This is the accepted version of a paper published in Water Research. This paper has been peer-rev... more This is the accepted version of a paper published in Water Research. This paper has been peer-reviewed but does not include the final publisher proof-corrections or journal pagination.
To investigate the effects of different bioaugmentation strategies for enhancing the biogas produ... more To investigate the effects of different bioaugmentation strategies for enhancing the biogas production from cow manure and evaluate microbial community patterns. Methods and Results: Co-inoculation with cow rumen fluid and cow rumen-derived enriched microbial consortia were evaluated in anaerobic batch tests at 36 o C and 41 o C. Singular addition of both rumen fluid and enriched bioaugmentation culture had a promising enhancement on methane yields; however, the highest methane yield (311 mL CH 4 / g VS at 41 o C) was achieved when the anaerobic seed sludge was co-inoculated together with rumen fluid and enriched bioaugmentation culture. Bacterial community profiles were investigated by Ion PGM Platform and specific lignocellulolytic bacteria dynamics in batch tests were assessed by qPCR. The temperature had minor effects on the abundance of bacterial community; in which Bacteroidetes and Firmicutes were the most abundant phyla in all digesters. Furthermore, Rikenellaceae, Clostridiaceae, Porphyromonadaceae, Bacteroidaceae and Ruminococcaceae played a crucial role during the anaerobic degradation of cow manure. There was an important impact of F. flavefaciens and R. albus at the 41 °C, which in turn positively affected the methane production. Conclusion: The degree of enhancement in biogas production can be upgraded by the coinoculation of rumen-derived bioaugmentation culture with anaerobic seed sludge with high methanogenic activity. Significance and Impact of the Study: A close look at the biotic interactions and their associations with abiotic factors might be valuable for evaluating rumen-related bioaugmentation applications.
During the 19th century, increasing human activity followed by great use of fossil fuels and the ... more During the 19th century, increasing human activity followed by great use of fossil fuels and the production of manifold aromatics including polycyclic aromatic hydrocarbons (PAHs) induced the generation of aromatic end-products. PAH are toxic to human health since they have been classified as pollutants and may reduce the biodiversity of natural ecosystems. They may form extensive global contaminants which pose a threat to entire world. This study focuses on summarizes recent information of PAHs biodegradation by aerobic and anaerobic fungi. Such information develops a new point of view on how organic molecules including PAHs are metabolically degraded in a complicated ecosystem and assists the foundation of new decontamination strategies due to the microbial interactions between fungi and their associates. Emerging integrative approaches including metagenomics, metatranscriptomics, metabolomics, and metaproteomics are studied in order to understand how these approaches give insight into decipher the molecular mechanisms of degradation of PAHs by fungi at the single species and community levels.
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.
Recent energy policies promote energy generations from green resources to meet sustainability cri... more Recent energy policies promote energy generations from green resources to meet sustainability criteria. Since Turkey is one of the largest agricultural producers globally, it has great biogas production potential. This study aims to evaluate the biomethane yields of the most abundant agroresidues in Turkey and to assess their potentials for contribution to biogas production. Within this scope, sunflower heads, tea residues, cotton stalks, and crop residues; wheat, rye, and triticale straws were collected from different regions of Turkey. Anaerobic batch digesters were conducted to investigate the biomethane production of the selected feedstock and operated for 30 days at 37°C. Each setup was conducted in triplicates and methane productions were monitored online. The main methane production route of the inoculum was determined as acetoclastic methanogenesis while Cloacimonetes, Firmicutes, and Bacteroidetes composed the core bacterial phyla. The greatest methane yield was observed in the digesters operated with the wheat straw followed (164 NmL/gVSinfluent) by triticale straw and sunflower head. The lowest yields were calculated for the digesters fed with the cotton stalks (71 NmL/gVSinfluent). To increase the biomethane potential yields in the anaerobic digesters operated with agro-residues and to make the anaerobic digesters more feasible, operational conditions should be optimized and physico-chemical and biological pre-treatment techniques and/or bioaugmentation applications should be integrated into the systems.
Performance and microbial community dynamics in an upflow anaerobic sludge bed (UASB) reactor cou... more Performance and microbial community dynamics in an upflow anaerobic sludge bed (UASB) reactor coupled with anaerobic ammonium oxidizing (Anammox) treating diluted chicken manure digestate (Total ammonia nitrogen; TAN=123±10 mg/L) were investigated for a 120-d operating period in the presence of anaerobic granular inoculum. Maximum TAN removal efficiency reached to above 80% with as low as 20 mg/L TAN concentrations in the effluent. Moreover, total COD (tCOD) with 807±215 mg/L in the influent was removed by 60-80%. High-throughput sequencing revealed that Proteobacteria, Actinobacteria, and Firmicutes were dominant phyla followed by Euryarchaeota and Bacteroidetes. The relative abundance of Planctomycetes significantly increased from 4% to 8-9% during the late days of the operation with decreased tCOD concentration, which indicated a more optimum condition to favor ammonia removal through anammox route. There was also significant association between the hzsA gene and ammonia removal in the UASB reactor.
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.
Biological treatment processes offer the ideal conditions in which a high diversity of microorgan... more Biological treatment processes offer the ideal conditions in which a high diversity of microorganisms can grow and develop. The wastewater produced during these processes is contaminated with antibiotics and, as such, they provide the ideal setting for the acquisition and proliferation of antibiotic resistance genes (ARGs). This research investigated the occurrence and variation in the ARGs found during the oneyear operation of the anaerobic sequencing batch reactors (SBRs) used to treat pharmaceutical wastewater that contained combinations of sulfamethoxazole-tetracycline-erythromycin (STE) and sulfamethoxazole-tetracycline (ST). The existence of eighteen ARGs encoding resistance to sulfamethoxazole (sul1, sul2, sul3), erythromycin (ermA, ermF, ermB, msrA, ereA), tetracycline (tetA, tetB, tetC, tetD, tetE, tetM, tetS, tetQ, tetW, tetX) and class І integron gene (intІ 1) in the STE and ST reactors was investigated by quantitative real-time PCR. Due to the limited availability of primers to detect ARGs, Illumina sequencing was also performed on the sludge and effluent of the STE and ST reactors. Although there was good reactor performance in the SBRs, which corresponds to min 80% COD removal efficiency, tetA, tetB, sul1, sul2 and ermB genes were among those ARGs detected in the effluent from STE and ST reactors. A comparison of the ARGs acquired from the STE and ST reactors revealed that the effluent from the STE reactor had a higher number of ARGs than that from the ST reactor; this could be due to the synergistic effects of erythromycin. According to the expression of genes results, microorganisms achieve tetracycline and erythromycin resistance through a combination of three mechanisms: efflux pumping protein, modification of the antibiotic target and modifying enzymes. There was also a significant association between the presence of the class 1 integron and sulfamethoxazole resistance genes.
This study focuses on the dynamics of VFA production from pretreated olive mill wastewater (OMW).... more This study focuses on the dynamics of VFA production from pretreated olive mill wastewater (OMW). Acidogenic anaerobic sequencing batch reactors (AcASBR) were operated with the pretreated OMW at hydraulic retention time (HRT) of 2 days and pH of 5,5 for different organic loading rates (OLRs) ranging from 5 gr COD/L to 40 gr COD/L. VFA production reached to the highest value of about 27000 mg/L with the increase in the organic load applied (20 gr COD/L). The highest acidification rate was calculated as 68%. Acetic acid was found to be as the dominant VFA compound for all stage of the study. At steady state, VFA production during a day-cycle period (24th hours) in AcASBR is also monitored, VFA production gradually increased after the 3rd and 6th hours (about 20%) and a rapid increase (about %40) was observed reaching the maximum at the end of the cycle (24th hours).
h i g h l i g h t s Higher methane yields and OTC reductions were achieved with twostage system. ... more h i g h l i g h t s Higher methane yields and OTC reductions were achieved with twostage system. Methanogens were not negatively affected by OTC in the two-stage digester. Methanosarcina spp. and syntrophic acetate-oxidizing bacteria are critical to methane production. Two-stage AD reduce negative effects of such antibiotics on microbial communities.
The aim of this study was to determine the potential of bioaugmentation with cellulolytic rumen m... more The aim of this study was to determine the potential of bioaugmentation with cellulolytic rumen microbiota to enhance the anaerobic digestion of lignocellulosic feedstock. An anaerobic cellulolytic culture was enriched from sheep rumen fluid using wheat straw as substrate under mesophilic conditions. To investigate the effects of bioaugmentation on methane production from straw, the enrichment culture was added to batch reactors in proportions of 2% (Set-1) and 4% (Set-2) of the microbial cell number of the standard inoculum slurry. The methane production in the bioaugmented reactors was higher than in the control reactors. After 30 days of batch incubation, the average methane yield was 154 mL N CH 4 g VS À1 in the control reactors. Addition of 2% enrichment culture did not enhance methane production, whereas in Set-2 the methane yield was increased by 27%. The bacterial communities were examined by 454 amplicon sequencing of 16S rRNA genes, while terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of mcrA genes was applied to analyze the methanogenic communities. The results highlighted that relative abundances of Ruminococcaceae and Lachnospiraceae increased during the enrichment. However, Cloacamonaceae, which were abundant in the standard inoculum, dominated the bacterial communities of all batch reactors. T-RFLP profiles revealed that Methanobacteriales were predominant in the rumen fluid, whereas the enrichment culture was dominated by Methanosarcinales. In the batch rectors, the most abundant methanogens were affiliated to Methanobacteriales and Methanomicrobiales. Our results suggest that bioaugmentation with sheep rumen enrichment cultures can enhance the performance of digesters treating lignocellulosic feedstock.
Ecotoxicology and Environmental Safety, Mar 1, 2016
This study investigated the abundance and diversity of soil n-alkane and polycyclic aromatic hydr... more This study investigated the abundance and diversity of soil n-alkane and polycyclic aromatic hydrocarbon (PAH)-degrading bacterial communities. It also investigated the quantity of the functional genes, the occurrence of horizontal gene transfer (HGT) in the identified bacterial communities and the effect that such HGT can have on biostimulation process. Illumina sequencing was used to detect the microbial diversity of petroleum-polluted soil prior to the biostimulation process, and quantitative real-time PCR was used to determine changes in the bacterial community and functional genes (alkB, phnAc and nah) expressions throughout the biostimulation of petroleum-contaminated soil. The illumine results revealed that γ-proteobacteria, Chloroflexi, Firmicutes, and δ-proteobacteria were the most dominant bacterial phyla in the contaminated site, and that most of the strains were Gram-negative. The results of the gene expression results revealed that gram-negative bacteria and alkB are critical to successful bioremediation. Failure to maintain the stability of hydrocarbon-degrading bacteria and functional gene will reduce the extend to which alkanes and PAHs are degraded. According to the results of the study, the application of a C:N:P ratio of was 100:15:1 in the biodegradation experiment resulted in the highest rate at which petroleum hydrocarbons were biodegraded. The diversity of pollutant-degrading bacteria and the effective transfer of degrading genes among resident microorganisms are essential factors for the successful biostimulation of petroleum hydrocarbons. As such, screening these factors throughout the biostimulation process represents an effective monitoring approach by which the success of the biostimulation can be assessed.
Environmental Science and Pollution Research, Mar 26, 2019
Nanomaterials (NMs) commercially used for various activities mostly end up in landfills. Reduced ... more Nanomaterials (NMs) commercially used for various activities mostly end up in landfills. Reduced biogas productions reported in landfill reactors create a need for more comprehensive research on these greatly-diverse microbial pools. In order to evaluate the impact of one of the most widely-used NMs, namely nano-zinc oxide (nano-ZnO), simulated bioreactor and conventional landfills were operated using real municipal solid waste (MSW) for 300 days with addition nano-ZnO. Leachate samples were taken at different phases and analyzed by 16S rRNA gene amplicon sequencing. The bacterial communities were distinctly characterized by Cloacamonaceae (phylum WWE1), Rhodocyclaceae (phylum Proteobacteria), Porphyromonadaceae (phylum Bacteroidetes), and Synergistaceae (phylum Synergistetes). The bacterial community in the bioreactors shifted at the end of the operation and was dominated by Rhodocyclaceae. There was not a major change in the bacterial community in the conventional reactors. The methanogenic archaeal diversity highly differed between the bioreactors and conventional reactors. The dominance of Methanomicrobiaceae was observed in the bioreactors during the peak methane-production period; however, their prominence shifted to WSA2 in the nano-ZnO-added bioreactor and to Methanocorpusculaceae in the control bioreactor towards the end. Methanocorpusculaceae was the most abundant family in both conventional control and nano-ZnO-containing reactors.
Organic matter degradation and bacterial communities associated to the thermophilic phase of comp... more Organic matter degradation and bacterial communities associated to the thermophilic phase of composting were compared using two different types of anaerobic digestates, one from a sewage sludge digester (SD), and the other from an agricultural digester (AD). The composting process exhibited similar variations in temperature, pH, moisture content and bacterial profiles, despite the inherent feedstock differences along with distinctive initial bacterial composition. According to the data obtained from 16S rRNA gene amplicon sequencing, SD constituted more than 20 bacterial phyla with Proteobacteria (21%) and Chloroflexi (21%) being predominant, meanwhile AD was represented by only 7 phyla in which Firmicutes was the most abundant phylum (73%). Nevertheless, bacterial community profiles of the two composting systems became more similarly represented at the phylum level, both dominated by Proteobacteria (65% in AD and 61% in SD), whereas Chromatiaceae and Sphingomonadaceae were the most abundant families in AD and SD, respectively. Highly diverse but similar bacterial communities were detected during the composting of different anaerobic digestates at the thermophilic phase.
Applied Microbiology and Biotechnology, Nov 19, 2017
The aim of this study was to develop an effective bioaugmentation concept for anaerobic digesters... more The aim of this study was to develop an effective bioaugmentation concept for anaerobic digesters treating lignocellulosic biomass such as straw. For that purpose, lignocellulose-degrading methanogenic communities were enriched on wheat straw from cow and goat rumen fluid as well as from a biogas reactor acclimated to lignocellulosic biomass (sorghum as mono-substrate). The bacterial communities of the enriched cultures and the different inocula were examined by 454 amplicon sequencing of 16S rRNA genes while the methanogenic archaeal communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the mcrA gene. Bacteroidetes was the most abundant phylum in all samples. Within the Bacteroidetes phylum, Bacteroidaceae was the most abundant family in the rumen-derived enrichment cultures, whereas Porphyromonadaceae was the predominant one in the reactor-derived culture. Additionally, the enrichment procedure increased the relative abundance of Ruminococcaceae (phylum: Firmicutes) in all cultures. T-RFLP profiles of the mcrA gene amplicons highlighted that the ruminal methanogenic communities were composed of hydrogenotrophic methanogens dominated by the order Methanobacteriales regardless of the host species. The methanogenic communities changed significantly during the enrichment procedure, but still the strict hydrogenotrophic Methanobacteriales and Methanomicrobiales were the predominant orders in the enrichment cultures. The bioaugmentation potential of the enriched methanogenic cultures will be evaluated in further studies.
Algal Research-Biomass Biofuels and Bioproducts, Apr 1, 2017
The aim of this study was to investigate the effects of bioaugmentation with anaerobic rumen fung... more The aim of this study was to investigate the effects of bioaugmentation with anaerobic rumen fungi at varied ratios of inoculums on the performance of anaerobic digesters of microalgae biomass for increasing methane production. Anaerobic rumen fungi, Anaeromyces, Neocallimastix, Orpinomyces and Piromyces, were used in this study and have groups of genes that originate from bacteria by the way of horizontal gene transfer. The results imply that rumen fungi improved the fermentation and degradation of microalgae biomass because they fostered cell wall degradation while methane production increased of 41% because of bioaugmentation with rumen fungi during anaerobic processes. Overall, the findings here indicate that bioaugmentation with a combination of rumen fungi in anaerobic process can represent an appropriate alternative to the use of chemical pretreatments of microalgae biomass. Thus, anaerobic rumen fungi have promise for enhancing biogas production from different microalgae and macroalgae species and also various lignocellulosic substrates.
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.
In this study, we aimed to develop an understanding of the triple effects of sulfamethoxazoleeryt... more In this study, we aimed to develop an understanding of the triple effects of sulfamethoxazoleerythromycin-tetracycline (ETS) and the dual effects of sulfamethoxazole-tetracycline (ST), erythromycin-sulfamethoxazole (ES) and erythromycin-tetracycline (ET) on the anaerobic treatment of pharmaceutical industry wastewater throughout a year of operation. Concentrations of the antibiotics in the influent were gradually increased until the metabolic collapse of the anaerobic sequencing batch reactors (SBRs), which corresponded to ETS (40 þ 3 þ 3 mg/L) and ST (25 þ 2.5 mg/L), ET (4 þ 4 mg/L) and ES (3 þ 40 mg/L). Acetate accumulation in the anaerobic SBRs, acetoclastic activity of the anaerobic sludge taken from different antibiotic feeding stages and also expression of acetyl-coA synthetase from the acetoclastic methanogenic pathway on the mRNA level were assessed. The results indicated that, while acetate accumulation and decrease of acetoclastic activity were observed after stage 3 in the ST and ES reactors, and stage 7 in the ETS and ET reactors, the expression of acetyl-coA synthetase was mostly decreased in the last stages in all SBRs, in which antibiotic mixture feeding was terminated. It might be speculated that acetoclastic methanogens have an important role in acetate degradation by expressing acetyl-coA synthetase.
This is a PDF file of an unedited manuscript that has been accepted for publication. As a service... more This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Highlights • This study investigated bioaugmentation with anaerobic rumen fungi to enhance the methane production • Methane production was found to increase by 60% with the addition of anaerobic rumen fungi • Controlling Bacteroidetes, Longilinea and Methanolinea sp. could promote the effective degradation of animal manure
This is the accepted version of a paper published in Water Research. This paper has been peer-rev... more This is the accepted version of a paper published in Water Research. This paper has been peer-reviewed but does not include the final publisher proof-corrections or journal pagination.
To investigate the effects of different bioaugmentation strategies for enhancing the biogas produ... more To investigate the effects of different bioaugmentation strategies for enhancing the biogas production from cow manure and evaluate microbial community patterns. Methods and Results: Co-inoculation with cow rumen fluid and cow rumen-derived enriched microbial consortia were evaluated in anaerobic batch tests at 36 o C and 41 o C. Singular addition of both rumen fluid and enriched bioaugmentation culture had a promising enhancement on methane yields; however, the highest methane yield (311 mL CH 4 / g VS at 41 o C) was achieved when the anaerobic seed sludge was co-inoculated together with rumen fluid and enriched bioaugmentation culture. Bacterial community profiles were investigated by Ion PGM Platform and specific lignocellulolytic bacteria dynamics in batch tests were assessed by qPCR. The temperature had minor effects on the abundance of bacterial community; in which Bacteroidetes and Firmicutes were the most abundant phyla in all digesters. Furthermore, Rikenellaceae, Clostridiaceae, Porphyromonadaceae, Bacteroidaceae and Ruminococcaceae played a crucial role during the anaerobic degradation of cow manure. There was an important impact of F. flavefaciens and R. albus at the 41 °C, which in turn positively affected the methane production. Conclusion: The degree of enhancement in biogas production can be upgraded by the coinoculation of rumen-derived bioaugmentation culture with anaerobic seed sludge with high methanogenic activity. Significance and Impact of the Study: A close look at the biotic interactions and their associations with abiotic factors might be valuable for evaluating rumen-related bioaugmentation applications.
During the 19th century, increasing human activity followed by great use of fossil fuels and the ... more During the 19th century, increasing human activity followed by great use of fossil fuels and the production of manifold aromatics including polycyclic aromatic hydrocarbons (PAHs) induced the generation of aromatic end-products. PAH are toxic to human health since they have been classified as pollutants and may reduce the biodiversity of natural ecosystems. They may form extensive global contaminants which pose a threat to entire world. This study focuses on summarizes recent information of PAHs biodegradation by aerobic and anaerobic fungi. Such information develops a new point of view on how organic molecules including PAHs are metabolically degraded in a complicated ecosystem and assists the foundation of new decontamination strategies due to the microbial interactions between fungi and their associates. Emerging integrative approaches including metagenomics, metatranscriptomics, metabolomics, and metaproteomics are studied in order to understand how these approaches give insight into decipher the molecular mechanisms of degradation of PAHs by fungi at the single species and community levels.
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.
Recent energy policies promote energy generations from green resources to meet sustainability cri... more Recent energy policies promote energy generations from green resources to meet sustainability criteria. Since Turkey is one of the largest agricultural producers globally, it has great biogas production potential. This study aims to evaluate the biomethane yields of the most abundant agroresidues in Turkey and to assess their potentials for contribution to biogas production. Within this scope, sunflower heads, tea residues, cotton stalks, and crop residues; wheat, rye, and triticale straws were collected from different regions of Turkey. Anaerobic batch digesters were conducted to investigate the biomethane production of the selected feedstock and operated for 30 days at 37°C. Each setup was conducted in triplicates and methane productions were monitored online. The main methane production route of the inoculum was determined as acetoclastic methanogenesis while Cloacimonetes, Firmicutes, and Bacteroidetes composed the core bacterial phyla. The greatest methane yield was observed in the digesters operated with the wheat straw followed (164 NmL/gVSinfluent) by triticale straw and sunflower head. The lowest yields were calculated for the digesters fed with the cotton stalks (71 NmL/gVSinfluent). To increase the biomethane potential yields in the anaerobic digesters operated with agro-residues and to make the anaerobic digesters more feasible, operational conditions should be optimized and physico-chemical and biological pre-treatment techniques and/or bioaugmentation applications should be integrated into the systems.
Performance and microbial community dynamics in an upflow anaerobic sludge bed (UASB) reactor cou... more Performance and microbial community dynamics in an upflow anaerobic sludge bed (UASB) reactor coupled with anaerobic ammonium oxidizing (Anammox) treating diluted chicken manure digestate (Total ammonia nitrogen; TAN=123±10 mg/L) were investigated for a 120-d operating period in the presence of anaerobic granular inoculum. Maximum TAN removal efficiency reached to above 80% with as low as 20 mg/L TAN concentrations in the effluent. Moreover, total COD (tCOD) with 807±215 mg/L in the influent was removed by 60-80%. High-throughput sequencing revealed that Proteobacteria, Actinobacteria, and Firmicutes were dominant phyla followed by Euryarchaeota and Bacteroidetes. The relative abundance of Planctomycetes significantly increased from 4% to 8-9% during the late days of the operation with decreased tCOD concentration, which indicated a more optimum condition to favor ammonia removal through anammox route. There was also significant association between the hzsA gene and ammonia removal in the UASB reactor.
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.
Biological treatment processes offer the ideal conditions in which a high diversity of microorgan... more Biological treatment processes offer the ideal conditions in which a high diversity of microorganisms can grow and develop. The wastewater produced during these processes is contaminated with antibiotics and, as such, they provide the ideal setting for the acquisition and proliferation of antibiotic resistance genes (ARGs). This research investigated the occurrence and variation in the ARGs found during the oneyear operation of the anaerobic sequencing batch reactors (SBRs) used to treat pharmaceutical wastewater that contained combinations of sulfamethoxazole-tetracycline-erythromycin (STE) and sulfamethoxazole-tetracycline (ST). The existence of eighteen ARGs encoding resistance to sulfamethoxazole (sul1, sul2, sul3), erythromycin (ermA, ermF, ermB, msrA, ereA), tetracycline (tetA, tetB, tetC, tetD, tetE, tetM, tetS, tetQ, tetW, tetX) and class І integron gene (intІ 1) in the STE and ST reactors was investigated by quantitative real-time PCR. Due to the limited availability of primers to detect ARGs, Illumina sequencing was also performed on the sludge and effluent of the STE and ST reactors. Although there was good reactor performance in the SBRs, which corresponds to min 80% COD removal efficiency, tetA, tetB, sul1, sul2 and ermB genes were among those ARGs detected in the effluent from STE and ST reactors. A comparison of the ARGs acquired from the STE and ST reactors revealed that the effluent from the STE reactor had a higher number of ARGs than that from the ST reactor; this could be due to the synergistic effects of erythromycin. According to the expression of genes results, microorganisms achieve tetracycline and erythromycin resistance through a combination of three mechanisms: efflux pumping protein, modification of the antibiotic target and modifying enzymes. There was also a significant association between the presence of the class 1 integron and sulfamethoxazole resistance genes.
This study focuses on the dynamics of VFA production from pretreated olive mill wastewater (OMW).... more This study focuses on the dynamics of VFA production from pretreated olive mill wastewater (OMW). Acidogenic anaerobic sequencing batch reactors (AcASBR) were operated with the pretreated OMW at hydraulic retention time (HRT) of 2 days and pH of 5,5 for different organic loading rates (OLRs) ranging from 5 gr COD/L to 40 gr COD/L. VFA production reached to the highest value of about 27000 mg/L with the increase in the organic load applied (20 gr COD/L). The highest acidification rate was calculated as 68%. Acetic acid was found to be as the dominant VFA compound for all stage of the study. At steady state, VFA production during a day-cycle period (24th hours) in AcASBR is also monitored, VFA production gradually increased after the 3rd and 6th hours (about 20%) and a rapid increase (about %40) was observed reaching the maximum at the end of the cycle (24th hours).
h i g h l i g h t s Higher methane yields and OTC reductions were achieved with twostage system. ... more h i g h l i g h t s Higher methane yields and OTC reductions were achieved with twostage system. Methanogens were not negatively affected by OTC in the two-stage digester. Methanosarcina spp. and syntrophic acetate-oxidizing bacteria are critical to methane production. Two-stage AD reduce negative effects of such antibiotics on microbial communities.
The aim of this study was to determine the potential of bioaugmentation with cellulolytic rumen m... more The aim of this study was to determine the potential of bioaugmentation with cellulolytic rumen microbiota to enhance the anaerobic digestion of lignocellulosic feedstock. An anaerobic cellulolytic culture was enriched from sheep rumen fluid using wheat straw as substrate under mesophilic conditions. To investigate the effects of bioaugmentation on methane production from straw, the enrichment culture was added to batch reactors in proportions of 2% (Set-1) and 4% (Set-2) of the microbial cell number of the standard inoculum slurry. The methane production in the bioaugmented reactors was higher than in the control reactors. After 30 days of batch incubation, the average methane yield was 154 mL N CH 4 g VS À1 in the control reactors. Addition of 2% enrichment culture did not enhance methane production, whereas in Set-2 the methane yield was increased by 27%. The bacterial communities were examined by 454 amplicon sequencing of 16S rRNA genes, while terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of mcrA genes was applied to analyze the methanogenic communities. The results highlighted that relative abundances of Ruminococcaceae and Lachnospiraceae increased during the enrichment. However, Cloacamonaceae, which were abundant in the standard inoculum, dominated the bacterial communities of all batch reactors. T-RFLP profiles revealed that Methanobacteriales were predominant in the rumen fluid, whereas the enrichment culture was dominated by Methanosarcinales. In the batch rectors, the most abundant methanogens were affiliated to Methanobacteriales and Methanomicrobiales. Our results suggest that bioaugmentation with sheep rumen enrichment cultures can enhance the performance of digesters treating lignocellulosic feedstock.
Ecotoxicology and Environmental Safety, Mar 1, 2016
This study investigated the abundance and diversity of soil n-alkane and polycyclic aromatic hydr... more This study investigated the abundance and diversity of soil n-alkane and polycyclic aromatic hydrocarbon (PAH)-degrading bacterial communities. It also investigated the quantity of the functional genes, the occurrence of horizontal gene transfer (HGT) in the identified bacterial communities and the effect that such HGT can have on biostimulation process. Illumina sequencing was used to detect the microbial diversity of petroleum-polluted soil prior to the biostimulation process, and quantitative real-time PCR was used to determine changes in the bacterial community and functional genes (alkB, phnAc and nah) expressions throughout the biostimulation of petroleum-contaminated soil. The illumine results revealed that γ-proteobacteria, Chloroflexi, Firmicutes, and δ-proteobacteria were the most dominant bacterial phyla in the contaminated site, and that most of the strains were Gram-negative. The results of the gene expression results revealed that gram-negative bacteria and alkB are critical to successful bioremediation. Failure to maintain the stability of hydrocarbon-degrading bacteria and functional gene will reduce the extend to which alkanes and PAHs are degraded. According to the results of the study, the application of a C:N:P ratio of was 100:15:1 in the biodegradation experiment resulted in the highest rate at which petroleum hydrocarbons were biodegraded. The diversity of pollutant-degrading bacteria and the effective transfer of degrading genes among resident microorganisms are essential factors for the successful biostimulation of petroleum hydrocarbons. As such, screening these factors throughout the biostimulation process represents an effective monitoring approach by which the success of the biostimulation can be assessed.
Environmental Science and Pollution Research, Mar 26, 2019
Nanomaterials (NMs) commercially used for various activities mostly end up in landfills. Reduced ... more Nanomaterials (NMs) commercially used for various activities mostly end up in landfills. Reduced biogas productions reported in landfill reactors create a need for more comprehensive research on these greatly-diverse microbial pools. In order to evaluate the impact of one of the most widely-used NMs, namely nano-zinc oxide (nano-ZnO), simulated bioreactor and conventional landfills were operated using real municipal solid waste (MSW) for 300 days with addition nano-ZnO. Leachate samples were taken at different phases and analyzed by 16S rRNA gene amplicon sequencing. The bacterial communities were distinctly characterized by Cloacamonaceae (phylum WWE1), Rhodocyclaceae (phylum Proteobacteria), Porphyromonadaceae (phylum Bacteroidetes), and Synergistaceae (phylum Synergistetes). The bacterial community in the bioreactors shifted at the end of the operation and was dominated by Rhodocyclaceae. There was not a major change in the bacterial community in the conventional reactors. The methanogenic archaeal diversity highly differed between the bioreactors and conventional reactors. The dominance of Methanomicrobiaceae was observed in the bioreactors during the peak methane-production period; however, their prominence shifted to WSA2 in the nano-ZnO-added bioreactor and to Methanocorpusculaceae in the control bioreactor towards the end. Methanocorpusculaceae was the most abundant family in both conventional control and nano-ZnO-containing reactors.
Organic matter degradation and bacterial communities associated to the thermophilic phase of comp... more Organic matter degradation and bacterial communities associated to the thermophilic phase of composting were compared using two different types of anaerobic digestates, one from a sewage sludge digester (SD), and the other from an agricultural digester (AD). The composting process exhibited similar variations in temperature, pH, moisture content and bacterial profiles, despite the inherent feedstock differences along with distinctive initial bacterial composition. According to the data obtained from 16S rRNA gene amplicon sequencing, SD constituted more than 20 bacterial phyla with Proteobacteria (21%) and Chloroflexi (21%) being predominant, meanwhile AD was represented by only 7 phyla in which Firmicutes was the most abundant phylum (73%). Nevertheless, bacterial community profiles of the two composting systems became more similarly represented at the phylum level, both dominated by Proteobacteria (65% in AD and 61% in SD), whereas Chromatiaceae and Sphingomonadaceae were the most abundant families in AD and SD, respectively. Highly diverse but similar bacterial communities were detected during the composting of different anaerobic digestates at the thermophilic phase.
Applied Microbiology and Biotechnology, Nov 19, 2017
The aim of this study was to develop an effective bioaugmentation concept for anaerobic digesters... more The aim of this study was to develop an effective bioaugmentation concept for anaerobic digesters treating lignocellulosic biomass such as straw. For that purpose, lignocellulose-degrading methanogenic communities were enriched on wheat straw from cow and goat rumen fluid as well as from a biogas reactor acclimated to lignocellulosic biomass (sorghum as mono-substrate). The bacterial communities of the enriched cultures and the different inocula were examined by 454 amplicon sequencing of 16S rRNA genes while the methanogenic archaeal communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the mcrA gene. Bacteroidetes was the most abundant phylum in all samples. Within the Bacteroidetes phylum, Bacteroidaceae was the most abundant family in the rumen-derived enrichment cultures, whereas Porphyromonadaceae was the predominant one in the reactor-derived culture. Additionally, the enrichment procedure increased the relative abundance of Ruminococcaceae (phylum: Firmicutes) in all cultures. T-RFLP profiles of the mcrA gene amplicons highlighted that the ruminal methanogenic communities were composed of hydrogenotrophic methanogens dominated by the order Methanobacteriales regardless of the host species. The methanogenic communities changed significantly during the enrichment procedure, but still the strict hydrogenotrophic Methanobacteriales and Methanomicrobiales were the predominant orders in the enrichment cultures. The bioaugmentation potential of the enriched methanogenic cultures will be evaluated in further studies.
Algal Research-Biomass Biofuels and Bioproducts, Apr 1, 2017
The aim of this study was to investigate the effects of bioaugmentation with anaerobic rumen fung... more The aim of this study was to investigate the effects of bioaugmentation with anaerobic rumen fungi at varied ratios of inoculums on the performance of anaerobic digesters of microalgae biomass for increasing methane production. Anaerobic rumen fungi, Anaeromyces, Neocallimastix, Orpinomyces and Piromyces, were used in this study and have groups of genes that originate from bacteria by the way of horizontal gene transfer. The results imply that rumen fungi improved the fermentation and degradation of microalgae biomass because they fostered cell wall degradation while methane production increased of 41% because of bioaugmentation with rumen fungi during anaerobic processes. Overall, the findings here indicate that bioaugmentation with a combination of rumen fungi in anaerobic process can represent an appropriate alternative to the use of chemical pretreatments of microalgae biomass. Thus, anaerobic rumen fungi have promise for enhancing biogas production from different microalgae and macroalgae species and also various lignocellulosic substrates.
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.
In this study, we aimed to develop an understanding of the triple effects of sulfamethoxazoleeryt... more In this study, we aimed to develop an understanding of the triple effects of sulfamethoxazoleerythromycin-tetracycline (ETS) and the dual effects of sulfamethoxazole-tetracycline (ST), erythromycin-sulfamethoxazole (ES) and erythromycin-tetracycline (ET) on the anaerobic treatment of pharmaceutical industry wastewater throughout a year of operation. Concentrations of the antibiotics in the influent were gradually increased until the metabolic collapse of the anaerobic sequencing batch reactors (SBRs), which corresponded to ETS (40 þ 3 þ 3 mg/L) and ST (25 þ 2.5 mg/L), ET (4 þ 4 mg/L) and ES (3 þ 40 mg/L). Acetate accumulation in the anaerobic SBRs, acetoclastic activity of the anaerobic sludge taken from different antibiotic feeding stages and also expression of acetyl-coA synthetase from the acetoclastic methanogenic pathway on the mRNA level were assessed. The results indicated that, while acetate accumulation and decrease of acetoclastic activity were observed after stage 3 in the ST and ES reactors, and stage 7 in the ETS and ET reactors, the expression of acetyl-coA synthetase was mostly decreased in the last stages in all SBRs, in which antibiotic mixture feeding was terminated. It might be speculated that acetoclastic methanogens have an important role in acetate degradation by expressing acetyl-coA synthetase.
This is a PDF file of an unedited manuscript that has been accepted for publication. As a service... more This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Highlights • This study investigated bioaugmentation with anaerobic rumen fungi to enhance the methane production • Methane production was found to increase by 60% with the addition of anaerobic rumen fungi • Controlling Bacteroidetes, Longilinea and Methanolinea sp. could promote the effective degradation of animal manure
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