Data for: Comparative biogeography of marine and terrestrial microbes and macrobiota using eDNA

Quantifying how patterns of biodiversity and their underlying processes vary across diverse environments and ecological communities is a long-standing challenge in biogeography. The logistics of sampling entire communities over different geographic scales are barriers to determining biogeographic theory and conceptual integration at large scales. Here, we use environmental DNA (eDNA) to overcome these challenges and examine biogeography hypotheses contrasting diversity in marine versus terrestrial realms and unicellular versus multicellular organisms. Within two days, we sampled three habitats (terrestrial, estuarine, marine) along a ~1,400 km coastal transect in California. We found that eDNA exhibited some novel and familiar alpha diversity patterns. Marine diversity was lower than terrestrial diversity in multicellular biota, though statistically indistinguishable in unicellular biota. Richness was modestly correlated within habitats and was generally higher in unicellular biota. Bet..., Sample collection: California Environmental DNA (CALeDNA) kits (n = 23) were sent to co-authors and collaborators across the state to sample 22 locations (Figure 2; Table S1). We used one kit for each location, except for Morro Bay (n = 2). At each location we sampled 3 habitats: marine, terrestrial and estuarine. Marine habitat was sampled at the swash zone, defined as the area of the beach influenced by wave action; the swash was characterized by sandy beach or rocky intertidal. Terrestrial habitat included dunes and bluffs. Estuarine habitat included the river mouth, tidal flat or tidal marsh. Habitats were characterized in more detail using the updated California Wildlife Habitat Relationship system (CWHR) for coastal habitats (Shaffer 2002). At each habitat we sampled 2 sites (Figure 2b), separated at least 33 m apart (Figure 2c, d), and collected 1.5 ml of sample (sand, sediment, or soil) in triplicate (each replicate being ~30 cm from another). In places where the swash habitat w..., , # Data for: Comparative biogeography of marine and terrestrial microbes and macrobiota using eDNA Raw reads were deposited in NCBI Sequence Read Archive (Accession: PRJNA702201). Photographs from the sampling sites and the habitat were taken and uploaded with the kobo tool app to the CALeDNA webpage under the Transect Research Project ([https://data.ucedna.com/research_projects/transect/pages/overview](https://data.ucedna.com/research_projects/transect/pages/overview)) ## DATA & CODE FILE OVERVIEW This data repository consists of 35 data files, 12 code scripts, and this README document, with the following data and code filenames and variables ### Data files and variables 1\. Final_metadata_Coast_balanced.csv Description: Metadata for sample collections, including coordinates, site description, environmental variables, and diversity indexes. Used with the taxonomy tables to create initial phyloseq objects. Variables: MatchName: Sample site's name assigned by CALeDNA naming scheme..., ,量化生物多样性模式及其背后的过程在不同环境与生态群落间的变化规律，是生物地理学领域长期存在的核心挑战。在不同地理尺度下对完整群落进行采样的实操障碍，制约了大尺度生物地理学理论的构建与概念整合。本研究借助环境DNA（environmental DNA, eDNA）攻克了上述难题，检验了对比海洋与陆地界域、单细胞与多细胞生物多样性的生物地理学假说。本研究于两天内沿加利福尼亚州境内约1400公里的海岸样带，完成了陆地、河口与海洋三类生境的采样工作。研究发现，环境DNA检测得到的α多样性模式兼具新颖性与经典特征：在多细胞生物类群中，海洋生境的多样性显著低于陆地生境；而在单细胞生物类群中，二者多样性差异无统计学意义。生境内的物种丰富度呈弱相关性，且单细胞生物类群的丰富度整体更高。β多样性…… # 样本采集： 加利福尼亚环境DNA（CALeDNA）试剂盒（n=23）被分发至全州的合作作者与合作者，用于22个采样点位的采集工作（图2；表S1）。除莫罗湾（n=2）外，每个采样点位仅使用1个试剂盒。每个采样点位均覆盖三类生境：海洋、陆地与河口。海洋生境采样于激浪带（即受波浪作用影响的海滩区域，以沙质海滩或岩相潮间带为典型特征）；陆地生境包括沙丘与崖坡；河口生境则涵盖河口、潮滩或潮汐沼泽。生境的详细分类依据更新后的沿海生境加州野生动物生境关系系统（California Wildlife Habitat Relationship system, CWHR）（Shaffer, 2002）完成。 在每类生境中，我们设置2个采样点（图2b），两点间距至少33米（图2c、d），并采集三份平行的1.5毫升样本（沙、沉积物或土壤），每份平行样本间距约30厘米。在激浪生境的采样区域…… # 数据集主题：基于环境DNA的海洋与陆地微生物及大型生物比较生物地理学研究 原始测序reads已提交至NCBI序列读取档案（NCBI Sequence Read Archive，登录号：PRJNA702201）。 采样点位与生境的照片已通过Kobo工具应用上传至CALeDNA网页的样带研究项目板块（[https://data.ucedna.com/research_projects/transect/pages/overview](https://data.ucedna.com/research_projects/transect/pages/overview)） ## 数据与代码文件概览 本数据集仓库包含35个数据文件、12个代码脚本及本README文档，具体数据与代码文件名称及变量如下： ### 数据文件及变量 1. Final_metadata_Coast_balanced.csv 描述：采样元数据，包含坐标、点位描述、环境变量及多样性指数，可与分类表结合构建初始phyloseq对象。 变量：MatchName：基于CALeDNA命名规则分配的采样点位名称……