Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
Center for Electromicrobiology, Aarhus University, Aarhus, Denmark.
ISME J. 2023 Apr;17(4):561-569. doi: 10.1038/s41396-023-01372-6. Epub 2023 Jan 25.
Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera: Candidatus Electronema, typically found in freshwater environments, and Candidatus Electrothrix, typically found in saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences and metagenome-assembled genome (MAG) phylogenies. However, most of the currently available MAGs are highly fragmented, incomplete, and thus likely miss key genes essential for deciphering the physiology of cable bacteria. Also, a closed, circular genome of cable bacteria has not been published yet. To address this, we performed Nanopore long-read and Illumina short-read shotgun sequencing of selected environmental samples and a single-strain enrichment of Ca. Electronema aureum. We recovered multiple cable bacteria MAGs, including two circular and one single-contig. Phylogenomic analysis, also confirmed by 16S rRNA gene-based phylogeny, classified one circular MAG and the single-contig MAG as novel species of cable bacteria, which we propose to name Ca. Electronema halotolerans and Ca. Electrothrix laxa, respectively. The Ca. Electronema halotolerans, despite belonging to the previously recognized freshwater genus of cable bacteria, was retrieved from brackish-water sediment. Metabolic predictions showed several adaptations to a high salinity environment, similar to the "saltwater" Ca. Electrothrix species, indicating how Ca. Electronema halotolerans may be the evolutionary link between marine and freshwater cable bacteria lineages.
缆线菌科的缆线菌是长约 1 厘米的丝状细菌，能够进行长距离的电子传递。目前，所有缆线菌都被分为两个候选属：通常在淡水环境中发现的 Candidatus Electronema 和通常在咸水环境中发现的 Candidatus Electrothrix。这个分类框架基于 16S rRNA 基因序列和宏基因组组装基因组 (MAG) 系统发育。然而，目前大多数可用的 MAG 高度碎片化，不完整，因此可能缺少解码缆线菌生理学的关键基因。此外，缆线菌的封闭、圆形基因组尚未公布。为了解决这个问题，我们对选定的环境样本和一株单菌株富集的 Ca. Electronema aureum 进行了纳米孔长读和 Illumina 短读 shotgun 测序。我们回收了多个缆线菌 MAG，包括两个圆形和一个单链。系统发育基因组分析，也通过基于 16S rRNA 基因的系统发育得到证实，将一个圆形 MAG 和一个单链 MAG 分类为缆线菌的新种，我们分别提议将其命名为 Ca. Electronema halotolerans 和 Ca. Electrothrix laxa。尽管 Ca. Electronema halotolerans 属于先前公认的淡水缆线菌属，但它是从半咸水沉积物中回收的。代谢预测显示出对高盐环境的几种适应，类似于“咸水”Ca. Electrothrix 种，表明 Ca. Electronema halotolerans 如何可能是海洋和淡水缆线菌谱系之间的进化联系。
