An examination of seasonal variation in taxonomic richness and community composition using eDNA on a tropical coral reef

Small volumes of water containing environmental DNA (eDNA) are
increasingly combined with metabarcoding to generate biodiversity data for
specific fractions of marine flora and fauna. To date, however, few
studies have utilized this technique to assess how well it captures
seasonal patterns in coral reef communities or how environmental or
methodological factors influence eDNA detections. In our study, we used
three eDNA metabarcoding assays primarily targeting bony fish,
elasmobranchs, as well as cnidarians and sponges (Cnidaria/Porifera)
combined with monthly seawater sampling to 1) investigate temporal
variation in taxonomic detections and 2) statistically test the potential
effect of season, sea surface temperature, timing of spawning (using moon
phase as a proxy), and sample preservation on taxon detection across a
12-month period in a model coral reef system (Big Vicki’s Reef, Lizard
Island, Great Barrier Reef, Australia). Species-level fish and genus-level
scleractinian coral detections from standardised visual surveys conducted
at the same coral reef, in addition to a curated list of all known fishes
recorded from the more expansive coral reef system, were used to validate
eDNA detections. Our eDNA dataset indicated that the number of taxa
detected were consistently highest in September for fish, and in February
followed by September for Cnidaria/Porifera. Conversely, detections were
lowest in June and July for all taxa. Some, but not all, of the
environmental and methodological variables explained the observed temporal
pattern in biological communities or systematic changes in the number of
taxa, and in some cases, this effect was taxon dependent. Our study also
highlights the significance of timing in eDNA biodiversity surveys
conducted on tropical coral reefs in the Southern Hemisphere. To obtain
the most meaningful estimates of site diversity, we recommend focusing
sampling efforts between early spring to early autumn. Alternatively,
allocating an entire year to sampling would better capture seasonal
variation and provide more comprehensive insights into coral reef
biodiversity.

携带环境DNA（environmental DNA, eDNA）的微量水体样本，正日益与元条形码（metabarcoding）技术结合，以获取特定类群海洋动植物的生物多样性数据。
然而迄今为止，鲜有研究运用该技术评估其在珊瑚礁群落中捕捉季节模式的效果，亦未探究环境或方法学因素如何影响eDNA的检出结果。
本研究依托澳大利亚大堡礁蜥蜴岛的Big Vicki’s Reef（维基礁）这一典型珊瑚礁系统，采用3种分别主要靶向硬骨鱼、软骨鱼纲，以及刺胞动物与海绵动物（刺胞动物门/多孔动物门）的eDNA元条形码检测方案，结合月度海水采样，完成两项研究目标：1）探究分类单元检出情况的时间变异；2）在12个月的周期内，统计检验季节、海表温度、以月相为替代指标的产卵时间，以及样本保存方式对分类单元检出的潜在影响。
本研究通过同期在该珊瑚礁开展的标准化目视调查所得到的物种级鱼类数据与属级石珊瑚检出结果，结合针对该更大范围珊瑚礁系统已记录的所有鱼类的精选名录，共同对eDNA检出结果进行验证。
本研究的eDNA数据集显示，鱼类的检出类群数量在9月始终处于最高水平；而刺胞动物门/多孔动物门的检出类群数量则在2月达到峰值，其次为9月。与之相反，所有类群的检出量在6月与7月均为最低。
部分（而非全部）环境与方法学变量能够解释观测到的生物群落时间模式，或分类单元数量的系统性变化；且在部分情形下，该影响具有类群特异性。
本研究同时凸显了采样时机对南半球热带珊瑚礁eDNA生物多样性调查的重要性。
为获得最具参考价值的样点生物多样性评估结果，我们建议将采样工作集中在早春至早秋时段。或者，若开展为期一整年的采样，则可更好地捕捉季节变异，从而对珊瑚礁生物多样性提供更全面的认知。