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Papers by Orhan Ince

Research paper thumbnail of Anaerobic sulfamethoxazole degradation is driven by homoacetogenesis coupled with hydrogenotrophic methanogenesis

Research paper thumbnail of Rumen bacteria at work: bioaugmentation strategies to enhance biogas production from cow manure

Journal of Applied Microbiology, Jan 22, 2018

Research paper thumbnail of Aerobic and anaerobic fungal metabolism and Omics insights for increasing polycyclic aromatic hydrocarbons biodegradation

Fungal Biology Reviews, Mar 1, 2017

Research paper thumbnail of Application of real-time PCR to determination of combined effect of antibiotics on Bacteria, Methanogenic Archaea, Archaea in anaerobic sequencing batch reactors

Water Research, Jun 1, 2015

This study evaluated the long-term effects of erythromycin-tetracycline-sulfamethoxazole (ETS) an... more This study evaluated the long-term effects of erythromycin-tetracycline-sulfamethoxazole (ETS) and sulfamethoxazole-tetracycline (ST) antibiotic combinations on the microbial community and examined the ways in which these antimicrobials impact the performance of anaerobic reactors. Quantitative real-time PCR was used to determine the effect that different antibiotic combinations had on the total and active Bacteria, Archae and Methanogenic Archae. Three primer sets that targeted metabolic genes encoding formylterahydrofolate synthetase, methyl-coenzyme M reductase and acetyl-coA synthetase were also used to determine the inhibition level on the mRNA expression of the homoacetogens, methanogens and specifically acetoclastic methanogens, respectively. These microorganisms play a vital role in the anaerobic degradation of organic waste and targeting these gene expressions offers operators or someone at a treatment plant the potential to control and the improve the anaerobic system. The results of the investigation revealed that acetogens have a competitive advantage over Archaea in the presence of ETS and ST combinations. Although the efficiency with which methane production takes place and the quantification of microbial populations in both the ETS and ST reactors decreased as antibiotic concentrations increased, the ETS batch reactor performed better than the ST batch reactor. According to the expression of genes results, the syntrophic interaction of acetogens and methanogens is critical to the performance of the ETS and ST reactors. Failure to maintain the stability of these microorganisms resulted in a decrease in the performance and stability of the anaerobic reactors.

Research paper thumbnail of Kâğit endüstrisi atiksularinda anaerobik mikrobiyal çeşitliliğin belirlenmesi

Research paper thumbnail of Comparative Assessment of Biogas Production Potential of the Most Abundant Agro-residues in Turkey

Fen-mühendislik dergisi, May 24, 2021

Research paper thumbnail of Microbial monitoring of ammonia removal in a UASB reactor treating pre-digested chicken manure with anaerobic granular inoculum

Bioresource Technology, Oct 1, 2017

Research paper thumbnail of Assessment of anaerobic bacterial diversity and its effects on anaerobic system stability and the occurrence of antibiotic resistance genes

Bioresource Technology, May 1, 2016

This study evaluated the link between anaerobic bacterial diversity and, the biodegradation of an... more This study evaluated the link between anaerobic bacterial diversity and, the biodegradation of antibiotic combinations and assessed how amending antibiotic combination and increasing concentration of antibiotics in a stepwise fashion influences the development of resistance genes in anaerobic reactors. The biodegradation, sorption and occurrence of the known antibiotic resistance genes (ARGs) of erythromycin and tetracycline were investigated using the processes of UV-HPLC and qPCR analysis respectively. Ion Torrent sequencing was used to detect microbial community changes in response to the addition of antibiotics. The overall results indicated that changes in the structure of a microbial community lead to changes in biodegradation capacity, sorption of antibiotics combinations and occurrence of ARGs. The enhanced biodegradation efficiency appeared to generate variations in the structure of the bacterial community. The results suggested that controlling the ultimate Gram-negative bacterial community, especially Acinetobacter-related populations, may promote the successful biodegradation of antibiotic combinations and reduce the occurrence of ARGs.

Research paper thumbnail of Development of antibiotic resistance genes in microbial communities during long-term operation of anaerobic reactors in the treatment of pharmaceutical wastewater

Water Research, Oct 1, 2015

Research paper thumbnail of Volatile fatty acid production dynamics during the acidification of pretreated olive mill wastewater

Bioresource Technology, Oct 1, 2017

Research paper thumbnail of A comprehensive microbial insight into single-stage and two-stage anaerobic digestion of oxytetracycline-medicated cattle manure

Chemical Engineering Journal, Nov 1, 2016

Research paper thumbnail of Effect of bioaugmentation by cellulolytic bacteria enriched from sheep rumen on methane production from wheat straw

Research paper thumbnail of Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach

Ecotoxicology and Environmental Safety, Mar 1, 2016

Research paper thumbnail of Linking nano-ZnO contamination to microbial community profiling in sanitary landfill simulations

Environmental Science and Pollution Research, Mar 26, 2019

Research paper thumbnail of Bacterial Succession in the Thermophilic Phase of Composting of Anaerobic Digestates

Waste and Biomass Valorization, Dec 3, 2018

Research paper thumbnail of Enrichment of lignocellulose-degrading microbial communities from natural and engineered methanogenic environments

Applied Microbiology and Biotechnology, Nov 19, 2017

Research paper thumbnail of Rumen anaerobic fungi create new opportunities for enhanced methane production from microalgae biomass

Algal Research-Biomass Biofuels and Bioproducts, Apr 1, 2017

Research paper thumbnail of Biogeographical distribution and diversity of bacterial and archaeal communities within highly polluted anoxic marine sediments from the marmara sea

Marine Pollution Bulletin, Aug 1, 2009

Physicochemical and microbiological characterization of anoxic sediments taken from seven highly ... more Physicochemical and microbiological characterization of anoxic sediments taken from seven highly polluted sites of the Marmara Sea was carried out. The 16S rRNA based microbial community structure analyses were performed using domain-specific PCR followed by denaturant gradient gel electrophoresis (DGGE) and sequencing of characteristic bands. The results showed that the microbial communities in these sediments were diverse and evenly distributed. Relating the prokaryotic and geochemical variables through statistical tools revealed that the microbial diversity in the sediments significantly related to depth, and S, Mn and Fe content of the sediments. Fermentative bacteria, denitrifying bacteria and hydrogenotrophic methanogens were dominant whereas sulfate reducing bacteria were absent in the DGGE patterns. This unusual microbial community structure implied that the newly discovered anaerobic methane oxidation coupled to denitrification process may occur in these subseafloor environments.

Research paper thumbnail of The joint acute effect of tetracycline, erythromycin and sulfamethoxazole on acetoclastic methanogens

Water Science and Technology, Feb 13, 2015

Research paper thumbnail of Improvement of biogas potential of anaerobic digesters using rumen fungi

Renewable Energy, Aug 1, 2017

Research paper thumbnail of Anaerobic sulfamethoxazole degradation is driven by homoacetogenesis coupled with hydrogenotrophic methanogenesis

Research paper thumbnail of Rumen bacteria at work: bioaugmentation strategies to enhance biogas production from cow manure

Journal of Applied Microbiology, Jan 22, 2018

Research paper thumbnail of Aerobic and anaerobic fungal metabolism and Omics insights for increasing polycyclic aromatic hydrocarbons biodegradation

Fungal Biology Reviews, Mar 1, 2017

Research paper thumbnail of Application of real-time PCR to determination of combined effect of antibiotics on Bacteria, Methanogenic Archaea, Archaea in anaerobic sequencing batch reactors

Water Research, Jun 1, 2015

This study evaluated the long-term effects of erythromycin-tetracycline-sulfamethoxazole (ETS) an... more This study evaluated the long-term effects of erythromycin-tetracycline-sulfamethoxazole (ETS) and sulfamethoxazole-tetracycline (ST) antibiotic combinations on the microbial community and examined the ways in which these antimicrobials impact the performance of anaerobic reactors. Quantitative real-time PCR was used to determine the effect that different antibiotic combinations had on the total and active Bacteria, Archae and Methanogenic Archae. Three primer sets that targeted metabolic genes encoding formylterahydrofolate synthetase, methyl-coenzyme M reductase and acetyl-coA synthetase were also used to determine the inhibition level on the mRNA expression of the homoacetogens, methanogens and specifically acetoclastic methanogens, respectively. These microorganisms play a vital role in the anaerobic degradation of organic waste and targeting these gene expressions offers operators or someone at a treatment plant the potential to control and the improve the anaerobic system. The results of the investigation revealed that acetogens have a competitive advantage over Archaea in the presence of ETS and ST combinations. Although the efficiency with which methane production takes place and the quantification of microbial populations in both the ETS and ST reactors decreased as antibiotic concentrations increased, the ETS batch reactor performed better than the ST batch reactor. According to the expression of genes results, the syntrophic interaction of acetogens and methanogens is critical to the performance of the ETS and ST reactors. Failure to maintain the stability of these microorganisms resulted in a decrease in the performance and stability of the anaerobic reactors.

Research paper thumbnail of Kâğit endüstrisi atiksularinda anaerobik mikrobiyal çeşitliliğin belirlenmesi

Research paper thumbnail of Comparative Assessment of Biogas Production Potential of the Most Abundant Agro-residues in Turkey

Fen-mühendislik dergisi, May 24, 2021

Research paper thumbnail of Microbial monitoring of ammonia removal in a UASB reactor treating pre-digested chicken manure with anaerobic granular inoculum

Bioresource Technology, Oct 1, 2017

Research paper thumbnail of Assessment of anaerobic bacterial diversity and its effects on anaerobic system stability and the occurrence of antibiotic resistance genes

Bioresource Technology, May 1, 2016

This study evaluated the link between anaerobic bacterial diversity and, the biodegradation of an... more This study evaluated the link between anaerobic bacterial diversity and, the biodegradation of antibiotic combinations and assessed how amending antibiotic combination and increasing concentration of antibiotics in a stepwise fashion influences the development of resistance genes in anaerobic reactors. The biodegradation, sorption and occurrence of the known antibiotic resistance genes (ARGs) of erythromycin and tetracycline were investigated using the processes of UV-HPLC and qPCR analysis respectively. Ion Torrent sequencing was used to detect microbial community changes in response to the addition of antibiotics. The overall results indicated that changes in the structure of a microbial community lead to changes in biodegradation capacity, sorption of antibiotics combinations and occurrence of ARGs. The enhanced biodegradation efficiency appeared to generate variations in the structure of the bacterial community. The results suggested that controlling the ultimate Gram-negative bacterial community, especially Acinetobacter-related populations, may promote the successful biodegradation of antibiotic combinations and reduce the occurrence of ARGs.

Research paper thumbnail of Development of antibiotic resistance genes in microbial communities during long-term operation of anaerobic reactors in the treatment of pharmaceutical wastewater

Water Research, Oct 1, 2015

Research paper thumbnail of Volatile fatty acid production dynamics during the acidification of pretreated olive mill wastewater

Bioresource Technology, Oct 1, 2017

Research paper thumbnail of A comprehensive microbial insight into single-stage and two-stage anaerobic digestion of oxytetracycline-medicated cattle manure

Chemical Engineering Journal, Nov 1, 2016

Research paper thumbnail of Effect of bioaugmentation by cellulolytic bacteria enriched from sheep rumen on methane production from wheat straw

Research paper thumbnail of Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach

Ecotoxicology and Environmental Safety, Mar 1, 2016

Research paper thumbnail of Linking nano-ZnO contamination to microbial community profiling in sanitary landfill simulations

Environmental Science and Pollution Research, Mar 26, 2019

Research paper thumbnail of Bacterial Succession in the Thermophilic Phase of Composting of Anaerobic Digestates

Waste and Biomass Valorization, Dec 3, 2018

Research paper thumbnail of Enrichment of lignocellulose-degrading microbial communities from natural and engineered methanogenic environments

Applied Microbiology and Biotechnology, Nov 19, 2017

Research paper thumbnail of Rumen anaerobic fungi create new opportunities for enhanced methane production from microalgae biomass

Algal Research-Biomass Biofuels and Bioproducts, Apr 1, 2017

Research paper thumbnail of Biogeographical distribution and diversity of bacterial and archaeal communities within highly polluted anoxic marine sediments from the marmara sea

Marine Pollution Bulletin, Aug 1, 2009

Physicochemical and microbiological characterization of anoxic sediments taken from seven highly ... more Physicochemical and microbiological characterization of anoxic sediments taken from seven highly polluted sites of the Marmara Sea was carried out. The 16S rRNA based microbial community structure analyses were performed using domain-specific PCR followed by denaturant gradient gel electrophoresis (DGGE) and sequencing of characteristic bands. The results showed that the microbial communities in these sediments were diverse and evenly distributed. Relating the prokaryotic and geochemical variables through statistical tools revealed that the microbial diversity in the sediments significantly related to depth, and S, Mn and Fe content of the sediments. Fermentative bacteria, denitrifying bacteria and hydrogenotrophic methanogens were dominant whereas sulfate reducing bacteria were absent in the DGGE patterns. This unusual microbial community structure implied that the newly discovered anaerobic methane oxidation coupled to denitrification process may occur in these subseafloor environments.

Research paper thumbnail of The joint acute effect of tetracycline, erythromycin and sulfamethoxazole on acetoclastic methanogens

Water Science and Technology, Feb 13, 2015

Research paper thumbnail of Improvement of biogas potential of anaerobic digesters using rumen fungi

Renewable Energy, Aug 1, 2017

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