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Seguel Suazo K, Dobbeleers T, Dries J. Bacterial community and filamentous population of industrial wastewater treatment plants in Belgium. Appl Microbiol Biotechnol 2024; 108:43. [PMID: 38180550 DOI: 10.1007/s00253-023-12822-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 10/27/2023] [Accepted: 11/23/2023] [Indexed: 01/06/2024]
Abstract
The discharge of industrial water requires the removal of its pollutants, where biological wastewater treatment plants (WWTPs) are the most used systems. Biological WWTPs make use of activated sludge (AS), where bacteria are responsible for the removal of pollutants. However, our knowledge of the microbial communities of industrial plants is limited. Understanding the microbial population is essential to provide solutions to industrial problems such as bulking. The aim of this study was to identify at a high taxonomic resolution the bacterial population of 29 industrial WWTPs using 16S rRNA amplicon sequencing. Our results revealed that the main functional groups were dominated by Thauera and Zoogloea within denitrifiers, Dechloromonas in phosphate-accumulating organisms, and Defluviicoccus in glycogen-accumulating organisms. The activated sludge characterization indicated that 59% of the industrial plants suffered from bulking sludge, with DSVI values of up to 448 mL g-1. From the bulking cases, 72% corresponded to filamentous bulking with Thiothrix as the most abundant filament; meanwhile, the other 28% corresponded to viscous bulking sludge in which Zoogloea was the most abundant genus. Furthermore, the bacterial population did not share a core of taxa across all industrial plants. However, 20 genera were present in at least 50% of the plants comprising the general core, including Thauera, Ca. Competibacter, and several undescribed microorganisms. Moreover, statistical analysis revealed that wastewater salinity strongly affected the microbial richness of the industrial plants. The bacterial population across industrial plants differed considerably from each other, resulting in unique microbial communities that are attributed to the specificity of their wastewaters. KEY POINTS: • The general core taxa of industrial plants were mostly made up of undescribed bacterial genera. • Filamentous bacteria constituted on average 4.1% read abundance of the industrial WWTPs. • Viscous bulking remains a significant type of bulking within industrial WWTPs.
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Affiliation(s)
- Karina Seguel Suazo
- Biochemical Wastewater Valorization and Engineering (BioWAVE), Faculty of Applied Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | - Thomas Dobbeleers
- Biochemical Wastewater Valorization and Engineering (BioWAVE), Faculty of Applied Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | - Jan Dries
- Biochemical Wastewater Valorization and Engineering (BioWAVE), Faculty of Applied Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium.
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Zhang R, He J, Wang M, Duan S, Zhang J. Nitrate and nitrite utilization during denitrifying phosphorus removal: Electron acceptor preference and feasible process combinations. BIORESOURCE TECHNOLOGY 2024; 406:131081. [PMID: 38977037 DOI: 10.1016/j.biortech.2024.131081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/30/2024] [Accepted: 07/04/2024] [Indexed: 07/10/2024]
Abstract
Denitrifying phosphorus removal (DPR), which is dominated by denitrifying polyphosphate-accumulating organisms (DPAOs), is a promising process for nitrogen and phosphorus removal. Denitrifying glycogen-accumulating organisms (DGAOs) and DPAOs typically coexist in the DPR sludge, complicating the study of DPAOs' denitrification capacity. In this study, two reactors were fed with nitrate and nitrite during the anoxic phase to cultivate nitrate-DPR and nitrite-DPR sludge. Both reactors yielded high and low DGAO abundance sludges, enabling the evaluation of the denitrification capacity of DPAOs. For the nitrate-DPR sludge, the nitrite reduction rate was 1.63 times higher than the nitrate reduction rate when DPAOs were the primary denitrifiers. For the nitrite-DPR sludge, the reduction rate of nitrite was more than three times that of nitrate, irrespective of DGAO abundance. These findings indicated that DPAOs preferred nitrite to nitrate and were well suited to reduce nitrite rather than reduce nitrate to supply nitrite.
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Affiliation(s)
- Ruimiao Zhang
- School of Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, PR China; State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, PR China.
| | - Junguo He
- School of Civil Engineering, Guangzhou University, Guangzhou 510006, PR China
| | - Mengfei Wang
- School of Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, PR China; State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, PR China
| | - Shengye Duan
- School of Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, PR China; State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, PR China
| | - Jie Zhang
- School of Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, PR China; State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, PR China
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Ai S, Chang C, Zhang H, Wang Z, Kang H, Bian D. Performance of micro-pressure double-cycle coupled membrane integrated bioreactor for the treatment of urban sewage. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:15525-15537. [PMID: 38296926 DOI: 10.1007/s11356-024-32164-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/19/2024] [Indexed: 02/02/2024]
Abstract
Based on the theory of nitrogen and phosphorus removal and technical requirements, a micro-pressure double-cycle bioreactor coupled with membrane components was used to treat municipal wastewater. The method realized the simultaneous removal of organic matter, nitrogen, and phosphorus in the same reactor and had the characteristics of membrane bioreactor process. Results showed that the average removal efficiency of COD, NH+4-N, TN, and TP were 93.74%, 95.1%, 71.85%, and 81.03%, respectively. During operation, Proteobacteria and Bacteroidetes were the main dominant bacteria, and they had complete nitrogen and phosphorus metabolic pathways. Owing to the low protein content in the mixture, the design of film placement in the micro-precipitation zone was conducive to alleviating the membrane pollution caused by the accumulation of protein, thereby improving the effluent quality and extending the service life of the membrane components.
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Affiliation(s)
- Shengshu Ai
- Key Laboratory of Urban Sewage Treatment of Jilin Province, Changchun Institute of Technology, Changchun, 130012, China
| | - Chunlin Chang
- Key Laboratory of Urban Sewage Treatment of Jilin Province, Changchun Institute of Technology, Changchun, 130012, China
| | - Haigang Zhang
- Key Laboratory of Urban Sewage Treatment of Jilin Province, Changchun Institute of Technology, Changchun, 130012, China
| | - Ziheng Wang
- Berlin Changchun High-Tech Wastewater Treatment Co. Ltd., 130000, Changchun, China
| | - Hua Kang
- Key Laboratory of Urban Sewage Treatment of Jilin Province, Changchun Institute of Technology, Changchun, 130012, China
| | - Dejun Bian
- Key Laboratory of Urban Sewage Treatment of Jilin Province, Changchun Institute of Technology, Changchun, 130012, China.
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China.
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Ravin NV, Muntyan MS, Smolyakov DD, Rudenko TS, Beletsky AV, Mardanov AV, Grabovich MY. Metagenomics Revealed a New Genus ' Candidatus Thiocaldithrix dubininis' gen. nov., sp. nov. and a New Species ' Candidatus Thiothrix putei' sp. nov. in the Family Thiotrichaceae, Some Members of Which Have Traits of Both Na +- and H +-Motive Energetics. Int J Mol Sci 2023; 24:14199. [PMID: 37762502 PMCID: PMC10532065 DOI: 10.3390/ijms241814199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG GKL-01 represented a new genus within the Thiotrichaceae family. The GC content of the GKL-01 DNA (44%) differed significantly from that of other known members of the genus Thiothrix (50.1-55.6%). We proposed to assign GKL-01 to a new species and genus 'Candidatus Thiocaldithrix dubininis' gen. nov., sp. nov. GKL-01. The phylogenetic analysis and estimated distances between MAG GKL-02 and the genomes of the previously described species of the genus Thiothrix allowed assigning GKL-02 to a new species with the proposed name 'Candidatus Thiothrix putei' sp. nov. GKL-02 within the genus Thiothrix. Genome data first revealed the presence of both Na+-ATPases and H+-ATPases in several Thiothrix species. According to genomic analysis, bacteria GKL-01 and GKL-02 are metabolically versatile facultative aerobes capable of growing either chemolithoautotrophically or chemolithoheterotrophically in the presence of hydrogen sulfide and/or thiosulfate or chemoorganoheterotrophically.
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Affiliation(s)
- Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect, 33-2, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Maria S. Muntyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
| | - Dmitry D. Smolyakov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (T.S.R.)
| | - Tatyana S. Rudenko
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (T.S.R.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect, 33-2, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect, 33-2, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Margarita Yu. Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (T.S.R.)
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History of the Study of the Genus Thiothrix: From the First Enrichment Cultures to Pangenomic Analysis. Int J Mol Sci 2022; 23:ijms23179531. [PMID: 36076928 PMCID: PMC9455678 DOI: 10.3390/ijms23179531] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Representatives of the genus Thiothrix are filamentous, sulfur-oxidizing bacteria found in flowing waters with counter-oriented sulfide and oxygen gradients. They were first described at the end of the 19th century, but the first pure cultures of this species only became available 100 years later. An increase in the number of described Thiothrix species at the beginning of the 21st century shows that the classical phylogenetic marker, 16S rRNA gene, is not informative for species differentiation, which is possible based on genome analysis. Pangenome analysis of the genus Thiothrix showed that the core genome includes genes for dissimilatory sulfur metabolism and central metabolic pathways, namely the Krebs cycle, Embden–Meyerhof–Parnas pathway, glyoxylate cycle, Calvin–Benson–Bassham cycle, and genes for phosphorus metabolism and amination. The shell part of the pangenome includes genes for dissimilatory nitrogen metabolism and nitrogen fixation, for respiration with thiosulfate. The dispensable genome comprises genes predicted to encode mainly hypothetical proteins, transporters, transcription regulators, methyltransferases, transposases, and toxin–antitoxin systems.
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Ravin NV, Rossetti S, Beletsky AV, Kadnikov VV, Rudenko TS, Smolyakov DD, Moskvitina MI, Gureeva MV, Mardanov AV, Grabovich MY. Two New Species of Filamentous Sulfur Bacteria of the Genus Thiothrix, Thiothrix winogradskyi sp. nov. and ‘Candidatus Thiothrix sulfatifontis’ sp. nov. Microorganisms 2022; 10:microorganisms10071300. [PMID: 35889019 PMCID: PMC9319827 DOI: 10.3390/microorganisms10071300] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 01/27/2023] Open
Abstract
The metagenome of foulings from sulfidic spring “Serovodorodny” (Tatarstan, Russia), where members of the genus Thiothrix was observed, was sequenced. Representatives of the phyla Gammaproteobacteria, Cyanobacteria and Campilobacteriota dominated in the microbial community. The complete genome of Thiothrix sp. KT was assembled from the metagenome. It displayed 93.93–99.72% 16S rRNA gene sequence identity to other Thiothrix species. The average nucleotide identity (ANI) и digital DNA-DNA hybridization (dDDH) showed that the genome designated KT represents a new species within the genus Thiothrix, ‘Candidatus Thiothrix sulfatifontis’ sp. nov. KT. The taxonomic status has been determined of the strain Thiothrix sp. CT3, isolated about 30 years ago and not assigned to any of Thiothrix species due to high 16S rRNA gene sequence identity with related species (i.e., 98.8–99.4%). The complete genome sequence of strain CT3 was determined. The ANI between CT3 and other Thiothrix species was below 82%, and the dDDH values were less than 40%, indicating that strain CT3 belongs to a novel species, Thiothrix winogradskyi sp. nov. A genome analysis showed that both strains are chemo-organoheterotrophs, chemolithotrophs (in the presence of hydrogen sulfide and thiosulfate) and chemoautotrophs. For the first time, representatives of Thiothrix showed anaerobic growth in the presence of thiosulfate.
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Affiliation(s)
- Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Simona Rossetti
- Water Research Institute, IRSA-CNR, Monterotondo, 00185 Rome, Italy;
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Tatyana S. Rudenko
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (T.S.R.); (D.D.S.); (M.I.M.); (M.V.G.)
| | - Dmitry D. Smolyakov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (T.S.R.); (D.D.S.); (M.I.M.); (M.V.G.)
| | - Marina I. Moskvitina
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (T.S.R.); (D.D.S.); (M.I.M.); (M.V.G.)
| | - Maria V. Gureeva
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (T.S.R.); (D.D.S.); (M.I.M.); (M.V.G.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Margarita Yu. Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (T.S.R.); (D.D.S.); (M.I.M.); (M.V.G.)
- Correspondence: ; Tel.: +7-473-2208877
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Begmatov S, Dorofeev AG, Kadnikov VV, Beletsky AV, Pimenov NV, Ravin NV, Mardanov AV. The structure of microbial communities of activated sludge of large-scale wastewater treatment plants in the city of Moscow. Sci Rep 2022; 12:3458. [PMID: 35236881 PMCID: PMC8891259 DOI: 10.1038/s41598-022-07132-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/03/2022] [Indexed: 12/21/2022] Open
Abstract
Microbial communities in wastewater treatment plants (WWTPs) play a key role in water purification. Microbial communities of activated sludge (AS) vary extensively based on plant operating technology, influent characteristics and WWTP capacity. In this study we performed 16S rRNA gene profiling of AS at nine large-scale WWTPs responsible for the treatment of municipal sewage from the city of Moscow, Russia. Two plants employed conventional aerobic process, one plant—nitrification/denitrification technology, and six plants were operated with the University of Cape Town (UCT) anaerobic/anoxic/oxic process. Microbial communities were impacted by the technology and dominated by the Proteobacteria, Bacteroidota and Actinobacteriota. WWTPs employing the UCT process enabled efficient removal of not only organic matter, but also nitrogen and phosphorus, consistently with the high content of ammonia-oxidizing Nitrosomonas sp. and phosphate-accumulating bacteria. The latter group was represented by Candidatus Accumulibacter, Tetrasphaera sp. and denitrifiers. Co-occurrence network analysis provided information on key hub microorganisms in AS, which may be targeted for manipulating the AS stability and performance. Comparison of AS communities from WWTPs in Moscow and worldwide revealed that Moscow samples clustered together indicating that influent characteristics, related to social, cultural and environmental factors, could be more important than a plant operating technology.
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Affiliation(s)
- Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071
| | - Alexander G Dorofeev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33‑2, Moscow, Russia, 119071
| | - Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071
| | - Nikolai V Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33‑2, Moscow, Russia, 119071
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071.
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, Moscow, Russia, 119071.
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Oren A, Garrity GM. CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35100104 DOI: 10.1099/ijsem.0.005186] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Nittami T, Batinovic S. Recent advances in understanding the ecology of the filamentous bacteria responsible for activated sludge bulking. Lett Appl Microbiol 2021; 75:759-775. [PMID: 34919734 DOI: 10.1111/lam.13634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/26/2021] [Accepted: 12/13/2021] [Indexed: 01/30/2023]
Abstract
Activated sludge bulking caused by filamentous bacteria is still a problem in wastewater treatment plants around the world. Bulking is a microbiological problem, and so its solution on species-specific basis is likely to be reached only after their ecology, physiology and metabolism is better understood. Culture-independent molecular methods have provided much useful information about this group of organisms, and in this review, the methods employed and the information they provide are critically assessed. Their application to understanding bulking caused by the most frequently seen filament in Japan, 'Ca. Kouleothrix', is used here as an example of how these techniques might be used to develop control strategies. Whole genome sequences are now available for some of filamentous bacteria responsible for bulking, and so it is possible to understand why these filaments might thrive in activated sludge plants, and provide clues as to how eventually they might be controlled specifically.
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Affiliation(s)
- T Nittami
- Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University, Yokohama, Japan
| | - S Batinovic
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Bundoora, Vic., Australia
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Ravin NV, Rudenko TS, Smolyakov DD, Beletsky AV, Rakitin AL, Markov ND, Fomenkov A, Sun L, Roberts RJ, Novikov AA, Karnachuk OV, Grabovich MY. Comparative Genome Analysis of the Genus Thiothrix Involving Three Novel Species, Thiothrix subterranea sp. nov. Ku-5, Thiothrix litoralis sp. nov. AS and " Candidatus Thiothrix anitrata" sp. nov. A52, Revealed the Conservation of the Pathways of Dissimilatory Sulfur Metabolism and Variations in the Genetic Inventory for Nitrogen Metabolism and Autotrophic Carbon Fixation. Front Microbiol 2021; 12:760289. [PMID: 34745068 PMCID: PMC8570282 DOI: 10.3389/fmicb.2021.760289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/28/2021] [Indexed: 11/24/2022] Open
Abstract
Two strains of filamentous, colorless sulfur bacteria were isolated from bacterial fouling in the outflow of hydrogen sulfide-containing waters from a coal mine (Thiothrix sp. Ku-5) and on the seashore of the White Sea (Thiothrix sp. AS). Metagenome-assembled genome (MAG) A52 was obtained from a sulfidic spring in the Volgograd region, Russia. Phylogenetic analysis based on the 16S rRNA gene sequences showed that all genomes represented the genus Thiothrix. Based on their average nucleotide identity and digital DNA-DNA hybridization data these new isolates and the MAG represent three species within the genus Thiothrix with the proposed names Thiothrix subterranea sp. nov. Ku-5T, Thiothrix litoralis sp. nov. AST, and “Candidatus Thiothrix anitrata” sp. nov. A52. The complete genome sequences of Thiothrix fructosivorans QT and Thiothrix unzii A1T were determined. Complete genomes of seven Thiothrix isolates, as well as two MAGs, were used for pangenome analysis. The Thiothrix core genome consisted of 1,355 genes, including ones for the glycolysis, the tricarboxylic acid cycle, the aerobic respiratory chain, and the Calvin cycle of carbon fixation. Genes for dissimilatory oxidation of reduced sulfur compounds, namely the branched SOX system (SoxAXBYZ), direct (soeABC) and indirect (aprAB, sat) pathways of sulfite oxidation, sulfur oxidation complex Dsr (dsrABEFHCEMKLJONR), sulfide oxidation systems SQR (sqrA, sqrF), and FCSD (fccAB) were found in the core genome. Genomes differ in the set of genes for dissimilatory reduction of nitrogen compounds, nitrogen fixation, and the presence of various types of RuBisCO.
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Affiliation(s)
- Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Tatyana S Rudenko
- Department of Biochemistry and Cell Physiology, Voronezh State University, Voronezh, Russia
| | - Dmitry D Smolyakov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Voronezh, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey L Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nikita D Markov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Voronezh, Russia
| | | | - Luo Sun
- New England Biolabs, Ipswich, MA, United States
| | | | - Andrey A Novikov
- Department of Physical and Colloid Chemistry, Gubkin Russian State University of Oil and Gas, Moscow, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Margarita Y Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Voronezh, Russia
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