Metabarcoding of modern soil DNA gives a highly local vegetation signal in Svalbard tundra

Abstract

Environmental DNA retrieved from modern soils (eDNA) and late-Quaternary palaeosols and sediments (aDNA and sedaDNA) promises insight into the composition of present and past terrestrial biotic communities, but few studies address the spatial relationship between recovered eDNA and contributing organisms. Svalbard's vascular plant flora is well known, and a cold climate enhances preservation of eDNA in soils. Thus, Svalbard plant communities are excellent systems for addressing the representation of plant eDNA in soil samples. In two valleys in the inner fjord region of Spitsbergen, we carried out detailed vegetation surveys of circular plots up to a 4-m radius. One or three near-surface soil samples from each plot were used for extraction and metabarcoding of soil-derived eDNA. Use of PCR replicates and appropriate filtering, plus a relevant reference metabarcode catalogue, provided taxon lists that reflected the local flora. There was high concordance between taxa recorded in plot vegetation and those in the eDNA, but floristic diversity was under-sampled, even at the scale of a 1-m radius plot. Most detected taxa grew within <0.5-1.0 m of the sampling point. Taxa present in vegetation but not in eDNA tended to occur further from the sampling point, and most had above-ground cover of <5%. Soil-derived eDNA provides a highly local floristic signal, and this spatial constraint should be considered in sampling designs. For palaeoecological or archaeological studies, multiple samples from a given soil horizon that are spatially distributed across the area of interest are likely to provide the most complete picture of species presence.

The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia

“…However, we note that campinas have an insular distribution in Amazonia, being surrounded by a “sea” of terra-firme forests 61,62 . OTU diversity in these patches could, potentially, be over-estimated due to DNA transported from nearby forest species, for instance through leaves, fungal spores and other debris 63 . This effect will be hard to test, but it is important to stress that the community composition of campinas was significantly different from the other habitats 40,64 and there is a rich micro-organismal community that is genuinely from campinas.…”

Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

“…This may relate to differences in preservation conditions for different taxa and at different locations and may also explain the variations we observed across samples in our two cores located only a few meters apart. There is still limited knowledge regarding the taphonomy of DNA in sediments (Yoccoz et al, 2012;Alsos et al, 2018;Edwards et al, 2018). Importantly, all of the three proxies only detect a fraction of the total diversity of the past vegetation (Allen and Huntley, 1999;Drake and Burrows, 2012;Birks and Birks, 2016;Alsos et al, 2018).…”

Holocene floristic diversity and richness in northeast Norway revealed by sedimentary ancient DNA (sedaDNA) and pollen

“…; Edwards et al . ). Recent investigation of the representation of contemporary vegetation in the DNA signal of superficial sediments in small lakes with limited inflowing streams from northern Norway revealed that 73 and 12% of the taxa detected in the DNA were recorded in vegetation surveys within 2 and 50 m of the lake shore, respectively (Alsos et al .…”