The making of sedimentary DNA: Insights from distribution patterns of DNA in sediments

Author(s):  
Laura S. Epp ◽  
Anan Ibrahim ◽  
Yi Wang ◽  
Lisa Gutbrod ◽  
Patrick Bartolin ◽  
...  

<p>Sedimentary ancient DNA has by now become a recognized source of information on past biodiversity change, but our understanding of its dynamics and taphonomy is still limited. While for environmental DNA in water, dedicated investigations on its provenance and degradation are being increasingly carried out, we know very little about sedimentary DNA, in particular with respect to aquatic organisms. We are therefore conducting investigations on the distribution of DNA in surface sediments and a short sediment core, with a focus on aquatic communities in the large and heterogeneous Lake Constance. Targeted organisms range from phyto- and zooplankton to fish and waterbirds. Initial results and comparison with sightings of rare species indicate that the DNA is not distributed uniformly or widely across the lake, especially for multicellular animals, but rather linked to the local presence of the organisms. This has implications for our understanding of how DNA enters the sediment and for paleoecological inferences derived from these records.</p>

2021 ◽  
Author(s):  
Yi Wang ◽  
Lisa Gutbrod ◽  
Myriam Schmid ◽  
Laura Epp

<p>Lake sedimentary ancient DNA has become a recognized source of information on past biodiversity change, but our understanding of its distribution and taphonomy is still limited. Here we collected 40 surface sediment samples from Lake Constance in southern Germany and characterized sedimentary DNA (sedDNA) heterogeneity through four metabarcoding PCRs on general eukaryotes, vascular plants, cyanobacteria and copepods.  We observed the variability of overall sedDNA being strongly correlated with sediment sample geographical locations, although this pattern varies within taxonomic groups. Specifically, geographical coordination and water depth explain 10.7% variability of terrestrial vascular plant sedDNA distribution, but the distribution of copepods is patchy and not correlated with sampling locations. Out study indicates that sedDNA is not distributed uniformly across the lake but rather linked to the movement of lake water and the local presence of the organisms.</p>


2019 ◽  
Vol 9 (17) ◽  
pp. 3450 ◽  
Author(s):  
Hyunbin Jo ◽  
Dong-Kyun Kim ◽  
Kiyun Park ◽  
Ihn-Sil Kwak

The nonlinearity and complexity of coastal ecosystems often cause difficulties when analyzing spatial and temporal patterns of ecological traits. Environmental DNA (eDNA) monitoring has provided an alternative to overcoming the aforementioned issues associated with classical monitoring. We determined aquatic community taxonomic composition using eDNA based on a meta-barcoding approach that characterizes the general ecological features in the Gwangyang Bay coastal ecosystem. We selected the V9 region of the 18S rDNA gene (18S V9), primarily because of its broad range among eukaryotes. Our results produced more detailed spatial patterns in the study area previously categorized (inner bay, main channel of the bay and outer bay) by Kim et al. (2019). Specifically, the outer bay zone was clearly identified by CCA using genus-level identification of aquatic organisms based on meta-barcoding data. We also found significant relationships between environmental factors. Therefore, eDNA monitoring based on meta-barcoding approach holds great potential as a complemental monitoring tool to identify spatial taxonomic distribution patterns in coastal areas.


Botanica ◽  
2019 ◽  
Vol 25 (1) ◽  
pp. 41-53 ◽  
Author(s):  
Ilona Jukonienė ◽  
Monika Subkaitė ◽  
Aurika Ričkienė

AbstractThe paper deals with bryophytes collected by Polish researchers from the mires in the eastern part of Lithuania in 1934–1940 and deposited at the Herbarium of W. Szafer Institute of Botany, Polish Academy of Sciences (KRAM). The collection provides data on bryophyte diversity and distribution patterns in the mires of Lithuania. The collection (868 specimens) was revised in 2016–2017. Almost 90% of all herbarium specimens were collected by Irena Dąbkowska. The specimens were identified by the collectors themselves or by Polish bryologist Zygmunt Czubiński; 254 specimens of the collection were not identified. After revision, a total of 112 bryophyte species were ascertained in the collection, two of these (Palustriella decipiens and Polytrichum swartzii) have not been reported to Lithuania before. The specimens were collected in 47 localities, the mires in nearly half of them at the moment are disturbed due to drainage or use for peat extraction. Information about the localities of rare species Hamatocaulis vernicosus, Meesia triquetra and Mesoptychia rutheana is valuable for the estimation of their population status.


2020 ◽  
Author(s):  
André O. Agostinis ◽  
Giorgi Dal Pont ◽  
Alexandre Borio ◽  
Aline Horodesky ◽  
Ana Paula da Silva Bertão ◽  
...  

AbstractThe study of environmental DNA (eDNA) is increasingly becoming a valuable tool to survey and monitor aquatic communities. However, there are important gaps in our understanding of the dynamics governing the distribution of eDNA under natural conditions. In this report we carry out controlled experiments to assess the extent and timing of eDNA distribution along the water column. A sample of known eDNA concentration was placed at the bottom of a 5-m high tube (20 cm in diameter and total volume of 160 L), and water samples were obtained at different depths over an 8 h-period. The presence of the target eDNA was assessed by qPCR analysis. This sampling protocol allowed for assessing the timescale for the diffusion of eDNA while minimizing the influence of turbulence. We demonstrate that, after a time-period of as little as 30 min, the eDNA had spread across the entire container. The implications of these results for eDNA sampling protocols in the field are discussed.


2020 ◽  
Vol 7 (7) ◽  
pp. 192045
Author(s):  
Faith A. M. Jones ◽  
Maria Dornelas ◽  
Anne E. Magurran

As pressures on biodiversity increase, a better understanding of how assemblages are responding is needed. Because rare species, defined here as those that have locally low abundances, make up a high proportion of assemblage species lists, understanding how the number of rare species within assemblages is changing will help elucidate patterns of recent biodiversity change. Here, we show that the number of rare species within assemblages is increasing, on average, across systems. This increase could arise in two ways: species already present in the assemblage decreasing in abundance but with no increase in extinctions, or additional species entering the assemblage in low numbers associated with an increase in immigration. The positive relationship between change in rarity and change in species richness provides evidence for the second explanation, i.e. higher net immigration than extinction among the rare species. These measurable changes in the structure of assemblages in the recent past underline the need to use multiple biodiversity metrics to understand biodiversity change.


Zootaxa ◽  
2020 ◽  
Vol 4819 (2) ◽  
pp. 216-264
Author(s):  
TÍMEA CHAMUTIOVÁ ◽  
LADISLAV HAMERLÍK ◽  
PETER BITUŠÍK

Here we present a summary of subfossil chironomids (Diptera: Chironomidae) found in the surface sediments of 52 Tatra Mts. lakes (Slovakia, Poland). Head capsules of 73 morphotypes of 5 subfamilies are described and illustrated. In addition to the previously documented subfossils by Brooks et al. (2007), we present 15 new morphotypes: Diamesa Tatra-type A, Diamesa Tatra-type B, Pseudodiamesa branickii-type, Pseudodiamesa nivosa-type, Pseudokiefferiella parva, Brillia bifida-type, Cricotopus (Paratrichocladius) skirwithensis-type, Cricotopus (Cricotopus) tremulus-type, Cricotopus/Orthocladius I, Eukiefferiella brevicalcar-type, Eukiefferiella claripennis-type B, Orthocladius (Orthocladius) dentifer-type, O. (Mesorthocladius) frigidus, Orthocladius (Euorthocladius) sp. and Tanytarsini indet. Most of these types have possibly broad distribution patterns in Europe. We believe that due to specific features of each region, this paper will serve as a helpful manual for limnologists and paleolimnologists working not only in the Tatra Mts. but also in the whole Carpathian region.


2017 ◽  
Vol 37 (6) ◽  
pp. 593-606 ◽  
Author(s):  
T. Leipe ◽  
M. Naumann ◽  
F. Tauber ◽  
H. Radtke ◽  
R. Friedland ◽  
...  

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