Unveiling Underwater Secrets with Aquatic Sampling Methods

Unveiling Underwater Secrets with Aquatic Sampling Methods

Figure 1: Habitat Surveying in Pine Gulch

The world beneath the water’s surface has always fascinated scientists and nature enthusiasts alike. Exploring and understanding aquatic ecosystems is crucial for the conservation and management of our precious natural resources. Traditional surveying methods although valuable, often come with limitations. However, recent advancements in scientific techniques have opened up new possibilities for investigating underwater habitats. One of these innovative approaches is environmental DNA (eDNA) sampling (Figure 2) combined with habitat surveys (Figure 1) and aquatic sampling techniques. In this blog post, I will delve into the world of field surveying techniques used to uncover and contribute to our understanding of aquatic ecosystems.

As a Mosaics in Science intern, I have been fortunate enough to get out into the field to sample sites for environmental DNA for several ESA-listed freshwater species such as steelhead (Oncorhynchus mykiss), California red-legged frog (Rana draytonii), foothill yellow-legged frog (Rana boylii), and northwestern pond turtle (Actinemys marmorata). With this, the fish crew at Point Reyes National Seashore have conducted habitat typing surveys to establish habitat areas that may act as a stronghold for these species. Aquatic sampling methods have involved electrofishing (Figure 3) and seining which are used to establish viable evidence of these populations within the watershed prior to the eDNA genetic analysis. 

Featured Photo Credit: Eric Wagner, Flickr

Figure 2: eDNA Sampling Equipment (Photo Credit: Smith-Root)
Figure 3: Electrofishing in Abbotts Creek

Fish eDNA sampling involves the collection and analysis of genetic material shed by fish into their environment. When fish swim in water bodies, they release various biological materials, such as skin cells, mucus, scales, and feces, each carrying their unique DNA signatures. These traces of DNA, collectively known as eDNA, can be detected and analyzed using laboratory techniques thus providing valuable insights into the fish species present in a particular habitat. Such a process involves three stages: sample collection, DNA extraction, and genetic analysis. Throughout my internship, I have been involved in sample collection at several sites within my host site, Point Reyes National Seashore. 

  1. Sample Collection: During fish eDNA sampling, water samples are collected from targeted aquatic habitats using specialized collection kits. These kits often include filters or preservatives that help capture and preserve the genetic material present in the water (Figure 2). 
  2. DNA Extraction: Once the water samples are obtained, scientists isolate and extract the DNA from the collected material. This step involves various laboratory protocols designed to remove contaminants and concentrate the genetic material for analysis.
  3. Genetic Analysis: The extracted DNA is then subjected to DNA sequencing or other molecular techniques to identify the fish species present in the sampled habitat. By comparing the obtained DNA sequences with existing genetic databases, researchers can determine the fish species that have left their genetic material traces in the water.
Along with eDNA sampling, at each site we collected length, width, and depth measurements, as well as water quality (dissolved oxygen, salinity, temperature, and specific conductivity). With the physical surveying methods (electrofishing or seining), we did three passes through the water in hopes of collecting samples with our targeted populations for additional evidence. 

To complement such sampling, habitat surveys play a vital role in understanding the environmental factors influencing fish communities. These surveys involve on-site observations (Figure 4), measurements, and data collection to assess the physical, chemical, and biological characteristics of riparian habitats. These techniques involve a stadia rod which is used to map the topography of the area as well as the vegetation present (large woody debris, root wads) that may provide suitable habitat for our targeted freshwater populations.

 By combining fish eDNA analysis with habitat surveys, we can gain a comprehensive understanding of the relationships between fish species and their habitats. Such information is imperative to managing our finite natural resources within this changing climate. Furthermore, these techniques offer a non-invasive, cost-effective, and efficient means of monitoring biodiversity, supporting conservation efforts, while also promoting sustainable management practices.

Figure 4: Sample Site for eDNA Collection in Kehoe Creek
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