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

科学钻探证明了地球深层微生物生物圈的丰富性，以及它在推动碳循环和营养循环方面的重要性。这些大型而研究不足的社区提出的一个主要问题是，他们如何应对渐进的埋葬和相关的能源饥饿。这个谜题的一个重要部分可能存在于极端缓慢的生长、休眠和微生物死亡之间的灰色区域；细菌内孢子可能在这一背景下发挥关键作用。内孢子是抗性细胞实体：代谢不活跃，休眠，结构独特，有能力监测它们的栖息地，以便在有利的条件下恢复生长。到目前为止，在海底生物量普查中对内生孢子的解释很差。事实上，DNA染色在多大程度上渗透到内孢子中仍然存在争议，因此内孢子可能是看不见的，或者是包括在计数的细胞池中的。另一种化学方法针对特定的生物标记物二吡啶甲酸(DPA)，最近产生了海底下内孢子丰度的第一个数据，并表明大量营养细胞伴随着同样大量的休眠内孢子。在这一观察的基础上，我们建议利用我们的大量适当保存的样本(例如，ODP201，IODP Exps)，对海底以下沉积物中的内孢子浓度进行一次基于DPA的调查。301、311、315、316、317、322、329、337)，以及其他致力于海底生命的探险。我们的目标是解决深层生物圈内孢子的生态相关性，并解决IODP科学计划确定的2013-2023年全球挑战中的两个：#5海底群落的起源、组成和全球意义；#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，即内孢子是主要的，没有充分考虑到对深层生物圈的贡献。为了验证这一点，我们将a)调查大量有细胞浓度和地球化学数据的深海海底样本中基于DPA的内孢子丰度，以及b)调查细胞计数在多大程度上包括内孢子。虽然我们实验室已经完全建立了DPA分析的分析方法，但要可靠地计数生物圈深处的内孢子，需要精炼DPA到孢子转换因子和关于DPA在沉积物中分配的信息。我们还假设，内生孢子不仅在埋葬期间能在极端条件下生存，而且可能在深层的、刺激活动的栖息地定居。为了测试这一点，我们将a)通过实验评估在地质时间尺度上保持存活的沉积内孢子的比率以及它们可能萌发的条件，以及b)确认微生物活动受到刺激的沉积层中内孢子萌发的生态相关性。

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.