Two New Species of Filamentous Sulfur Bacteria of the Genus , Sp. Nov. and ' Thiothrix Sulfatifontis' Sp. Nov

Overview

Journal Microorganisms

Specialty Microbiology

Date 2022 Jul 27

PMID 35889019

Authors

Nikolai V Ravin

Simona Rossetti

Alexey V Beletsky

Vitaly V Kadnikov

Tatyana S Rudenko

Dmitry D Smolyakov

Marina I Moskvitina

Maria V Gureeva

Andrey V Mardanov

Margarita Yu Grabovich

Affiliations

Soon will be listed here.

Abstract

The metagenome of foulings from sulfidic spring "Serovodorodny" (Tatarstan, Russia), where members of the genus was observed, was sequenced. Representatives of the phyla , and dominated in the microbial community. The complete genome of sp. KT was assembled from the metagenome. It displayed 93.93-99.72% 16S rRNA gene sequence identity to other 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 sulfatifontis' sp. nov. KT. The taxonomic status has been determined of the strain sp. CT3, isolated about 30 years ago and not assigned to any of 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 species was below 82%, and the dDDH values were less than 40%, indicating that strain CT3 belongs to a novel species, 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 showed anaerobic growth in the presence of thiosulfate.

Citing Articles

Wastewater Treatment with Bacterial Representatives of the Morphotype.

Gureeva M, Muntyan M, Ravin N, Grabovich M Int J Mol Sci. 2024; 25(16).

PMID: 39201777 PMC: 11355018. DOI: 10.3390/ijms25169093.

Genomic and morphological characterization of a new Thiothrix species from a sulfide hot spring of the Zmeinaya bay (Northern Baikal, Russia).

Chernitsyna S, Elovskaya I, Bukin S, Bukin Y, Pogodaeva T, Kwon D Antonie Van Leeuwenhoek. 2024; 117(1):23.

PMID: 38217803 DOI: 10.1007/s10482-023-01918-w.

and : New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus .

Ravin N, Smolyakov D, Markov N, Beletsky A, Mardanov A, Rudenko T Microorganisms. 2023; 11(10).

PMID: 37894178 PMC: 10609254. DOI: 10.3390/microorganisms11102521.

Metagenomics Revealed a New Genus ' Thiocaldithrix dubininis' gen. nov., sp. nov. and a New Species ' Thiothrix putei' sp. nov. in the Family , Some Members of Which Have Traits of Both Na- and H-Motive Energetics.

Ravin N, Muntyan M, Smolyakov D, Rudenko T, Beletsky A, Mardanov A Int J Mol Sci. 2023; 24(18).

PMID: 37762502 PMC: 10532065. DOI: 10.3390/ijms241814199.

History of the Study of the Genus : From the First Enrichment Cultures to Pangenomic Analysis.

Ravin N, Rudenko T, Smolyakov D, Beletsky A, Gureeva M, Samylina O Int J Mol Sci. 2022; 23(17).

PMID: 36076928 PMC: 9455678. DOI: 10.3390/ijms23179531.

References

Lee I, Kim Y, Park S, Chun J . OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol. 2015; 66(2):1100-1103. DOI: 10.1099/ijsem.0.000760. View

Parks D, Chuvochina M, Waite D, Rinke C, Skarshewski A, Chaumeil P . A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018; 36(10):996-1004. DOI: 10.1038/nbt.4229. View

Rubio-Rincon F, Welles L, Lopez-Vazquez C, Nierychlo M, Abbas B, Geleijnse M . Long-term effects of sulphide on the enhanced biological removal of phosphorus: The symbiotic role of Thiothrix caldifontis. Water Res. 2017; 116:53-64. DOI: 10.1016/j.watres.2017.03.017. View

Yao J, Liu J, Zhang Y, Xu S, Hong Y, Chen Y . Adding an anaerobic step can rapidly inhibit sludge bulking in SBR reactor. Sci Rep. 2019; 9(1):10843. PMC: 6659659. DOI: 10.1038/s41598-019-47304-3. View

Edgar R . Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010; 26(19):2460-1. DOI: 10.1093/bioinformatics/btq461. View

Rossetti S, Blackall L, Levantesi C, Uccelletti D, Tandoi V . Phylogenetic and physiological characterization of a heterotrophic, chemolithoautotrophic Thiothrix strain isolated from activated sludge. Int J Syst Evol Microbiol. 2003; 53(Pt 5):1271-1276. DOI: 10.1099/ijs.0.02647-0. View

Wang Z, Meng F, He X, Zhou Z, Huang L, Liang S . Optimisation and performance of NaClO-assisted maintenance cleaning for fouling control in membrane bioreactors. Water Res. 2014; 53:1-11. DOI: 10.1016/j.watres.2013.12.040. View

Walker B, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S . Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014; 9(11):e112963. PMC: 4237348. DOI: 10.1371/journal.pone.0112963. View

Alcaide M, Tchigvintsev A, Martinez-Martinez M, Popovic A, Reva O, Lafraya A . Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata by using functional metagenomics. Appl Environ Microbiol. 2015; 81(6):2125-36. PMC: 4345394. DOI: 10.1128/AEM.03387-14. View

10.

Li Y, Tang K, Zhang L, Zhao Z, Xie X, Chen C . Coupled Carbon, Sulfur, and Nitrogen Cycles Mediated by Microorganisms in the Water Column of a Shallow-Water Hydrothermal Ecosystem. Front Microbiol. 2018; 9:2718. PMC: 6282030. DOI: 10.3389/fmicb.2018.02718. View

11.

Frey B, Rime T, Phillips M, Stierli B, Hajdas I, Widmer F . Microbial diversity in European alpine permafrost and active layers. FEMS Microbiol Ecol. 2016; 92(3). DOI: 10.1093/femsec/fiw018. View

12.

Mardanov A, Gruzdev E, Smolyakov D, Rudenko T, Beletsky A, Gureeva M . Genomic and Metabolic Insights into Two Novel Species from Enhanced Biological Phosphorus Removal Systems. Microorganisms. 2020; 8(12). PMC: 7767063. DOI: 10.3390/microorganisms8122030. View

13.

Wick R, Schultz M, Zobel J, Holt K . Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 2015; 31(20):3350-2. PMC: 4595904. DOI: 10.1093/bioinformatics/btv383. View

14.

Rossmassler K, Hanson T, Campbell B . Diverse sulfur metabolisms from two subterranean sulfidic spring systems. FEMS Microbiol Lett. 2016; 363(16). DOI: 10.1093/femsle/fnw162. View

15.

de Graaff D, van Loosdrecht M, Pronk M . Stable granulation of seawater-adapted aerobic granular sludge with filamentous Thiothrix bacteria. Water Res. 2020; 175:115683. DOI: 10.1016/j.watres.2020.115683. View

16.

Haja D, Wu C, Poole 2nd F, Sugar J, Williams S, Jones A . Characterization of thiosulfate reductase from Pyrobaculum aerophilum heterologously produced in Pyrococcus furiosus. Extremophiles. 2019; 24(1):53-62. DOI: 10.1007/s00792-019-01112-9. View

17.

Konstantinidis K, Tiedje J . Towards a genome-based taxonomy for prokaryotes. J Bacteriol. 2005; 187(18):6258-64. PMC: 1236649. DOI: 10.1128/JB.187.18.6258-6264.2005. View

18.

Brettin T, Davis J, Disz T, Edwards R, Gerdes S, Olsen G . RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015; 5:8365. PMC: 4322359. DOI: 10.1038/srep08365. View

19.

Salcedo Moyano A, Delforno T, Subtil E . Simultaneous nitrification-denitrification (SND) using a thermoplastic gel as support: pollutants removal and microbial community in a pilot-scale biofilm membrane bioreactor. Environ Technol. 2021; :1-15. DOI: 10.1080/09593330.2021.1950843. View

20.

Okabe S, Odagiri M, Ito T, Satoh H . Succession of sulfur-oxidizing bacteria in the microbial community on corroding concrete in sewer systems. Appl Environ Microbiol. 2006; 73(3):971-80. PMC: 1800771. DOI: 10.1128/AEM.02054-06. View