1
|
Linz D, Partridge CG, Hassett MC, Sienkiewicz N, Tyrrell K, Henderson A, Tardani R, Lu J, Steinman AD, Vesper S. Changes in Cyanobacterial Phytoplankton Communities in Lake-Water Mesocosms Treated with Either Glucose or Hydrogen Peroxide. Microorganisms 2024; 12:1925. [PMID: 39338598 PMCID: PMC11434412 DOI: 10.3390/microorganisms12091925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 09/20/2024] [Accepted: 09/20/2024] [Indexed: 09/30/2024] Open
Abstract
When cyanobacterial phytoplankton form harmful cyanobacterial blooms (HCBs), the toxins they produce threaten freshwater ecosystems. Hydrogen peroxide is often used to control HCBs, but it is broadly toxic and dangerous to handle. Previously, we demonstrated that glucose addition to lake water could suppress the abundance of cyanobacteria. In this study, glucose was compared to hydrogen peroxide for the treatment of cyanobacterial phytoplankton communities. The six-week study was conducted in the large mesocosms facility at Grand Valley State University's Annis Water Resources Institute in Michigan. To 1000 L of Muskegon Lake water, glucose was added at either 150 mg or 30 mg glucose/L. Hydrogen peroxide was added at 3 mg/L to two 1000 L mesocosms. And two mesocosms were left untreated as controls. Triplicate 100 mL samples were collected weekly from each mesocosm, which were then filtered and frozen at -80 °C for 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing results revealed that hydrogen peroxide treatment quickly reduced the relative abundance of the cyanobacteria compared to the control mesocosms, but the cyanobacteria population returned over the course of the 6-week study. On the other hand, both glucose concentrations caused a rapid proliferation of multiple low abundance proteobacterial and bacteroidotal taxa resulting in notable increases in taxonomic richness over the duration of the study and reducing the relative abundance of cyanobacteria. Although hydrogen peroxide quickly suppressed the cyanobacteria, the population later returned to near starting levels. The glucose suppressed the cyanobacterial phytoplankton apparently by promoting competitive heterotrophic bacteria.
Collapse
Affiliation(s)
- David Linz
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
| | - Charlyn G Partridge
- Annis Water Resources Institute, Graduate School, Grand Valley State University, Allendale, MI 49441, USA
| | - Michael C Hassett
- Annis Water Resources Institute, Graduate School, Grand Valley State University, Allendale, MI 49441, USA
| | - Nathan Sienkiewicz
- United States Environmental Protection Agency, Cincinnati, OH 45268, USA
| | - Katie Tyrrell
- Annis Water Resources Institute, Graduate School, Grand Valley State University, Allendale, MI 49441, USA
| | - Aimèe Henderson
- United States Environmental Protection Agency, Cincinnati, OH 45268, USA
| | - Renee Tardani
- Annis Water Resources Institute, Graduate School, Grand Valley State University, Allendale, MI 49441, USA
| | - Jingrang Lu
- United States Environmental Protection Agency, Cincinnati, OH 45268, USA
| | - Alan D Steinman
- Annis Water Resources Institute, Graduate School, Grand Valley State University, Allendale, MI 49441, USA
| | - Stephen Vesper
- United States Environmental Protection Agency, Cincinnati, OH 45268, USA
| |
Collapse
|
2
|
Yan R, Abdullah, Ahmed I, Jiang L, Tuliebieke T, Xing Z, Li H, Zhang Y, Zhang T, Tian X, Zhang H. The metabarcoding of Grubs: Traditional herbal medicine of Scarabaeidae larvae. Gene 2024; 910:148303. [PMID: 38401835 DOI: 10.1016/j.gene.2024.148303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/04/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
Grubs, called Qicao in China, have a long tradition as herbal medicine in East Asia. These larvae belong to the diverse family Scarabaeidae and are typically harvested from the wild during their immature stage based on morphological characteristics. However, rapid and accurate identification becomes challenging when relying solely on external morphological features, as the lack of clarity on biological sources raises safety concerns for clinical applications. The application of DNA metabarcoding provides a solution by enabling the determination of the biological source of a large sample. In the current study, we collected 19 batches of Grubs, consisting of 11,539 individuals, from the market and analyzed their biological composition through metabarcoding. We identified 49 Amplicon Sequence Variants (ASVs), 21 of which were Grubs. The 21 ASVs were classified into seven Molecular Operational Taxonomic Units (MOTUs) through species delimitation, which revealed that commercially available Grubs are predominantly sourced from Protaetia brevitarsis seulensis, while species of Rutelinae, Anomala, and Holotrichia were also abundant in some commercial batches. Among the identified ASVs, 28 belonged to non-Grub species and indicated adulteration from different animal families; high abundances of these ASVs were detected for Bombycidae, Tabanidae, and Viviparidae. Our findings underscore the complexity of Grubs' species composition and advocate for a deeper understanding of the wildlife sources contributing to herbal products. This research contributes valuable insights into the molecular identification of Grubs, paving the way for enhanced quality assurance in traditional medicine applications to provide safe and effective medicines for humanity.
Collapse
Affiliation(s)
- Rushan Yan
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Abdullah
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad 45710, Pakistan; Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards Band Science (KRISS), Daejeon 34113, Republic of Korea
| | - Lu Jiang
- Key Laboratory of Economic and Applied Entomology of Liaoning Province, College of Plant Protection, Shenyang Agricultural University, Shenyang Liaoning, 110866, China.
| | - Tenukeguli Tuliebieke
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Zhimei Xing
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Hui Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Yue Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Tingting Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Xiaoxuan Tian
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Huanyu Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.
| |
Collapse
|
3
|
Linz D, Struewing I, Sienkiewicz N, Steinman AD, Partridge CG, McIntosh K, Allen J, Lu J, Vesper S. Periodic Addition of Glucose Suppressed Cyanobacterial Abundance in Additive Lake Water Samples during the Entire Bloom Season. JOURNAL OF WATER RESOURCE AND PROTECTION 2024; 16:140-155. [PMID: 38487714 PMCID: PMC10936582 DOI: 10.4236/jwarp.2024.162009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Previously, we showed that prophylactic addition of glucose to Harsha Lake water samples could inhibit cyanobacteria growth, at least for a short period of time. The current study tested cyanobacterial control with glucose for the entire Harsha Lake bloom season. Water samples (1000 ml) were collected weekly from Harsha Lake during the algal-bloom season starting June 9 and lasting until August 24, 2022. To each of two 7-liter polypropylene containers, 500 ml of Harsha Lake water was added, and the containers were placed in a controlled environment chamber. To one container labeled "Treated," 0.15 g of glucose was added, and nothing was added to the container labeled "Control." After that, three 25 ml samples from each container were collected and used for 16S rRNA gene sequencing each week. Then 1000 ml of Harsha Lake water was newly collected each week, with 500 ml added to each container, along with the addition of 0.15 g glucose to the "Treated" container. Sequencing data were used to examine differences in the composition of bacterial communities between Treated and Control containers. Treatment with glucose altered the microbial communities by 1) reducing taxonomic diversity, 2) largely eliminating cyanobacterial taxa, and 3) increasing the relative abundance of subsets of non-cyanobacterial taxa (such as Proteobacteria and Actinobacteriota). These effects were observed across time despite weekly inputs derived directly from Lake water. The addition of glucose to a container receiving weekly additions of Lake water suppressed the cyanobacterial populations during the entire summer bloom season. The glucose appears to stimulate the diversity of certain bacterial taxa at the expense of the cyanobacteria.
Collapse
Affiliation(s)
- David Linz
- United States Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Ian Struewing
- United States Environmental Protection Agency, Cincinnati, Ohio, USA
| | | | - Alan David Steinman
- Annis Water Resources Institute, Grand Valley State University, Muskegon, USA
| | | | - Kyle McIntosh
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Joel Allen
- United States Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Jingrang Lu
- United States Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Stephen Vesper
- United States Environmental Protection Agency, Cincinnati, Ohio, USA
| |
Collapse
|
4
|
Warter MM, Tetzlaff D, Ring AM, Christopher J, Kissener HL, Funke E, Sparmann S, Mbedi S, Soulsby C, Monaghan MT. Environmental DNA, hydrochemistry and stable water isotopes as integrative tracers of urban ecohydrology. WATER RESEARCH 2024; 250:121065. [PMID: 38159541 DOI: 10.1016/j.watres.2023.121065] [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: 10/10/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Urbanization and the persistent environmental changes present a major challenge for urban freshwaters and availability of water for humans and wildlife. In order to increase understanding of urban ecohydrology, we investigated the variability of planktonic bacteria and benthic diatoms - as two key biological indicators - coupled with insights from hydrochemistry and stable water isotopes across four urban streams characterized by different dominant water sources in Berlin, the German capital, over a period of one year (2021-2022). DNA metabarcoding results show that substantial spatio-temporal variability exists across urban streams in terms of microbial diversity and richness, with clear links to abiotic factors and nutrient concentrations. Bacterial communities showed clear distinction between effluent-impacted and non-effluent impacted streams as well as clear seasonal turnover. In-stream benthic diatom assemblages also showed robust seasonal variation as well as high species diversity. Our multiple-tracer approach is relevant for emerging questions regarding the increased use of treated effluent to supplement declining baseflows, the assessment of stream restoration projects and the impact of storm drainage and surface pollution on aquatic ecosystem health. eDNA analysis allows analysis of spatial and temporal patterns not feasibly studied with traditional analyses of macroinvertebrates. This can ultimately be leveraged for future water resource management and restoration planning and monitoring of urban freshwater systems across metropolitan areas.
Collapse
Affiliation(s)
| | - Dörthe Tetzlaff
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Department of Geography, Humboldt University of Berlin, Berlin, Germany; Northern Rivers Institute, University of Aberdeen, St. Mary's Building, Kings College, Old Aberdeen, Scotland, United Kingdom
| | - Ann-Marie Ring
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Jan Christopher
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Hanna L Kissener
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Elisabeth Funke
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Sarah Sparmann
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Susan Mbedi
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Berlin, Germany; Museum für Naturkunde - Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany
| | - Chris Soulsby
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Department of Geography, Humboldt University of Berlin, Berlin, Germany; Chair of Water Resources Management and Modeling of Hydrosystems, Technical University Berlin, Berlin, Germany
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institute of Biology, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
5
|
Jeon Y, Struewing I, McIntosh K, Tidd M, Webb L, Ryu H, Mash H, Lu J. Spatial and Temporal Variability of Saxitoxin-Producing Cyanobacteria in U.S. Urban Lakes. Toxins (Basel) 2024; 16:70. [PMID: 38393148 PMCID: PMC10892283 DOI: 10.3390/toxins16020070] [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] [Received: 12/26/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Harmful cyanobacterial blooms (HCBs) are of growing global concern due to their production of toxic compounds, which threaten ecosystems and human health. Saxitoxins (STXs), commonly known as paralytic shellfish poison, are a neurotoxic alkaloid produced by some cyanobacteria. Although many field studies indicate a widespread distribution of STX, it is understudied relative to other cyanotoxins such as microcystins (MCs). In this study, we assessed eleven U.S. urban lakes using qPCR, sxtA gene-targeting sequencing, and 16S rRNA gene sequencing to understand the spatio-temporal variations in cyanobacteria and their potential role in STX production. During the blooms, qPCR analysis confirmed the presence of the STX-encoding gene sxtA at all lakes. In particular, the abundance of the sxtA gene had a strong positive correlation with STX concentrations in Big 11 Lake in Kansas City, which was also the site with the highest quantified STX concentration. Sequencing analysis revealed that potential STX producers, such as Aphanizomenon, Dolichospermum, and Raphidiopsis, were present. Further analysis targeting amplicons of the sxtA gene identified that Aphanizomenon and/or Dolichospermum are the primary STX producer, showing a significant correlation with sxtA gene abundances and STX concentrations. In addition, Aphanizomenon was associated with environmental factors, such as conductivity, sulfate, and orthophosphate, whereas Dolichospermum was correlated with temperature and pH. Overall, the results herein enhance our understanding of the STX-producing cyanobacteria and aid in developing strategies to control HCBs.
Collapse
Affiliation(s)
- Youchul Jeon
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Ian Struewing
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Kyle McIntosh
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Marcie Tidd
- United States Environmental Protection Agency, Region 8, Lakewood, CO 80225, USA
| | - Laura Webb
- United States Environmental Protection Agency, Region 7, Kansas City, KS 66101, USA
| | - Hodon Ryu
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Heath Mash
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Jingrang Lu
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| |
Collapse
|
6
|
Wu L, Osugi T, Inagawa T, Okitsu J, Sakamoto S, Minamoto T. Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons. Mol Ecol Resour 2024; 24:e13875. [PMID: 37830396 DOI: 10.1111/1755-0998.13875] [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] [Received: 02/07/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
Periodic monitoring can provide important information for the protection of endangered fish, sustainable use of fishery resources and management of alien species. Previous studies have attempted to monitor fish using non-invasive environmental DNA (eDNA) technology, generally employing quantitative PCR to quantify the eDNA concentration. However, the throughput was limited. High-throughput metabarcoding technology can detect the DNA of multiple species simultaneously in a single experiment but does not provide sufficient quantification. In this study, we applied a quantitative metabarcoding approach to simultaneously quantify the eDNA concentration of an entire fish assemblage in a small reservoir over two summer seasons. Traditional surveys were also conducted to investigate the individuals of fish. The eDNA concentrations were quantified using quantitative metabarcoding, and the fish species detected using this approach were highly consistent with the results of traditional fish monitoring. A significant positive relationship was observed between the eDNA concentration and fish species abundance. Seasonal changes in fish community structure were estimated using eDNA concentrations, which may reveal the activity seasons of different fish. The eDNA concentrations of different fish species peaked at different water temperatures, reflecting the differential responses of fish species to this environmental factor. Finally, by detecting outlier eDNA concentrations, the spawning activities of 13 fish species were estimated, 12 of which were roughly consistent with the current knowledge of fish spawning periods. These results indicate that quantitative eDNA metabarcoding with dozens of sampling times is useful for the simultaneous ecological monitoring of multiple fish species.
Collapse
Affiliation(s)
- Luhan Wu
- Graduate School of Human Development and Environment, Kobe University, Kobe City, Hyogo, Japan
| | | | | | | | | | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Kobe City, Hyogo, Japan
| |
Collapse
|
7
|
Hu H, Wei XY, Liu L, Wang YB, Jia HJ, Bu LK, Pei DS. Supervised machine learning improves general applicability of eDNA metabarcoding for reservoir health monitoring. WATER RESEARCH 2023; 246:120686. [PMID: 37812979 DOI: 10.1016/j.watres.2023.120686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/11/2023]
Abstract
Effective and standardized monitoring methodologies are vital for successful reservoir restoration and management. Environmental DNA (eDNA) metabarcoding sequencing offers a promising alternative for biomonitoring and can overcome many limitations of traditional morphological bioassessment. Recent attempts have even shown that supervised machine learning (SML) can directly infer biotic indices (BI) from eDNA metabarcoding data, bypassing the cumbersome calculation process of BI regardless of the taxonomic assignment of eDNA sequences. However, questions surrounding the general applicability of this taxonomy-free approach to monitoring reservoir health remain unclear, including model stability, feature selection, algorithm choice, and multi-season biomonitoring. Here, we firstly developed a novel biological integrity index (Me-IBI) that integrates multitrophic interactions and environmental information, based on taxonomy-assigned eDNA metabarcoding data. The Me-IBI can better distinguish the actual health status of the Three Gorges Reservoir (TGR) than physicochemical assessments and have a clear response to human activity. Then, taking this reliable Me-IBI as a supervised label, we compared the impact of selecting different numbers of features and SML algorithms on the stability and predictive performance of the model for predicting ecological conditions in multiple seasons using taxonomy-free eDNA metabarcoding data. We discovered that even with a small number of features, different SML algorithms can establish a stable model and obtain excellent predictive performance. Finally, we proposed a four-step strategy for standardized routine biomonitoring using SML tools. Our study firstly explores the general applicability problem of the taxonomy-free eDNA-SML approach and establishes a solid foundation for the large-scale and standardized biomonitoring application.
Collapse
Affiliation(s)
- Huan Hu
- Chongqing Jiaotong University, Chongqing, 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xing-Yi Wei
- Chongqing Jiaotong University, Chongqing, 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Li Liu
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yuan-Bo Wang
- Chongqing Jiaotong University, Chongqing, 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Huang-Jie Jia
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Ling-Kang Bu
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China.
| |
Collapse
|
8
|
Aunins AA, Mueller SJ, Fike JA, Cornman RS. Assessing arthropod diversity metrics derived from stream environmental DNA: spatiotemporal variation and paired comparisons with manual sampling. PeerJ 2023; 11:e15163. [PMID: 37020852 PMCID: PMC10069422 DOI: 10.7717/peerj.15163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Background Benthic invertebrate (BI) surveys have been widely used to characterize freshwater environmental quality but can be challenging to implement at desired spatial scales and frequency. Environmental DNA (eDNA) allows an alternative BI survey approach, one that can potentially be implemented more rapidly and cheaply than traditional methods. Methods We evaluated eDNA analogs of BI metrics in the Potomac River watershed of the eastern United States. We first compared arthropod diversity detected with primers targeting mitochondrial 16S (mt16S) and cytochrome c oxidase 1 (cox1 or COI) loci to that detected by manual surveys conducted in parallel. We then evaluated spatial and temporal variation in arthropod diversity metrics with repeated sampling in three focal parks. We also investigated technical factors such as filter type used to capture eDNA and PCR inhibition treatment. Results Our results indicate that genus-level assessment of eDNA compositions is achievable at both loci with modest technical noise, although database gaps remain substantial at mt16S for regional taxa. While the specific taxa identified by eDNA did not strongly overlap with paired manual surveys, some metrics derived from eDNA compositions were rank-correlated with previously derived biological indices of environmental quality. Repeated sampling revealed statistical differences between high- and low-quality sites based on taxonomic diversity, functional diversity, and tolerance scores weighted by taxon proportions in transformed counts. We conclude that eDNA compositions are efficient and informative of stream condition. Further development and validation of scoring schemes analogous to commonly used biological indices should allow increased application of the approach to management needs.
Collapse
Affiliation(s)
- Aaron A. Aunins
- Eastern Ecological Research Center, U.S. Geological Survey, Kearneysville, West Virginia, United States
| | - Sara J. Mueller
- Wildlife and Fisheries Sciences Program, The Pennsylvania State College, State College, Pennsylvania, United States
| | - Jennifer A. Fike
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States
| | - Robert S. Cornman
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States
| |
Collapse
|
9
|
Linz DM, Sienkiewicz N, Struewing I, Stelzer EA, Graham JL, Lu J. Metagenomic mapping of cyanobacteria and potential cyanotoxin producing taxa in large rivers of the United States. Sci Rep 2023; 13:2806. [PMID: 36797305 PMCID: PMC9935515 DOI: 10.1038/s41598-023-29037-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Cyanobacteria and cyanotoxin producing cyanobacterial blooms are a trending focus of current research. Many studies focus on bloom events in lentic environments such as lakes or ponds. Comparatively few studies have explored lotic environments and fewer still have examined the cyanobacterial communities and potential cyanotoxin producers during ambient, non-bloom conditions. Here we used a metagenomics-based approach to profile non-bloom microbial communities and cyanobacteria in 12 major U.S. rivers at multiple time points during the summer months of 2019. Our data show that U.S. rivers possess microbial communities that are taxonomically rich, yet largely consistent across geographic location and time. Within these communities, cyanobacteria often comprise significant portions and frequently include multiple species with known cyanotoxin producing strains. We further characterized these potential cyanotoxin producing taxa by deep sequencing amplicons of the microcystin E (mcyE) gene. We found that rivers containing the highest levels of potential cyanotoxin producing cyanobacteria consistently possess taxa with the genetic potential for cyanotoxin production and that, among these taxa, the predominant genus of origin for the mcyE gene is Microcystis. Combined, these data provide a unique perspective on cyanobacteria and potential cyanotoxin producing taxa that exist in large rivers across the U.S. and can be used to better understand the ambient conditions that may precede bloom events in lotic freshwater ecosystems.
Collapse
Affiliation(s)
- David M Linz
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, USA
| | - Nathan Sienkiewicz
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, USA
| | - Ian Struewing
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, USA
| | | | | | - Jingrang Lu
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, USA.
| |
Collapse
|
10
|
Vesper S, Sienkiewicz N, Struewing I, Linz D, Lu J. Prophylactic Addition of Glucose Suppresses Cyanobacterial Abundance in Lake Water. Life (Basel) 2022; 12:life12030385. [PMID: 35330137 PMCID: PMC8949225 DOI: 10.3390/life12030385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/21/2022] [Accepted: 03/04/2022] [Indexed: 11/23/2022] Open
Abstract
To mitigate harmful cyanobacterial blooms (HCBs), toxic algicides have been used, but alternative methods of HCB prevention are needed. Our goal was to test the prophylactic addition of glucose to inhibit HCB development, using Microcystis and the toxin microcystin as the HCB model. Water samples were collected weekly, from 4 June to 2 July, from Harsha Lake in southwestern Ohio during the 2021 algal bloom season. From each weekly sample, a 25 mL aliquot was frozen for a 16S rRNA gene sequencing analysis. Then, 200 mL of Harsha Lake water was added to each of the three culture flasks, and glucose was added to create concentrations of 0 mM (control), 1.39 mM, or 13.9 mM glucose, respectively. The microcystin concentration in each flask was measured after 1 and 2 weeks of incubation. The results showed an 80 to 90% reduction in microcystin concentrations in glucose-treated water compared to the control. At the end of the second week of incubation, a 25 mL sample was also obtained from each of the culture flasks for molecular analysis, including a 16S rRNA gene sequencing and qPCR-based quantification of Microcystis target genes. Based on these analyses, the glucose-treated water contained significantly lower Microcystis and microcystin producing gene (mcy) copy numbers than the control. The 16S rRNA sequencing analysis also revealed that Cyanobacteria and Proteobacteria were initially the most abundant bacterial phyla in the Harsha Lake water, but as the summer progressed, Cyanobacteria became the dominant phyla. However, in the glucose-treated water, the Cyanobacteria decreased and the Proteobacteria increased in weekly abundance compared to the control. This glucose-induced proteobacterial increase in abundance was driven primarily by increases in two distinct families of Proteobacteria: Devosiaceae and Rhizobiaceae. In conclusion, the prophylactic addition of glucose to Harsha Lake water samples reduced Cyanobacteria’s relative abundance, Microcystis numbers and microcystin concentrations and increased the relative abundance of Proteobacteria compared to the control.
Collapse
|
11
|
Charvoz L, Apothéloz-Perret-Gentil L, Reo E, Thiébaud J, Pawlowski J. Monitoring newt communities in urban area using eDNA metabarcoding. PeerJ 2021; 9:e12357. [PMID: 34900410 PMCID: PMC8628619 DOI: 10.7717/peerj.12357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022] Open
Abstract
Newts are amphibians commonly present in small ponds or garden pools in urban areas. They are protected in many countries and their presence is monitored through visual observation and/or trapping. However, newts are not easy to spot as they are small, elusive and often hidden at the bottom of water bodies. In recent years, environmental DNA (eDNA) has become a popular tool for detecting newts, with a focus on individual species using qPCR assays. Here, we assess the effectiveness of eDNA metabarcoding compared to conventional visual surveys of newt diversity in 45 ponds within urban areas of Geneva canton, Switzerland. We designed newt-specific mitochondrial 16S rRNA primers, which assign the majority of amplicons to newts, and were able to detect four species known to be present in the region, including the invasive subspecies Lissotriton vulgaris meridionalis, native to the Italian peninsula, that has been introduced in the Geneva area recently. The obtained eDNA results were congruent overall with conventional surveys, confirming the morphological observations in the majority of cases (67%). In 25% of cases, a species was only detected genetically, while in 8% of cases, the observations were not supported by eDNA metabarcoding. Our study confirms the usefulness of eDNA metabarcoding as a tool for the effective and non-invasive monitoring of newt community and suggests its broader use for the survey of newt diversity in urban area at larger scales.
Collapse
Affiliation(s)
- Léo Charvoz
- Department of Genetics and Evolution, University of Geneva, Geneva, Geneva, Switzerland
| | - Laure Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Geneva, Switzerland
- ID-Gene ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland
| | - Emanuela Reo
- Department of Genetics and Evolution, University of Geneva, Geneva, Geneva, Switzerland
| | - Jacques Thiébaud
- KARCH-GE (Swiss Coordination Center for the Protection of Amphibians and Reptiles)—Geneva Regional Branch, Switzerland, Geneva, Geneva, Switzerland
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Geneva, Switzerland
- ID-Gene ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland
- Polish Academy of Sciences, Institute of Oceanology, Sopot, Pomerania, Poland
| |
Collapse
|
12
|
Xie R, Zhao G, Yang J, Wang Z, Xu Y, Zhang X, Wang Z. eDNA metabarcoding revealed differential structures of aquatic communities in a dynamic freshwater ecosystem shaped by habitat heterogeneity. ENVIRONMENTAL RESEARCH 2021; 201:111602. [PMID: 34214559 DOI: 10.1016/j.envres.2021.111602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Freshwater ecosystems have been threatened by complicated disturbances from both natural and anthropogenic variables, especially in dynamic and complex river basins. The environmental DNA (eDNA)-based approach provides a broader spectrum and higher throughput way of biomonitoring for biodiversity assessment compared with traditional morphological survey. Most eDNA metabarcoding studies have been limited to a few specific taxa/groups and habitat scopes. Here we applied the eDNA metabarcoding to characterize the structures and spatial variations of zooplankton and fish communities among different habitat types in a highly dynamic and complex freshwater ecosystem of the Daqing River basin (DRB). The results showed that varied species spectra of zooplankton and fish communities were identified and unique dominant species occurred across habitats. Additionally, markedly spatial distributions of biotic community structures were observed in areas with different habitat characteristics. Natural variables, including geographic distances and gradient ratio, as well as anthropogenic factors of chemical oxygen demand (COD) and organic chemicals demonstrated significant effects but different outcomes on the structures of zooplankton and fish communities. Moreover, the relative abundances of specific aquatic taxa were associated with the gradient of particular environmental variables. This case study verified the distribution patterns and differentiation mechanisms of biotic communities under habitat heterogeneity could be captured by application of eDNA biomonitoring. And habitat-specific and even species-specific environmental stressors would be diagnosed for improving management of complex river basins.
Collapse
Affiliation(s)
- Ruili Xie
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gaofeng Zhao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Zhihao Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Yiping Xu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China.
| | - Zijian Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| |
Collapse
|
13
|
Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
Collapse
Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
| |
Collapse
|
14
|
Shadrin DM. DNA Barcoding: Applications. RUSS J GENET+ 2021. [DOI: 10.1134/s102279542104013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
15
|
Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates. WATER 2021. [DOI: 10.3390/w13030331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs.
Collapse
|
16
|
Zizka VMA, Weiss M, Leese F. Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. METABARCODING AND METAGENOMICS 2020. [DOI: 10.3897/mbmg.4.51925] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genetic diversity is the most basal level of biodiversity and determines the evolutionary capacity of species to adapt to changing environments, yet it is typically neglected in routine biomonitoring and stressor impact assessment. For a comprehensive analysis of stressor impacts on genetic diversity, it is necessary to assess genetic variants simultaneously in many individuals and species. Such an assessment is not as straightforward and usually limited to one or few focal species. However, nowadays species diversity can be assessed by analysing thousands of individuals of a community simultaneously with DNA metabarcoding. Recent bioinformatic advances also allow for the extraction of exact sequence variants (ESVs or haplotypes) in addition to Operational Taxonomic Units (OTUs). By using this new capability, we here evaluated if the analysis of intraspecific mitochondrial diversity in addition to species diversity can provide insights into responses of stream macrozoobenthic communities to environmental stressors. For this purpose, we analysed macroinvertebrate bulk samples of three German river systems with different stressor levels using DNA metabarcoding. While OTU and haplotype number were negatively correlated with stressor impact, this association was not as clear when studying haplotype diversity across all taxa. However, stressor responses were found for sensitive EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa and those exceedingly resistant to organic stress. An increase in haplotype number per OTU and haplotype diversity of sensitive taxa was observed with an increase in ecosystem quality and stability, while the opposite pattern was detected for pollution resistant taxa. However, this pattern was less prominent than expected based on the strong differences in stressor intensity between sites. To compare genetic diversity among communities in river systems, we focussed on OTUs, which were present in all systems. As OTU composition differed strongly between rivers, this led to the exclusion of a high number of OTUs, especially in diverse river systems of good quality, which potentially diminished the increase in intraspecific diversity. To better understand responses of intraspecific genetic diversity to environmental stressors, for example in river ecosystems, it would be important to increase OTU overlap between compared sites, e.g. by sampling a narrower stressor gradient, and to perform calibrated studies controlling for the number of individuals and their haplotypes. However, this pioneer study shows that the extraction of haplotypes from DNA metabarcoding datasets is a promising source of information to simultaneously assess intraspecific diversity changes in response to environmental impacts for a metacommunity.
Collapse
|