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Insights into microbial diversity in wastewater treatment systems: How far have we come? Biotechnol Adv 2016; 34:790-802. [DOI: 10.1016/j.biotechadv.2016.04.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/15/2016] [Accepted: 04/07/2016] [Indexed: 11/16/2022]
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Kim BC, Seung Jeon B, Kim S, Kim H, Um Y, Sang BI. Caproiciproducens galactitolivorans gen. nov., sp. nov., a bacterium capable of producing caproic acid from galactitol, isolated from a wastewater treatment plant. Int J Syst Evol Microbiol 2015; 65:4902-4908. [PMID: 26474980 DOI: 10.1099/ijsem.0.000665] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly anaerobic, Gram-stain-positive, non-spore-forming, rod-shaped bacterial strain, designated BS-1T, was isolated from an anaerobic digestion reactor during a study of bacteria utilizing galactitol as the carbon source. Its cells were 0.3-0.5 μm × 2-4 μm, and they grew at 35-45 °C and at pH 6.0-8.0. Strain BS-1T produced H2, CO2, ethanol, acetic acid, butyric acid and caproic acid as metabolic end products of anaerobic fermentation. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that strain BS-1T represented a novel bacterial genus within the family Ruminococcaceae, Clostridium Cluster IV. The type strains that were most closely related to strain BS-1T were Clostridium sporosphaeroides KCTC 5598T (94.5 %), Clostridium leptum KCTC 5155T (94.3 %), Ruminococcus bromii ATCC 27255T (92.1 %) and Ethanoligenens harbinense YUAN-3T (91.9 %). Strain BS-1T had 17.6 % and 20.9 % DNA-DNA relatedness values with C. sporosphaeroides DSM 1294T and C. leptum DSM 753T, respectively. The major components of the cellular fatty acids were C16 : 0 dimethyl aldehyde (DMA) (22.1 %), C16 : 0 aldehyde (14.1 %) and summed feature 11 (iso-C17 : 0 3-OH and/or C18 : 2 DMA; 10.0 %). The genomic DNA G+C content was 50.0 mol%. Phenotypic and phylogenetic characteristics allowed strain BS-1T to be clearly distinguished from other taxa of the genus Clostridium Cluster IV. On the basis of these data, the isolate is considered to represent a novel genus and novel species within Clostridium Cluster IV, for which the name Caproiciproducens galactitolivorans gen. nov., sp. nov. is proposed. The type species is BS-1T ( = JCM 30532T and KCCM 43048T).
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Affiliation(s)
- Byung-Chun Kim
- The Research Institute of Industrial Science, Hanyang University, 17 Hangdang-dong, Seongdong-gu, Seoul 133-791, Republic of Korea
| | - Byoung Seung Jeon
- Department of Chemical Engineering, Hanyang University, 17 Hangdang-dong, Seongdong-gu, Seoul 133-791, Republic of Korea
| | - Seil Kim
- Division of Metrology for Quality of Life, Center for Bioanalysis, Korea Research Institute of Standards and Science, 267 Gajeong-Ro, Yuseong-Gu, Daejeon 305-340, Republic of Korea
| | - Hyunook Kim
- Department of Environmental Engineering, University of Seoul, 90 Jeonnong-dong, Dongdaemun-Ku, Seoul 130-743, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute and Science and Technology, 39-1 Hawolgok-dong, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Byoung-In Sang
- Department of Chemical Engineering, Hanyang University, 17 Hangdang-dong, Seongdong-gu, Seoul 133-791, Republic of Korea
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Ieropoulos I, Gálvez A, Greenman J. Effects of sulphate addition and sulphide inhibition on microbial fuel cells. Enzyme Microb Technol 2013. [PMID: 23199736 DOI: 10.1016/j.enzmictec.2012.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The effects of adding sulphate in: (i) standard activated sludge microbial fuel cells (MFCs) and (ii) larger-scale leachate-treating columns - both as individual units and as a system connected in cascade - are reported. S-replete power output was ∼2-fold higher than that of the S-deplete MFC. Furthermore, the effects of evolved sulphide (S(2-)) inhibition were investigated. The overall decrease in power output from the sulphide inhibitor (Na(2)MoO(4)) additions was 83% for the S-replete and 90% for the S-deplete. The second phase with the leachate treating units shows an improvement of 32-86% (depended on leachate strength) in current output as a result of adding sulphate. When leachate column MFCs were connected fluidically in series, the amount of Na(2)SO(4) made available downstream was decreasing (increase in power was 99%, 40% and 12% for columns in cascade). Results demonstrated the beneficial effects of added sulphur sources to both activated sludge and leachate-treating MFCs.
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Affiliation(s)
- I Ieropoulos
- Bristol Robotics Laboratory, Environment and Technology Faculty, University of the West of England, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK.
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Pearce DA, Gast CJ, Lawley B, Ellis-Evans JC. Bacterioplankton community diversity in a maritime Antarctic lake, determined by culture-dependent and culture-independent techniques. FEMS Microbiol Ecol 2012; 45:59-70. [PMID: 19719607 DOI: 10.1016/s0168-6496(03)00110-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Abstract The biodiversity of the pelagic bacterioplankton community of a maritime Antarctic freshwater lake was examined by cultivation-dependent and cultivation-independent techniques to determine predominant bacterioplankton populations present. The culture-dependent techniques used were direct culture and observation, polymerase chain reaction amplification of 16S rRNA gene fragments, restriction fragment length polymorphism (RFLP) analysis followed by selective sequencing and fatty acid methyl ester analysis. The culture-independent techniques used were 16S ribosomal DNA gene cloning, RFLP analysis and sequencing, in situ hybridisation with group-specific, fluorescently labelled oligonucleotide probes and cloning and sequencing of dominant denaturing gradient gel electrophoresis products. Significant differences occurred between the results obtained with each method. However, sufficient overlap existed between the different methods to identify potentially significant groups. At least six different bacterial divisions including 24 genera were identified using culture-dependent techniques, and eight different bacterial divisions, including 23 genera, were identified using culture-independent techniques. Only five genera, Corynebacterium, Cytophaga, Flavobacterium, Janthinobacterium and Pseudomonas, could be identified using both sets of techniques, which represented four different bacterial divisions. Significantly for Antarctic freshwater lakes, pigment production is found within members of each of these genera. This work illustrates the importance of a comprehensive polyphasic approach in the analysis of lake bacterioplankton, and supports the ecological relevance of results obtained in earlier entirely culture-based studies.
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Affiliation(s)
- D A Pearce
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
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Vázquez-Rodríguez GA, Beltrán-Hernández RI, Coronel-Olivares C, Rols JL. Standardization of activated sludge for biodegradation tests. Anal Bioanal Chem 2011; 401:1127-37. [DOI: 10.1007/s00216-011-5212-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 06/23/2011] [Accepted: 06/24/2011] [Indexed: 11/28/2022]
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Jin D, Wang P, Bai Z, Wang X, Peng H, Qi R, Yu Z, Zhuang G. Analysis of bacterial community in bulking sludge using culture-dependent and -independent approaches. J Environ Sci (China) 2011; 23:1880-1887. [PMID: 22432314 DOI: 10.1016/s1001-0742(10)60621-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The bacterial community of a bulking sludge from a municipal wastewater treatment plant with anoxic-anaerobic-oxic process was investigated by combination of cultivation and 16S rRNA gene clone library analysis for understanding the causes of bulking. A total of 28 species were obtained from 63 isolates collected from six culture media. The most cultivable species belonged to gamma-Proteobacteria including Klebsiella sp., Pseudomonas sp., Aeromonas sp. and Acinetobacter sp. Further analysis of these strains by repetitive sequence based on polymerase chain reaction (rep-PCR) technology showed that rep-PCR yielded discriminatory banding patterns within the same genus using REP and BOX primer sets. While the culture-independent assessment revealed that beta-Proteobacteria was the dominant group in the bulking sample. Sequence analysis revealed that the highest proportion (14.7%) of operational taxonomic units was 98% similar to Candidatus Accumulibacter phosphatis, which is used to remove phosphorous from wastewater. Our results indicated that combining different approaches can produce complementary information, thus generate a more accurate view of microbial community in bulking sludge.
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Affiliation(s)
- Decai Jin
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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Bafana A, Chakrabarti T, Krishnamurthi K, Devi SS. Biodiversity and dye decolourization ability of an acclimatized textile sludge. BIORESOURCE TECHNOLOGY 2008; 99:5094-5098. [PMID: 17983742 DOI: 10.1016/j.biortech.2007.09.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 09/24/2007] [Accepted: 09/26/2007] [Indexed: 05/25/2023]
Abstract
In the present study, sludge sample from biological treatment plant of a textile industry was acclimatized for decolourization of azo dye Direct Black 38 (DB38). A continuous culture experiment showed that the acclimatized sludge could decolourize 76% of 100mg/l DB38. Bacterial community in the sludge was analyzed using culture-independent molecular approach to get the complete picture of its diversity. RFLP analysis of its 16S rRNA gene library divided the clones into 14 distinct groups. Phylogenetic analysis of these groups showed that they belonged to five different bacterial lineages: beta- and gamma-Proteobacteria (3 and 4 respectively), Bacteroidetes (2), Firmicutes (4) and Actinobacteria (1). The largest number of clones was found to cluster in the gamma-Proteobacteria (54%), followed by Firmicutes (19%), beta-Proteobacteria (14%), Bacteroidetes (10%) and Actinobacteria (3%).
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Affiliation(s)
- Amit Bafana
- Environmental Biotechnology Division, National Environmental Engineering Research Institute, Nagpur 440 020, India
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Viñas M, Sabaté J, Guasp C, Lalucat J, Solanas AM. Culture-dependent and -independent approaches establish the complexity of a PAH-degrading microbial consortium. Can J Microbiol 2006; 51:897-909. [PMID: 16333329 DOI: 10.1139/w05-090] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A microbial consortium (AM) obtained by sequential enrichment in liquid culture with a polycyclic aromatic hydrocarbon (PAH) mixture of three- and four-ringed PAHs as a sole source of carbon and energy was examined using a triple-approach method based on various cultivation strategies, denaturing gradient gel electrophoresis (DGGE), and the screening of 16S and 18S rRNA gene clone libraries. Eleven different sequences by culture-dependent techniques and seven by both DGGE and clone libraries were obtained. The comparison of three variable regions (V3-V5) of the 16S rRNA gene between the sequences obtained yielded 19 different microbial components. Proteobacteria were the dominant group, representing 83% of the total, while the Cytophaga-Flexibacter-Bacteroides group (CFB) was 11% and the Ascomycota fungi 6%. Beta-proteobacteria were predominant in the DGGE and clone library methods, whereas they were a minority in culturable strains. The highest diversity and number of noncoincident sequences were achieved by the cultivation method that showed members of the alpha-, beta-, and gamma-Proteobacteria; CFB bacterial group; and Ascomycota fungi. Only six of the 11 strains isolated showed PAH-degrading capability. The bacterial strain (AMS7) and the fungal strain (AMF1), which were similar to Sphingomonas sp. and Fusarium sp., respectively, achieved the greatest PAH depletion. The results indicate that polyphasic assessment is necessary for a proper understanding of the composition of a microbial consortium.
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MESH Headings
- Ascomycota/classification
- Ascomycota/genetics
- Ascomycota/isolation & purification
- Ascomycota/metabolism
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/metabolism
- Bacteroides/classification
- Bacteroides/genetics
- Bacteroides/isolation & purification
- Bacteroides/metabolism
- Biodegradation, Environmental
- Biodiversity
- Cytophaga/classification
- Cytophaga/genetics
- Cytophaga/isolation & purification
- Cytophaga/metabolism
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Electrophoresis, Polyacrylamide Gel
- Flexibacter/classification
- Flexibacter/genetics
- Flexibacter/isolation & purification
- Flexibacter/metabolism
- Fungi/classification
- Fungi/genetics
- Fungi/isolation & purification
- Fungi/metabolism
- Molecular Sequence Data
- Phylogeny
- Polycyclic Aromatic Hydrocarbons/metabolism
- Proteobacteria/classification
- Proteobacteria/genetics
- Proteobacteria/isolation & purification
- Proteobacteria/metabolism
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/genetics
- Sequence Homology, Nucleic Acid
- Soil Microbiology
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Affiliation(s)
- Marc Viñas
- Department of Microbiology, University of Barcelona, Diagonal 645, E-08028 Barcelona, Spain
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Watanabe K, Baker PW. Environmentally relevant microorganisms. J Biosci Bioeng 2005; 89:1-11. [PMID: 16232691 DOI: 10.1016/s1389-1723(00)88043-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/1999] [Accepted: 12/03/1999] [Indexed: 11/19/2022]
Abstract
The development of molecular microbial ecology in the 1990s has allowed scientists to realize that microbial populations in the natural environment are much more diverse than microorganisms so far isolated in the laboratory. This finding has exerted a significant impact on environmental biotechnology, since knowledge in this field has been largely dependent on studies with pollutant-degrading bacteria isolated by conventional culture methods. Researchers have thus started to use molecular ecological methods to analyze microbial populations relevant to pollutant degradation in the environment (called environmentally relevant microorganisms, ERMs), although further effort is needed to gain practical benefits from these studies. This review highlights the utility and limitations of molecular ecological methods for understanding and advancing environmental biotechnology processes. The importance of the combined use of molecular ecological and physiological methods for identifying ERMs is stressed.
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Affiliation(s)
- K Watanabe
- Marine Biotechnology Institute, Kamaishi Laboratories, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
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Orsini M, Romano-Spica V. A microwave-based method for nucleic acid isolation from environmental samples. Lett Appl Microbiol 2001; 33:17-20. [PMID: 11442808 DOI: 10.1046/j.1472-765x.2001.00938.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS A simple and rapid method was described for DNA isolation directly from activated sludge or other environmental sources, including soil and sediments. METHODS AND RESULTS The present method is based on microwave thermal shock and provides DNA suitable for further analysis. It is also effective for RNA extraction. CONCLUSION The protocol is effective, easy, fast and does not require the use of expensive equipment or reagents. SIGNIFICANCE AND IMPACT OF THE STUDY The described method can be applied to difficult substrates in environmental microbiology studies.
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Affiliation(s)
- M Orsini
- Institute of Hygiene, Catholic University Medical School, Rome, Italy
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Characterization of a 4-methylbenzoate-degrading methanogenic consortium as determined by small-subunit rDNA sequence analysis. J Biosci Bioeng 2001. [DOI: 10.1016/s1389-1723(01)80272-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Sakano Y, Kerkhof L. Assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools. Appl Environ Microbiol 1998; 64:4877-82. [PMID: 9835577 PMCID: PMC90937 DOI: 10.1128/aem.64.12.4877-4882.1998] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofiltration has been used for two decades to remove odors and various volatile organic and inorganic compounds in contaminated off-gas streams. Although biofiltration is widely practiced, there have been few studies of the bacteria responsible for the removal of air contaminants in biofilters. In this study, molecular techniques were used to identify bacteria in a laboratory-scale ammonia biofilter. Both 16S rRNA and ammonia monooxygenase (amoA) genes were used to characterize the heterotrophic and ammonia-oxidizing bacteria collected from the biofilter during a 102-day experiment. The overall diversity of the heterotrophic microbial population appeared to decrease by 38% at the end of the experiment. The community structure of the heterotrophic population also shifted from predominantly members of two subdivisions of the Proteobacteria (the beta and gamma subdivisions) to members of one subdivision (the gamma subdivision). An overall decrease in the diversity of ammonia monooxygenase genes was not observed. However, a shift from groups dominated by organisms containing Nitrosomonas-like and Nitrosospira-like amoA genes to groups dominated by organisms containing only Nitrosospira-like amoA genes was observed. In addition, a new amoA gene was discovered. This new gene is the first freshwater amoA gene that is closely affiliated with Nitrosococcus oceanus and the particulate methane monooxygenase gene from the methane oxidizers belonging to the gamma subdivision of the Proteobacteria.
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Affiliation(s)
- Y Sakano
- Department of Environmental Sciences and Institute of Marine and Coastal Sciences, Cook College, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903-0231, USA
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