Environmental DNA sequencing will allow scientists to discover Amazon piscine variety with out catching fish


A view of the river the place environmental DNA was collected for comparability with captured specimens. The researchers intention to deposit in public databases sequences of genetic materials representing all orders and households and most genera of Amazonian fish. Credit: David de Santana

A scientific expedition within the Javari River basin on the border between Brazil, Colombia and Peru has proven use of environmental DNA sequencing to be possible to research fish variety within the Amazon. The eDNA technique consists of extracting molecules of DNA current in water samples and figuring out the species to which they belong by way of genetic markers. 

An article on the analysis revealed within the journal Scientific Reports additionally discusses the constraints of the approach for the examine of environments as extremely numerous as Amazonia.

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“We need to continue catching and identifying animals by traditional methods in order to create libraries of genetic material. They will serve as a reference for comparing whatever is found in water samples. As the technique advances, in a few years we may be able to know about all the fish species current in a spot with out catching them,” stated Carlos David de Santana, a analysis affiliate on the Smithsonian Institution’s National Museum of Natural History within the United States and first writer of the article.

The examine was a part of the challenge “Diversity and evolution of Gymnotiformes”, supported by FAPESP and led by Naércio Menezes, a professor on the University of São Paulo’s Zoology Museum (MZ-USP) in Brazil. “The extraction of DNA from water samples creates expectations that are highly favorable to protection of the environment, as the usual methods for collecting samples of aquatic animals include the use of nets and other fishing gear with a negative impact,” stated Menezes, a co-author of the article.

The group of researchers spent 18 days on the Javari River, amassing water samples at three of 46 areas the place they collected fish specimens. The variety of species represented reached the stunning total of 443, and 60 had been new to science.

At the websites from which water for eDNA evaluation was collected, 201 species had been caught utilizing conventional strategies. However, solely 58, or 26% of the total, had been recognized with precision on the species stage from evaluation of the eDNA.

“A possible explanation is lack of reference genetic material in databases that can be used for purposes of comparison. In addition, many species in these locations are entirely new and have never been identified before using conventional techniques,” stated Gislene Torrente-Vilara, a professor on the Federal University of São Paulo’s Institute of Marine Sciences (IMAR-UNIFESP) in Santos and a co-author of the article.

Torrente-Vilara led the expedition as a part of the Amazon Fish challenge, a world collaboration that was supported by FAPESP and resulted in a brand new understanding of the distribution of fish species within the area. 

DNA in 100 milliliters of water

To sequence the eDNA, the researchers first collected 100-milliliter floor water samples at three predetermined areas. The samples had been filtered and combined with an answer to forestall degradation of the eDNA.

The 12S mitochondrial RNA gene is the marker most generally used worldwide to determine fish species from eDNA. To discover this small piece of genetic code within the water samples, the researchers used DNA extraction kits designed for evaluation of each blood and tissue. Excrement and animal components current within the water will be “captured” by the approach.

However, 12S is a slowly evolving piece of genetic code and won’t be adequate to determine all fish specimens on the species stage as a result of many species within the Amazon diverged greater than as soon as tens of millions of years in the past (not too long ago in evolutionary phrases).

For the identical purpose, eDNA sequencing supplied a exact portrait solely of the orders represented within the samples. It additionally differentiated the communities that stay in giant rivers from people who inhabit small streams deep within the forest (igarapés).

The Amazon basin is house to the very best freshwater fish variety on the earth, with greater than 2,700 scientifically described species belonging to 18 orders, 60 households, and over 500 genera. 

“Even with an adequate library, it would be very difficult to identify everything at the species level with just this marker,” Santana stated. “Two electric eels that diverged recently, for example, Electrophorus voltai and E. electricus, could appear to be a single species.”

The researchers count on the approach to enhance sufficient within the years forward for multiple DNA sample to be sequenced concurrently, in order that species will be outlined exactly. Until then it will likely be essential to create genetic reference libraries, and Santana plans to catalog genetic materials from not less than all fish households and most fish genera within the Amazon.

In this context, the authors stress that pure historical past museums are excellent establishments for creating genetic reference libraries and storing environmental samples. As applied sciences advance, the fabric deposited will be sequenced with rising precision.

“Museums conserve samples of biodiversity for a very long time and make them available for study by future generations. To keep genetic material viable for such long periods, however, they need to implement cryogenic facilities, or significantly expand the ones they have, rearranging their physical layout and acquiring massive amounts of equipment, such as ultra low temperature freezers and liquid nitrogen tanks,” stated Aléssio Datovo, one other co-author of the article and fish curator at MZ-USP, the primary establishment in Brazil to gather samples of eDNA.

The approach can be used for environmental monitoring, and even to have interaction colleges and riverine communities in conservation initiatives through citizen science applications. 

Using DNA to look for fish species

More info:
C. David de Santana et al, The vital function of pure historical past museums in advancing eDNA for biodiversity research: a case examine with Amazonian fishes, Scientific Reports (2021). DOI: 10.1038/s41598-021-97128-3

Environmental DNA sequencing will allow scientists to discover Amazon piscine variety with out catching fish (2021, November 23)
retrieved 23 November 2021
from https://phys.org/news/2021-11-environmental-dna-sequencing-enable-scientists.html

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