scholarly journals Application of environmental DNA for monitoring and management of aquatic biological invasions: Emerging trends and advancements towards best practice

2021 ◽  
Vol 4 ◽  
Author(s):  
Emily Chen
Keyword(s):  
Invasive Species ◽  
Experimental Design ◽  
Native Species ◽  
Best Practice ◽  
Environmental Dna ◽  
Extraction Methods ◽  
Indigenous Species ◽  
Recent Emergence ◽  
Species Specific ◽  
Sampling Procedures

Introduction Aquatic Invasive Species (AIS) are a growing concern for global biodiversity as humans continue to accelerate the transport of non-indigenous species beyond their natural range. These species may possess traits that allow them to thrive in new environmental conditions such as non-selective feeding and high reproductive output, causing ecological harm through competition with native species for limited local resources. Consequently, environmental DNA (eDNA) has come to the forefront of AIS management in recent years as a promising method to detect or monitor invasive species using rapid and non-invasive sampling to complement traditional surveying. As eDNA’s potential is explored and beginning to be adopted for a variety of applications around the world, it is increasingly important to synthesize the trends in field and laboratory protocols from different working groups to establish guidelines that will allow greater comparability between studies and improve experimental design. Methodology and Results This meta-analytic study collated and reviewed information from previously published eDNA studies that targeted AIS in freshwater and marine environments to recognize current patterns in sampling techniques, laboratory protocols, and potential geographic or taxonomic biases. A total of 492 records from 192 full-text articles were used in the analysis, composed of 408 species-specific and 84 metabarcoding records. With regards to sampling procedures, many studies were not explicit enough for true replicability, lacking critical information such as the volume of filtered water and details of storage conditions. There was no observable trend for eDNA extraction methods in either species-specific or metabarcoding approaches, with choice of extraction method being mostly arbitrary among laboratories as well as influenced by the recent emergence of dedicated commercial kits . Discussion This analysis revealed a wide variety of choices for collecting and processing eDNA samples, so it is recommended that there should be some sort of standardized workflow diagram or decision tree for every stage of the experimental design in order for researchers to determine what approaches best meet their research objectives. There is also a clear need for improving metadata reporting guidelines; although the relevance of some criteria depends on the goals and limitations of specific projects, there should be a standardized minimum set of parameters to be reported for each eDNA study, from environmental variables to decontamination practices to PCR conditions. This will increase consistency and transparency through all stages of eDNA research, which is key to collectively improving methodologies and moving forward in this field.

scholarly journals Emerging fungal pathogen of an invasive grass: Implications for competition with native plant species

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0237894
Author(s):  
Amy E. Kendig ◽  
Vida J. Svahnström ◽  
Ashish Adhikari ◽  
Philip F. Harmon ◽  
S. Luke Flory
Keyword(s):  
Invasive Species ◽  
Plant Species ◽  
Fungal Pathogen ◽  
Native Species ◽  
Grass Species ◽  
Leaf Spot Disease ◽  
Native Plant ◽  
Invasive Grass ◽  
Native Plant Species ◽  
Species Specific

Infectious diseases and invasive species can be strong drivers of biological systems that may interact to shift plant community composition. For example, disease can modify resource competition between invasive and native species. Invasive species tend to interact with a diversity of native species, and it is unclear how native species differ in response to disease-mediated competition with invasive species. Here, we quantified the biomass responses of three native North American grass species (Dichanthelium clandestinum, Elymus virginicus, and Eragrostis spectabilis) to disease-mediated competition with the non-native invasive grass Microstegium vimineum. The foliar fungal pathogen Bipolaris gigantea has recently emerged in Microstegium populations, causing a leaf spot disease that reduces Microstegium biomass and seed production. In a greenhouse experiment, we examined the effects of B. gigantea inoculation on two components of competitive ability for each native species: growth in the absence of competition and biomass responses to increasing densities of Microstegium. Bipolaris gigantea inoculation affected each of the three native species in unique ways, by increasing (Dichanthelium), decreasing (Elymus), or not changing (Eragrostis) their growth in the absence of competition relative to mock inoculation. Bipolaris gigantea inoculation did not, however, affect Microstegium biomass or mediate the effect of Microstegium density on native plant biomass. Thus, B. gigantea had species-specific effects on native plant competition with Microstegium through species-specific biomass responses to B. gigantea inoculation, but not through modified responses to Microstegium density. Our results suggest that disease may uniquely modify competitive interactions between invasive and native plants for different native plant species.

Improving reliability in environmental DNA detection surveys through enhanced quality control

2017 ◽  
Vol 68 (2) ◽  
pp. 388 ◽  
Author(s):  
Elise M. Furlan ◽  
Dianne Gleeson
Keyword(s):  
Quality Control ◽  
Native Species ◽  
Conservation Management ◽  
Environmental Dna ◽  
Positive Control ◽  
False Negatives ◽  
Method Error ◽  
Target Dna ◽  
Species Specific ◽  
Australian Freshwater

Species-specific environmental DNA (eDNA) surveys are increasingly being used to infer species presence in an environment. Current inadequacies in quality control increase concern for false negatives, which can have serious ramifications for both the management of invasive species and the conservation of native species. eDNA surveys involve a multi-step process to sample, capture, extract and amplify target DNA from the environment. We outline various positive control options and show that many of the commonly used controls are capable of detecting false negatives arising during the amplification stage only. We suggest a secondary, generic primer, designed to co-amplify endogenous DNA sampled during species-specific eDNA surveys, constitutes a superior positive control to monitor method success throughout all stages of eDNA analysis. We develop a species-specific European carp (Cyprinus carpio) assay and a generic fish assay for use as an endogenous control for eDNA surveys in Australian freshwater systems where fish are known to be abundant. We use these assays in a multiplex on eDNA samples that are simultaneously sampled, captured, extracted and amplified. This positive control allows us to distinguish method error from informative non-amplification results, improving reliability in eDNA surveys, which will ultimately lead to better informed conservation management decisions.

scholarly journals Characterization and Comparison of Bacterial Communities of an Invasive and Two Native Caribbean Seagrass Species Sheds Light on the Possible Influence of the Microbiome on Invasive Mechanisms

2021 ◽  
Vol 12 ◽  
Author(s):  
Tania Aires ◽  
Tamara M. Stuij ◽  
Gerard Muyzer ◽  
Ester A. Serrão ◽  
Aschwin H. Engelen
Keyword(s):  
Invasive Species ◽  
Bacterial Communities ◽  
Invasion Success ◽  
Positive Interactions ◽  
Indigenous Species ◽  
Seagrass Species ◽  
Invasion Mechanisms ◽  
New Findings ◽  
Leaves And Roots ◽  
Species Specific

Invasive plants, including marine macrophytes, are one of the most important threats to biodiversity by displacing native species and organisms depending on them. Invasion success is dependent on interactions among living organisms, but their study has been mostly limited to negative interactions while positive interactions are mostly underlooked. Recent studies suggested that microorganisms associated with eukaryotic hosts may play a determinant role in the invasion process. Along with the knowledge of their structure, taxonomic composition, and potential functional profile, understanding how bacterial communities are associated with the invasive species and the threatened natives (species-specific/environmentally shaped/tissue-specific) can give us a holistic insight into the invasion mechanisms. Here, we aimed to compare the bacterial communities associated with leaves and roots of two native Caribbean seagrasses (Halodule wrightii and Thalassia testudinum) with those of the successful invader Halophila stipulacea, in the Caribbean island Curaçao, using 16S rRNA gene amplicon sequencing and functional prediction. Invasive seagrass microbiomes were more diverse and included three times more species-specific core OTUs than the natives. Associated bacterial communities were seagrass-specific, with higher similarities between natives than between invasive and native seagrasses for both communities associated with leaves and roots, despite their strong tissue differentiation. However, with a higher number of OTUs in common, the core community (i.e., OTUs occurring in at least 80% of the samples) of the native H. wrightii was more similar to that of the invader H. stipulacea than T. testudinum, which could reflect more similar essential needs (e.g., nutritional, adaptive, and physiological) between native and invasive, in contrast to the two natives that might share more environment-related OTUs. Relative to native seagrass species, the invasive H. stipulacea was enriched in halotolerant bacterial genera with plant growth-promoting properties (like Halomonas sp. and Lysinibacillus sp.) and other potential beneficial effects for hosts (e.g., heavy metal detoxifiers and quorum sensing inhibitors). Predicted functional profiles also revealed some advantageous traits on the invasive species such as detoxification pathways, protection against pathogens, and stress tolerance. Despite the predictive nature of our findings concerning the functional potential of the bacteria, this investigation provides novel and important insights into native vs. invasive seagrasses microbiome. We demonstrated that the bacterial community associated with the invasive seagrass H. stipulacea is different from native seagrasses, including some potentially beneficial bacteria, suggesting the importance of considering the microbiome dynamics as a possible and important influencing factor in the colonization of non-indigenous species. We suggest further comparison of H. stipulacea microbiome from its native range with that from both the Mediterranean and Caribbean habitats where this species has a contrasting invasion success. Also, our new findings open doors to a more in-depth investigation combining meta-omics with bacterial manipulation experiments in order to confirm any functional advantage in the microbiome of this invasive seagrass.

scholarly journals Potensi Environmental DNA (e-DNA) Untuk Pemantauan dan Konservasi Keanekaragaman Hayati

2021 ◽  
Vol 11 (1) ◽  
pp. 75
Author(s):  
Siti Marfuah ◽  
Beivy Jonathan Kolondam ◽  
Trina Ekawati Tallei
Keyword(s):  
Invasive Species ◽  
Molecular Markers ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Native Species ◽  
Biological Diversity ◽  
Secondary Data ◽  
Environmental Dna ◽  
Review Article ◽  
Oxidase Subunit

(Article History: Received January 6, 2021; Revised February 12, 2021; Accepted February 28, 2021) ABSTRAK Hilangnya spesies dan adanya spesies invasif dalam suatu habitat dapat menjadi ancaman bagi spesies asli dalam satu ekosistem. Untuk itu diperlukan teknik terkini yang mampu mendeteksi keberadaan suatu organisme. Salah satu teknik yang dapat mendeteksi organisme target di lingkungan secara cepat dan akurat yaitu environmental DNA (e-DNA).Tujuan dari ulasan artikel ini yaitu untuk mengeksplorasi kemampuan e-DNA secara ekogenomik untuk pemantauan dan konservasi keanekaragaman hayati. Ulasan artikel ini menggunakan data sekunder yang diperoleh dari berbagai database yang berbasis dalam jaringan. Hasil analisis memperlihatkan bahwa dengan menggunakan pendekatan e-DNA pemantauan dan konsevasi keanekaragaman hayati dapat dideteksi sesuai dengan taksonomi organisme dan penanda molekuler. Penanda molekuler Cytochrome c Oxidase subunit 1 (COI) mampu mendeteksi berbagai spesies baik langka dan invasif. Dengan demikian dapat disimpulkan bahwa pendekatan e-DNA dapat dijadikan sebagai metode untuk pemantauan dan konsevasi keanekaragaman hayati pada berbagai ekosistem.Kata - kata kunci: environmental DNA; keanekaragaman hayati dan konservasi; penanda molekuler  ABSTRACTThe loss of species and the presence of invasive species in a habitat can be a threat to native species in an ecosystem. So we need the latest techniques that are able to detect the presence of an organism. One technique that can detect target organisms in the environment quickly and accurately is environmental DNA (e-DNA). The purpose of this review article is to explore the ecogenomic ability of e-DNA for monitoring and conservation of biodiversity. This article reviews using secondary data obtained from various network-based databases. The results of the analysis show that by using the e-DNA approach, monitoring and conservation of biological diversity can be detected according to the taxonomy of organisms and molecular markers. Cytochrome c Oxidase subunit 1 (COI) molecular markers are capable of detecting a variety of both rare and invasive species. Thus it can be concluded that the e-DNA approach can be used as a method for monitoring and conservation of biological diversity in various ecosystems.Keywords: environmental DNA; biodiversity and conservation; molecular markers

scholarly journals Environmental DNA (eDNA) detection of marine aquatic invasive species (AIS) in Eastern Canada using a targeted species-specific qPCR approach

2020 ◽  
Vol 11 (2) ◽  
pp. 201-217
Author(s):  
Francis LeBlanc ◽  
Valérie Belliveau ◽  
Erica Watson ◽  
Chantal Coomber ◽  
Nathalie Simard ◽  
...  
Keyword(s):  
Invasive Species ◽  
Environmental Dna ◽  
Aquatic Invasive Species ◽  
Eastern Canada ◽  
Species Specific

scholarly journals Exploiting intraspecific competitive mechanisms to control invasive cane toads ( Rhinella marina )

2012 ◽  
Vol 279 (1742) ◽  
pp. 3436-3442 ◽  
Author(s):  
Michael R. Crossland ◽  
Takashi Haramura ◽  
Angela A. Salim ◽  
Robert J. Capon ◽  
Richard Shine
Keyword(s):  
Invasive Species ◽  
Communication Systems ◽  
Native Species ◽  
Negative Effects ◽  
Specific Chemical ◽  
Rhinella Marina ◽  
Invasive Species Control ◽  
Tropical Australia ◽  
Competitive Mechanisms ◽  
Species Specific

If invasive species use chemical weapons to suppress the viability of conspecifics, we may be able to exploit those species-specific chemical cues for selective control of the invader. Cane toads ( Rhinella marina ) are spreading through tropical Australia, with negative effects on native species. The tadpoles of cane toads eliminate intraspecific competitors by locating and consuming newly laid eggs. Our laboratory trials show that tadpoles find those eggs by searching for the powerful bufadienolide toxins (especially, bufogenins) that toads use to deter predators. Using those toxins as bait, funnel-traps placed in natural waterbodies achieved near-complete eradication of cane toad tadpoles with minimal collateral damage (because most native (non-target) species are repelled by the toads' toxins). More generally, communication systems that have evolved for intraspecific conflict provide novel opportunities for invasive-species control.

scholarly journals Responses of native and invasive woody seedlings to combined competition and drought are species-specific

2020 ◽  
Author(s):  
Andrea Bueno ◽  
Karin Pritsch ◽  
Judy Simon
Keyword(s):  
Invasive Species ◽  
Water Supply ◽  
Soil Water ◽  
Native Species ◽  
Woody Species ◽  
Total Soluble Protein ◽  
Summer Drought ◽  
Species Invasions ◽  
Species Specific ◽  
N Acquisition

Abstract Woody species invasions are a major threat to native communities with intensified consequences during increased periods of summer drought as predicted for the future. Competition for growth-limiting nitrogen (N) between native and invasive tree species might represent a key mechanism underlying the invasion process, because soil water availability and N acquisition of plants are closely linked. To study whether the traits of invasive species provide an advantage over natives in Central Europe in the competition for N under drought, we conducted a greenhouse experiment. We analysed the responses of three native (i.e., Fagus sylvatica, Quercus robur, and Pinus sylvestris) and two invasive woody species (i.e., Prunus serotina and Robinia pseudoacacia) to competition in terms of their organic and inorganic N acquisition, as well as allocation of N to N pools in the leaves and fine roots. In our study, competition resulted in reduced growth and changes in internal N pools in both native and invasive species mediated by the physiological characteristics of the target species, the competitor, as well as soil water supply. N acquisition, however, was not affected by competition indicating that changes in growth and N pools were rather linked to the remobilization of stored N. Drought led to reduced N acquisition, growth and total soluble protein-N levels, while total soluble amino acid-N levels increased, most likely as osmoprotectants as an adaptation to the reduced water supply. Generally, the consequences of drought were enhanced with competition across all species. Comparing the invasive competitors, P. serotina was a greater threat to the native species than R. pseudoacacia. Furthermore, deciduous and coniferous native species affected the invasives differently, with the species-specific responses being mediated by soil water supply.

scholarly journals Monthly eDNA Monitoring of an Invasive Bryozoan, Bugulina californica, in Seawater Using Species-Specific Markers

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1966
Author(s):  
Philjae Kim ◽  
Tae-Joong Yoon ◽  
Sook Shin
Keyword(s):  
Invasive Species ◽  
Dna Analysis ◽  
Early Stage ◽  
Environmental Dna ◽  
Pcr Analysis ◽  
Monitoring Method ◽  
Ship Hulls ◽  
Seawater Samples ◽  
Species Specific ◽  
Invasive Bryozoan

Environmental DNA (eDNA) method used by many ecologists as effective investigation tool can detect endangered species, rare species, and invasive species. In case of invasive species, eDNA method help to monitor the target species when the species was hard to detect through the traditional survey such as the early stage of invasion, low abundance, and larva or juvenile stage. The bryozoan, Bugulina californica, was known as a marine fouling invasive species in Korea since its first reported in 1978. This species expanded nationwide, and damages to ascidian aquaculture through attached on the ship hulls and artificial facilities. To monitor the distribution and biomass of invasive bryozoan, B. californica, the qPCR analysis of environmental DNA was performed on seawater samples from 12 harbors. In this study, we designed species-specific markers which can calculate the detected DNA copies of B. californica, and the presence and monitoring of this species can be more accurately estimated by environmental DNA analysis than by traditional survey, in which it is difficult to identify the species. Real-time PCR analysis using environmental DNA is an effective monitoring method that can determine both the distribution and the monthly change in biomass of B. californica in Korea.

scholarly journals Challenges in eDNA Detection of the Invasive European Green Crab, Carcinus Maenas

2021 ◽  
Author(s):  
Ariella M. Danziger ◽  
Markus Frederich
Keyword(s):  
Invasive Species ◽  
Visual Detection ◽  
Gulf Of Maine ◽  
Carcinus Maenas ◽  
Environmental Dna ◽  
Green Crab ◽  
Local Fauna ◽  
Irreversible Damage ◽  
European Green Crab ◽  
Species Specific

Abstract The early detection of invasive species is essential to cease the spread of the species before it can cause irreversible damage to the environment. The analysis of environmental DNA (eDNA) has emerged as a non-harmful method to detect the presence of a species before visual detection and is a promising approach to monitor invasive species. Few studies have investigated the use of eDNA for arthropods, as their exoskeleton is expected to limit the release of eDNA into the environment. We tested published primers for the invasive European green crab, Carcinus maenas, in the Gulf of Maine and found them not species-specific enough for reliable use outside of the area for which they were designed for. We then designed new primers, tested them against a broad range of local faunal species, and validated these primers in a field study. We demonstrate that eDNA analyses can be used for crustaceans with an exoskeleton and suggest that primers and probe sequences must be tested on local fauna at each location of use to ensure no positive amplification of these other species.

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