Anaerobic Protist Survival in Microcosms is Dependent on Microbiome Metabolic Function

Syntrophy is a type of symbiotic cooperation, performed through metabolic interaction between partners. Syntrophic interactions between prokaryotes are common in low-oxygen environments, however, whether such interactions exist between microbial eukaryotes (protists) and prokaryotes is under explored. Previous investigations uncovered a potentially syntrophic interaction between the anaerobic breviate protist Lenisia limosa and the bacterium Arcobacter sp. EP1. This interaction provides benefits to both partners via hydrogen transfer whereby hydrogen produced by the protist is consumed by Arcobacter. Whether this relationship is conserved in other members in the Breviatea remains unexplored and yet critical to understand the scope and impact of these symbiotic associations in oxygen minimum zones (OMZs). Here, we address this knowledge gap, by exploring the metabolism and evolutionary relationship of diverse breviate species. We find that Arcobacteracea species and breviate-related sequences co-occur in the same environmental sequencing projects. These observations suggest that the symbiosis previously described between Lenisia limosa and Arcobacter sp. EP1 might be pervasive in Breviatea. To expand on these data, we present metagenome-assembled genomes of the prokaryotic communities of four undescribed breviate isolates and 16S amplicon sequencing data of anoxic cultures with different electron acceptors. We find that diverse Arcobacter-like species co-occur in all of the cultures and that the abundance of some of the Arcobacteracea species is higher in anaerobic conditions with nitrate. Based on the proteome prediction and the amplicon data, we speculate that some Arcobacteracea species could use the H2 produced by the breviates for dissimilatory nitrate reduction, engaging in a similar metabolic interaction like the one occurring in L. limosa and Arcobacter sp. EP1.互养共生（Syntrophy）是一类通过共生伙伴间代谢互作实现的共生合作模式。原核生物间的互养互作在低氧环境中普遍存在，但目前对于微生物真核生物（原生生物protists）与原核生物间是否存在此类互作的研究仍较为匮乏。既往研究曾在厌氧性短膜虫类（breviate）原生生物Lenisia limosa与弓形杆菌属（Arcobacter）菌株EP1（Arcobacter sp. EP1）之间发现了潜在的互养互作关系。该互作通过氢转移使双方均获益：原生生物产生的氢气被Arcobacter消耗利用。目前仍不清楚该共生关系是否在其他短膜虫类（Breviatea）类群中保守存在，而明确这一点对于理解此类共生关联在低氧区（oxygen minimum zones, OMZs）中的分布范围与影响至关重要。本研究通过解析多样短膜虫类物种的代谢与演化关系，填补了这一认知空白。我们发现，螺杆菌科（Arcobacteraceae）物种与短膜虫类相关序列在同一环境测序项目中共同出现。上述结果表明，此前在Lenisia limosa与Arcobacter sp. EP1之间发现的共生关系，可能广泛存在于短膜虫类类群中。为拓展上述研究数据，本研究公开了4株未被描述的短膜虫类分离株的原核生物群落宏基因组组装基因组（metagenome-assembled genomes, MAGs），以及不同电子受体条件下厌氧培养物的16S扩增子测序数据。研究发现，所有培养物中均存在多种类Arcobacter物种，且部分螺杆菌科物种在添加硝酸盐的厌氧条件下丰度更高。基于蛋白质组预测结果与扩增子测序数据，我们推测部分螺杆菌科物种可利用短膜虫类产生的氢气进行异化硝酸盐还原，从而形成与Lenisia limosa和Arcobacter sp. EP1间类似的代谢互作关系。