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Chernitsyna SM, Elovskaya IS, Bukin SV, Bukin YS, Pogodaeva TV, Kwon DA, Zemskaya TI. Genomic and morphological characterization of a new Thiothrix species from a sulfide hot spring of the Zmeinaya bay (Northern Baikal, Russia). Antonie Van Leeuwenhoek 2024; 117:23. [PMID: 38217803 DOI: 10.1007/s10482-023-01918-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/08/2023] [Indexed: 01/15/2024]
Abstract
A survey for bacteria of the genus Thiothrix indicated that they inhabited the area where the water of the Zmeiny geothermal spring (northern basin of Lake Baikal, Russia) mixed with the lake water. In the coastal zone of the lake oxygen (8.25 g/L) and hydrogen sulfide (up to 1 mg/L) were simultaneously present at sites of massive growth of these particular Thiothrix bacteria. Based on the analysis of the morphological characteristics and sequence of individual genes (16S rRNA, rpoB and tilS), we could not attribute the Thiothrix from Lake Baikal to any of the known species of this genus. To determine metabolic capabilities and phylogenetic position of the Thiothrix sp. from Lake Baikal, we analyzed their whole genome. Like all members of this genus, the bacteria from Lake Baikal were capable of organo-heterotrophic, chemolithoheterotrophic, and chemolithoautotrophic growth and differed from its closest relatives in the spectrum of nitrogen and sulfur cycle genes as well as in the indices of average nucleotide identity (ANI < 75-94%), amino acid identity (AAI < 94%) and in silico DNA-DNA hybridization (dDDH < 17-57%), which were below the boundary of interspecies differences, allowing us to identify them as novel candidate species.
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Affiliation(s)
| | | | - S V Bukin
- Limnological Institute SB RAS, Irkutsk, Russia
| | - Yu S Bukin
- Limnological Institute SB RAS, Irkutsk, Russia
| | | | - D A Kwon
- Institute of Genome Analysis, Moscow, Russia
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Ravin NV, Smolyakov DD, Markov ND, Beletsky AV, Mardanov AV, Rudenko TS, Grabovich MY. tilS and rpoB: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus Thiothrix. Microorganisms 2023; 11:2521. [PMID: 37894178 PMCID: PMC10609254 DOI: 10.3390/microorganisms11102521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/01/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Currently, the phylogeny of the genus Thiothrix is based on comparative whole genome analysis because of the high homology of the 16S ribosomal RNA gene sequences within the genus. We analyzed the possibility of using various conservative genes as phylogenetic markers for the genus Thiothrix. We found that the levels of similarity of the nucleotide sequences of the tRNA(Ile)-lysidine synthase (tilS) and the β subunit of RNA polymerase (rpoB) genes are in good agreement with the average nucleotide identity (ANI) values between the genomes of various representatives of the genus Thiothrix. The genomes of Thiothrix strains MK1, WS, DNT52, DNT53, and H33 were sequenced. Taxonomic analysis using both whole genomes and the tilS gene consistently showed that MK1 and WS belong to Thiothrix lacustris, while DNT52, DNT53, and H33 belong to Thiothrix subterranea. The tilS gene fragments were subjected to high-throughput sequencing to profile the Thiothrix mat of a sulfidic spring, which revealed the presence of known species of Thiothrix and new species-level phylotypes. Thus, the use of tilS and rpoB as phylogenetic markers will allow for rapid analyses of pure cultures and natural communities for the purpose of phylogenetic identification of representatives of the genus Thiothrix.
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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.); (A.V.M.)
| | - Dmitry D. Smolyakov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (N.D.M.); (T.S.R.)
| | - Nikita D. Markov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (N.D.M.); (T.S.R.)
| | - 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.); (A.V.M.)
| | - 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.); (A.V.M.)
| | - Tatyana S. Rudenko
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (N.D.M.); (T.S.R.)
| | - Margarita Yu. Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (N.D.M.); (T.S.R.)
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Matsuura N, Masakke Y, Karthikeyan S, Kanazawa S, Honda R, Yamamoto-Ikemoto R, Konstantinidis KT. Metagenomic insights into the effect of sulfate on enhanced biological phosphorus removal. Appl Microbiol Biotechnol 2021; 105:2181-2193. [PMID: 33555362 DOI: 10.1007/s00253-021-11113-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/25/2020] [Accepted: 01/12/2021] [Indexed: 11/30/2022]
Abstract
Excess phosphorus in water supplies causes eutrophication, which degrades water quality. Hence, the efficient removal of phosphorus from wastewater represents a highly desirable process. Here, we evaluated the effect of sulfate concentration on enhanced biological phosphorus removal (EBPR), in which phosphorus is typically removed under anaerobic-oxic cycles, with sulfate reduction the predominant process in the anaerobic phase. Two sequencing batch EBPR reactors operated under high- (SBR-H) vs. low-sulfate (SBR-L) concentrations for 189 days and under three periods, i.e., start-up, sufficient acetate, and limited acetate. Under acetate-rich conditions, phosphorus removal efficiency was > 90% for both reactors; however, under acetate-limited conditions, only 34% and 91.3% of the phosphorus were removed for the SBR-L and the SBR-H, respectively. Metagenomic sequencing of the reactors showed that the relative abundance of the polyphosphate-accumulating and sulfur-reducing bacteria (SRB) was higher in the SBR-H, consistent with its higher phosphorus removal activity. Ten high-quality metagenome-assembled genomes, including one closely related to the genus Thiothrix disciformis (99.81% average amino acid identity), were recovered and predicted to simultaneously metabolize phosphorus and sulfur by the presence of phosphorus (ppk, ppx, pst, and pit) and sulfur (sul, sox, dsr, sqr, apr, cys, and sat) metabolism marker genes. The omics-based analysis provided a holistic view of the microbial ecosystem in the EBPR process and revealed that SRB and Thiothrix play key roles in the presence of high sulfate.Key points• We observed high phosphorus-removal efficiency in high-sulfate EBPR.• Metagenome-based analysis revealed sulfate-related metabolic mechanisms in EBPR.• SRB and PAOs showed interrelationships in the EBPR-sulfur systems.
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Affiliation(s)
- Norihisa Matsuura
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan.
| | - Yalkhin Masakke
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Smruthi Karthikeyan
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sui Kanazawa
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Ryoko Yamamoto-Ikemoto
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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Mardanov AV, Gruzdev EV, Smolyakov DD, Rudenko TS, Beletsky AV, Gureeva MV, Markov ND, Berestovskaya YY, Pimenov NV, Ravin NV, Grabovich MY. Genomic and Metabolic Insights into Two Novel Thiothrix Species from Enhanced Biological Phosphorus Removal Systems. Microorganisms 2020; 8:E2030. [PMID: 33353182 DOI: 10.3390/microorganisms8122030] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 12/15/2022] Open
Abstract
Two metagenome-assembled genomes (MAGs), obtained from laboratory-scale enhanced biological phosphorus removal bioreactors, were analyzed. The values of 16S rRNA gene sequence identity, average nucleotide identity, and average amino acid identity indicated that these genomes, designated as RT and SSD2, represented two novel species within the genus Thiothrix, 'Candidatus Thiothrix moscowensis' and 'Candidatus Thiothrix singaporensis'. A complete set of genes for the tricarboxylic acid cycle and electron transport chain indicates a respiratory type of metabolism. A notable feature of RT and SSD2, as well as other Thiothrix species, is the presence of a flavin adenine dinucleotide (FAD)-dependent malate:quinone oxidoreductase instead of nicotinamide adenine dinucleotide (NAD)-dependent malate dehydrogenase. Both MAGs contained genes for CO2 assimilation through the Calvin-Benson-Bassam cycle; sulfide oxidation (sqr, fccAB), sulfur oxidation (rDsr complex), direct (soeABC) and indirect (aprBA, sat) sulfite oxidation, and the branched Sox pathway (SoxAXBYZ) of thiosulfate oxidation to sulfur and sulfate. All these features indicate a chemoorganoheterotrophic, chemolithoautotrophic, and chemolithoheterotrophic lifestyle. Both MAGs comprise genes for nitrate reductase and NO-reductase, while SSD2 also contains genes for nitrite reductase. The presence of polyphosphate kinase and exopolyphosphatase suggests that RT and SSD2 could accumulate and degrade polyhosphates during the oxic-anoxic growth cycle in the bioreactors, such as typical phosphate-accumulating microorganisms.
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de Graaff DR, van Loosdrecht MCM, Pronk M. Stable granulation of seawater-adapted aerobic granular sludge with filamentous Thiothrix bacteria. Water Res 2020; 175:115683. [PMID: 32179272 DOI: 10.1016/j.watres.2020.115683] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/21/2020] [Accepted: 03/01/2020] [Indexed: 06/10/2023]
Abstract
Many sources of wastewater contain sulfides, which can cause excessive growth of filamentous bacteria such as Thiothrix sp. resulting in bulking sludge in conventional activated sludge systems. Granular sludge systems could potentially also suffer from the growth of filamentous bacteria. Uptake of easily degradable COD by the relatively slow growing Ca. Accumulibacter phosphatis bacteria and the absence of strong diffusion gradients due to plug flow feeding through the settled granular sludge bed are assumed to be the dominant factors for successful granulation. Sulfides will remain after this anaerobic phase and cause growth of sulfide-consuming bacteria such as Thiothrix sp. Here we observed the impact of growth of Thiothrix sp bacteria in a laboratory aerobic granular sludge reactor by feeding a mixture of acetate and thiosulfate in the influent. Thiothrix sp, proliferated when 18% of the influent COD was due to thiosulfate, forming 51.4 ± 8.3% of the total granular biomass. Despite the strong presence of these filamentous bacteria a well settling sludge was maintained (SVI10 equal to 13.3 mL/g). These results confirm that sludge morphology is not necessarily a reflection of the cell morphology of the bacteria, but is highly influence by reactor operation. It also reiterates the fact that compact biofilms are formed when the substrate consumption rate is lower than the substrate transport rate.
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Affiliation(s)
- Danny R de Graaff
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Mario Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, the Netherlands; Royal HaskoningDHV, Laan 1914 35, Amersfoort, 3800 AL, the Netherlands
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Rey-Martínez N, Badia-Fabregat M, Guisasola A, Baeza JA. Glutamate as sole carbon source for enhanced biological phosphorus removal. Sci Total Environ 2019; 657:1398-1408. [PMID: 30677906 DOI: 10.1016/j.scitotenv.2018.12.064] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
Enhanced Biological Phosphorus Removal (EBPR) is based on the enrichment of sludge in polyphosphate accumulating organisms (PAO). Candidatus Accumulibacter is the bacterial community member most commonly identified as PAO in EBPR systems when volatile fatty acids (VFA) are the carbon source. However, it is necessary to understand the role of non-Accumulibacter PAO in the case of wastewater with low VFA content. This work shows the first successful long-term operation of an EBPR system with glutamate as sole carbon and nitrogen source, resulting in the enrichment of sludge in the genus Thiothrix (37%), the family Comamonadaceae (15.6%) and Accumulibacter (7.7%). The enrichment was performed in an anaerobic/anoxic/oxic (A2/O) continuous pilot plant, obtaining stable biological N and P removal. This microbial community performed anaerobic P-release with only 18-29% of the observed PHA storage in Accumulibacter-enriched sludge and with slight glycogen storage instead of consumption, indicating the involvement of other carbon storage routes not related to PHA and glycogen. Thiothrix could be clearly involved in P-removal because it is able of accumulating Poly-P, probably without PHA synthesis, but with glutamate involvement. On the other hand, Comamonadaceae could participate in degradation of glutamate and denitrification, but its involvement in P-uptake cannot be reliably concluded.
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Affiliation(s)
- Natalia Rey-Martínez
- GENOCOV, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Spain.
| | - Marina Badia-Fabregat
- GENOCOV, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Spain.
| | - Albert Guisasola
- GENOCOV, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Spain.
| | - Juan Antonio Baeza
- GENOCOV, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Spain.
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Wu X, Huang J, Lu Z, Chen G, Wang J, Liu G. Thiothrix eikelboomii interferes oxygen transfer in activated sludge. Water Res 2019; 151:134-143. [PMID: 30594082 DOI: 10.1016/j.watres.2018.12.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 06/09/2023]
Abstract
This study revealed that, Thiothrix eikelboomii, a well-known filamentous bacterium that causes sludge bulking, could also interfere oxygen transfer during wastewater treatment. The volumetric oxygen transfer coefficient (KLa) in filamentous-bulking sludge (FBS) was found to be 43% lower than that in floc-forming sludge (FFS) at similar biomass concentrations, partially because the filamentous bacteria had increased the sludge apparent viscosity. The KLa value for FBS, however, was still significantly lower than that for FFS even if both sludges had similar apparent viscosity. Numerous tiny and free-swimming filaments were observed to attach on the air bubble surface, presumably reducing the liquid film renewal and increasing the liquid film thickness. Moreover, the filaments were co-coated with extracellular polymeric substances of protein and polysaccharide, which could make them performing like "amphiphilic molecules" of surfactants to hinder oxygen transfer. Therefore, the particular surface property of filaments and their interaction with air bubbles could also impact oxygen transfer. Thiothrix eikelboomii was identified to be the responsible filamentous bacterium that lowered the KLa value, while other filamentous bacteria with short filaments did not interfere oxygen transfer. This study implies that controlling sludge bulking benefits not only sludge settling but also oxygen transfer.
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Affiliation(s)
- Xianwei Wu
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials, And Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, 510632, China
| | - Ju Huang
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials, And Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, 510632, China
| | - Zichuan Lu
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials, And Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, 510632, China
| | - Gaofeng Chen
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials, And Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, 510632, China
| | - Jianmin Wang
- Department of Civil, Architectural and Environmental Engineering, Missouri University of Science and Technology, Rolla, MO, 65409, USA
| | - Guoqiang Liu
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials, And Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, 510632, China.
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Narihiro T, Nobu MK, Hori T, Aoyagi T, Sato Y, Inaba T, Aizawa H, Tamaki H, Habe H. Effects of the Wastewater Flow Rate on Interactions between the Genus Nitrosomonas and Diverse Populations in an Activated Sludge Microbiome. Microbes Environ 2018; 34:89-94. [PMID: 30584187 PMCID: PMC6440735 DOI: 10.1264/jsme2.me18108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The present study characterized the interactions of microbial populations in activated sludge systems during the operational period after an increase in the wastewater flow rate and consequential ammonia accumulation using a 16S rRNA gene sequencing-based network analysis. Two hundred microbial populations accounting for 81.8% of the total microbiome were identified. Based on a co-occurrence analysis, Nitrosomonas-type ammonia oxidizers had one of the largest number of interactions with diverse bacteria, including a bulking-associated Thiothrix organism. These results suggest that an increased flow rate has an impact on constituents by changing ammonia concentrations and also that Nitrosomonas- and Thiothrix-centric responses are critical for ammonia removal and microbial community recovery.
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Affiliation(s)
- Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Masaru Konishi Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hidenobu Aizawa
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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Boden R, Scott KM. Evaluation of the genus Thiothrix Winogradsky 1888 (Approved Lists 1980) emend. Aruga et al. 2002: reclassification of Thiothrix disciformis to Thiolinea disciformis gen. nov., comb. nov., and of Thiothrix flexilis to Thiofilum flexile gen. nov., comb nov., with emended description of Thiothrix. Int J Syst Evol Microbiol 2018; 68:2226-2239. [PMID: 29851374 DOI: 10.1099/ijsem.0.002816] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thiothrix is the type genus of the Thiotrichaceae in the Thiotrichales of the Gammaproteobacteria, comprising nine species of sulfur-oxidising filamentous bacteria, which are variously autotrophic, heterotrophic or have mixed metabolic modes. Within the genus, four species show 16S rRNA gene identities lower the Yarza threshold for the rank of genus (94.5 %) - Thiothrix disciformis, Thiothrix flexilis, Thiothrix defluvii and Thiothrix eikelboomii - as they show no affiliation to extant genera, a polyphasic study was undertaken including biochemical, physiological and genomic properties and phylogeny based on the 16S rRNA gene (rrs), recombination protein A (RecA), polynucleotide nucleotidyltransferase (Pnp), translation initiation factor IF-2 (InfB), glyceraldehyde-3-phosphate dehydrogenase (GapA), glutaminyl-tRNA synthetase (GlnS), elongation factor EF-G (FusA) and concatamers of 53 ribosomal proteins encoded by rps, rpl and rpm operons, all of which support the reclassification of these species. We thus propose Thiolinea gen. nov. and Thiofilum gen. nov. for which the type species are Thiolinea disciformis gen. nov., comb. nov. and Thiofilum flexile gen. nov., comb. nov. We also propose that these genera are each circumscribed into novel families Thiolinaceae fam. nov. and Thiofilaceae fam. nov., and that Leucothrix and Cocleimonas are circumscribed into Leucotrichaceaefam. nov. and provide emended descriptions of Thiothrix and Thiotrichaceae.
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Affiliation(s)
- Rich Boden
- Sustainable Earth Institute, University of Plymouth, Plymouth, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Kathleen M Scott
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
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Sharrar AM, Flood BE, Bailey JV, Jones DS, Biddanda BA, Ruberg SA, Marcus DN, Dick GJ. Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin. Front Microbiol 2017; 8:791. [PMID: 28533768 PMCID: PMC5421297 DOI: 10.3389/fmicb.2017.00791] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 04/18/2017] [Indexed: 11/25/2022] Open
Abstract
Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight. De novo assembly and binning of metagenomic data from these two communities yielded near complete genomes and revealed representatives of two families of LSB. The Isolated Sinkhole community was dominated by novel members of the Beggiatoaceae that are phylogenetically intermediate between known freshwater and marine groups. Several of these Beggiatoaceae had 16S rRNA genes that contained introns previously observed only in marine taxa. The Alpena fountain was dominated by populations closely related to Thiothrix lacustris and an SM1 euryarchaeon known to live symbiotically with Thiothrix spp. The SM1 genomic bin contained evidence of H2-based lithoautotrophy. Genomic bins of both the Thiothrix and Beggiatoaceae contained genes for sulfur oxidation via the rDsr pathway, H2 oxidation via Ni-Fe hydrogenases, and the use of O2 and nitrate as electron acceptors. Mats at both sites also contained Deltaproteobacteria with genes for dissimilatory sulfate reduction (sat, apr, and dsr) and hydrogen oxidation (Ni-Fe hydrogenases). Overall, the microbial mats at the two sites held low-diversity microbial communities, displayed evidence of coupled sulfur cycling, and did not differ largely in their metabolic potentials, despite the environmental differences. These results show that groundwater-fed communities in an artesian fountain and in submerged sinkholes of Lake Huron are a rich source of novel LSB, associated heterotrophic and sulfate-reducing bacteria, and archaea.
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Affiliation(s)
- Allison M Sharrar
- Department of Earth and Environmental Sciences, University of Michigan, Ann ArborMI, USA
| | - Beverly E Flood
- Department of Earth Sciences, University of Minnesota, MinneapolisMN, USA
| | - Jake V Bailey
- Department of Earth Sciences, University of Minnesota, MinneapolisMN, USA
| | - Daniel S Jones
- Department of Earth Sciences, University of Minnesota, MinneapolisMN, USA.,BioTechnology Institute, University of Minnesota, MinneapolisMN, USA
| | - Bopaiah A Biddanda
- Annis Water Resources Institute, Grand Valley State University, MuskegonMI, USA
| | - Steven A Ruberg
- NOAA-Great Lakes Environmental Research Laboratory, Ann ArborMI, USA
| | - Daniel N Marcus
- Department of Earth and Environmental Sciences, University of Michigan, Ann ArborMI, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann ArborMI, USA
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