混合营养是细菌在海洋中生存的重要营养策略。然而,主要兼养类群的全球相关性和同一性在很大程度上仍然难以捉摸。这里,我们结合了系统发育,宏基因组,以及根据我们的深海原位孵化和全球数据进行的超转录组学分析,以表征普遍存在的杆菌科。杆菌科的系统发育树分为三个大分支,其中进化枝A和B的成员几乎都来自陆地环境,而C进化枝除了一些陆地起源外,还广泛分布在各种海洋栖息地。所有进化枝都含有推定参与甲壳素降解的基因,硫化物氧化,氢氧化,硫代硫酸盐氧化,反硝化,异化硝酸盐还原成铵,微需氧呼吸,和金属(铁/锰)还原。此外,在进化枝C,找到了更多独特的途径,包括硫代硫酸盐歧化,乙醇发酵,甲烷氧化,脂肪酸氧化,钴胺素合成,和硫酸盐的异化还原,高氯酸盐,和砷酸盐。在这个进化支中,以UBA6211和CAIJNA01为代表的两个兼养型念珠菌属,它们含有推定参与反三羧酸固定碳途径的基因。此外,深海原位孵化中的代谢组学数据表明,后者属是一种混合营养,通过耦合硫氧化和反硝化以及代谢有机物来进行碳固定。此外,全球代谢组学数据证实了在所有海洋区域和深度的相应基因表达中,杆菌科的普遍分布和全球相关性。总的来说,这些结果突出了先前未被识别的杆菌科对碳的贡献,氮,和全球海洋中的硫循环。重要海洋微生物对全球碳循环和生态关系产生了深远的影响。混合营养,同时利用自养和异养营养,对全球碳循环产生重大影响。该报告描述了一组未培养的细菌,这些细菌在庞大的颗粒有机物的“热时间”中蓬勃发展,并在原位有机矿化过程中表现出混合营养策略。与进化枝A和B相比,在进化枝C中恢复了更多独特的代谢途径,包括用于碳固定的反向三羧酸途径,硫代硫酸盐歧化,甲烷氧化,和脂肪酸氧化。来自塔拉海洋探险的全球转移转录组数据证实了细菌科的普遍存在分布和广泛的转录活性,其基因的表达与碳固定有关,甲烷氧化,多硫化合物氧化,以及所有海洋区域和深度的反硝化。
Mixotrophy is an important trophic strategy for bacterial survival in the ocean. However, the global relevance and identity of the major mixotrophic taxa remain largely elusive. Here, we combined phylogenetic, metagenomic, and metatranscriptomic analyses to characterize ubiquitous Arcobacteraceae based on our deep-sea in situ incubations and the global data. The phylogenomic tree of Arcobacteraceae is divided into three large clades, among which members of clades A and B are almost all from terrestrial environments, while those of clade C are widely distributed in various marine habitats in addition to some terrestrial origins. All clades harbor genes putatively involved in chitin degradation, sulfide oxidation, hydrogen oxidation, thiosulfate oxidation,
denitrification, dissimilatory nitrate reduction to ammonium, microaerophilic respiration, and metal (iron/manganese) reduction. Additionally, in clade C, more unique pathways were retrieved, including thiosulfate disproportionation, ethanol fermentation, methane oxidation, fatty acid oxidation, cobalamin synthesis, and dissimilatory reductions of sulfate, perchlorate, and arsenate. Within this clade, two mixotrophic Candidatus genera represented by UBA6211 and CAIJNA01 harbor genes putatively involved in the reverse tricarboxylic acid pathway for carbon fixation. Moreover, the metatranscriptomic data in deep-sea in situ incubations indicated that the latter genus is a mixotroph that conducts carbon fixation by coupling sulfur oxidation and
denitrification and metabolizing organic matter. Furthermore, global metatranscriptomic data confirmed the ubiquitous distribution and global relevance of Arcobacteraceae in the expression of those corresponding genes across all oceanic regions and depths. Overall, these results highlight the contribution of previously unrecognized Arcobacteraceae to carbon, nitrogen, and sulfur cycling in global oceans.IMPORTANCEMarine microorganisms exert a profound influence on global carbon cycling and ecological relationships. Mixotrophy, characterized by the simultaneous utilization of both autotrophic and heterotrophic nutrition, has a significant impact on the global carbon cycling. This report characterizes a group of uncultivated bacteria Arcobacteraceae that thrived on the \"hot time\" of bulky particulate organic matter and exhibited mixotrophic strategy during the in situ organic mineralization. Compared with clades A and B, more unique metabolic pathways were retrieved in clade C, including the reverse tricarboxylic acid pathway for carbon fixation, thiosulfate disproportionation, methane oxidation, and fatty acid oxidation. Global metatranscriptomic data from the Tara Oceans expeditions confirmed the ubiquitous distribution and extensive transcriptional activity of Arcobacteraceae with the expression of genes putatively involved in carbon fixation, methane oxidation, multiple sulfur compound oxidation, and
denitrification across all oceanic regions and depths.