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

单细胞微生物具有高度的多样性，在自然生态系统的功能中扮演着不同的角色，但要认识到微生物群体中遗传、形态和生理多样性之间的相互关系是具有挑战性的。在一个典型的例子中，共生藻科的微藻包括许多只能用分子数据来区分的物种。共生菌科是各种海洋无脊椎动物的共生体，但可能最为人所知的是珊瑚礁生态系统健康和持续的关键。该小组将于2021年8月主办一次虚拟研讨会，以确定并在专家之间就共生科多样性的评估达成进一步的共识。通过将协商一致的方法正式化并广泛传播，这次研讨会正在创建一个更具协作性和更受欢迎的研究社区，并确保所有现有的研究人员以及进入该领域的研究人员对申请赠款、进行研究和发表论文充满信心，这些论文纳入了共生科多样性的工作。这次研讨会确定了额外的前瞻性研究优先事项，以期在未来5-10年内取得方法学上的进步。解决微生物的分子多样性是一项重大的技术挑战，特别是对于共生菌科的甲藻。这些与珊瑚和其他海洋无脊椎动物相关的微藻内共生体具有巨大的基因组、高重复含量和其他独特的方面，这些方面阻碍了它们的分子特征。随着测序技术的进步，我们对共生菌科的多样性也有了更多的了解，从20世纪60年代一个广泛分布的物种的假设发展到现在包括15个不同的属，可能有数百个物种。这一发现过程充满了争议，因为最有用的系统发育标记-超多样化的内部转录间隔区2(ITS2)-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，采样的珊瑚组织包含可能来自多个共生科分类群的共生体细胞群，使表征伴侣特异性的努力复杂化。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体物种或仅仅是多个种内变异。这一中心冲突导致了关于珊瑚-藻类协会的灵活性以及它们可能如何应对正在进行的气候变化的不同学派。下一代测序提供了更多的数据，但同样的基础性解释问题仍然存在。这个团队聚集了来自世界各地的共生科先驱专家(从经验丰富的老兵到新近毕业的博士)，他们都一致认为，为了推动这一领域的发展，可以而且必须确定和推进共识解释框架。与会者正在制定一份导致两个研讨会产品的“共识路线图”：1.一份NSF白皮书；2.一份开放获取、同行评议的手稿。通过研讨会前的调查、四次研讨会、研讨会后的合作和出版物，该小组总结了当前的做法，并推荐了识别和分析共生菌科遗传多样性的关键方法，涉及三个“保护伞”：1.群落、2.种群和3.品系。通过利用先前为2022年国际珊瑚礁专题讨论会开发的一个单独的迷你讲习班，该讲习班的书面产品正在分发给更广泛的珊瑚礁和保育界。研讨会参与者还强调了未来十年应有助于填补部分剩余知识缺口的新技术和研究重点。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.