THE EXTRACT

August 2022

Kia ora koutou,

Welcome to the latest edition of The Extract, a roundup of highlights from the wilderness over the last couple of months. Our thoughts go out to all those affected by the recent flooding around the motu, including our underwater friends. Here in Wellington a mysterious yellow orb has appeared in the sky - which we hope is an omen for mild weather ahead.

Have you found anything interesting in your eDNA results? We love hearing feedback, especially where unexpected critters are detected. This month we had two surprise species show up in a single batch of samples from the Pūharakekenui Styx River - a native bat and a… Capybara?! The large South American rodent was traced back to the Willowbank Wildlife Reserve a few km upstream of the sampling spot, and there is a team gearing up with detectors to try to track down the bats. You can find out more in the full Stuff article here.

Species name change for Koi carp in Aotearoa

The system of taxonomy (the naming and classifying of things) is designed to evolve as we improve our understanding of evolutionary lineages, divergence and speciation. This means that taxon names and their relationships with other taxa are constantly being revisited and refined.

A growing body of research including this DOC report indicates that the Koi carp we have here in Aotearoa is an Asian lineage called Cyprinus rubrofuscus, rather than the European lineage Cyprinus carpio as previously thought. Regardless of their taxonomic classification, Koi are a highly invasive fish, and have spread rapidly through Te Ika-a-Māui since the 1960s. They are a destructive presence in our waterways, reducing water clarity by stirring up mud when they feed, and destroying native plant and fish habitat.

Based on the advice of pest fish experts Prof. Nick Ling (University of Waikato), Dave West (DOC) and Kerry Bodmin (DOC), we have now updated our reference database and historic Cyprinus carpio eDNA records to the more accurate Cyprinus rubrofuscus.

Although this may seem like a minor change, it does carry with it the need for several legislative adjustments. Aotearoa’s Unwanted Organism Register formerly included Cyprinus carpio but not Cyprinus rubrofuscus, so an application needed to be made to MPI to assign Unwanted Organism status for Cyprinus rubrofuscus. This has now been granted, meaning that Cyprinus rubrofuscus is now subject to the same regulations and restriction of sale and distribution as Cyprinus carpio.

However according to Kerry Bodmin, several management issues may still remain for Regional Councils and DOC where legislation and plans refer to the old name Cyprinus carpio.

Our computers are currently re-processing and updating all of the historic eDNA sample reports to reflect this name change on the Wilderlab explorer map. This means that koi eDNA records will now be searchable using the term ‘Cyprinus rubrofuscus’ rather than ‘Cyprinus carpio’ in the advanced taxon search option. This includes this record that really muddied the waters when it revealed koi DNA in a central Hawke’s Bay farm pond (full article here).

If you’d like to receive an updated version of your eDNA results that reflect this name change, don’t hesitate to contact our team at info@wilderlab.co.nz.

eRNA metabarcoding helps track SARS-CoV-2 in Aotearoa’s wastewater

Unless you’ve been living under a rock (no offence to our cryptobenthic readers) you will have heard that wastewater testing is being used around the world to track the spread of COVID-19. Small fragments of viral RNA in public sewersheds can be used to understand the dynamics of COVID infections in a population in near-real-time. This approach isn’t reliant on self-reporting or PCR analysis of nasal swabs, and has the ability to detect surges in case numbers or the appearance of new strains before they are detected by genomic surveillance.

Over the past few months, Wilderlab has been working closely with the ESR wastewater team to further develop surveillance methods to strengthen the national COVID monitoring effort in Aotearoa New Zealand.

The ESR and Wilderlab teams have designed, optimized and validated four metabarcoding assays for high-throughput testing and identification of different COVID RNA variants. The assays can approximate the proportions each COVID variant in the wastewater without the need to sequence SARS-CoV-2 genomes from large numbers of nasal swabs. This enables a scalable and timely approach to COVID surveillance as new variants arrive and spread through the regions.

These ‘microbarcoding’ assays focus on very short but variable sections of the viral spike protein coding region. They are extremely sensitive at detecting trace amounts of RNA, even where nucleic acids are degraded and fragmented in wastewater treatment plants.

Wilderlab now processes wastewater extracts from 20 sentinel sites around the country each week to contribute data to ESR’s Wastewater Variant Analysis and Wastewater Surveillance Dashboard. As new COVID variants arise and are sequenced overseas, the sharing of full genome data allows us to design and validate new assays to ensure we’ll be able to detect the variant as soon as it shows up in our wastewater systems.

If you’d like to learn more, here is a deep dive into the nation’s wastewater from University of Auckland microbiologist Dr. Siouxsie Wiles and ESR Principal Scientist Prof. Mike Bunce.

Extract more from your eDNA data with the shinywheels app

You may have seen our colourful ‘wheels of life’ appear around the place. We developed these to help people visualize and communicate the breadth of biodiversity in eDNA results beyond just spreadsheets. Due to the popularity of these diagrams, our data scientist (Susan) and community engagement coordinator (Amy), developed a new app that enables you to create your very own wheel of life just by uploading your eDNA results spreadsheet. What’s more, we have curated a large library of free silhouettes that you can access to really bring your wheel of life to life!

This application is still in development, but if you’re interested in trying it out we’d love to hear any feedback about how you’ve found using it. You can find the shinywheels app here, and some helpful instructions on how to use it here.

Real-time data access: Into the Wilderness

Our standard method of communicating results to our clients is via email and in spreadsheet format. These data tables represent our best effort at identifying taxa from the eDNA sequences at the time at which they are sent. However, being static result tables, they don’t benefit from the updates that are constantly being applied to the underlying eDNA data that are stored on our servers as new reference sequences become available. Furthermore, static result tables are not always shared between departments in large organizations, resulting in fragmented data and reporting.

To remedy this, Wilderlab has developed an API (Application Programming Interface) that enables clients to access their updated data in real-time. This ensures that the most up-to-date species detection records are always available to our clients, and helps facilitate the export of eDNA results to environmental data storage platforms such as Kisters/KiEco.

Get in touch with our team at info@wilderlab.co.nz if you think your organization would benefit from having API access. You can also check out our API and R package tutorial here.

Growing library of resources from Wai Tuwhera o te Taiao

As part of the Environmental Protection Authority’s community science programme Wai Tuwhero o te Taiao, the EPA and Wilderlab teams have been putting together a library of resources to help support participants get the most value from their eDNA activities.

These resources include guidance on optimal survey design, replication, interpreting data, and some suggested approaches for translating and communicating important eDNA findings to the wider community.

The team also holds monthly webinars to explore different aspects of eDNA monitoring and applications. These recordings have all been made available on the Wai Tuwhero o te Taiao website.