Department of Civil and Environmental Engineering, Michigan State University, A135, 1449 Engineering Research Court, East Lansing, MI, 48824, USA.
Curr Microbiol. 2024 Aug 20;81(10):314. doi: 10.1007/s00284-024-03829-z.
Propanotrophs are a focus of interest because of their ability to degrade numerous environmental contaminants. To explore the phylogeny of microorganisms containing the propane monooxygenase gene cluster (prmABCD), NCBI bacterial genomes and publicly available soil associated metagenomes (from soils, rhizospheres, tree roots) were both examined. Nucleic acid sequences were collected only if all four subunits were located together, were of the expected length and were annotated as propane monooxygenase subunits. In the bacterial genomes, this resulted in data collection only from the phyla Actinomycetota and Pseudomonadota. For the soil associated metagenomes, reads from four studies were subject to quality control, assembly and annotation. Following this, the propane monooxygenase subunit nucleic acid sequences were collected and aligned to the collected bacterial sequences. In total, forty-two propane monooxygenase gene clusters were annotated from the soil associated metagenomes. The majority aligned closely to those from the Actinomycetota, followed by the Alphaproteobacteria, then the Betaproteobacteria. Actinomycetota aligning propane monooxygenase sequences were obtained from all four datasets and most closely aligned to the genera Kribbella and Amycolatopsis. Alphaproteobacteria aligning sequences largely originated from metagenomes associated with miscanthus and switchgrass rhizospheres and primarily aligned with the genera Bradyrhizobium, Acidiphilium and unclassified Rhizobiales. Betaproteobacteria aligning sequences were obtained from only the Red Oak root metagenomes and primarily aligned with the genera Paraburkholderia, Burkholderia and Caballeronia. Interestingly, sequences from the environmental metagenomes were not closely aligned to those from well-studied propanotrophs, such as Mycobacterium and Rhodococcus. Overall, the study highlights the previously unreported diversity of putative propanotrophs in environmental samples. The common occurrence of propane monooxygenase gene clusters has implications for their potential use for contaminant biodegradation.
丙烷营养菌是研究的重点，因为它们能够降解多种环境污染物。为了探索含有丙烷单加氧酶基因簇（prmABCD）的微生物的系统发育，我们同时检查了 NCBI 细菌基因组和公开的土壤相关宏基因组（来自土壤、根际、树的根部）。只有当所有四个亚基都在一起，具有预期的长度并且被注释为丙烷单加氧酶亚基时，才收集核酸序列。在细菌基因组中，这导致仅从放线菌门和假单胞菌门收集数据。对于与土壤相关的宏基因组，对来自四项研究的读数进行质量控制、组装和注释。之后，收集丙烷单加氧酶亚基核酸序列并与收集的细菌序列进行比对。总共从与土壤相关的宏基因组中注释了 42 个丙烷单加氧酶基因簇。大多数与放线菌门密切相关，其次是α变形菌纲，然后是β变形菌纲。从四个数据集都获得了与丙烷单加氧酶序列相匹配的放线菌门，与 Kribbella 和 Amycolatopsis 属最匹配。与 α变形菌纲相匹配的序列主要来自与柳枝稷和芒草根际相关的宏基因组，主要与 Bradyrhizobium、Acidiphilium 和未分类的根瘤菌目属相匹配。与β变形菌纲相匹配的序列仅从红橡木根宏基因组中获得，与 Paraburkholderia、Burkholderia 和 Caballeronia 属最匹配。有趣的是，环境宏基因组中的序列与经过充分研究的丙烷营养菌（如 Mycobacterium 和 Rhodococcus）的序列不密切匹配。总的来说，该研究强调了环境样本中潜在丙烷营养菌的多样性以前没有报道过。丙烷单加氧酶基因簇的普遍存在表明它们在污染物生物降解方面有潜在的应用。
