Weiten Arne, Kalvelage Kristin, Becker Patrick, Reinhardt Richard, Hurek Thomas, Reinhold-Hurek Barbara, Rabus Ralf
General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany.
Max-Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
Microb Physiol. 2021;31(1):16-35. doi: 10.1159/000513167. Epub 2021 Jan 21.
The betaproteobacterial genus Aromatoleum comprises facultative denitrifiers specialized in the anaerobic degradation of recalcitrant organic compounds (aromatic and terpenoid). This study reports on the complete and manually annotated genomes of Ar. petrolei ToN1T (5.41 Mbp) and Ar. bremense PbN1T (4.38 Mbp), which cover the phylogenetic breadth of the genus Aromatoleum together with previously genome sequenced Ar. aromaticum EbN1T [Rabus et al., Arch Microbiol. 2005 Jan;183(1):27-36]. The gene clusters for the anaerobic degradation of aromatic and terpenoid (strain ToN1T only) compounds are scattered across the genomes of strains ToN1T and PbN1T. The richness in mobile genetic elements is shared with other Aromatoleum spp., substantiating that horizontal gene transfer should have been a major driver in shaping the genomes of this genus. The composite catabolic network of strains ToN1T and PbN1T comprises 88 proteins, the coding genes of which occupy 86.1 and 76.4 kbp (1.59 and 1.75%) of the respective genome. The strain-specific gene clusters for anaerobic degradation of ethyl-/propylbenzene (strain PbN1T) and toluene/monoterpenes (strain ToN1T) share high similarity with their counterparts in Ar. aromaticum strains EbN1T and pCyN1, respectively. Glucose is degraded via the ED-pathway in strain ToN1T, while gluconeogenesis proceeds via the reverse EMP-pathway in strains ToN1T, PbN1T, and EbN1T. The diazotrophic, endophytic lifestyle of closest related genus Azoarcus is known to be associated with nitrogenase and type-6 secretion system (T6SS). By contrast, strains ToN1T, PbN1T, and EbN1T lack nif genes for nitrogenase (including cofactor synthesis and enzyme maturation). Moreover, strains PbN1T and EbN1T do not possess tss genes for T6SS, while strain ToN1T does and facultative endophytic "Aromatoleum" sp. CIB is known to even have both. These findings underpin the functional heterogeneity among Aromatoleum members, correlating with the high plasticity of their genomes.
β-变形菌纲的芳香油菌属包含兼性反硝化菌，专门进行难降解有机化合物（芳香族和萜类）的厌氧降解。本研究报告了石油芳香油菌ToN1T（5410 kbp）和布雷默芳香油菌PbN1T（4380 kbp）的完整且经人工注释的基因组，它们与之前已进行基因组测序的芳香油菌EbN1T [拉布斯等人，《微生物学档案》。2005年1月；183(1):27 - 36] 共同涵盖了芳香油菌属的系统发育广度。芳香族和萜类化合物（仅ToN1T菌株）的厌氧降解基因簇分散在ToN1T和PbN1T菌株的基因组中。移动遗传元件的丰富性与其他芳香油菌属物种相同，这证实水平基因转移应该是塑造该属基因组的主要驱动力。ToN1T和PbN1T菌株的复合分解代谢网络包含88种蛋白质，其编码基因分别占各自基因组的86.1和76.4 kbp（1.59%和1.75%）。乙基/丙基苯（PbN1T菌株）和甲苯/单萜类（ToN1T菌株）厌氧降解的菌株特异性基因簇分别与其在芳香油菌EbN1T和pCyN1菌株中的对应基因簇具有高度相似性。ToN1T菌株中葡萄糖通过ED途径降解，而在ToN1T、PbN1T和EbN1T菌株中糖异生通过反向EMP途径进行。已知与其亲缘关系最近的偶氮弧菌属的固氮内生生活方式与固氮酶和6型分泌系统（T6SS）有关。相比之下，ToN1T、PbN1T和EbN1T菌株缺乏固氮酶的nif基因（包括辅因子合成和酶成熟）。此外，PbN1T和EbN1T菌株不具有T6SS的tss基因，而ToN1T菌株具有，并且已知兼性内生的“芳香油菌”CIB菌株两者都有。这些发现强调了芳香油菌属成员之间的功能异质性，这与其基因组的高可塑性相关。
