Ettinger Cassandra L, Vann Laura E, Eisen Jonathan A
Genome Center, University of California, Davis, Davis, California, USA.
Department of Evolution and Ecology, University of California, Davis, Davis, California, USA.
Appl Environ Microbiol. 2021 May 26;87(12):e0279520. doi: 10.1128/AEM.02795-20.
Seagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and seagrass studies, despite terrestrial fungi having critical functional roles as decomposers, pathogens, or endophytes in global ecosystems. Here, we characterize the distribution of fungi associated with the seagrass using leaves, roots, and rhizosphere sediment from 16 locations across its full biogeographic range. Using high-throughput sequencing of the ribosomal internal transcribed spacer (ITS) region and 18S rRNA gene, we first measured fungal community composition and diversity. We then tested hypotheses of neutral community assembly theory and the degree to which deviations suggested that amplicon sequence variants (ASVs) were plant selected or dispersal limited. Finally, we identified a core mycobiome and investigated the global distribution of differentially abundant ASVs. We found that the fungal community is significantly different between sites and that the leaf mycobiome follows a weak but significant pattern of distance decay in the Pacific Ocean. Generally, there was evidence for both deterministic and stochastic factors contributing to community assembly of the mycobiome, with most taxa assembling through stochastic processes. The core leaf and root mycobiomes were dominated by unclassified Sordariomycetes spp., unclassified Chytridiomycota lineages (including Lobulomycetaceae spp.), unclassified Capnodiales spp., and sp. It is clear from the many unclassified fungal ASVs and fungal functional guilds that knowledge of marine fungi is still rudimentary. Further studies characterizing seagrass-associated fungi are needed to understand the roles of these microorganisms generally and when associated with seagrasses. Fungi have important functional roles when associated with land plants, yet very little is known about the roles of fungi associated with marine plants, like seagrasses. In this study, we report the results of a global effort to characterize the fungi associated with the seagrass across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases that general knowledge of seagrass-associated fungi and marine fungi is lacking. This work serves as an important foundational step toward future work investigating the functional ramifications of fungi in the marine ecosystem.
海草是海洋开花植物，在全球沿海环境中提供关键的生态系统服务。尽管陆地真菌在全球生态系统中作为分解者、病原体或内生菌发挥着关键的功能作用，但在微生物群落和海草研究中，海洋真菌常常被忽视。在这里，我们利用海草在其完整生物地理范围内16个地点的叶片、根系和根际沉积物，对与之相关的真菌分布进行了表征。通过对核糖体内部转录间隔区（ITS）区域和18S rRNA基因进行高通量测序，我们首先测量了真菌群落组成和多样性。然后，我们检验了中性群落组装理论的假设，以及偏离该理论的程度，这些偏离表明扩增子序列变体（ASV）是植物选择的还是受扩散限制的。最后，我们确定了一个核心真菌群落，并研究了差异丰富的ASV的全球分布。我们发现，不同地点之间的真菌群落存在显著差异，并且在太平洋地区，叶片真菌群落呈现出一种微弱但显著的距离衰减模式。一般来说，有证据表明确定性和随机性因素都对真菌群落的组装有贡献，大多数分类群是通过随机过程组装的。核心叶片和根系真菌群落主要由未分类的粪壳菌纲物种、未分类的壶菌门谱系（包括Lobulomycetaceae物种）、未分类的小煤炱目物种和sp.组成。从许多未分类的真菌ASV和真菌功能类群可以明显看出，我们对海洋真菌的了解仍然很基础。需要进一步开展表征与海草相关真菌的研究，以全面了解这些微生物的作用以及它们与海草相关时的作用。真菌与陆地植物相关时具有重要的功能作用，但对于与海洋植物如海草相关的真菌的作用却知之甚少。在本研究中，我们报告了一项全球范围内的研究结果，旨在表征海草在其完整生物地理范围内相关真菌的特征。尽管我们定义了一个假定的全球核心真菌群落，但从许多与现有数据库不匹配的真菌序列和预测的功能类群可以明显看出，我们缺乏对与海草相关真菌和海洋真菌的一般认识。这项工作是未来研究真菌在海洋生态系统中功能影响的重要基础步骤。
