1
|
Zambrano-Romero A, Ramirez-Villacis DX, Barriga-Medina N, Sierra-Alvarez R, Trueba G, Ochoa-Herrera V, Leon-Reyes A. Comparative Methods for Quantification of Sulfate-Reducing Bacteria in Environmental and Engineered Sludge Samples. BIOLOGY 2023; 12:985. [PMID: 37508415 PMCID: PMC10375983 DOI: 10.3390/biology12070985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]
Abstract
This study aimed to compare microscopic counting, culture, and quantitative or real-time PCR (qPCR) to quantify sulfate-reducing bacteria in environmental and engineered sludge samples. Four sets of primers that amplified the dsrA and apsA gene encoding the two key enzymes of the sulfate-reduction pathway were initially tested. qPCR standard curves were constructed using genomic DNA from an SRB suspension and dilutions of an enriched sulfate-reducing sludge. According to specificity and reproducibility, the DSR1F/RH3-dsr-R primer set ensured a good quantification based on dsrA gene amplification; however, it exhibited inconsistencies at low and high levels of SRB concentrations in environmental and sulfate-reducing sludge samples. Ultimately, we conducted a qPCR method normalized to dsrA gene copies, using a synthetic double-stranded DNA fragment as a calibrator. This method fulfilled all validation criteria and proved to be specific, accurate, and precise. The enumeration of metabolically active SRB populations through culture methods differed from dsrA gene copies but showed a plausible positive correlation. Conversely, microscopic counting had limitations due to distinguishing densely clustered organisms, impacting precision. Hence, this study proves that a qPCR-based method optimized with dsrA gene copies as a calibrator is a sensitive molecular tool for the absolute enumeration of SRB populations in engineered and environmental sludge samples.
Collapse
Affiliation(s)
- Aracely Zambrano-Romero
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Dario X Ramirez-Villacis
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Noelia Barriga-Medina
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, The University of Arizona, P.O. Box 210011, Tucson, AZ 85721-0011, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Valeria Ochoa-Herrera
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Antonio Leon-Reyes
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| |
Collapse
|
2
|
Dynamics of Microbial Communities during the Removal of Copper and Zinc in a Sulfate-Reducing Bioreactor with a Limestone Pre-Column System. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19031484. [PMID: 35162506 PMCID: PMC8835105 DOI: 10.3390/ijerph19031484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/15/2022] [Accepted: 01/25/2022] [Indexed: 11/30/2022]
Abstract
Biological treatment using sulfate-reducing bacteria (SRB) is a promising approach to remediate acid rock drainage (ARD). Our purpose was to assess the performance of a sequential system consisting of a limestone bed filter followed by a sulfate-reducing bioreactor treating synthetic ARD for 375 days and to evaluate changes in microbial composition. The treatment system was effective in increasing the pH of the ARD from 2.7 to 7.5 and removed total Cu(II) and Zn(II) concentrations by up to 99.8% and 99.9%, respectively. The presence of sulfate in ARD promoted sulfidogenesis and changed the diversity and structure of the microbial communities. Methansarcina spp. was the most abundant amplicon sequence variant (ASV); however, methane production was not detected. Biodiversity indexes decreased over time with the bioreactor operation, whereas SRB abundance remained stable. Desulfobacteraceae, Desulfocurvus, Desulfobulbaceae and Desulfovibrio became more abundant, while Desulfuromonadales, Desulfotomaculum and Desulfobacca decreased. Geobacter and Syntrophobacter were enriched with bioreactor operation time. At the beginning, ASVs with relative abundance <2% represented 65% of the microbial community and 21% at the end of the study period. Thus, the results show that the microbial community gradually lost diversity while the treatment system was highly efficient in remediating ARD.
Collapse
|
3
|
Caizán-Juanarena L, ter Heijne A, Weijma J, Yntema D, Suárez-Zuluaga DA, Buisman CJ. Screening for electrical conductivity in anaerobic granular sludge from full-scale wastewater treatment reactors. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
4
|
Qian Z, Tianwei H, Mackey HR, van Loosdrecht MCM, Guanghao C. Recent advances in dissimilatory sulfate reduction: From metabolic study to application. WATER RESEARCH 2019; 150:162-181. [PMID: 30508713 DOI: 10.1016/j.watres.2018.11.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/25/2018] [Accepted: 11/08/2018] [Indexed: 05/24/2023]
Abstract
Sulfate-reducing bacteria (SRB) are a group of diverse anaerobic microorganisms omnipresent in natural habitats and engineered environments that use sulfur compounds as the electron acceptor for energy metabolism. Dissimilatory sulfate reduction (DSR)-based techniques mediated by SRB have been utilized in many sulfate-containing wastewater treatment systems worldwide, particularly for acid mine drainage, groundwater, sewage and industrial wastewater remediation. However, DSR processes are often operated suboptimally and disturbances are common in practical application. To improve the efficiency and robustness of SRB-based processes, it is necessary to study SRB metabolism and operational conditions. In this review, the mechanisms of DSR processes are reviewed and discussed focusing on intracellular and extracellular electron transfer with different electron donors (hydrogen, organics, methane and electrodes). Based on the understanding of the metabolism of SRB, responses of SRB to environmental stress (pH-, temperature-, and salinity-related stress) are summarized at the species and community levels. Application in these stressed conditions is discussed and future research is proposed. The feasibility of recovering energy and resources such as biohydrogen, hydrocarbons, polyhydroxyalkanoates, magnetite and metal sulfides through the use of SRB were investigated but some long-standing questions remain unanswered. Linking the existing scientific understanding and observations to practical application is the challenge as always for promotion of SRB-based techniques.
Collapse
Affiliation(s)
- Zeng Qian
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hao Tianwei
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China; Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Hamish Robert Mackey
- Division of Sustainable Development, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | | | - Chen Guanghao
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China; Water Technology Center, The Hong Kong University of Science and Technology, Hong Kong, China; Hong Kong Branch of Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, The Hong Kong University of Science and Technology, Hong Kong, China; Wastewater Treatment Laboratory, FYT Graduate School, The Hong Kong University of Science and Technology, Nansha, Guangzhou, China.
| |
Collapse
|
5
|
Wang H, Vuorela M, Keränen AL, Lehtinen TM, Lensu A, Lehtomäki A, Rintala J. Development of microbial populations in the anaerobic hydrolysis of grass silage for methane production. FEMS Microbiol Ecol 2010; 72:496-506. [DOI: 10.1111/j.1574-6941.2010.00850.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
6
|
Liu FH, Wang SB, Zhang JS, Zhang J, Yan X, Zhou HK, Zhao GP, Zhou ZH. The structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis. J Appl Microbiol 2009; 106:952-66. [PMID: 19187154 DOI: 10.1111/j.1365-2672.2008.04064.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To identify the bacterial and archaeal composition in a mesophilic biogas digester treating pig manure and to compare the consistency of two 16S rDNA-based methods to investigate the microbial structure. METHODS AND RESULTS Sixty-nine bacterial operational taxonomic units (OTU) and 25 archaeal OTU were identified by sequencing two 16S rDNA clone libraries. Most bacterial OTU were identified as phyla of Firmicutes (47.2% of total clones), Bacteroides (35.4%) and Spirochaetes (13.2%). Methanoculleus bourgensis (29.0%), Methanosarcina barkeri (27.4%) and Methanospirillum hungatei (10.8%) were the dominant methanogens. Only 9% of bacterial and 20% of archaeal OTU matched cultured isolates at a similarity index of >or=97%. About 78% of the dominant bacterial (with abundance >3%) and 83% of archaeal OTU were recovered from the denaturing gradient gel electrophoresis (DGGE) bands of V3 regions in 16S rDNAs. CONCLUSIONS In the digester, most bacterial and archaeal species were uncultured; bacteria belonging to Firmicutes, Bacteroides and Spirochaetes seem to take charge of cellulolysis, proteolysis, acidogenesis, sulfur-reducing and homoacetogenesis; the most methanogens were typical hydrogenotrophic or hydrogenotrophic/aceticlastic; DGGE profiles reflected the dominant microbiota. SIGNIFICANCE AND IMPACT OF THE STUDY This study gave a first insight of the overall microbial structure in a rural biogas digester and also indicated DGGE was useful in displaying its dominant microbiota.
Collapse
Affiliation(s)
- F H Liu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | | | | | | | | | | | | |
Collapse
|
7
|
Celis LB, Villa-Gómez D, Alpuche-Solís AG, Ortega-Morales BO, Razo-Flores E. Characterization of sulfate-reducing bacteria dominated surface communities during start-up of a down-flow fluidized bed reactor. J Ind Microbiol Biotechnol 2008; 36:111-21. [DOI: 10.1007/s10295-008-0478-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 09/17/2008] [Indexed: 11/28/2022]
|