Endospores in the deep marine biosphere: Distribution, abundance and function

科学钻探已经证明了地球深层微生物生物圈的丰富性，以及它在推动碳和营养循环方面的重要性。这些大型和未充分研究的社区提出的一个主要问题是他们如何处理渐进式埋葬和相关的能源饥饿。这个难题的一个重要部分可能存在于极其缓慢的生长，休眠和微生物死亡之间的灰色区域;细菌内生孢子可能在这种情况下发挥关键作用。内生孢子是抗性细胞实体：代谢不活跃，休眠，结构独特，具有监测其栖息地的能力，以便在有利条件下恢复生长。内生孢子迄今为止在海底生物量普查中没有得到很好的解释。事实上，DNA染色剂渗透到内生孢子中的程度仍然存在争议，因此内生孢子可能保持不可见或被包括在计数的细胞池中。另一种针对特定生物标志物吡啶二羧酸（DPA）的化学方法最近首次获得了海底下内生孢子丰度的数据，并表明大量营养细胞伴随着同样大量的休眠内生孢子。基于这一观察结果，我们提出了一个基于DPA的海底沉积物内生孢子浓度调查，使用我们的大型档案馆，这些档案馆保存了我们小组参与ODP和IODP考察所获得的适当样本（例如，ODP航段201，IODP Exps. 301，311，315，316，317，322，329，337），以及其他致力于海底生活的探险。我们的目标是解决深层生物圈内生孢子的生态相关性，并解决2013-2023年IODP科学计划定义的两个全球挑战：#5海底生物群落的起源，组成和全球意义是什么？#6海底生物的极限是什么？我们的研究是由这样一个假设驱动的，即内生孢子是深层生物圈的主要贡献者，但这一假设并不充分。为了验证这一点，我们将a）在大量深海底样品中调查基于DPA的内生孢子丰度，这些样品存在背景细胞浓度和地球化学数据，以及B）调查细胞计数在多大程度上包括内生孢子。虽然DPA分析的分析方法是完全建立在我们的实验室中，可靠的计数内生孢子在深层生物圈中需要细化DPA孢子转换因子和信息的DPA在沉积物中的分区。我们还假设内生孢子不仅在埋葬过程中的极端条件下生存，但可能会殖民深，活动刺激的栖息地。为了测试这一点，我们将a）实验性地评估在地质时间尺度上保持活力的沉积内生孢子的比率以及它们可能发芽的条件，以及B）确认在微生物活性受到刺激的沉积层中内生孢子发芽的生态相关性。

Scientific drilling has demonstrated the abundance of Earth's deep microbial biosphere, and its importance in driving carbon and nutrient cycles. A major question presented by these large and understudied communities is how they deal with progressive burial and associated energy starvation. One important piece of this puzzle may reside in the gray area between extremely slow growth, dormancy, and microbial death; bacterial endospores may play a critical role in this context. Endospores are resistant cellular entities: metabolically inactive, dormant, and structurally unique, with the ability to monitor their habitat in order to resume growth under favorable conditions. Endospores have so far been poorly accounted for in censuses of subseafloor biomass. Indeed, it remains controversial to what extent DNA stains penetrate into endospores, which therefore might either have remained invisible or been included in the pool of counted cells. An alternative chemical approach, targeting the specific biomarker dipicolinic acid (DPA), has recently produced the first data of endospore abundance in the subseafloor and suggests that the vast population of vegetative cells is accompanied by an equally large population of dormant endospores. Building on this observation we propose a DPA-based survey of endospore concentration in subseafloor sediments, using our large archive of appropriately preserved samples resulting from our group's participation in ODP and IODP expeditions (e.g., ODP Leg 201, IODP Exps. 301, 311, 315, 316, 317, 322, 329, 337), and other expeditions dedicated to subseafloor life. We aim to tackle the ecological relevance of endospores in the deep biosphere and to address two of the global challenges defined by the IODP Science Plan for 2013-2023: #5 What are the origin, composition, and global significance of subseafloor communities and #6 What are the limits of life in the subseafloor? Our research is driven by the hypothesis that endospores are major and insufficiently accounted for contributors to the deep biosphere. To test this we will a) survey DPA-based endospore abundance in a large set of deep subseafloor samples for which contextual cell concentration and geochemical data exists, and b) investigate to which extent cell counts include endospores. While the analytical method for DPA analysis is fully established in our lab, reliable enumeration of endospores in the deep biosphere requires refinement of DPA to spore conversion factors and information on the partitioning of DPA in the sediment. We also hypothesize that endospores not only survive extreme conditions during burial, but may colonize deep, activity-stimulating habitats. To test this we will a) experimentally evaluate the ratio of sedimentary endospores that remain viable over geological time scales and the conditions under which they may germinate and b) confirm the ecological relevance of endospore germination in sediment layers where microbial activity is stimulated.