proteins that interact with other microbes, host and/or environment. These proteins are exported by the coordinated activities of the protein secretion machinery present in the cell. A group of bacteriophage, called filamentous phage, have the ability to hijack bacterial protein secretion machinery in order to amplify and assemble via a secretion-like process. This ability has been harnessed in the use of filamentous phage of Escherichia coli in biotechnology applications, including screening large libraries of variants for binding to "bait" of interest, from tissues in vivo to pure proteins or even inorganic substrates. In this review we discuss the roles of secretome proteins in pathogenic and non-pathogenic bacteria and corresponding secretion pathways. We describe the basics of phage display technology and its variants applied to discovery of bacterial proteins that are implicated in colonization of host tissues and pathogenesis, as well as vaccine candidates through filamentous phage display library screening. Secretome selection aided by next-generation sequence analysis was successfully applied for selective display of the secretome at a microbial community scale, the latter revealing the richness of secretome functions of interest and surprising versatility in filamentous phage display of secretome proteins from large number of Gram-negative as well as Gram-positive bacteria and archaea.
PB  - Frontiers Media Sa, Lausanne
T2  - Frontiers in Microbiology
T1  - Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display
VL  - 7
DO  - 10.3389/fmicb.2016.00429
ER  - 

@article{
author = "Gagić, Dragana and Ćirić, Milica and Wen, Wesley X. and Ng, Filomena and Rakonjac, Jasna",
year = "2016",
abstract = "Microbial surface and secreted proteins (the secretome) contain a large number of proteins that interact with other microbes, host and/or environment. These proteins are exported by the coordinated activities of the protein secretion machinery present in the cell. A group of bacteriophage, called filamentous phage, have the ability to hijack bacterial protein secretion machinery in order to amplify and assemble via a secretion-like process. This ability has been harnessed in the use of filamentous phage of Escherichia coli in biotechnology applications, including screening large libraries of variants for binding to "bait" of interest, from tissues in vivo to pure proteins or even inorganic substrates. In this review we discuss the roles of secretome proteins in pathogenic and non-pathogenic bacteria and corresponding secretion pathways. We describe the basics of phage display technology and its variants applied to discovery of bacterial proteins that are implicated in colonization of host tissues and pathogenesis, as well as vaccine candidates through filamentous phage display library screening. Secretome selection aided by next-generation sequence analysis was successfully applied for selective display of the secretome at a microbial community scale, the latter revealing the richness of secretome functions of interest and surprising versatility in filamentous phage display of secretome proteins from large number of Gram-negative as well as Gram-positive bacteria and archaea.",
publisher = "Frontiers Media Sa, Lausanne",
journal = "Frontiers in Microbiology",
title = "Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display",
volume = "7",
doi = "10.3389/fmicb.2016.00429"
}

Gagić, D., Ćirić, M., Wen, W. X., Ng, F.,& Rakonjac, J.. (2016). Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display. in Frontiers in Microbiology
Frontiers Media Sa, Lausanne., 7.
https://doi.org/10.3389/fmicb.2016.00429

Gagić D, Ćirić M, Wen WX, Ng F, Rakonjac J. Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display. in Frontiers in Microbiology. 2016;7.
doi:10.3389/fmicb.2016.00429 .

Gagić, Dragana, Ćirić, Milica, Wen, Wesley X., Ng, Filomena, Rakonjac, Jasna, "Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display" in Frontiers in Microbiology, 7 (2016),
https://doi.org/10.3389/fmicb.2016.00429 . .

TY  - JOUR
AU  - Gagić, Dragana
AU  - Ćirić, Milica
AU  - Wen, Wesley X.
AU  - Ng, Filomena
AU  - Rakonjac, Jasna
PY  - 2016
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/943
PB  - Frontiers Media Sa, Lausanne
T2  - Frontiers in Microbiology
T1  - Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display
VL  - 7
DO  - 10.3389/fmicb.2016.00927
ER  - 

@article{
author = "Gagić, Dragana and Ćirić, Milica and Wen, Wesley X. and Ng, Filomena and Rakonjac, Jasna",
year = "2016",
publisher = "Frontiers Media Sa, Lausanne",
journal = "Frontiers in Microbiology",
title = "Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display",
volume = "7",
doi = "10.3389/fmicb.2016.00927"
}

Gagić, D., Ćirić, M., Wen, W. X., Ng, F.,& Rakonjac, J.. (2016). Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display. in Frontiers in Microbiology
Frontiers Media Sa, Lausanne., 7.
https://doi.org/10.3389/fmicb.2016.00927

Gagić D, Ćirić M, Wen WX, Ng F, Rakonjac J. Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display. in Frontiers in Microbiology. 2016;7.
doi:10.3389/fmicb.2016.00927 .

Gagić, Dragana, Ćirić, Milica, Wen, Wesley X., Ng, Filomena, Rakonjac, Jasna, "Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display" in Frontiers in Microbiology, 7 (2016),
https://doi.org/10.3389/fmicb.2016.00927 . .

TY  - JOUR
AU  - Ćirić, Milica
AU  - Moon, Christina D.
AU  - Leahy, Sinead C.
AU  - Creevey, Christopher J.
AU  - Altermann, Eric
AU  - Attwood, Graeme T.
AU  - Rakonjac, Jasna
AU  - Gagić, Dragana
PY  - 2014
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/718
AB  - Background: In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. Results: By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre. Conclusions: As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis.
PB  - BMC, London
T2  - BMC Genomics
T1  - Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community
VL  - 15
DO  - 10.1186/1471-2164-15-356
ER  - 

@article{
author = "Ćirić, Milica and Moon, Christina D. and Leahy, Sinead C. and Creevey, Christopher J. and Altermann, Eric and Attwood, Graeme T. and Rakonjac, Jasna and Gagić, Dragana",
year = "2014",
abstract = "Background: In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. Results: By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre. Conclusions: As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis.",
publisher = "BMC, London",
journal = "BMC Genomics",
title = "Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community",
volume = "15",
doi = "10.1186/1471-2164-15-356"
}

Ćirić, M., Moon, C. D., Leahy, S. C., Creevey, C. J., Altermann, E., Attwood, G. T., Rakonjac, J.,& Gagić, D.. (2014). Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. in BMC Genomics
BMC, London., 15.
https://doi.org/10.1186/1471-2164-15-356

Ćirić M, Moon CD, Leahy SC, Creevey CJ, Altermann E, Attwood GT, Rakonjac J, Gagić D. Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. in BMC Genomics. 2014;15.
doi:10.1186/1471-2164-15-356 .

Ćirić, Milica, Moon, Christina D., Leahy, Sinead C., Creevey, Christopher J., Altermann, Eric, Attwood, Graeme T., Rakonjac, Jasna, Gagić, Dragana, "Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community" in BMC Genomics, 15 (2014),
https://doi.org/10.1186/1471-2164-15-356 . .