SpongeDNA - Bolstering marine biodiversity exploration and monitoring through natural environmental DNA samplers

我们的星球正在经历生物多样性丧失的戏剧性阶段，这威胁到生态系统和我们所依赖的服务的不稳定。为了记录这种变化的程度和速度，并准备避免和/或管理它们，我们必须准确和广泛地评估和监测跨空间和时间的生物多样性模式。然而，可靠的物种清单是具有挑战性的、昂贵的、耗时的，并且难以实现跨分类群的标准化。对于海洋来说尤其如此，海洋是地球上最大、最难以接近的栖息地。利用DNA序列对物种进行区分和编目，逐渐提高了我们描述生态系统、管理资源和改进政策的能力。然后在过去的十年里，高通量平行DNA测序技术的出现改变了这个领域，这使得从水、沉积物、粪便、食品等中提取复杂生物混合物的分类成分在技术上成为可能，而且成本低廉。从动物在其栖息地自然脱落的细胞物质中提取“环境DNA”（eDNA）已成为一种流行的生态工具，特别是在水生科学中。事实上，鲸鱼和细菌的DNA可以用同样的方式“捕获”和筛选，这些发现可以在保护生物学、渔业和水产养殖、环境管理和流行病学方面有重要的应用。然而，从所研究的环境中收集水远非直截了当。首先，大多数收集水的方法在可靠地代表海洋浩瀚的能力上是有限的。此外，水样品中的目标eDNA通常非常稀释，这需要过滤，这是一个耗时的过程，容易受到交叉污染，并且严重依赖塑料。为了规避这些问题，世界各地的几个研究团队正在投资于高科技解决方案，例如各种形式的自动水下航行器，包括“dna探测机器人”。然而，这些系统运行起来非常昂贵，难以在迫切需要生物多样性信息的许多栖息地部署，并且主要依赖于单一物种检测试剂盒。我们的团队最近证明了海绵（多孔门——世界上最有效的水过滤器）在其组织中浓缩颗粒，从中可以检索和筛选周围生物群的痕量DNA。由于海绵也存在于每一个海洋栖息地中，并且可以进行非致命性采样，这为利用大自然自己的记录设备作为生物观察者提供了令人兴奋的前景，从而通过高度降低的成本和最小的环境影响，绕过了eDNA工作流程中一些最繁琐的步骤。该项目将彻底研究各种机制，以便将这一诱人的前景转化为探索和监测世界海洋生物多样性的操作工具。我们将：i)量化海绵组织中DNA的降解时间；Ii)比较圈养环境和野生环境下海绵与水样的物种检测能力；iii)评估海绵“自然采样DNA”（nsDNA）在底栖和远洋栖息地的表现，并考虑各种海绵形态；iv)探索海绵nsDNA在识别保护区内外生物多样性格局中的作用；v)评估nsDNA方法作为记录生物多样性的机会主义和“公民科学”工具的潜力。该项目将提供一种经济实惠、低技术含量的生物监测工具（高科技自动化设备的替代或补充），同时全面了解“自然环境DNA采样器”可以为海洋生物多样性评估做出最大贡献的情况。

Our planet is undergoing a dramatic phase of biodiversity loss, which threatens to destabilise ecosystems and the services upon which we rely. In order to document the extent and the rate of such changes and be prepared to avert and/or manage them, we must accurately and extensively assess and monitor biodiversity patterns across space and time. Yet, reliable species inventories are challenging, expensive, time-consuming to obtain, and difficult to standardise across taxa. This is particularly true for the oceans, the largest and least accessible habitats on Earth.The use of DNA sequences for distinguishing and cataloguing species has progressively improved our ability to characterise ecosystems, manage resources and improve policy. Then in the last decade, the field was transformed by the advent of high through-put parallel DNA sequencing technologies, which made it technically possible and inexpensive to reveal taxonomic compositions of complex biological mixtures extracted from water, sediments, faeces, food products and more. The retrieval of "environmental DNA" (eDNA) from cellular material naturally shed by animals in their habitat has become a popular ecological tool, especially in aquatic science. Indeed, DNA can be 'captured' and screened in the same way for whales and bacteria, and the findings can have important applications in conservation biology, fisheries and aquaculture, environmental management and epidemiology.However, the collection of water from the environment under study is far from straightforward. First of all, most water-collecting methods are limited in their capacity to reliably represent the vastness of the ocean. Furthermore, the target eDNA from aqueous samples is typically very diluted, which requires filtration, a time-consuming process, vulnerable to cross-contamination, and heavily reliant on plastic. To circumvent some of these issues, several research teams across the world are now investing in high-tech solutions, such as various forms of automated underwater vehicles, including "DNA-detecting robots". However, these systems are very expensive to run, difficult to deploy in many habitats where biodiversity information is urgently required, and mostly reliant on single-species detection kits.Our team recently demonstrated that sponges (phylum Porifera - the world's most efficient water-filterers) concentrate particles in their tissues, from which trace DNA of the surrounding biota can be retrieved and screened. Since sponges are also present in every marine habitat - and are amenable to non-lethal sampling - this offers the exciting prospect of harnessing Nature's own recording devices as biological observers, and hence by-pass some of the most cumbersome steps along the eDNA workflow, through highly reduced costs and minimal environmental impact. This project will thoroughly investigate the mechanisms that will enable to transform this attractive prospect into an operational tool for exploring and monitoring biodiversity across the world's oceans. We will: i) quantify the degradation time of the DNA trapped in sponge tissues; ii) compare species detection ability of sponges with that of water samples in both captive and wild settings; iii) evaluate sponge "natural sampler DNA" (nsDNA) performance in both benthic and pelagic habitats, and considering a variety of sponge morphologies; iv) explore the usefulness of sponge nsDNA to identify biodiversity patterns inside and outside protected areas; v) evaluate the potential of the nsDNA approach as opportunistic and 'citizen science' tools for recording biodiversity.The project will deliver an affordable, low-tech bio-monitoring tool (alternative or complementary to high-tech automated equipment) alongside a thorough understanding of the scenarios under which 'natural environmental DNA samplers' can offer the greatest contribution to marine biodiversity assessment.