Eukaryotic diversity in late Pleistocene marine sediments around a shallow methane hydrate deposit in the Japan Sea

Abstract

Marine sediments contain eukaryotic DNA deposited from overlying water columns. However, a large proportion of deposited eukaryotic DNA is aerobically biodegraded in shallow marine sediments. Cold seep sediments are often anaerobic near the sediment-water interface, so eukaryotic DNA in such sediments is expected to be preserved. We investigated deeply buried marine sediments in the Japan Sea, where a methane hydrate deposit is associated with cold seeps. Quantitative PCR analysis revealed the reproducible recovery of eukaryotic DNA in marine sediments at depths up to 31.0 m in the vicinity of the methane hydrate deposit. In contrast, the reproducible recovery of eukaryotic DNA was limited to a shallow depth (8.3 m) in marine sediments not adjacent to the methane hydrate deposit in the same area. Pyrosequencing of an 18S rRNA gene variable region generated 1,276-3,307 reads per sample, which was sufficient to cover the biodiversity based on rarefaction curves. Phylogenetic analysis revealed that most of the eukaryotic DNA originated from radiolarian genera of the class Chaunacanthida, which have SrSO skeletons, the sea grass genus Zostera, and the seaweed genus Sargassum. Eukaryotic DNA originating from other planktonic fauna and land plants was also detected. Diatom sequences closely related to Thalassiosira spp., indicative of cold climates, were obtained from sediments deposited during the last glacial period (MIS-2). Plant sequences of the genera Alnus, Micromonas, and Ulmus were found in sediments deposited during the warm interstadial period (MIS-3). These results suggest the long-term persistence of eukaryotic DNA from terrestrial and aquatic sources in marine sediments associated with cold seeps, and that the genetic information from eukaryotic DNA from deeply buried marine sediments associated with cold seeps can be used to reconstruct environments and ecosystems from the past.

Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA

“…Therefore, sedimentary eDNA could complement aqueous eDNA in eDNA biomonitoring for species composition because the sedimentary eDNA should reflect a longer timescale, as shown in this study, and a narrower spatial scale, owing to its physical properties, than aqueous eDNA. In addition, although the analysis of eDNA from sediment cores can reconstruct information on past biological communities by targeting various taxa (e.g., plants: Pansu et al, ; eukaryotes: Kouduka et al, ; rabbits: Ficetola et al, ), knowledge of the characteristics of extracellular sedimentary eDNA of macro‐organisms and detection methods remains limited, especially for sediment core samples. Therefore, further research related to detection methods and analysis is needed to achieve more sensitive detection and accurate estimation of bioinformation using ancient eDNA from sediment cores.…”

Endolithic Microbial Habitats Hosted in Carbonate Nodules Currently Forming within Sediment at a High Methane Flux Site in the Sea of Japan

“…After the initial discovery of a massive gas hydrate outcropping on the seafloor in the Umitaka Spur [40,41], the eastern margin of the Sea of Japan has been intensively investigated from the perspectives of geology, geochemistry, geomicrobiology, and as a future energy resource [42][43][44][45][46][47][48][49]. The study site is located southwest of the Oki Trough in the Sea of Japan (Figure 1), and has recently been confirmed as a gas hydrate accumulation area [45].…”

Reconstruction of the Eukaryotic Communities in Beppu Bay Over the Past 50 Years Based on Sedimentary DNA Barcoding

“…Paleoenvironmental reconstructions have been conducted based on microfossils, biomarkers, isotopes, and other proxies. Environmental DNA technology is increasingly being used to understand contemporary ecosystems and environments (Schuster, 2008), but its application in paleoenvironmental analyses remains limited aside from a few pioneering studies (e.g., Boere, Rijpstra, et al., 2011; Boere, Sinninghe Damsté, et al., 2011; Capo et al., 2015, 2016; Coolen et al., 2004, 2013; Corinaldesi et al., 2011; Giguet‐Covex et al., 2014; Kouduka et al., 2017; Pansu et al., 2015). DNA is the most comprehensive indicator of organism identity.…”