Collaborative Research: Building consensus around the quantification and interpretation of Symbiodiniaceae diversity

单细胞微生物是高度多样化的，在自然生态系统的功能中发挥着各种作用，但认识微生物群体的遗传、形态和生理多样性如何相互关联是具有挑战性的。在一个示例性案例中，共生藻科的微藻包括许多只能使用分子数据来区分的物种。共生体科是各种海洋无脊椎动物的共生体，但最著名的可能是珊瑚礁生态系统健康和持久的关键。该团队将于2021年8月举办一次虚拟研讨会，以确定并在专家之间就共生体科多样性的评估达成进一步共识。通过将共识方法正式化并广泛传播，该研讨会正在创建一个更具协作性和欢迎性的研究社区，并确保所有现有的研究人员以及进入该领域的研究人员都能自信地申请资助，进行研究，并发表包含共生生物科多样性工作的论文。本次研讨会将确定额外的前瞻性研究重点，以预测未来5-10年方法上的进步。解决微生物的分子多样性是一项重大的技术挑战，特别是对共生体科的鞭毛藻。这些与珊瑚和其他海洋无脊椎动物相关的微藻内共生生物具有大量基因组，高重复内容和其他独特的方面，这些方面阻碍了它们的分子表征。随着测序技术的进步，我们对共生体科多样性的了解也在不断发展，从20世纪60年代推测的一个广泛分布的物种发展到现在包括15个不同的属和可能的数百个物种。这一发现过程充满了争议，因为最有用的系统发育标记——超多样化内部转录间隔2 （ITS2）区域——很难以一致的方式解释。核糖体阵列是多拷贝的，它在不同的谱系中以不同的速度进化，并且受到协同进化的影响，所有这些都使系统发育重建复杂化。此外，珊瑚组织样本中含有可能来自多个共生体科分类群的共生细胞群，这使鉴定伴侣特异性的工作复杂化。早期的争论集中在独特的ITS2序列在多大程度上表明存在多个共生物种或仅仅是多个种内变体。这一核心冲突导致了不同流派对珊瑚-藻类结合的灵活性以及它们如何应对持续的气候变化的看法。下一代测序提供了更多的数据，但同样的基础解释问题仍然存在。这个团队正在聚集来自世界各地的共生体科先锋专家（从经验丰富的老兵到新毕业的博士），他们都一致认为，为了推动该领域的发展，可以而且必须确定和推进一个共识的解释框架。参与者正在生成一个“共识路线图”，导致两个研讨会产品：1。NSF白皮书；和2。一份开放获取、同行评审的手稿。通过研讨会前的调查、四次研讨会、研讨会后的合作和出版，该团队总结了目前的实践，并推荐了识别和分析共生体科遗传多样性的关键方法。社区,2。人口，和3。菌株。本次研讨会的书面成果将通过之前为2022年国际珊瑚礁研讨会开发的一个单独的小型研讨会分发给更广泛的珊瑚礁和保护界。研讨会参与者还强调了未来十年的新技术和研究重点，这应该有助于填补一些剩余的知识空白。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Single-celled microorganisms are highly diverse and play various roles in the function of natural ecosystems, but it is challenging to recognize how genetic, morphological, and physiological diversity relate to each other in microbial groups. In an exemplary case, micro-algae in the family Symbiodiniaceae comprise many species that can only be distinguished using molecular data. Symbiodinaceae function as symbionts of various marine invertebrates, but are perhaps best known as the key to coral reef ecosystem health and persistence. The team is hosting a virtual workshop in August 2021 to identify and build further consensus among experts regarding the assessment of Symbiodiniaceae diversity. By formalizing consensus approaches and disseminating them broadly, this workshop is creating a more collaborative and welcoming research community and ensuring that all current researchers, as well as those entering the field, feel confident applying for grants, conducting research, and publishing papers that incorporate work on Symbiodiniaceae diversity. This workshop is defining additional forward-thinking research priorities that anticipate methodological advances over the next 5-10 years. Resolving the molecular diversity of microorganisms is a major technical challenge, particularly for dinoflagellates in the family Symbiodiniaceae. These micro-algal endosymbionts that associate with corals and other marine invertebrates feature massive genomes, high repeat content, and other unique aspects that have hindered their molecular characterization. As sequencing technologies have advanced, so too has our understanding of Symbiodiniaceae diversity, which has grown from the presumption of one widespread species in the 1960s to now encompass fifteen divergent genera and likely hundreds of species. This process of discovery has been fraught with controversy, as the most useful phylogenetic marker–the hyperdiverse internal transcribed spacer 2 (ITS2) region–is frustratingly difficult to interpret in a consistent manner. The ribosomal array is multicopy, it evolves at different rates in different lineages, and it is subject to concerted evolution, all of which complicate phylogenetic reconstructions. Moreover, sampled coral tissues contain populations of symbiont cells that can potentially be from multiple Symbiodiniaceae taxa, complicating efforts to characterize partner specificity. Early debates focused on the extent to which unique ITS2 sequences indicated the presence of multiple symbiont species or simply multiple intraspecific variants. This central conflict has led to different schools of thought about how flexible coral-algal associations can be, and how they might respond to ongoing climate change. Next-generation sequencing has provided more data, but the same foundational interpretive issues remain. This team is gathering pioneering Symbiodiniaceae experts from around the world (ranging from seasoned veterans to newly-minted PhDs) who all collectively agree that a consensus interpretive framework can and must be identified and advanced in order to move the field forward. The participants are generating a ‘consensus road map’ leading to two workshop products: 1. an NSF white paper; and 2. an open-access, peer-reviewed manuscript. Through pre-workshop surveys, four workshop sessions, post-workshop collaboration, and publication, the team is summarizing current practices and recommending key methods for identifying and analyzing Symbiodiniaceae genetic diversity across three ‘umbrellas’: 1. communities, 2. populations, and 3. strains. The written products from this workshop are being distributed to the wider reef and conservation community by leveraging a separate mini-workshop previously developed for the 2022 International Coral Reef Symposium. Workshop participants are also highlighting new technologies and research priorities for the next decade that should help fill some of the remaining knowledge gaps.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.