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

我们的星球正在经历一个生物多样性急剧丧失的阶段，这可能会破坏生态系统和我们所依赖的服务的稳定。为了记录这种变化的程度和速度，并做好准备避免和/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，可靠的物种库存是具有挑战性的，昂贵的，耗时的，难以跨越类群。海洋是地球上最大但最难进入的生境，利用DNA序列对物种进行区分和编目，逐步提高了我们保护生态系统、管理资源和改进政策的能力。然后在过去的十年中，该领域被高通量并行DNA测序技术的出现所改变，这使得从水，沉积物，粪便，食品等中提取的复杂生物混合物的分类组成在技术上成为可能且成本低廉。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学工具，特别是在水产科学中。事实上，DNA可以被“捕获”，并以同样的方式筛选鲸鱼和细菌，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。首先，大多数水收集方法的能力有限，无法可靠地代表海洋的浩瀚。此外，来自水性样品的靶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，并且严重依赖于塑料。为了规避其中的一些问题，世界各地的几个研究团队现在正在投资高科技解决方案，例如各种形式的自动水下航行器，包括“DNA检测机器人”。然而，这些系统运行起来非常昂贵，很难在许多急需生物多样性信息的栖息地部署，并且主要依赖于单一物种的检测试剂盒。我们的团队最近证明，海绵（多孔动物门-世界上最有效的水过滤器）将颗粒集中在它们的组织中，从中可以检索和筛选周围生物群的微量DNA。由于海绵也存在于每一个海洋栖息地--并且可以进行非致命性采样--这提供了一个令人兴奋的前景，即利用大自然自己的记录设备作为生物观察者，从而通过大幅降低成本和最小的环境影响，绕过eDNA工作流程中沿着一些最繁琐的步骤。该项目将彻底调查能够将这一诱人的前景转变为探索和监测世界各海洋生物多样性的实用工具的机制。我们将：（一）量化海绵组织中捕获的DNA的降解时间;（二）比较捕获和野生环境中海绵与水样的物种检测能力;（三）评估海绵“天然采样器DNA”在海底和远洋生境中的性能，并考虑各种海绵形态; ㈣探讨海绵nsDNA在确定保护区内外生物多样性模式方面的用途; 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。该项目将提供一个负担得起的，在这方面，我们将使用低技术生物监测工具（替代或补充高技术自动化设备），同时深入了解“自然环境DNA采样器”可为海洋生物多样性评估作出最大贡献的情景。

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.