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Lu S, Zeng H, Xiong F, Yao M, He S. Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1368-1384. [PMID: 38512561 DOI: 10.1007/s11427-023-2493-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 03/23/2024]
Abstract
Environmental DNA (eDNA) monitoring, a rapidly advancing technique for assessing biodiversity and ecosystem health, offers a noninvasive approach for detecting and quantifying species from various environmental samples. In this review, a comprehensive overview of current eDNA collection and detection technologies is provided, emphasizing the necessity for standardization and automation in aquatic ecological monitoring. Furthermore, the intricacies of water bodies, from streams to the deep sea, and the associated challenges they pose for eDNA capture and analysis are explored. The paper delineates three primary eDNA survey methods, namely, bringing back water, bringing back filters, and bringing back data, each with specific advantages and constraints in terms of labor, transport, and data acquisition. Additionally, innovations in eDNA sampling equipment, including autonomous drones, subsurface samplers, and in-situ filtration devices, and their applications in monitoring diverse taxa are discussed. Moreover, recent advancements in species-specific detection and eDNA metabarcoding are addressed, highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of biodiversity. The implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological data. Lastly, the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term biomonitoring. We propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring, aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.
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Affiliation(s)
- Suxiang Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
- School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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Sakata A, Sado T, Oka SI, Ushio M, Miya M. Collection of environmental DNA from stemflow for monitoring arboreal biodiversity: Preliminary validation using lichens. MethodsX 2023; 11:102448. [PMID: 38023308 PMCID: PMC10630645 DOI: 10.1016/j.mex.2023.102448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
The forest canopy harbors a diverse array of organisms. However, monitoring their biodiversity poses challenges due to limited accessibility and the vast taxonomic diversity. To address these challenges, we present a novel method for capturing arboreal biodiversity by harnessing stemflow as a source of DNA from organisms inhabiting trees. Our method involves encircling the tree trunk with gauze, directing the stemflow along the gauze into a funnel, and collecting it in a plastic bag. We employed dual collection systems to retrieve environmental DNA (eDNA) from the stemflow: the gauze trap, designed to capture macroscopic biological fragments, and the plastic bag trap, which collected the stemflow itself. The trapped fragments and stemflow were separately filtered, and eDNA was subsequently extracted from the filter membranes. To validate our method, we focused on foliose lichens, which are easily observable on tree surfaces. We performed eDNA metabarcoding and successfully detected a majority of the observed foliose lichen species, including those not identified through visual observation alone.•We have developed a non-invasive and straightforward method for monitoring arboreal biodiversity by collecting eDNA from stemflow, which has been validated using lichens for its efficacy.•This cost-effective approach minimizes disruptions to tree ecosystems and is expected to provide an efficient means of sampling and monitoring arboreal organisms.
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Affiliation(s)
- Ayumi Sakata
- Natural History Museum and Institute, Chiba, Japan
| | - Tetsuya Sado
- Natural History Museum and Institute, Chiba, Japan
| | | | - Masayuki Ushio
- Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Masaki Miya
- Natural History Museum and Institute, Chiba, Japan
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Ushio M, Saito H, Tojo M, Nagano AJ. An ecological network approach for detecting and validating influential organisms for rice growth. eLife 2023; 12:RP87202. [PMID: 37702717 PMCID: PMC10499375 DOI: 10.7554/elife.87202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] Open
Abstract
How to achieve sustainable food production while reducing environmental impacts is a major concern in agricultural science, and advanced breeding techniques are promising for achieving such goals. However, rice is usually grown under field conditions and influenced by surrounding ecological community members. How ecological communities influence the rice performance in the field has been underexplored despite the potential of ecological communities to establish an environment-friendly agricultural system. In the present study, we demonstrate an ecological-network-based approach to detect potentially influential, previously overlooked organisms for rice (Oryza sativa). First, we established small experimental rice plots, and measured rice growth and monitored ecological community dynamics intensively and extensively using quantitative environmental DNA metabarcoding in 2017 in Japan. We detected more than 1000 species (including microbes and macrobes such as insects) in the rice plots, and nonlinear time series analysis detected 52 potentially influential organisms with lower-level taxonomic information. The results of the time series analysis were validated under field conditions in 2019 by field manipulation experiments. In 2019, we focused on two species, Globisporangium nunn and Chironomus kiiensis, whose abundance was manipulated in artificial rice plots. The responses of rice, namely, the growth rate and gene expression patterns, were measured before and after the manipulation. We confirmed that, especially in the G. nunn-added treatment, rice growth rate and gene expression pattern were changed. In the present study, we demonstrated that intensive monitoring of an agricultural system and the application of nonlinear time series analysis were helpful to identify influential organisms under field conditions. Although the effects of the manipulations were relatively small, the research framework presented here has future potential to harness the ecological complexity and utilize it in agriculture. Our proof-of-concept study would be an important basis for the further development of field-basis system management.
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Affiliation(s)
- Masayuki Ushio
- Hakubi Center, Kyoto UniversityKyotoJapan
- Center for Ecological Research, Kyoto UniversityOtsuJapan
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, KowloonHong Kong SARChina
| | - Hiroki Saito
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural SciencesOkinawaJapan
| | - Motoaki Tojo
- Graduate School of Agriculture, Osaka Metropolitan UniversityOsakaJapan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku UniversityOtsuJapan
- Institute for Advanced Biosciences, Keio UniversityTsuruokaJapan
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DeHart HM, Gasser MT, Dixon J, Thielen P. An aquatic environmental DNA filtration system to maximize recovery potential and promote filtration approach standardization. PeerJ 2023; 11:e15360. [PMID: 37456865 PMCID: PMC10349554 DOI: 10.7717/peerj.15360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/16/2023] [Indexed: 07/18/2023] Open
Abstract
Background Aquatic environmental DNA (eDNA) has emerged as a promising approach to identify organisms in freshwater and marine environments. While the recovery of eDNA from water most commonly involves capture of biological debris on a filter matrix, practitioners are yet to converge on standardized approaches for filtration, particularly in the field. This lack of standardization has resulted in inconsistent handling of samples following collection, limiting interpretation of results across studies and burdening groups with inconvenient storage and transport logistics that may compromise eDNA integrity. Methods A simple to assemble and low-cost ($350 USD) water filtration system is demonstrated that can be used in field and laboratory settings to reduce time between sample acquisition and eDNA filtration, maximizing eDNA sample recovery. Quantitative PCR is used to show the utility of the platform for laboratory and marine eDNA analysis. Results The resulting eDNA collection system is easily transported in a rugged water-resistant case, operates for more than eight hours on a 12-volt lead-acid battery, and has an unobstructed filtration rate of 150.05 ± 7.01 mL/min and 151.70 ± 6.72 mL/min with 0.22 µm and 0.45 µm Sterivex filters, respectively. We show that immediate sample filtration increases eDNA recovery in the laboratory, and demonstrate collections in aquaria and marine environments. We anticipate that providing easy to obtain, open hardware designs for eDNA sample collection will increase standardization of aquatic eDNA collection methods and improve cross-study comparisons.
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Affiliation(s)
- Hayley M. DeHart
- Research and Exploratory Development Department, The Johns Hopkins University, Laurel, MD, United States of America
| | - Mark T. Gasser
- Research and Exploratory Development Department, The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States of America
| | - Jarret Dixon
- Force Projection Sector, The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States of America
| | - Peter Thielen
- Research and Exploratory Development Department, The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States of America
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Yoneya K, Ushio M, Miki T. Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant. Sci Rep 2023; 13:7125. [PMID: 37173307 PMCID: PMC10182007 DOI: 10.1038/s41598-023-32862-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 04/04/2023] [Indexed: 05/15/2023] Open
Abstract
Reliable survey of arthropods is a crucial for their conservation, community ecology, and pest control on terrestrial plants. However, efficient and comprehensive surveys are hindered by challenges in collecting arthropods and identifying especially small species. To address this issue, we developed a non-destructive environmental DNA (eDNA) collection method termed "plant flow collection" to apply eDNA metabarcoding to terrestrial arthropods. This involves spraying distilled or tap water, or using rainfall, which eventually flows over the surface of the plant, and is collected in a container that is set at the plant base. DNA is extracted from collected water and a DNA barcode region of cytochrome c oxidase subunit I (COI) gene is amplified and sequenced using a high-throughput Illumina Miseq platform. We identified more than 64 taxonomic groups of arthropods at the family level, of which 7 were visually observed or artificially introduced species, whereas the other 57 groups of arthropods, including 22 species, were not observed in the visual survey. These results show that the developed method is possible to detect the arthropod eDNA remained on plants although our sample size was small and the sequence size was unevenly distributed among the three water types tested.
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Affiliation(s)
- Kinuyo Yoneya
- Faculty of Agriculture, Kindai University, 3327-204, Nakamachi, Nara, 631-8505, Japan.
- Center for Biodiversity Science, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan.
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, 606-8501, Japan
- Center for Ecological Research, Kyoto University, Otsu, 520-2113, Japan
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Takeshi Miki
- Center for Biodiversity Science, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
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Patin NV, Goodwin KD. Capturing marine microbiomes and environmental DNA: A field sampling guide. Front Microbiol 2023; 13:1026596. [PMID: 36713215 PMCID: PMC9877356 DOI: 10.3389/fmicb.2022.1026596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/22/2022] [Indexed: 01/15/2023] Open
Abstract
The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.
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Affiliation(s)
- Nastassia Virginia Patin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States,*Correspondence: Nastassia Virginia Patin,
| | - Kelly D. Goodwin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States
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Inoue N, Sato M, Furuichi N, Imaizumi T, Ushio M. The relationship between eDNA density distribution and current fields around an artificial reef in the waters of Tateyama Bay, Japan. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.87415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Monitoring of artificial reefs (ARs) has been conducted through such methods as visual censuses, surveys using fishing gear, and echo sounder. These methods have disadvantages: visual census is not possible at ARs in deeper waters, fishing gear surveys are invasive to fish individuals, and echo sounders have difficulty in species identification. A new AR monitoring method is required to compensate for these disadvantages. While eDNA has become a valid monitoring tool for marine biodiversities, it is influenced by degradation and transport of the molecules that affect information about the spatio-temporal distribution of fish. An understanding of the relationship between current fields and eDNA distribution, particularly in open waters, is critical when using eDNA as an index for fish aggregation at ARs. We investigated the relationship between eDNA distribution and current fields around an AR for four dominant species (Engraulis japonicus, Parapristipoma trilineatum, Scomber spp and Trachurus japonicus) in Tateyama Bay, Japan. The highest density of fish schools is formed directly above or at the upstream side of ARs. If we assume that the center of eDNA originates at these locations at an AR and eDNA is simply transported by currents, a higher density of eDNA would distribute downstream from the AR. However, our results indicate that eDNA distribution is in accord with actual fish distribution, namely eDNA densities are more abundant in the upstream side of ARs. We thus consider that eDNA distribution is more influenced by actual distribution patterns than by the transport processes.
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Jiménez Elvira N, Ushio M, Sakai S. Are microbes growing on flowers evil? Effects of old flower microbes on fruit set in a wild ginger with one-day flowers, Alpinia japonica (Zingiberaceae). METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.84331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Flowers are colonized and inhabited by diverse microbes. Flowers have various mechanisms to suppress microbial growth, such as flower volatiles, reactive oxygen and secondary compounds. Besides, plants rapidly replace flowers that have a short lifespan, and old flowers senesce. They may contribute to avoiding adverse effects of the microbes. In this study, we investigate if the flower microbial community on old flowers impedes fruit and seed production in a wild ginger with one-day flowers. We focus on microbes on old flowers because they may be composed of microbes that would grow during flowering if the flowers did not have mechanisms to suppress microbial growth. We inoculated newly opened flowers with old flower microbes, and monitored the effects on fruit and seed set. We also assessed prokaryotic communities on the flowers using 16S rRNA amplicon sequencing. We found six bacterial amplicon sequence variants (ASVs) whose proportions were increased on the inoculated flowers. These ASVs were also found on flower buds and flowers that were bagged by net or paper during anthesis, suggesting that they had been present in small numbers prior to flowering. Fruit set was negatively associated with the proportions of these ASVs, while seed set was not. The results suggest that old flowers harbor microbial communities different from those at anthesis, and that the microbes abundant on old flowers negatively affect plant reproduction. Although it has received little attention, antagonistic microbes that rapidly proliferate on the flowers may have affected the evolution of various flower characteristics such as flower volatiles and life span.
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Matsuoka S, Sugiyama Y, Nagano M, Doi H. Influence of DNA extraction kits on freshwater fungal DNA metabarcoding. PeerJ 2022; 10:e13477. [PMID: 35651749 PMCID: PMC9150701 DOI: 10.7717/peerj.13477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/01/2022] [Indexed: 01/17/2023] Open
Abstract
Background Environmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes. Methods DNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extractmicrobial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results; i.e., operational taxonomic unit (OTU) number and composition of the extracted samples. Results No PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals.
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Affiliation(s)
- Shunsuke Matsuoka
- Field Science Education and Research Center, Kyoto University, Kyoto, Japan
| | - Yoriko Sugiyama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Mariko Nagano
- Department of Bioenvironmental Design, Kyoto University of Advanced Science, Kameoka, Japan
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, Kobe, Japan
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Abstract
How patterns in community diversity emerge is a long-standing question in ecology. Studies suggested that community diversity and interspecific interactions are interdependent. However, evidence from high-diversity ecological communities is lacking because of practical challenges in characterizing speciose communities and their interactions. Here, I analysed time-varying interaction networks that were reconstructed using 1197 species, DNA-based ecological time series taken from experimental rice plots and empirical dynamic modelling, and introduced 'interaction capacity', namely, the sum of interaction strength that a single species gives and receives, as a potential driver of community diversity. As community diversity increases, the number of interactions increases exponentially but the mean interaction capacity of a community becomes saturated, weakening interspecific interactions. These patterns are modelled with simple mathematical equations, based on which I propose the 'interaction capacity hypothesis': that interaction capacity and network connectance can be two fundamental properties that influence community diversity. Furthermore, I show that total DNA abundance and temperature influence interaction capacity and connectance nonlinearly, explaining a large proportion of diversity patterns observed in various systems. The interaction capacity hypothesis enables mechanistic explanations of community diversity. Therefore, analysing ecological community data from the viewpoint of interaction capacity would provide new insight into community diversity.
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Affiliation(s)
- Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto 606-8501, Japan,Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
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Serrana JM, Watanabe K. Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16S rRNA amplicon sequencing. BMC Microbiol 2022; 22:33. [PMID: 35057747 PMCID: PMC8772107 DOI: 10.1186/s12866-022-02441-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Sequential membrane filtration as a pre-processing step for capturing sediment-associated microorganisms could provide good quality and integrity DNA that can be preserved and kept at ambient temperatures before community profiling through culture-independent molecular techniques. However, the effects of sample pre-processing via filtration on DNA-based profiling of sediment-associated microbial community diversity and composition are poorly understood. Specifically, the influences of pre-processing on the quality and quantity of extracted DNA, high-throughput DNA sequencing reads, and detected microbial taxa need further evaluation. RESULTS We assessed the impact of pre-processing freshwater sediment samples by sequential membrane filtration (from 10, 5 to 0.22 μm pore size) for 16S rRNA-based community profiling of sediment-associated microorganisms. Specifically, we examined if there would be method-driven differences between non- and pre-processed sediment samples regarding the quality and quantity of extracted DNA, PCR amplicon, resulting high-throughput sequencing reads, microbial diversity, and community composition. We found no significant difference in the qualities and quantities of extracted DNA and PCR amplicons, and the read abundance after bioinformatics processing (i.e., denoising and chimeric-read filtering steps) between the two methods. Although the non- and pre-processed sediment samples had more unique than shared amplicon sequence variants (ASVs), we report that their shared ASVs accounted for 74% of both methods' absolute read abundance. More so, at the genus level, the final collection filter identified most of the genera (95% of the reads) captured from the non-processed samples, with a total of 51 false-negative (2%) and 59 false-positive genera (3%). We demonstrate that while there were differences in shared and unique taxa, both methods revealed comparable microbial diversity and community composition. CONCLUSIONS Our observations highlight the feasibility of pre-processing sediment samples for community analysis and the need to further assess sampling strategies to help conceptualize appropriate study designs for sediment-associated microbial community profiling.
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Affiliation(s)
- Joeselle M Serrana
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 790-8577, Japan
| | - Kozo Watanabe
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 790-8577, Japan.
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Formel N, Enochs IC, Sinigalliano C, Anderson SR, Thompson LR. Subsurface automated samplers for eDNA (SASe) for biological monitoring and research. HARDWAREX 2021; 10:e00239. [PMID: 35607674 PMCID: PMC9123479 DOI: 10.1016/j.ohx.2021.e00239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 10/04/2021] [Accepted: 10/09/2021] [Indexed: 05/05/2023]
Abstract
Sampling of environmental DNA (eDNA) in seawater is an increasingly common approach to non-invasively assess marine biodiversity, detect cryptic or invasive species, and monitor specific groups of organisms. Despite this remarkable utility, collection and filtration of eDNA samples in the field still requires considerable time and effort. Recent advancements in automated water samplers have standardized the eDNA collection process, allowing researchers to collect eDNA day or night, sample in locations that are difficult to access, and remove the need for highly trained personnel to perform sampling. However, the high cost of purchasing or building these samplers represents a financial hurdle to widespread application. To overcome this difficulty, we have designed and built a low-cost subsurface automated sampler for eDNA (SASe). Each sampler is submersible to 55 m, can filter a pre-programmable volume of water, and preserves eDNA at the site of collection. SASe samplers have replaceable filters and a low build cost (∼280 USD vs. >100,000 USD for other eDNA samplers), which facilitates repeated field sampling at fine spatial and temporal scales. Lab testing has shown the SASe to be as effective as a standard desktop peristaltic pump for sampling, preserving, and recovering marine eDNA. SASe design files and operating code are open-source, promoting the use of this tool to meet a range of future eDNA research applications, including project-specific customizations to the current design.
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Affiliation(s)
- Nathan Formel
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, NOAA, 4301 Rickenbacker Cswy, Miami, FL 33149, USA
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, 4600 Rickenbacker Cswy, Miami, FL 33149, USA
| | - Ian C. Enochs
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, NOAA, 4301 Rickenbacker Cswy, Miami, FL 33149, USA
| | - Chris Sinigalliano
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, NOAA, 4301 Rickenbacker Cswy, Miami, FL 33149, USA
| | - Sean R. Anderson
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, NOAA, 4301 Rickenbacker Cswy, Miami, FL 33149, USA
- Northern Gulf Institute, Mississippi State University, 2 Research Blvd, Starkville, MS 39759, USA
| | - Luke R. Thompson
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, NOAA, 4301 Rickenbacker Cswy, Miami, FL 33149, USA
- Northern Gulf Institute, Mississippi State University, 2 Research Blvd, Starkville, MS 39759, USA
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Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey. Sci Rep 2021; 11:19477. [PMID: 34593907 PMCID: PMC8484675 DOI: 10.1038/s41598-021-98926-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/08/2021] [Indexed: 01/03/2023] Open
Abstract
Since the early 1970s, many artificial reefs (ARs) have been deployed in Japanese coastal waters to create fisheries grounds. Recently, researchers began to use environmental DNA (eDNA) methods for biodiversity monitoring of aquatic species. A metabarcoding approach using internal standard DNAs [i.e., quantitative MiSeq sequencing (qMiSeq)] makes it possible to monitor eDNA concentrations of multiple species simultaneously. This method can improve the efficiency of monitoring AR effects on fishes. Our study investigated distributions of marine fishes at ARs and surrounding stations in the open oceanographic environment of Tateyama Bay, central Japan, using qMiSeq and echo sounder survey. Using the qMiSeq with 12S primers, we found higher quantities of fish eDNAs at the ARs than at surrounding stations and different fish species compositions between them. Comparisons with echo sounder survey also showed positive correlations between fish eDNA concentration and echo intensity, which indicated a highly localized signal of eDNA at each sampling station. These results suggest that qMiSeq is a promising technique to complement conventional methods to monitor distributions of multiple fish species.
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Matsuoka S, Sugiyama Y, Shimono Y, Ushio M, Doi H. Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding. Environ Microbiol 2021; 23:4797-4806. [PMID: 34258854 DOI: 10.1111/1462-2920.15669] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 11/27/2022]
Abstract
Investigation of seasonal variation in fungal communities is essential for understanding biodiversity and ecosystem functions. However, the conventional sampling method, with substrate removal and high spatial heterogeneity of community composition, makes surveying the seasonality of fungal communities challenging. Recently, water environmental DNA (eDNA) analysis has been explored for its utility in biodiversity surveys. In this study, we assessed whether the seasonality of fungal communities can be detected by monitoring eDNA in a forest stream. We conducted monthly water sampling in a forest stream over 2 years and used DNA metabarcoding to identify fungal eDNA. The stream water contained DNA from functionally diverse aquatic and terrestrial fungi, such as plant decomposers, parasites and mutualists. The variation in the fungal assemblage showed a regular annual periodicity, meaning that the assemblages in a given season were similar, irrespective of the year or sampling. Furthermore, the strength of the annual periodicity varied among functional groups. Our results suggest that forest streams may act as a 'trap' for terrestrial fungal DNA derived from different habitats, allowing the analysis of fungal DNA in stream water to provide information about the temporal variation in fungal communities in both the aquatic and the surrounding terrestrial ecosystems.
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Affiliation(s)
- Shunsuke Matsuoka
- Graduate School of Information Science, University of Hyogo, Kobe, Japan
| | - Yoriko Sugiyama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Yoshito Shimono
- Graduate School of Bioresources, Mie University, Tsu, Japan.,Osaka Museum of Nature History, Osaka, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, Japan.,Center for Ecological Research, Kyoto University, Kyoto, Japan
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, Kobe, Japan
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15
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Field application of an improved protocol for environmental DNA extraction, purification, and measurement using Sterivex filter. Sci Rep 2020; 10:21531. [PMID: 33298993 PMCID: PMC7725969 DOI: 10.1038/s41598-020-77304-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/10/2020] [Indexed: 11/29/2022] Open
Abstract
Environmental DNA (eDNA) is increasingly popular as a useful non-invasive method to monitor and study biodiversity and community structure in freshwater and marine environments. To effectively extract eDNA from the filter surface is a fundamental factor determining the representativeness of the samples. We improved the eDNA extraction efficiency of an established Sterivex method by 12- to 16-fold using a larger volume of lysis buffer mix coupled with backflushing the cartridges. The DNeasy extraction column could be overloaded when the environmental sample input is high, possibly due to a higher nonspecific binding present in environmental samples, thus resulting in a relatively lower quantity measured. Therefore, we included an internal control DNA in the extraction to monitor the extraction and purification efficiencies in field samples, which is crucial for quantification of original eDNA concentration. The use of Takara Probe qPCR Mix supplemented with protein-based additives improved the robustness of the real time PCR assay on inhibitor-rich environmental samples, but prior purification by Qiagen PowerClean Pro Cleanup kit could be essential for inhibitor-rich water samples, even though the recovery rate was unexpectedly low (average 33.0%). The improved extraction and quantification complement the qualitative analyses including metabarcoding and metagenomics in field application.
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16
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Tsuji S, Shibata N, Sawada H, Ushio M. Quantitative evaluation of intraspecific genetic diversity in a natural fish population using environmental DNA analysis. Mol Ecol Resour 2020; 20:1323-1332. [PMID: 32452621 DOI: 10.1111/1755-0998.13200] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/01/2020] [Accepted: 05/18/2020] [Indexed: 01/04/2023]
Abstract
Recent advances in environmental DNA (eDNA) analysis using high-throughput sequencing (HTS) enable evaluation of intraspecific genetic diversity in a population. As the intraspecific genetic diversity provides invaluable information for wildlife conservation and management, there is an increasing demand to apply eDNA analysis to population genetics and the phylogeography by quantitative evaluation of intraspecific diversity. However, quantitative evaluations of intraspecific genetic diversity using eDNA is not straightforward because the number of eDNA sequence reads obtained by HTS may not be an index of the quantity of eDNA. In this study, to quantitatively evaluate genetic diversity using eDNA analysis, we applied a quantitative eDNA metabarcoding method using the internal standard DNAs. We targeted Ayu (Plecoglossus altivelis altivelis) and added internal standard DNAs with known copy numbers to each eDNA sample obtained from three rivers during the library preparation process. The sequence reads of each Ayu haplotype were successfully converted to DNA copy numbers based on the relationship between the copy numbers and sequence reads of the internal standard DNAs. In all rivers, the calculated copy number of each haplotype showed a significant positive correlation with the haplotype frequency estimated by a capture-based survey. Furthermore, estimates of genetic indicators such as nucleotide diversity based on the eDNA copy numbers were comparable with those estimated based on a capture-based study. Our results demonstrate that eDNA analysis with internal standard DNAs enables reasonable quantification of intraspecific genetic diversity, and this method could thus be a promising tool in the field of population genetics and phylogeography.
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Affiliation(s)
- Satsuki Tsuji
- Graduate School of Science, Kyoto University, Kyoto, Japan.,Faculty of Science and Technology/Graduate School of Science and Technology, Ryukoku University, Otsu, Japan
| | - Naoki Shibata
- Faculty of Science and Technology/Graduate School of Science and Technology, Ryukoku University, Otsu, Japan
| | - Hayato Sawada
- Faculty of Science and Technology/Graduate School of Science and Technology, Ryukoku University, Otsu, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto, Japan.,Center for Ecological Research, Kyoto University, Otsu, Japan.,Japan Science and Technology Agency, PRESTO, Kawaguchi, Japan
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17
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Doi H. Idea paper: Community‐interaction analyses contribute to improving the performance of microbial fuel cells. Ecol Res 2020. [DOI: 10.1111/1440-1703.12134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Hideyuki Doi
- Graduate School of Simulation Studies University of Hyogo Kobe Japan
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18
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Ushio M. Idea paper: Predicting culturability of microbes from population dynamics under field conditions. Ecol Res 2020. [DOI: 10.1111/1440-1703.12104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Masayuki Ushio
- Hakubi Center Kyoto University Kyoto Japan
- Center for Ecological Research Kyoto University Otsu Shiga Japan
- PRESTO Japan Science and Technology Agency Kawaguchi Saitama Japan
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