Malfertheiner Lukas, Martínez-Pérez Clara, Zhao Zihao, Herndl Gerhard J, Baltar Federico
Department of Functional and Evolutionary Ecology, University of Vienna, 1090 Vienna, Austria.
Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zurich, Switzerland.
Biology (Basel). 2022 Apr 14;11(4):599. doi: 10.3390/biology11040599.
The bacterial SAR324 cluster is ubiquitous and abundant in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 30% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding genes (instead of the previously used 16S rRNA single gene marker), the former cluster SAR324 has been classified since 2018 as its own phylum. Yet, very little is known about its phylogeny and metabolic potential. We downloaded all publicly available SAR324 genomes (65) from all natural environments and reconstructed 18 new genomes using publicly available oceanic metagenomic data and unpublished data from the waters underneath the Ross Ice Shelf. We calculated a global SAR324 phylogenetic tree and identified six clusters (namely 1A, 1B, 2A, 2B, 2C and 2D) within this clade. Genome annotation and metatranscriptome read mapping showed that SAR324 clades possess a flexible array of genes suited for survival in various environments. Clades 2A and 2C are mostly present in the surface mesopelagic layers of global oceans, while clade 2D dominates in deeper regions. Our results show that SAR324 has a very versatile and broad metabolic potential, including many heterotrophic, but also autotrophic pathways. While one surface water associated clade (2A) seems to use proteorhodopsin to gain energy from solar radiation, some deep-sea genomes from clade 2D contain the complete Calvin-Benson-Bassham cycle gene repertoire to fix carbon. This, in addition to a variety of other genes and pathways for both oxic (e.g., dimethylsulfoniopropionate degradation) and anoxic (e.g., dissimilatory sulfate reduction, anaerobic benzoate degradation) conditions, can help explain the ubiquitous presence of SAR324 in aquatic habitats.
细菌SAR324簇在海洋中普遍存在且数量丰富，尤其是在热液喷口周围和深海，在那里它可占整个细菌群落的30%。根据使用多个通用蛋白质编码基因（而非先前使用的16S rRNA单基因标记）生成的新分类法，自2018年起，前SAR324簇已被归类为一个独立的门。然而，人们对其系统发育和代谢潜力知之甚少。我们从所有自然环境中下载了所有公开可用的SAR324基因组（65个），并使用公开可用的海洋宏基因组数据和罗斯冰架下海域的未发表数据重建了18个新基因组。我们计算了一个全球SAR324系统发育树，并在这个进化枝中识别出六个簇（即1A、1B、2A、2B、2C和2D）。基因组注释和宏转录组读数映射表明，SAR324进化枝拥有一系列灵活的基因，适合在各种环境中生存。2A和2C簇主要存在于全球海洋的表层中层水域，而2D簇在较深区域占主导地位。我们的结果表明，SAR324具有非常多样和广泛的代谢潜力，包括许多异养途径，也有自养途径。虽然一个与地表水相关的进化枝（2A）似乎利用视紫红质从太阳辐射中获取能量，但2D进化枝的一些深海基因组包含完整的卡尔文-本森-巴斯姆循环基因库来固定碳。这一点，再加上针对有氧（如二甲基磺丙酸降解）和无氧（如异化硫酸盐还原、厌氧苯甲酸降解）条件的各种其他基因和途径，有助于解释SAR324在水生栖息地中普遍存在的原因。
