From politics to Facebook, transparency is on all our minds. And science, of
course, depends on transparency to advance.
A big barrier to transparency in scientific research is the cost of viewing
peer reviewed articles. A simple Google® Scholar search on a topic of your
choosing will result in thousands of articles, many of which you might want to
read. Unfortunately, to review an article requires payment of $30 or more. Who
can afford that?
The mission of open access sites like PLOS-Public Library of Science (http://journals.plos.org/) is to breach the cost barrier and promote the free flow of peer reviewed
research.
Granted, the focus of PLOS seems to be on medical research. And yet, even so,
an article by ExxonMobil researchers Prosset and Hedgpeth, is a part of the
trove of treasures in this collection.
Viva transparency!
///////
Effects of
bioturbation on environmental DNA migration through soil media
Christopher M. Prosser
& Bryan M. Hedgpeth
PLOS Published: April 24, 2018 •
https://doi.org/10.1371/journal.pone.0196430
Contributed equally to this work with: Christopher M. Prosser, Bryan M.
Hedgpeth
Roles: Conceptualization, Methodology, Writing
* E-mail: Christopher.m.prosser@exxonmobil.com
ORCID: http://orcid.org/0000-0002-5209-1878 Bryan M. Hedgpeth
Affiliation: ExxonMobil Biomedical Sciences
Incorporated, Annandale, NJ, United States of America
Abstract
Extracting and identifying genetic material from environmental media (i.e.
water and soil) presents a unique opportunity for researchers to assess biotic
diversity and ecosystem health with increased speed and decreased cost as
compared to traditional methods (e.g. trapping). The heterogeneity of soil
mineralogy, spatial and temporal variations however present unique challenges
to sampling and interpreting results. Specifically, fate/transport of genetic
material in the terrestrial environment represents a substantial data gap. Here
we investigate to what degree, benthic fauna transport genetic material through
soil. Using the red worm (Eisenia fetida), we investigate how natural movement
through artificial soil affect the transport of genetic material. All
experiments were run in Frabill® Habitat® II worm systems with approximately 5
cm depth of artificial soil. We selected an ªexoticº source of DNA not expected
to be present in soil, zebrafish (Danio rerio) tissue. Experiment groups
contained homogenized zebrafish tissue placed in a defined location combined
with a varying number of worms (10, 30 or 50 worms per experimental group).
Experimental groups comprised two controls and three treatment groups
(representing different worm biomass) in triplicate. A total of 210 soil
samples were randomly collected over the course of 15 days to investigate the
degree of genetic transfer, and the rate of detection. Positive detections were
identified in 14% - 38% of samples across treatment groups, with an overall
detection rate of 25%. These findings highlight two important issues when
utilizing environmental DNA for biologic assessments. First, benthic fauna are
capable of redistributing genetic material through a soil matrix. Second,
despite a defined sample container and abundance of worm biomass, as many as
86% of the samples were negative. This has substantial implications for
researchers and managers who wish to interpret environmental DNA results from
terrestrial systems. Studies such as these will aid in future study protocol
design and sample collection methodology. Introduction Accurate biodiversity
assessments are a central component to compliance with environmental regulations.
In the United States, for example, environmental impact statements under the National
Environmental Policy Act require extensive baseline information on
biodiversity. Similarly, quantitative biodiversity assessments are important
for assessing the progress of habitat reclamation efforts. However, traditional
biodiversity monitoring relies on direct (ex. traps, sightings) or indirect
(ex. tracks, calls) observation of organisms. Especially true for direct
methods such as trapping or netting, these activities are often time consuming,
expensive, and impractical in remote or hard to reach regions. Over the past
decade, technological advances have resulted in the ability to detect the
presence of organisms through amplification of environmental DNA (eDNA). eDNA is
a generic term collectively referring to all genetic material that can be
extracted from environmental media. Examples are extracellular DNA fragments,
hair, feces, blood, free microbial cells, pollen or any other source by which
cells and/or tissue may enter the environment [1]. Due to high precision, species-specific
detection and low rates of false positives, eDNA has been increasingly utilized
for an array of studies including biodiversity assessments, mapping of species
distributions, and detection of invasive and endangered species [1±5].
DNA-based ecosystem monitoring can have distinct advantages over traditional
sampling methods, including being less invasive/less destructive than
trapping/netting. Sampling only environmental media (water, soil, sediment),
reduces stress and danger of entrapment of valuable (e.g. endangered) species
in nets or snares. The DNA sequencing of bulk material containing the DNA of
dozens or hundreds of species would have been cost-prohibitive with older low
throughput DNA sequencing platforms (e.g. Sanger sequencing). However, with
next generation DNA sequencers (NGS), which use high-throughput technologies
such as massively parallel sequencing, it is now possible to generate millions
of DNA reads from bulk material in a short period of time [6]. Additionally, newer
DNA sequencing technologies boast low detection limits (10−8 ng/μL) allowing
for low levels of genetic material to be amplified and sequenced. To date, the
majority of eDNA studies have focused on aquatic and/or wetland systems [3, 7±9].
This is most likely due to methodological advantages of sampling aquatic media.
For example, lotic and lentic systems provide defined boundaries within which
to sample and relatively large volumes of water (as large as several liters)
can be filtered to concentrate available genetic material. In contrast to eDNA
analysis from aquatic/marine systems, there is generally a paucity of data from
terrestrial habitats. Soil matrices present unique challenges that are not encountered
in aquatic systems. For example, the volume of soil used in extractions is
typically a limiting factor (~0.25g soil per extraction). Additionally, little
is known on eDNA fate and mobility in terrestrial systems over time and space
(i.e. once deposited, there is little data to predict transport and/or
persistence). A non-detect may be a false-negative if in fact the complexity of
soil matrix precludes homogenous distribution of genetic material thus limiting
spatial area from which it can be detected. As compared to aqueous media, the
chemical complexity and reactivity of soils displays a greater degree of
spatial and temporal heterogeneity, raising questions about eDNA mobility in
soils. Soil mineralogy (e.g. clay, sand, silt) and subsequent mixtures (e.g.
silty clays) will greatly influence the amount of surface reactive particles
present, and thus the adsorption of genetic material within that matrix [10].
Physicochemical interactions influencing eDNA mobility within the soil matrix
are highly variable and will depend on DNA fragment size, soil mineralogy,
hydrophobicity, pH and ionic strength [11]. Persistence of eDNA in soils has
also received limited attention and is incompletely understood. The presence of
clay and soil colloids has been suggested to prohibit enzymatic degradation of
genetic material thus potentially prolonging its availability for detection
[12,13]. In anoxic environments, such as lake sediment, eDNA has been recovered
dating back thousands of years [14]. Conversely, eDNA can also be taken up by
bacteria as a source of nutrition expediting its removal from the environment [10].
Such uncertainties have led to wide estimates in persistence ranging from days
to years in the top 15 cm of soil [15]. To date, few field studies have been
conducted specifically focused on eDNA extraction from soil. However, in recent
years researchers have investigated soil samples from natural wetland habitats
[16] as well as in more spatially defined zoos and parks [17]. Fahner et al.
[16] investigated large-scale plant monitoring using DNA metabarcoding.
Researchers collected core samples from the Ramsar designated Peace-Athabasca
Delta in Wood Buffalo National Park, Alberta, Canada with the goal of
identifying standard DNA markers designed to evaluate floral biodiversity. An
important approach in this study was the targeting of full length amplicons (400±900
base pairs), demonstrating this length is not so extensively degraded to
preclude their use in biodiversity assessment. Andersen et al. [17]
investigated a fundamental relationship between known species abundance and
detectable levels of eDNA. Researchers isolated and amplified eDNA from known species
in safari parks, zoological gardens, and farms and found that detectable eDNA
generally reflected the diversity of animals on the landscape. However, these
researchers reported patchy detection (as low as 31%) from soil surface.
Researchers also reported eDNA extraction efficiency was inversely proportional
to organic carbon content of the soil. The vast majority of studies to date
have focused on the presence/absence of DNA in the environment; however, such
studies do little to investigate eDNA fate and transport. While there are some
exceptions in aquatic systems (i.e. [8]), there is a noticeable data gap investigating
such effects in terrestrial systems. While the deposition of genetic material
through normal processes (e.g. hair loss) is generally accepted, the degree to
which physical (e.g. wind/rain) and biological (bioturbation) processes
disseminate genetic material through terrestrial media are not well understood.
As eDNA continues to grow as a tool for use in ecological assessments, a
fundamental understanding of detection rate, and the risk of false negatives in
terrestrial media will bolster data interpretation. Given the paucity of data
related to eDNA fate and transport within terrestrial environments, the scope
of this study focused on whether bioturbation will transport eDNA through soil.
Our study was designed to investigate if normal biotic activity (e.g. the
natural movement of worms through soil) would transport detectable levels of
genetic material from a single, well defined depositional source, to adjacent
areas. The redworm (Eisenia fetida) was used in controlled laboratory
experiments to examine if, and to what degree bioturbation moves DNA from a
single deposition source through soil.
source: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0196430
///////
Here are some excerpts from the PLOS Web site …
///////
Founded in 2001 as an alternative to the
growing constraints of traditional scientific publishing, the Public Library of
Science (PLOS) rapidly evolved into a driving force in the Open Access
movement.
source: https://www.plos.org/history
///////
Your Research, Our Resources
QUALITY Scientists that peer review and
serve on editorial boards for PLOS are experts committed to reporting, ethics
and publishing guidelines. This means every article published with PLOS is the
most robust it can be.
SPEED From submission to acceptance,
PLOS publishing processes are tightly focused to eliminate unnecessary
publication delays.
INFLUENCE Policymakers, educators,
journalists and organizations around the world turn to trustworthy research
published in PLOS journals. In 2017, nearly 4,000 research articles were
covered by news sources such as the BBC, NPR, The New York Times and The
Guardian. That's a 15% increase from our 2016 coverage.
OPEN ACCESS FOR MAXIMUM IMPACT PLOS
research attracts more than 15 million article views per month. Articles are
immediately and freely available under a Creative Commons Attribution License
(CC BY).
ARTICLE-LEVEL METRICS (ALMS) PubMed,
Scopus, Web of Science and Google Scholar feature PLOS articles. At PLOS, all
these sources feed into ALMs to help demonstrate the influence of your work.
DATA AVAILABLITY Authors commit to
making the data underlying their conclusions fully available, when at all
possible. This enables validation, replication and reproducibility—all
increasing the value of research. source: source: https://www.plos.org/why-publish-with-plos
///////
TIP:
Search the PLOS Web (http://journals.plos.org/plosone/)
using whatever term you are interested in … like, for example, desulfurization.
Then read to your heart’s content.
No comments:
Post a Comment