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A microcosm study of surface sediment environmental DNA: decay observation, abundance estimation, and fragment length comparison. Nan Wei, Fumiyuki Nakajima, and Tomohiro Tobino Environ. Sci. Technol., Just Accepted Manuscript • DOI: 10.1021/acs.est.8b04956 • Publication Date (Web): 28 Sep 2018 Downloaded from http://pubs.acs.org on September 30, 2018
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Graphic Abstract 158x113mm (150 x 150 DPI)
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Title:
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A microcosm study of surface sediment environmental DNA: decay observation,
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abundance estimation, and fragment length comparison.
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Authors:
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† † † Nan Wei , Fumiyuki Nakajima* , Tomohiro Tobino
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Affiliations:
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† Department of Urban Engineering, The University of Tokyo, Hongo 7-3-1,
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Bunkyo-ku, Tokyo 113-8656, Japan
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Corresponding Author:
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Fumiyuki Nakajima
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Department of Urban Engineering, The University of Tokyo,
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Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan
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E-mail:
[email protected] 22
Tel: +81-3-5841-6260
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Abstract
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Interpretation of environmental DNA (eDNA) is a major problem hindering the
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application of this emerging technology for environmental monitoring. The decay
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characteristics and bioabundance estimation of different DNA fragment lengths are
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largely unknown, especially for eDNA captured from surface sediments. An estuarine
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amphipod, Grandidierella japonica was used as the target species in this study. We
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conducted a lab-scale experiment using DNA extraction to clarify the effect of
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bacteria on eDNA decay. We also conducted a microcosm experiment using
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amphipods to clarify interpretations of information regarding eDNA decay and
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bioabundance estimation by using two fragments with different lengths (126 bp and
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358 bp). It was found that the bacteria concentration accelerated eDNA decay, and
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long fragments were more susceptible to bacteria, thus decaying faster, than short
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fragments in the exponential decay period. The fresh eDNA (collected within 24 hours
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of removing the amphipods) was more indicative of bioabundance than old eDNA
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(collected 240~480 hours after removing amphipods), and short fragments better
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reflected bioabundance than long fragments. Finally, we compared the half-life of
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eDNA in surface sediment with that in a water sample and found that the temporal
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scales of surface sediment and water are similar (days to weeks). Our results suggest
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that surface sediment also has the potential to monitor the environment at a temporal
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scale similar to water.
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Key words: surface sediment; eDNA decay; abundance estimation; DNA fragment;
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qPCR
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Introduction
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Environmental DNA (eDNA) refers to the DNA captured from environmental
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samples which may contain tissue, feces, and mucus from organisms living in a
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certain area. The eDNA approach enables the detection of species in a non-invasive
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way, rather than directly sampling the species, making it much more cost effective
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than conventional biomonitoring methods. Since the emergence of environmental
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DNA around 2010, the applications of eDNA have been expanded from qualitatively
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detecting absence/presence of species with conventional polymerase chain reaction
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(PCR) to quantitatively estimating the abundance or richness of species by
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quantitative PCR (qPCR) or DNA metabarcoding1-3. However, there are still some
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knowledge gaps hindering the interpretation of eDNA information: for instance, the
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temporal scale of eDNA persistence especially in surface sediment, estimation of
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bioabundance, and development of DNA primer.
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The persistence of eDNA can be defined as the continuance of DNA after the
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removal of its source organisms4, reflecting the temporal scale for inference from
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eDNA. In the water phase, eDNA samples have a shorter temporal scale due to rapid
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eDNA degradation (eDNA remains detectable after removing the organisms for 25
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days4, 21 days5, 7~14 days6, 1~14 days7, 2~7 days8 and 2~54 days9). In the sediment
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phase the persistence period varies in a much larger range depending on the sample
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type: sediment cores reflect DNA information as far back as 4000 years10, 6000
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years11, and 12600 years12, or even longer13; surface sediment reflects a relatively
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current range of around 132 days14. Nevertheless, there are very limited studies about
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eDNA in surface sediment14, 15, the temporal scale of eDNA persistence in surface
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sediment is largely unknown, and needs further examination16. eDNA degradation
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happens ubiquitously. The effects of medium state17, temperature9,
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, sunlight9,
(UV), and pH9 on eDNA degradation were reported by previous studies, while the
effect of bacteria is not yet clear7, 18, and should be analyzed further.
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Positive relationships between eDNA from water samples and species
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abundance or biomass have been reported by previous studies6, 20-26, although the
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correlations were not obvious. Both linear and exponential relationships were
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obtained, and the correlation coefficients ranged from 0.03 to 0.93. There was a lack
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of knowledge about the relationship between species abundance and surface sediment
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eDNA. Moreover, we found that very limited studies investigated the benthic species,
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which are often used as indicator species for water quality assessment.
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PCR is an essential step for most eDNA approaches, where the DNA
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fragment length is one of the crucial factors. A recent study27 successfully amplified
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a >16 kb fragment of DNA from eDNA, while the most commonly applied fragment
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length is
