TY  - JOUR
AU  - Bajkić, Sanja
AU  - Narančić, Tanja
AU  - Đokić, Lidija
AU  - Đorđević, Dragana
AU  - Nikodinović-Runić, Jasmina
AU  - Morić, Ivana
AU  - Vasiljević, Branka
PY  - 2013
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/615
AB  - The bacterial diversity of the surface and deep sediment of the Copper Mining and Smelting Complex Bor, Serbia, was investigated using culture-dependent and culture-independent approaches. Sequencing analysis of 16S rDNA libraries revealed greater bacterial diversity in the surface sediment of the mining complex (MS) in comparison to deeper mine sediment (MU). While in the MS sample members of seven different phylogenetic groups were detected, in the MU sample library representatives of only three different groups were detected. The use of a culture-dependent approach revealed the presence of only three bacterial groups in both samples: Actinobacteria, Firmicutes and Proteobacteria, while six isolates exhibiting the highest metal tolerance were members of Arthrobacter and Staphylococcus genera. The most promising isolate, MSI08, was able to grow in the presence of high concentrations of Cd2+ (535 μM), Ni2+(17 mM) and Cr6+ (38.5 mM) and as such this indigenous strain has potential in the bioremediation of the contaminated surrounds of the city of Bor.
PB  - Srpsko biološko društvo, Beograd, i dr.
T2  - Archives of Biological Sciences
T1  - Microbial diversity and isolation of multiple metal-tolerant bacteria from surface and underground pits within the copper mining and smelting complex Bor
EP  - 386
IS  - 1
SP  - 375
VL  - 65
DO  - 10.2298/ABS1301375B
ER  - 

@article{
author = "Bajkić, Sanja and Narančić, Tanja and Đokić, Lidija and Đorđević, Dragana and Nikodinović-Runić, Jasmina and Morić, Ivana and Vasiljević, Branka",
year = "2013",
abstract = "The bacterial diversity of the surface and deep sediment of the Copper Mining and Smelting Complex Bor, Serbia, was investigated using culture-dependent and culture-independent approaches. Sequencing analysis of 16S rDNA libraries revealed greater bacterial diversity in the surface sediment of the mining complex (MS) in comparison to deeper mine sediment (MU). While in the MS sample members of seven different phylogenetic groups were detected, in the MU sample library representatives of only three different groups were detected. The use of a culture-dependent approach revealed the presence of only three bacterial groups in both samples: Actinobacteria, Firmicutes and Proteobacteria, while six isolates exhibiting the highest metal tolerance were members of Arthrobacter and Staphylococcus genera. The most promising isolate, MSI08, was able to grow in the presence of high concentrations of Cd2+ (535 μM), Ni2+(17 mM) and Cr6+ (38.5 mM) and as such this indigenous strain has potential in the bioremediation of the contaminated surrounds of the city of Bor.",
publisher = "Srpsko biološko društvo, Beograd, i dr.",
journal = "Archives of Biological Sciences",
title = "Microbial diversity and isolation of multiple metal-tolerant bacteria from surface and underground pits within the copper mining and smelting complex Bor",
pages = "386-375",
number = "1",
volume = "65",
doi = "10.2298/ABS1301375B"
}

Bajkić, S., Narančić, T., Đokić, L., Đorđević, D., Nikodinović-Runić, J., Morić, I.,& Vasiljević, B.. (2013). Microbial diversity and isolation of multiple metal-tolerant bacteria from surface and underground pits within the copper mining and smelting complex Bor. in Archives of Biological Sciences
Srpsko biološko društvo, Beograd, i dr.., 65(1), 375-386.
https://doi.org/10.2298/ABS1301375B

Bajkić S, Narančić T, Đokić L, Đorđević D, Nikodinović-Runić J, Morić I, Vasiljević B. Microbial diversity and isolation of multiple metal-tolerant bacteria from surface and underground pits within the copper mining and smelting complex Bor. in Archives of Biological Sciences. 2013;65(1):375-386.
doi:10.2298/ABS1301375B .

Bajkić, Sanja, Narančić, Tanja, Đokić, Lidija, Đorđević, Dragana, Nikodinović-Runić, Jasmina, Morić, Ivana, Vasiljević, Branka, "Microbial diversity and isolation of multiple metal-tolerant bacteria from surface and underground pits within the copper mining and smelting complex Bor" in Archives of Biological Sciences, 65, no. 1 (2013):375-386,
https://doi.org/10.2298/ABS1301375B . .

TY  - JOUR
AU  - Minovska, Gordana
AU  - Narančić, Tanja
AU  - Mandić, Mina
AU  - Šenerović, Lidija
AU  - Vasiljević, Branka
AU  - Nikodinović-Runić, Jasmina
PY  - 2013
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/691
AB  - Identifikacija i karakterizacija novih gena koji pripadaju putevima mikrobiološke razgradnje aromatičnih jedinjenja je od velikog značaja, jer su se pokazali kao izuzetno dobri biokatalizatori. U ovoj studiji, korišćenjem PCR metodologije, analizirano je prisustvo pet različitih gena iz biodegradativnog puta aromatičnih jedinjenja među 19 sredinskih izolata sa sposobnošću razgradnje širokog spektra aromatičnih jedinjenja. U slučaju 4-oksalokrotonat tautomeraze i toluen dioksigenaze, koji su detektovani kod većine sredinskih izolata, sekvence fragmenata su ukazivale na veoma ograničen diverzitet ova dva gena i visoku homologiju sa već poznatim sekvencama opisanim kod vrsta roda Pseudomonas. Korišćenjem degenerisanih prajmera konstruisanih na osnovu poznatih katehol-i naftalendioksigenaznih gena vrlo mali broj fragmenata je amplifikovan kod sredinskih izolata. Samo dve katehol 2,3-dioksigenaze iz dva izolata roda Bacillus su sekvenciranjem ukazale na različitost u odnosu na poznate sekvence, a pokazale međusobnu sličnost od 80-90%. Potencijalno tri nove katehol 1,2-dioksigenaze su identifikovane kod Bacillus sp. TN102, Gordonia sp. TN103 i Rhodococcus sp. TN112. Visok stepen homologije tautomeraza i toluen dioksigenaza među sredinskim izolatima izolovanim iz zagađene sredine ukazuje na horizontalni transfer gena, dok je ograničen uspeh u detektovanju preostala tri gena ukazao na potencijal da se među ovim izolatima mogu naći nove varijante gena iz puteva razgradnje aromatičnih jedinjenja.
AB  - Identification and characterization of novel genes belonging to microbial aromatic biodegradation pathway is of great importance as they have been proven versatile biocatalysts. In this study, the selection of 19 environmental bacterial isolates capable to degrade a wide range of aromatic compounds has been screened for the presence of five genes from the lower and the upper aromatic biodegradation pathway using PCR methodology. In the case of 4-oxalocrotonate tautomerase and toluene dioxygenases, although present in the most of environmental isolates, very limited diversity of the genes has been encountered. Highly conserved sequences of these genes in environmental samples revealed high homology with gene sequences of the characterized corresponding genes from Pseudomonas putida species. The screen using degenerate primers based on known catechol-and naphthalene dioxygenases sequences resulted in a limited number of amplified fragments. Only two catechol 2,3-dioxygenase from two Bacillus isolates were amplified and showed no significant similarities with dioxygenases from characterized organisms, but 80-90% identities with partial catechol 2,3-dioxygenase sequences from uncultured organisms. Potentially three novel catechol 1,2-dioxygenases were identified from Bacillus sp. TN102, Gordonia sp. TN103 and Rhodococcus sp. TN112. Highly homologous tautomerase and toluene dioxygenases amongst environmental samples isolated from the contaminated environment suggested horizontal gene transfer while limited success in PCR detection of the other three genes indicates that these isolates may still be a source of novel genes.
PB  - Društvo genetičara Srbije, Beograd
T2  - Genetika-Belgrade
T1  - Ograničen diverzitet gena iz puteva razgradnje aromatičnih jedinjenja među zemljišnim bakterijskim izolatima sa sposobnošću razgradnje aromatičnih jedinjenja
T1  - Limited aromatic pathway genes diversity amongst aromatic compound degrading soil bacterial isolates
EP  - 716
IS  - 3
SP  - 703
VL  - 45
DO  - 10.2298/GENSR1303703M
ER  - 

@article{
author = "Minovska, Gordana and Narančić, Tanja and Mandić, Mina and Šenerović, Lidija and Vasiljević, Branka and Nikodinović-Runić, Jasmina",
year = "2013",
abstract = "Identifikacija i karakterizacija novih gena koji pripadaju putevima mikrobiološke razgradnje aromatičnih jedinjenja je od velikog značaja, jer su se pokazali kao izuzetno dobri biokatalizatori. U ovoj studiji, korišćenjem PCR metodologije, analizirano je prisustvo pet različitih gena iz biodegradativnog puta aromatičnih jedinjenja među 19 sredinskih izolata sa sposobnošću razgradnje širokog spektra aromatičnih jedinjenja. U slučaju 4-oksalokrotonat tautomeraze i toluen dioksigenaze, koji su detektovani kod većine sredinskih izolata, sekvence fragmenata su ukazivale na veoma ograničen diverzitet ova dva gena i visoku homologiju sa već poznatim sekvencama opisanim kod vrsta roda Pseudomonas. Korišćenjem degenerisanih prajmera konstruisanih na osnovu poznatih katehol-i naftalendioksigenaznih gena vrlo mali broj fragmenata je amplifikovan kod sredinskih izolata. Samo dve katehol 2,3-dioksigenaze iz dva izolata roda Bacillus su sekvenciranjem ukazale na različitost u odnosu na poznate sekvence, a pokazale međusobnu sličnost od 80-90%. Potencijalno tri nove katehol 1,2-dioksigenaze su identifikovane kod Bacillus sp. TN102, Gordonia sp. TN103 i Rhodococcus sp. TN112. Visok stepen homologije tautomeraza i toluen dioksigenaza među sredinskim izolatima izolovanim iz zagađene sredine ukazuje na horizontalni transfer gena, dok je ograničen uspeh u detektovanju preostala tri gena ukazao na potencijal da se među ovim izolatima mogu naći nove varijante gena iz puteva razgradnje aromatičnih jedinjenja., Identification and characterization of novel genes belonging to microbial aromatic biodegradation pathway is of great importance as they have been proven versatile biocatalysts. In this study, the selection of 19 environmental bacterial isolates capable to degrade a wide range of aromatic compounds has been screened for the presence of five genes from the lower and the upper aromatic biodegradation pathway using PCR methodology. In the case of 4-oxalocrotonate tautomerase and toluene dioxygenases, although present in the most of environmental isolates, very limited diversity of the genes has been encountered. Highly conserved sequences of these genes in environmental samples revealed high homology with gene sequences of the characterized corresponding genes from Pseudomonas putida species. The screen using degenerate primers based on known catechol-and naphthalene dioxygenases sequences resulted in a limited number of amplified fragments. Only two catechol 2,3-dioxygenase from two Bacillus isolates were amplified and showed no significant similarities with dioxygenases from characterized organisms, but 80-90% identities with partial catechol 2,3-dioxygenase sequences from uncultured organisms. Potentially three novel catechol 1,2-dioxygenases were identified from Bacillus sp. TN102, Gordonia sp. TN103 and Rhodococcus sp. TN112. Highly homologous tautomerase and toluene dioxygenases amongst environmental samples isolated from the contaminated environment suggested horizontal gene transfer while limited success in PCR detection of the other three genes indicates that these isolates may still be a source of novel genes.",
publisher = "Društvo genetičara Srbije, Beograd",
journal = "Genetika-Belgrade",
title = "Ograničen diverzitet gena iz puteva razgradnje aromatičnih jedinjenja među zemljišnim bakterijskim izolatima sa sposobnošću razgradnje aromatičnih jedinjenja, Limited aromatic pathway genes diversity amongst aromatic compound degrading soil bacterial isolates",
pages = "716-703",
number = "3",
volume = "45",
doi = "10.2298/GENSR1303703M"
}

Minovska, G., Narančić, T., Mandić, M., Šenerović, L., Vasiljević, B.,& Nikodinović-Runić, J.. (2013). Ograničen diverzitet gena iz puteva razgradnje aromatičnih jedinjenja među zemljišnim bakterijskim izolatima sa sposobnošću razgradnje aromatičnih jedinjenja. in Genetika-Belgrade
Društvo genetičara Srbije, Beograd., 45(3), 703-716.
https://doi.org/10.2298/GENSR1303703M

Minovska G, Narančić T, Mandić M, Šenerović L, Vasiljević B, Nikodinović-Runić J. Ograničen diverzitet gena iz puteva razgradnje aromatičnih jedinjenja među zemljišnim bakterijskim izolatima sa sposobnošću razgradnje aromatičnih jedinjenja. in Genetika-Belgrade. 2013;45(3):703-716.
doi:10.2298/GENSR1303703M .

Minovska, Gordana, Narančić, Tanja, Mandić, Mina, Šenerović, Lidija, Vasiljević, Branka, Nikodinović-Runić, Jasmina, "Ograničen diverzitet gena iz puteva razgradnje aromatičnih jedinjenja među zemljišnim bakterijskim izolatima sa sposobnošću razgradnje aromatičnih jedinjenja" in Genetika-Belgrade, 45, no. 3 (2013):703-716,
https://doi.org/10.2298/GENSR1303703M . .

TY  - JOUR
AU  - Đokić, Lidija
AU  - Narančić, Tanja
AU  - Nikodinović-Runić, Jasmina
AU  - Bajkić, Sanja
AU  - Vasiljević, Branka
PY  - 2011
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/507
AB  - Two novel Bacillus sp. were isolated from a soil sample from a bank of the Tamiš river in close proximity to a petrochemical facility. They were capable of utilizing a broad range of aromatic compounds as a sole source of carbon and energy (including phenol, benzene, toluene, biphenyl, naphthalene). The isolates were designated as Bacillus sp. TN41 and TN42, based on their 16S rDNA sequence. Their catabolic potential was compared to two Bacillus sp. strains (PS1 and PS11) isolated from the rhizosphere of the endemorelict plant Ramonda serbica. Specific activities of phenol hydroxylase, catechol 1,2-dioxygenase and catechol 2,3-dioxygenase were analyzed from crude cell extracts of the isolates, as well as the temperature and pH effects on enzyme activity. Although all four isolates had the ability to degrade a similar range of aromatic compounds, the specific activities of the enzymes indicative of aromatic compound catabolism of TN isolates were 2 to 90-fold lower compared to the PS isolates. Phenol hydroxylase and catechol dioxygenases exhibited broad temperature (10°C-80°C) and pH (4-9) activity ranges in all four Bacillus isolates. While phenol inhibited both phenol hydroxylase and catechol dioxygenases in the TN strains, it was an inducer for phenol hydroxylase in the PS strains.
PB  - Srpsko biološko društvo, Beograd, i dr.
T2  - Archives of Biological Sciences
T1  - Four Bacillus sp. soil isolates capable of degrading phenol, toluene, biphenyl, naphthalene and other aromatic compounds exhibit different aromatic catabolic potentials
EP  - 1068
IS  - 4
SP  - 1057
VL  - 63
DO  - 10.2298/ABS1104057D{stroke}
ER  - 

@article{
author = "Đokić, Lidija and Narančić, Tanja and Nikodinović-Runić, Jasmina and Bajkić, Sanja and Vasiljević, Branka",
year = "2011",
abstract = "Two novel Bacillus sp. were isolated from a soil sample from a bank of the Tamiš river in close proximity to a petrochemical facility. They were capable of utilizing a broad range of aromatic compounds as a sole source of carbon and energy (including phenol, benzene, toluene, biphenyl, naphthalene). The isolates were designated as Bacillus sp. TN41 and TN42, based on their 16S rDNA sequence. Their catabolic potential was compared to two Bacillus sp. strains (PS1 and PS11) isolated from the rhizosphere of the endemorelict plant Ramonda serbica. Specific activities of phenol hydroxylase, catechol 1,2-dioxygenase and catechol 2,3-dioxygenase were analyzed from crude cell extracts of the isolates, as well as the temperature and pH effects on enzyme activity. Although all four isolates had the ability to degrade a similar range of aromatic compounds, the specific activities of the enzymes indicative of aromatic compound catabolism of TN isolates were 2 to 90-fold lower compared to the PS isolates. Phenol hydroxylase and catechol dioxygenases exhibited broad temperature (10°C-80°C) and pH (4-9) activity ranges in all four Bacillus isolates. While phenol inhibited both phenol hydroxylase and catechol dioxygenases in the TN strains, it was an inducer for phenol hydroxylase in the PS strains.",
publisher = "Srpsko biološko društvo, Beograd, i dr.",
journal = "Archives of Biological Sciences",
title = "Four Bacillus sp. soil isolates capable of degrading phenol, toluene, biphenyl, naphthalene and other aromatic compounds exhibit different aromatic catabolic potentials",
pages = "1068-1057",
number = "4",
volume = "63",
doi = "10.2298/ABS1104057D{stroke}"
}

Đokić, L., Narančić, T., Nikodinović-Runić, J., Bajkić, S.,& Vasiljević, B.. (2011). Four Bacillus sp. soil isolates capable of degrading phenol, toluene, biphenyl, naphthalene and other aromatic compounds exhibit different aromatic catabolic potentials. in Archives of Biological Sciences
Srpsko biološko društvo, Beograd, i dr.., 63(4), 1057-1068.
https://doi.org/10.2298/ABS1104057D{stroke}

Đokić L, Narančić T, Nikodinović-Runić J, Bajkić S, Vasiljević B. Four Bacillus sp. soil isolates capable of degrading phenol, toluene, biphenyl, naphthalene and other aromatic compounds exhibit different aromatic catabolic potentials. in Archives of Biological Sciences. 2011;63(4):1057-1068.
doi:10.2298/ABS1104057D{stroke} .

Đokić, Lidija, Narančić, Tanja, Nikodinović-Runić, Jasmina, Bajkić, Sanja, Vasiljević, Branka, "Four Bacillus sp. soil isolates capable of degrading phenol, toluene, biphenyl, naphthalene and other aromatic compounds exhibit different aromatic catabolic potentials" in Archives of Biological Sciences, 63, no. 4 (2011):1057-1068,
https://doi.org/10.2298/ABS1104057D{stroke} . .

TY  - JOUR
AU  - Đokić, Lidija
AU  - Savić, M.
AU  - Narančić, Tanja
AU  - Vasiljević, Branka
PY  - 2010
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/447
AB  - Ramonda serbica i Ramonda nathaliae, retke biljke 'vaskrsnice' koje rastu na Balkanskom poluostrvu, u odgovoru na stres produkuju velike količine fenola. Bakterijske zajednice poreklom iz rizosfere ovih biljaka analizirane su metagenomskim pristupom. Fluorescentna 'in situ' hibridizacija (FISH) i DAPI bojenje pokazali su da u analiziranim zemljištima ima svega 5% metabolički aktivnih bakterija. Upotrebom prajmera specifičnih za bakterijsku DNK umnoženi su geni za 16S rDNK i konstruisane su dve genske biblioteke. Biblioteke su pretraživane uz pomoć RFLP metode. Od ukupno 192 klona dobijena iz uzorka rizosfere R. nathaliae identifikovano je 35 operativnih taksonomskih jedinica (OTJ), dok je iz uzorka rizosfere R. serbica dobijeno 13 OTJ od ukupno 80 klonova. Predstavnici svake OTJ su sekvencirani. Analizirane zajednice odlikuje veoma mali diverzitet i većina dobijenih sekvenci je pokazala malu sličnost sa DNK sekvencama do sada kultivisanih bakterija.
AB  - Ramonda serbica and Ramonda nathaliae, rare resurrection plants growing in the Balkan Peninsula, produce a high amount of phenolic compounds as a response to stress. The composition and size of bacterial communities in two rhizosphere soil samples of these plants were analyzed using a metagenomic approach. Fluorescent in situ hybridization (FISH) experiments together with DAPI staining showed that the metabolically active bacteria represent only a small fraction, approximately 5%, of total soil bacteria. Using universal bacteria - specific primers 16S rDNA genes were amplified directly from metagenomic DNAs and two libraries were constructed. The Restriction Fragment Length Polymorphism (RLFP) method was used in library screening. Amongst 192 clones, 35 unique operational taxonomic units (OTUs) were determined from the rhizosphere of R. nathaliae, and 13 OTUs out of 80 clones in total from the library of R. serbica. Representative clones from each OTU were sequenced. The majority of sequences from metagenomes showed very little similarity to any cultured bacteria. In conclusion, the bacterial communities in the studied soil samples showed quite poor diversity.
PB  - Srpsko biološko društvo, Beograd, i dr.
T2  - Archives of Biological Sciences
T1  - Metagenomska analiza zemljišnih mikrobioloških zajednica
T1  - Metagenomic analysis of soil microbial communities
EP  - 564
IS  - 3
SP  - 559
VL  - 62
DO  - 10.2298/ABS1003559D
ER  - 

@article{
author = "Đokić, Lidija and Savić, M. and Narančić, Tanja and Vasiljević, Branka",
year = "2010",
abstract = "Ramonda serbica i Ramonda nathaliae, retke biljke 'vaskrsnice' koje rastu na Balkanskom poluostrvu, u odgovoru na stres produkuju velike količine fenola. Bakterijske zajednice poreklom iz rizosfere ovih biljaka analizirane su metagenomskim pristupom. Fluorescentna 'in situ' hibridizacija (FISH) i DAPI bojenje pokazali su da u analiziranim zemljištima ima svega 5% metabolički aktivnih bakterija. Upotrebom prajmera specifičnih za bakterijsku DNK umnoženi su geni za 16S rDNK i konstruisane su dve genske biblioteke. Biblioteke su pretraživane uz pomoć RFLP metode. Od ukupno 192 klona dobijena iz uzorka rizosfere R. nathaliae identifikovano je 35 operativnih taksonomskih jedinica (OTJ), dok je iz uzorka rizosfere R. serbica dobijeno 13 OTJ od ukupno 80 klonova. Predstavnici svake OTJ su sekvencirani. Analizirane zajednice odlikuje veoma mali diverzitet i većina dobijenih sekvenci je pokazala malu sličnost sa DNK sekvencama do sada kultivisanih bakterija., Ramonda serbica and Ramonda nathaliae, rare resurrection plants growing in the Balkan Peninsula, produce a high amount of phenolic compounds as a response to stress. The composition and size of bacterial communities in two rhizosphere soil samples of these plants were analyzed using a metagenomic approach. Fluorescent in situ hybridization (FISH) experiments together with DAPI staining showed that the metabolically active bacteria represent only a small fraction, approximately 5%, of total soil bacteria. Using universal bacteria - specific primers 16S rDNA genes were amplified directly from metagenomic DNAs and two libraries were constructed. The Restriction Fragment Length Polymorphism (RLFP) method was used in library screening. Amongst 192 clones, 35 unique operational taxonomic units (OTUs) were determined from the rhizosphere of R. nathaliae, and 13 OTUs out of 80 clones in total from the library of R. serbica. Representative clones from each OTU were sequenced. The majority of sequences from metagenomes showed very little similarity to any cultured bacteria. In conclusion, the bacterial communities in the studied soil samples showed quite poor diversity.",
publisher = "Srpsko biološko društvo, Beograd, i dr.",
journal = "Archives of Biological Sciences",
title = "Metagenomska analiza zemljišnih mikrobioloških zajednica, Metagenomic analysis of soil microbial communities",
pages = "564-559",
number = "3",
volume = "62",
doi = "10.2298/ABS1003559D"
}

Đokić, L., Savić, M., Narančić, T.,& Vasiljević, B.. (2010). Metagenomska analiza zemljišnih mikrobioloških zajednica. in Archives of Biological Sciences
Srpsko biološko društvo, Beograd, i dr.., 62(3), 559-564.
https://doi.org/10.2298/ABS1003559D

Đokić L, Savić M, Narančić T, Vasiljević B. Metagenomska analiza zemljišnih mikrobioloških zajednica. in Archives of Biological Sciences. 2010;62(3):559-564.
doi:10.2298/ABS1003559D .

Đokić, Lidija, Savić, M., Narančić, Tanja, Vasiljević, Branka, "Metagenomska analiza zemljišnih mikrobioloških zajednica" in Archives of Biological Sciences, 62, no. 3 (2010):559-564,
https://doi.org/10.2298/ABS1003559D . .