Thomas Elaina, Groussman Mora J, Coesel Sacha N, Hawco Nicholas J, Bundy Randelle M, Armbrust E Virginia
School of Oceanography, University of Washington, Seattle, WA, United States.
Department of Oceanography, University of Hawai'i Mānoa, Honolulu, HI, United States.
Front Microbiol. 2025 Sep 1;16:1602162. doi: 10.3389/fmicb.2025.1602162. eCollection 2025.
Protists are ubiquitous across the ocean, holding different roles in the food web depending on their trophic capabilities. Many protists are mixotrophs, which are capable of both photosynthesizing and ingesting prey. However, there is limited knowledge of which protist species are mixotrophs in nature, as well as their activity and distribution throughout the ocean. Here, we present Marine PRotist trophic Mode predictor (MarPRISM), a refined XGBoost-based machine learning model for predicting the trophic mode (phototrophy, mixotrophy, and heterotrophy) of marine protist species based on transcriptional profiles. We used MarPRISM to generate 1,462 trophic mode predictions for 28 environmental protist species based on 335 metatranscriptomes collected across the North Pacific Ocean, from the surface to 130 m depth, over the diel cycle, and within nutrient-amended incubations. Eight environmental species were identified as having mixotrophic capabilities, including six dinoflagellates, one bolidophyte, and one haptophyte. The species with mixotrophic capabilities varied in how they shifted their trophic mode across the surface ocean and in response to the experimental amendment of nitrate and iron. Limited light availability appeared to lead one species to shift from mixotrophy at the surface toward heterotrophy between 41 and 130 m depth. We used transcript abundance to evaluate the abundance of species with different trophic capabilities (species with mixotrophic capabilities, phototrophic specialists, and heterotrophic specialists). At the surface within the subtropical gyre, transcript abundance was similar among protist species with different trophic capabilities. In the gyre, the protist community was nitrate-limited, and experimental nitrate amendment favored phototrophic specialists. Increasing nitrate availability with latitude was correlated with phototrophic specialists being the dominant protist trophic group in the transition zone between the subtropical and subpolar gyres under high nitrogen availability. In contrast, under lower nitrogen conditions in the transition zone, protist species with different trophic capabilities comprised equal portions of the surface community. Light and nitrate availability influenced the transcript abundance of phototrophic specialists across depth; phototrophic specialists had high transcript abundance at 130 m in the subtropical gyre and at the surface in the transition zone, while species with mixotrophic capabilities and heterotrophic specialists showed less variation in transcript abundance with depth.
原生生物在海洋中无处不在，根据其营养能力在食物网中扮演不同角色。许多原生生物是混合营养型，既能进行光合作用又能捕食猎物。然而，对于自然界中哪些原生生物物种是混合营养型，以及它们在整个海洋中的活动和分布，我们了解有限。在此，我们展示了海洋原生生物营养模式预测器（MarPRISM），这是一种基于XGBoost的经过改进的机器学习模型，用于根据转录谱预测海洋原生生物物种的营养模式（光合营养、混合营养和异养）。我们使用MarPRISM，基于在北太平洋从海面到130米深度、在日周期内以及在添加营养物质的培养实验中收集的335个宏转录组，对28种环境原生生物物种进行了1462次营养模式预测。鉴定出8种环境物种具有混合营养能力，包括6种甲藻、1种球石藻和1种定鞭藻。具有混合营养能力的物种在整个表层海洋中以及对硝酸盐和铁的实验性添加做出反应时，其营养模式转变方式各不相同。光照可用性有限似乎导致一个物种从表层的混合营养转变为41米至130米深度之间的异养。我们使用转录本丰度来评估具有不同营养能力的物种（具有混合营养能力的物种、光合营养专家和异养专家）的丰度。在亚热带环流的表层，具有不同营养能力的原生生物物种之间的转录本丰度相似。在环流中，原生生物群落受到硝酸盐限制，实验性硝酸盐添加有利于光合营养专家。随着纬度升高硝酸盐可用性增加，在高氮可用性下，光合营养专家是亚热带和亚极地环流之间过渡带中占主导地位的原生生物营养群体。相比之下，在过渡带较低氮条件下，具有不同营养能力的原生生物物种在表层群落中所占比例相等。光照和硝酸盐可用性影响了光合营养专家在不同深度的转录本丰度；光合营养专家在亚热带环流130米深处和过渡带表层具有较高的转录本丰度，而具有混合营养能力的物种和异养专家的转录本丰度随深度变化较小。
