What is eDNA?

eDNA, or environmental DNA, is genetic material shed by organisms into their environment. It can be found in various forms, such as attached to particles, dissolved in water, within cells, or in fecal matter from predators. Due to DNA's stable double helical structure, it degrades slowly, allowing for the detection of both living and dead organisms. eDNA presence does not necessarily indicate a living organism.

 

What is eRNA?

eRNA, or environmental RNA, is a single-stranded nucleic acid that can take various shapes and forms, making it less stable than DNA and prone to quicker environmental degradation. This rapid breakdown means that detecting eRNA provides a strong indication of active life during sampling. Additionally, based on the target transcript, eRNA can tell you what genes organisms living in the environment express.

 

What is Metabolic Activity?

Metabolic activity refers to the processes involved in metabolism, the life-sustaining chemical reactions in organisms. In eRNA and eDNA studies, researchers focus on specific sections of nucleic acids, particularly housekeeping genes, which are essential for basic cellular functions and are always active if the cell is alive. These genes are transcribed into RNA, a process that serves as a marker for metabolic activity and, by extension, life.

 

Housekeeping genes are essential for maintaining cellular functions, with their transcription rates serving as a proxy for metabolism. These genes are consistently expressed across cell types, providing a stable baseline for comparison. Since metabolism influences energy production and nutrient utilization, metabolic rate changes coincide with housekeeping gene expression alterations.

 

What is Transcriptomics?

Transcriptomics is the study of the entire set of RNA transcripts produced by the genome. It involves analyzing the RNA transcribed from DNA, which serves as a template to create messages (RNA) in a process called transcription. While genomics focuses on the study of the entire set of genes (DNA) within an organism, transcriptomics focuses on understanding all the RNA molecules transcribed from these genes, providing insights into which genes are actively being expressed and how they are regulated in different conditions.

 

Pros and Cons of eDNA

Pros:

• High Sensitivity: DNA's stability allows for detecting organisms that are currently living, have recently lived, or were present in an environment at some point, providing a comprehensive overview of an ecosystem's biodiversity.

• Invasive Species Detection: Useful for risk assessments by detecting the DNA of invasive species before they can establish a self-sustaining population, aiding in early intervention strategies.

• Endangered Species Monitoring: Helps identify areas with significant DNA concentrations of native and endangered species, guiding conservation and management efforts even if the organisms are not alive.

Cons:

• Presence ≠ Current Life: High DNA stability means it can persist long after an organism has died, so detection doesn't guarantee the organism is alive or active in the area.

 

Pros and Cons of eRNA

Pros:

• Indicative of Active Life: RNA's rapid degradation makes it a reliable indicator of current life, offering insights into the presence and activity of organisms at the time of sampling.

• Gene Expression Analysis: RNA allows for examining which genes are being actively transcribed, providing valuable information on the physiological state of organisms, including stress responses and other environmental effects on population health.

• Population Dynamics and Health: Through transcriptome monitoring and sequencing, RNA can reveal detailed insights into organisms' population dynamics and health within an ecosystem.

Cons:

• Rapid Degradation: RNA's instability and quick breakdown in the environment could make sampling and preservation more challenging, requiring timely processing to represent current conditions accurately. This problem is solved through the use of the Osprey System.

• Limited Historical Data: Unlike DNA, RNA does not offer insights into past populations or long-term presence due to its transient nature, focusing instead on current biological activities.

 

How do eRNA and eDNA complement each other?

eRNA complements eDNA testing initiatives by providing a more comprehensive understanding of an ecosystem's current biological state. While eDNA offers insights into the organisms that have lived or are living in an area, eRNA adds a layer of information about what is actively alive and functioning at the time of sampling.

 

For instance, in the case of invasive species management, the presence of eDNA might indicate that invasive species, such as quagga mussels, have been or are present in a lake. However, the absence of eRNA in the exact locations, especially near decontamination points, suggests that while the DNA of these organisms is detectable, there are no living invasive organisms at those points, indicating that management efforts to prevent live invasions are effective.

 

Similarly, in studying fish populations like trout, eDNA can identify the various species present in a habitat. At the same time, eRNA can provide insights into these populations' active behaviors and health, such as responses to environmental stressors or predatory activities.

 

In essence, eRNA offers a dynamic view of the ecosystem, complementing the broader historical perspective of eDNA. Together, they deliver a fuller picture of both the presence and the physiological state of organisms within an ecosystem, enhancing our understanding of biodiversity, population dynamics, and the effectiveness of conservation strategies.

 

Why is RNA a helpful tool when looking for cryptic species that are hard to capture or see with the human eye?

RNA is beneficial for detecting cryptic or microscopic species that are challenging to observe with the human eye due to their elusive nature, small size, or habitat inaccessibility. Many species, including certain salamanders and microscopic organisms, reside in environments or within niches that are difficult or impossible to access for physical sampling physically. Furthermore, some species may appear visually similar, making it difficult to accurately identify them based solely on visual inspection, even for experts.

 

The sensitivity of molecular tools like RNA analysis allows for detecting and identifying species from minimal biological material, sometimes from just a single molecule. This molecular approach provides a significant advantage over traditional survey methods, offering precise identification without requiring direct observation or collection of the organisms. Consequently, RNA analysis is a more efficient, cost-effective, and accurate method for studying biodiversity, especially for species that are hard to detect through conventional means.

 

As a lake owner concerned about potential invasive species, how can eDNA and eRNA technologies help me assess their presence and impact on my water asset?

 

If you're a water asset owner concerned about invasive species in your lake, eDNA, and eRNA technologies can provide invaluable insights into these species' presence and activity levels, helping you devise effective management strategies.

 

eDNA Analysis:

• Offers a "heat map" of the invasive species' distribution within the lake, indicating areas of high prevalence or significant influx.

• It helps identify the invasive species' largest populations or the lake's main entry points, such as near boat ramps or inlets.

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eRNA Analysis:

• Provides a different type of "heat map" that reflects the activity levels of the invasive species populations.

• It shows where these populations are most active or growing, which might differ from where they are most prevalent (as indicated by eDNA).

 

By combining the data from both eDNA and eRNA analyses, you gain a comprehensive view of the invasive species' presence and activity:

• Prevention Efforts: Areas with high eDNA concentrations, especially where eRNA is also detected, are critical for focusing prevention efforts to stop further spread. These might include entry points or areas with recent invasive species introductions.

• Mitigation Efforts: Regions with significant eRNA activity indicate where the invasive species is thriving and possibly reproducing. These areas require direct intervention to control or eradicate the active populations.

 

This dual-layered approach enables targeted actions, ensuring resources are allocated efficiently to prevent new introductions and mitigate the impact of existing populations, ultimately helping preserve the health and biodiversity of your aquatic ecosystem.
 

How can eDNA and eRNA technologies assist in monitoring the status and health of specific or endangered species within my ecosystem?

 

To understand the status and health of desired or endangered species within your aquatic ecosystem, eDNA and eRNA technologies offer comprehensive insights across various scenarios.

 

Environmental and Species Act (ESA) Compliance for Development Projects:

• eDNA Analysis: Provides a historical overview of where desired or endangered species have been most prevalent, aiding in assessing potential impacts of construction projects like developments, roads, or bridges on these populations. It helps identify areas where design modifications may be necessary to minimize adverse effects.

• eRNA Analysis: Offers real-time data on active populations, highlighting critical areas requiring protection during planning and construction to avoid disrupting vital habitats.

 

Biodiversity Credits and Conservation Banking:

• Longitudinal Monitoring: Regular eDNA and eRNA sampling over time can track changes in the presence and activity of indicator species, guiding conservation efforts to ensure their healthy recovery and sustainable management.

• Seasonal Variance: Understanding seasonal changes in species activity and biodiversity helps optimize management practices, such as restricting area use during sensitive periods to support ecosystem restoration and growth.

 

Overall Biodiversity and Ecosystem Health:

• Biodiversity Assessment: eDNA provides a snapshot of total biodiversity, indicating whether it is increasing or decreasing and how it varies seasonally.

• Population and Health Insights: eRNA analysis reveals which genes are actively transcribed, including stress and metabolic genes, offering a deeper understanding of the physiological state of species and their responses to environmental factors.

 

By leveraging these technologies, water asset owners and conservationists can make informed decisions to support the sustainability and health of their ecosystems, ensuring the protection and prosperity of both common and endangered species.

 

Does someone from EQO need to visit my lake to conduct the tests?

EQO does not require physical visits to conduct sampling. We provide the necessary equipment designed for anyone to use, allowing for sample collection without specialized expertise quickly. Our role focuses on performing the subsequent analysis, enabling consultants to deliver enhanced client services.
 

Can we simply collect a grab sample and send it to the lab for analysis?

To ensure accurate analysis, especially for RNA, which is sensitive and requires specific handling, we recommend using our specialized Osprey survey system rather than just collecting a water sample manually. This system is designed for high-volume sampling, minimizing contamination and preserving the sample effectively at the point of collection with a specific buffer, which is crucial for reliable RNA analysis.

 

High-volume sampling is crucial for obtaining a representative sample of an area, especially when dealing with eDNA and eRNA, which can vary significantly from site to site and degrade quickly in the environment. The literature strongly supports high-volume sampling to capture a comprehensive ecosystem snapshot, ensuring that even rare RNA sequences prone to rapid breakdown are detected. This approach enhances the sensitivity and reliability of the sampling process, providing a more accurate reflection of the biodiversity and activity within a specific area.

 

Can you assist in creating a strategy to improve the health of species in my lake?

While we can interpret the results and offer insights into the health and status of species in your lake, we do not provide direct consultancy services to develop management or restoration plans. Our role is to assist in understanding the data, enabling consultants to create an effective strategy based on our analyses.
 

Is EQO a certified engineering firm?

EQO is not a certified engineering firm, and we do not have certified engineers on staff. We recommend contacting a certified engineering firm to collaborate on projects requiring gathering and applying insights from our services. We are also happy to suggest reputable firms we have previously worked with in your area.

 

Can EQO provide insights into the effectiveness of my current efforts to eradicate an invasive species or protect an endangered species through data and analytics?

EQO can supply data and analytics to assess the impact of your remediation efforts. However, we do not certify the outcomes of these strategies, nor do we design remediation plans.
 

Which species groups are you able to identify through your detection methods?

Amphibians, Mollusks, Macroinvertebrates, Fish, Microbiome, Aquatic Mammals, Aquatic Plants