Mujakić Izabela, Cabello-Yeves Pedro J, Villena-Alemany Cristian, Piwosz Kasia, Rodriguez-Valera Francisco, Picazo Antonio, Camacho Antonio, Koblížek Michal
Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences , Třeboň, Czechia.
Department of Ecosystem Biology, Faculty of Science, University of South Bohemia , České Budějovice, Czechia.
Microbiol Spectr. 2023 Sep 21;11(5):e0111223. doi: 10.1128/spectrum.01112-23.
Gemmatimonadota is a diverse bacterial phylum commonly found in environments such as soils, rhizospheres, fresh waters, and sediments. So far, the phylum contains just six cultured species (five of them sequenced), which limits our understanding of their diversity and metabolism. Therefore, we analyzed over 400 metagenome-assembled genomes (MAGs) and 5 culture-derived genomes representing Gemmatimonadota from various aquatic environments, hydrothermal vents, sediments, soils, and host-associated (with marine sponges and coral) species. The principal coordinate analysis based on the presence/absence of genes in Gemmatimonadota genomes and phylogenomic analysis documented that marine and host-associated Gemmatimonadota were the most distant from freshwater and wastewater species. A smaller genome size and coding sequences (CDS) number reduction were observed in marine MAGs, pointing to an oligotrophic environmental adaptation. Several metabolic pathways are restricted to specific environments. For example, genes for anoxygenic phototrophy were found only in freshwater, wastewater, and soda lake sediment genomes. There were several genomes from soda lake sediments and wastewater containing type IC/ID ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Various genomes from wastewater harbored bacterial type II RuBisCO, whereas RuBisCO-like protein was found in genomes from fresh waters, soil, host-associated, and marine sediments. Gemmatimonadota does not contain nitrogen fixation genes; however, the gene, involved in the reduction of NO, was present in genomes from most environments, missing only in marine water and host-associated Gemmatimonadota. The presented data suggest that Gemmatimonadota evolved as an organotrophic species relying on aerobic respiration and then remodeled its genome inventory when adapting to particular environments. IMPORTANCE Gemmatimonadota is a rarely studied bacterial phylum consisting of a handful of cultured species. Recent culture-independent studies documented that these organisms are distributed in many environments, including soil, marine, fresh, and waste waters. However, due to the lack of cultured species, information about their metabolic potential and environmental role is scarce. Therefore, we collected Gemmatimonadota metagenome-assembled genomes (MAGs) from different habitats and performed a systematic analysis of their genomic characteristics and metabolic potential. Our results show how Gemmatimonadota have adapted their genomes to different environments.
芽单胞菌门是一个多样化的细菌门，常见于土壤、根际、淡水和沉积物等环境中。到目前为止，该门仅包含六个已培养的物种（其中五个已测序），这限制了我们对其多样性和代谢的了解。因此，我们分析了400多个宏基因组组装基因组（MAG）和5个来自不同水生环境、热液喷口、沉积物、土壤以及与宿主相关（与海洋海绵和珊瑚相关）物种的芽单胞菌门培养基因组。基于芽单胞菌门基因组中基因的有无进行的主坐标分析和系统发育基因组分析表明，海洋和与宿主相关的芽单胞菌门与淡水和废水物种的亲缘关系最远。在海洋MAG中观察到较小的基因组大小和编码序列（CDS）数量减少，这表明其适应贫营养环境。几种代谢途径仅限于特定环境。例如，无氧光合作用基因仅在淡水、废水和苏打湖沉积物基因组中发现。有几个来自苏打湖沉积物和废水的基因组含有IC/ID型核酮糖-1,5-二磷酸羧化酶/加氧酶（RuBisCO）。来自废水的各种基因组含有细菌II型RuBisCO，而在淡水、土壤、与宿主相关的以及海洋沉积物的基因组中发现了类RuBisCO蛋白。芽单胞菌门不包含固氮基因；然而，参与NO还原的基因存在于大多数环境的基因组中，仅在海水和与宿主相关的芽单胞菌门中缺失。所呈现的数据表明，芽单胞菌门进化为依赖有氧呼吸的有机营养物种，然后在适应特定环境时重塑其基因组组成。重要性芽单胞菌门是一个很少被研究的细菌门，仅由少数几个已培养的物种组成。最近的非培养研究表明，这些生物分布在许多环境中，包括土壤、海洋、淡水和废水。然而，由于缺乏已培养的物种，关于它们的代谢潜力和环境作用的信息很少。因此，我们从不同栖息地收集了芽单胞菌门的宏基因组组装基因组（MAG），并对其基因组特征和代谢潜力进行了系统分析。我们的结果展示了芽单胞菌门如何使其基因组适应不同的环境。
