Comparative genome analysis of the Sphaerotilus-Leptothrix group supports the unification of the genera Sphaerotilus and Leptothrix into a single emended genus Sphaerotilus

IF 3.2 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology Pub Date : 2025-11-01 Epub Date: 2025-10-18 DOI:10.1016/j.syapm.2025.126666

Dmitry D. Smolyakov , Alexey V. Beletsky , Tatyana S. Rudenko , Maria V. Gureeva , Nikolai V. Ravin , Margarita Y. Grabovich

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引用次数: 0

Abstract

The Sphaerotilus-Leptothrix group comprises two genera studied for 200 years. Attempts to unite these genera were made repeatedly, but have caused controversy due to differences in phenotypic characters identified in a small number of pure cultures. According to the latest release of Genome Taxonomy Database, Sphaerotilus and Leptothrix are combined into a single genus, Sphaerotilus. In this study, we analyzed 20 high-quality genomes forming 7 clusters on a phylogenetic tree constructed from concatenated sequences of 120 conserved genes, and investigated the distribution of metabolic genes. The Sphaerotilus-Leptothrix group formed a distinct monophyletic lineage within the family Sphaerotilaceae, where Leptothrix species were distributed among Sphaerotilus species. The average amino acid identities between the Sphaerotilus-Leptothrix genomes vary from 65 to 94.21%. All analyzed genomes contained genes of glycolysis, tricarboxylic acid cycle, and glyoxylate cycle. Genes for enzymes of dissimilatory sulfur metabolism were found, including oxidation of sulfide (sqr, fccAB), thiosulfate (soxAXBYZCD), elemental sulfur (rDSR) and sulfite (soeABC). Genes for manganese oxidation (mnxG, mofABC), previously considered unique to Leptothrix, were found in a number of other representatives of the combined genus. Also, some representatives contained genes for dissimilatory nitrate reduction and nitrogen fixation; autotrophic CO₂ fixation via the Calvin cycle; potential iron oxidation (cyc2, mtoAB). The identified metabolic pathways indicate a wide range of ecological strategies and occupied niches, determined by chemoorganoheterotrophic, chemolithoautotrophic and chemolithoheterotrophic nutritional types. Thus, the data obtained from phylogenetic analysis, large-scale genome analysis and assessment of metabolic potential support the unification of the genera Sphaerotilus and Leptothrix as a single genus Sphaerotilus.

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Sphaerotilus-Leptothrix组的比较基因组分析支持Sphaerotilus属和Leptothrix属统一为一个修订的Sphaerotilus属。

Sphaerotilus-Leptothrix类群包括两个属，研究了200年。人们多次尝试将这些属统一起来，但由于在少数纯培养物中发现的表型特征差异而引起争议。根据最新发布的基因组分类数据库，Sphaerotilus和Leptothrix被合并为一个属Sphaerotilus。在本研究中，我们分析了20个高质量基因组，在120个保守基因的串联序列构建的系统发育树上形成7个集群，并研究了代谢基因的分布。Sphaerotilus-Leptothrix类群在Sphaerotilaceae家族中形成了一个独特的单系谱系，其中Leptothrix物种分布在Sphaerotilus物种中。细螺旋体和球螺旋体基因组氨基酸的平均同源性在65% ~ 94.21%之间。所有分析的基因组都包含糖酵解、三羧酸循环和乙醛酸循环基因。发现了硫代谢的异化酶基因，包括硫化物氧化（sqr, fccAB）、硫代硫酸盐（soxAXBYZCD）、单质硫（rDSR）和亚硫酸盐（soeABC）。锰氧化基因（mnxG, mofABC），以前被认为是细螺旋体所特有的，在许多其他联合属的代表中被发现。另外，一些代表植物含有异化还原硝酸盐和固氮基因；通过卡尔文循环自养二氧化碳固定；潜在的铁氧化（cyc2, mtoAB）。所确定的代谢途径表明了广泛的生态策略和占据的生态位，由化学有机异养、化学岩石自养和化学岩石异养营养类型决定。因此，从系统发育分析、大规模基因组分析和代谢潜力评估中获得的数据支持了Sphaerotilus属和Leptothrix作为Sphaerotilus一个属的统一。

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来源期刊

Systematic and applied microbiology 生物-生物工程与应用微生物

CiteScore

7.50

自引率

5.90%

发文量

审稿时长

22 days

期刊介绍： Systematic and Applied Microbiology deals with various aspects of microbial diversity and systematics of prokaryotes. It focuses on Bacteria and Archaea; eukaryotic microorganisms will only be considered in rare cases. The journal perceives a broad understanding of microbial diversity and encourages the submission of manuscripts from the following branches of microbiology: