The first detection of marine fish DNA in sediment sequences going back 300 years

November 16, 2020

Long-term variability in the 'abundance' of a macro-organism could provide fundamental information for evaluating its evolution, its responses to climate changes and human impact, enabling management and preservation strategies. Biological monitoring in aquatic systems has provided evidence of long-term variability in the abundance of macro-organisms. However, almost all such records span less than a century; there are none which span centuries or more. Aquatic bottom sediments have provided records of species abundance on longer time scales, although previous studies addressed marine fish species using fossil remains (mainly fish scales) and reconstructed abundance for only seven fish taxons. Thus, there remains a distinct lack of information on long-term changes in abundance for many marine fish species and other macro-organisms in aquatic systems.

This study focused on an approach using sedimentary DNA which is a potentially powerful tool for reconstructing lengthy records of fish species. We first tested the existence of fish DNA in the marine sediment sequences in a Japanese bay. Then we tested the utility of sedimentary DNA in reconstructing past fish abundance by comparing fish sedimentary DNA concentrations with fish scale concentrations and landing data.

Sediment core samples collected from Beppu Bay in the Seto Inland Sea, Japan, were used to quantify sedimentary DNA of three major fish species (Japanese anchovy, Japanese sardine, and jack mackerel) by applying quantitative Polymerase Chain Reaction (qPCR) methods. The result showed that the DNA of these fish species were detected in sediment sequences spanning the last 300 years. Observed temporal changes in fish DNA concentrations on decadal and centennial time scales are consistent with those of landings in Japan for all three species and with those of sardine fish scale concentrations. Thus, sedimentary DNA could be used to track decadal-centennial dynamics of fish abundance in marine.

Using environmental DNA is a widely accepted approach for biological monitoring that is easy, fast and inexpensive without the need for taxonomic expertise for the physical identification of a species. However, such monitoring started only recently; the data collection interval not being less than 10 years. In contrast, the use of sedimentary DNA is expected to instantly obtain lengthy retrospective monitoring data of abundance if the water has a sedimentary basin in which DNA is continuously deposited and stably preserved. This approach has not been used because it remains unclear whether sedimentary DNA concentrations reflect the abundance of an aquatic species. Our findings suggest that the use of sedimentary DNA is a viable technique for tracking past changes in fish abundance, and also could be used to reconstruct the abundance of macro-organisms inhabiting water. Sedimentary DNA technology could support monitoring efforts during the 21st century as a potential tool for decifering the long-term dynamics of macro-organisms before the monitoring started or at a place lacking lengthy monitering observations.

Ehime University

Related DNA Articles from Brightsurf:

A new twist on DNA origami
A team* of scientists from ASU and Shanghai Jiao Tong University (SJTU) led by Hao Yan, ASU's Milton Glick Professor in the School of Molecular Sciences, and director of the ASU Biodesign Institute's Center for Molecular Design and Biomimetics, has just announced the creation of a new type of meta-DNA structures that will open up the fields of optoelectronics (including information storage and encryption) as well as synthetic biology.

Solving a DNA mystery
''A watched pot never boils,'' as the saying goes, but that was not the case for UC Santa Barbara researchers watching a ''pot'' of liquids formed from DNA.

Junk DNA might be really, really useful for biocomputing
When you don't understand how things work, it's not unusual to think of them as just plain old junk.

Designing DNA from scratch: Engineering the functions of micrometer-sized DNA droplets
Scientists at Tokyo Institute of Technology (Tokyo Tech) have constructed ''DNA droplets'' comprising designed DNA nanostructures.

Does DNA in the water tell us how many fish are there?
Researchers have developed a new non-invasive method to count individual fish by measuring the concentration of environmental DNA in the water, which could be applied for quantitative monitoring of aquatic ecosystems.

Zigzag DNA
How the cell organizes DNA into tightly packed chromosomes. Nature publication by Delft University of Technology and EMBL Heidelberg.

Scientists now know what DNA's chaperone looks like
Researchers have discovered the structure of the FACT protein -- a mysterious protein central to the functioning of DNA.

DNA is like everything else: it's not what you have, but how you use it
A new paradigm for reading out genetic information in DNA is described by Dr.

A new spin on DNA
For decades, researchers have chased ways to study biological machines.

From face to DNA: New method aims to improve match between DNA sample and face database
Predicting what someone's face looks like based on a DNA sample remains a hard nut to crack for science.

Read More: DNA News and DNA Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to