Resident or invasive species? Environmental DNA can provide reliable answers

Resident or invasive species? Environmental DNA can provide reliable answers

Resident or invasive species? Environmental DNA can provide reliable answers

Environmental DNA can be successfully applied to identify vertebrates in a tropical lake improving our capacity to map and monitor species.
Panoramic view of Bacalar Lake including the 40-m deep Esmeralda sinkhole.

PHOTO CREDIT: Manuel Elías-Gutiérrez

Monitoring life within large bodies of water – those species that should and shouldn’t live there – can be very expensive and time consuming. To overcome these limitations, efforts in many temperate regions employ methods that use environmental DNA (eDNA), enabling effective and targeted detection of invasive and resident endangered species.

Our study is the first to demonstrate that eDNA-based monitoring can be successfully applied to target the whole fish community in a tropical freshwater system and its adjacent wetlands.

Between 1980 -1990, eDNA was the term introduced to define particulate DNA and it was used to detect and describe microbial communities in marine sediments and phytoplankton communities in the water column1. However, eDNA is presently defined as the genetic material left behind by eukaryotic organisms in the environment, reflecting a rise in the use of eDNA for the detection of vertebrate and invertebrate species in aquatic systems1. The popularity of using eDNA has increased following the development of next-generation sequencing, advances in quantitative PCR (qPCR), and the growth of DNA barcodes libraries such as the Barcode of Life Data System (BOLD), providing a quicker and more taxonomically comprehensive tool for biodiversity assessments.

 

South end of lake Bacalar with the sinkhole Cenote Azul.
PHOTO CREDIT: Manuel Elías-Gutiérrez

Lake Bacalar is the largest epicontinental habitat in Mexico’s Yucatan Peninsula, and it is renowned for its striking blue color, clarity of the water, and for the world’s largest occurrence of living stromatolites, a calcareous mound built up of layers of lime-secreting cyanobacteria. Due to the presence of sediments derived from karst limestone, it represents the world’s largest fresh groundwater-feed ecosystem. The northern part of Lake Bacalar is connected to a complex system of lagoons and the southern part has an indirect connection to the sea via a wetland system that connects with Hondo River and enters Chetumal Bay. This river has been heavily impacted by the discharge of organic waste and pesticides, by vegetation clearing, and by the introduction of invasive fish such as tilapia and the Amazon sailfin catfish (Pterygoplichthys pardalis) 2-4, first detected in 2013 4. The Amazon sailfin catfish is a serious threat to the fragile stromatolite ecosystem due to its burrowing habits and competition with local fish. The impact of declining water quality and the rise of invasive species on the native fish fauna needs to be carefully monitored in aid of conservation efforts of Lake Bacalar.

A team of researchers from the Instituto Tecnológico de Chetumal and El Colegio de la Frontera Sur sampled eight localities in December 2015, and January and April 2016. After each of 14 sampling events, water and sediment samples were immediately placed on ice before transportation to the lab in Chetumal. To minimize eDNA degradation, we filtered water samples within seven hours of collection. All filters and sediments were stored at -18°C before being transported on ice from Chetumal to the Centre for Biodiversity Genomics in Guelph, Canada, where DNA extraction was undertaken.

 

Water sampling between stromatolites.
PHOTO CREDIT: Miguel Valadez

We sequenced short fragments (<200 bp) of the cytochrome c oxidase I (COI) gene on Ion Torrent PGM or S5 platforms. In total, we recovered eDNA sequences from 75 species of vertebrates including 47 fishes, 15 birds, seven mammals, five reptiles, and one amphibian. Although all species are known from this region, six fish species represent new records for the study area, while two require verification (Vieja fenestrata and Cyprinodon beltrani /simus), because their presence is unlikely in this ecosystem. While there were species (two birds, two mammals, one reptile) only detected from sediments, water samples recovered a much higher diversity (52 species), indicating better eDNA preservation in the slightly alkaline Bacalar water.  Because DNA from the Amazon sailfin catfish was not detected, we used a mock eDNA experiment that confirmed our methods were effective.

Interesting findings include the detection of rare species, such as an anteater Tamandua mexicana, which was detected by both PGM and S5 instruments from a river sample (Juan Sarabia), and migratory birds, such as warbler Oreothlypis peregrina known to overwinter in the Yucatan Peninsula.

Docks in front of Bacalar town
PHOTO CREDIT: Miguel Valadez

Our study indicates that eDNA can be successfully applied to monitor vertebrates in a tropical oligotrophic lake as well as more eutrophic (higher primary production) wetlands and can aid conservation and monitoring programs in tropical areas by improving our capacity to map occurrence records for resident and invasive species.

Our next step is to convince Mexican and international stakeholders to implement these methodologies and establish a permanent biomonitoring system for this and other pristine freshwater ecosystems found in Yucatan Peninsula. This work is necessary to detect effects of climate change, declining water quality, and the increasing tourism activities in this region.

References:

1. Díaz-Ferguson EE, Moyer GR (2014) History, applications, methodological issues and perspectives for the use of environmental DNA (eDNA) in marine and freshwater environments. Revista de Biología Tropical 62: 1273-1284. DOI: 10.15517/RBT.V62I4.13231

2. Wakida-Kusunoki AT, Luis Enrique Amador-del Ángel (2011) Aspectos biológicos del pleco invasor Pterygoplichthys pardalis (Teleostei : Loricariidae) en el río Palizada, Campeche, México. Revista Mexicana de Biodiversidad 82: 870-878

3. Alfaro REM, Fisher JP, Courtenay W, Ramírez Martínez C, Orbe-Mendoza A, Escalera Gallardo C, et al. (2009) Armored catfish (Loricariidae) trinational risk assessment guidlines for aquatic alien invasive species. Test cases for the snakeheads (Channidae) and armored catfishes (Loricariidae) in North American inland waters. Montreal, Canada: Commission for Environmental Cooperation. pp. 25-49.

4. Schmitter-Soto JJ, Quintana R, Valdéz-Moreno ME, Herrera-Pavón RL, Esselman PC (2015) Armoured catfish (Pterygoplichthys pardalis) in the Hondo River basin, Mexico-Belize. Mesoamericana 19: 9-19.

Written by

Natalia V. Ivanova

Natalia V. Ivanova

Centre for Biodiversity Genomics, Guelph, ON, Canada

Martha Valdez-Moreno

Martha Valdez-Moreno

El Colegio de la Frontera Sur, Unidad Chetumal, Chetumal, Mexico

Manuel Elías-Gutiérrez

Manuel Elías-Gutiérrez

El Colegio de la Frontera Sur, Unidad Chetumal, Chetumal, Mexico

May 15, 2019
PDF
https://doi.org/10.21083/ibol.v9i1.5474

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Diagnosing a rare human disease in Mexico’s lowlands

Diagnosing a rare human disease in Mexico’s lowlands

Diagnosing a rare human disease in Mexico’s lowlands

The first multidisciplinary study using DNA barcodes as a medical diagnostic tool forms a unique collaborative group comprised of medical practitioners and scientists.

Scanning electron micrograph of the anterior part of Lagochilascaris minor.
PHOTO CREDIT: Manuel Elías-Gutiérrez

Roundworms (Nematoda) are one of the most diverse groups of invertebrates. Lagochilascaris minor, a parasitic nematode often found in wild cats such as jaguars and pumas, as well as in domestic cats and dogs, has only rarely been known to infect humans. However, a recent case in the Yucatan Peninsula has brought about a very unique collaboration between medical practitioners and scientists.

Lagochilascaris minor has been reported in the Americas, commonly in South America where the eggs have been found in public parks1. However, identifying L. minor with conventional methods can be misleading as they resemble other ascaridoid eggs.

When a 23-year old man from a village in the forests of southern Quintana Roo state (Yucatan Peninsula) came into the local hospital in July 2016, physicians were surprised to find that a parasite had destroyed the mastoid apophysis, the lateral sinus, and part of the cerebellum. After a radical mastoidectomy and medical treatment for 63 days, the patient made a full recovery. After removal, the parasite was identified as L. minor using DNA barcodes and morphology. While the method of infection is uncertain, it is thought to be through direct exposure to the eggs or through the consumption of uncooked meat from wild animals.

Coronal computerized tomography scan of the human patient. Arrow indicates destruction of the left mastoid bone.
PHOTO CREDIT: Hospital General de Chetumal, Mexico
While it has been a challenge to successful identify Nematoda using genetic markers in the past, high-quality DNA barcode sequences were obtained using semi-degenerate primers designed for micro-crustaceans2. A comparison with 81 ascaridoids obtained from the Barcode of Life Data System (BOLD) revealed its position in a unique clade, most closely related to Baylisascaris procyonis.

This is the first multidisciplinary study involving DNA barcodes as a diagnostic medical tool in a human patient. This field of research can be promising because we can get a precise identification of the parasites in any stage of their life cycle. Diagnosis using DNA barcoding will allow the recognition of the infection parameters, transmission, and more precise epidemiology of parasites. With this information, we can not only diagnose the disease but also prevent it by finding the infectious stages, the intermediate hosts, or the vectors in the environment.

All sequences of Lagochilascaris are in the public project ‘NECHE Lagochilascaris from Yucatan’ in BOLD. This study is published in the Journal of Parasitology.

References:

  1. de Moura MQ, Jeske S, Gallina T, Borsuk S, Berne MEA, Villela MM (2012) First report of Lagochilascaris (Nematoda: Ascarididae) eggs in a public park in Southern Brazil. Veterinary Parasitology 184(2-4): 359-361. https://doi.org/10.1016/j.vetpar.2011.09.019
  2. Prosser SW, Velarde-Aguilar MG, Leon-Regagnon V, Hebert PD (2013) Advancing nematode barcoding: A primer cocktail for the cytochrome c oxidase subunit I gene from vertebrate parasitic nematodes. Molecular Ecology Resources 13(6): 1108-1115. https://doi.org/10.1111/1755-0998.12082

Written by

David González-Solís

David González-Solís

El Colegio de la Frontera Sur, Chetumal, México

Manuel Elías-Gutiérrez

Manuel Elías-Gutiérrez

El Colegio de la Frontera Sur, Chetumal, México

Jenny Alejandra Prado-Bernal

Clínica Carranza, Chetumal, México

Miguel Alfredo García-de la Cruz

Hospital General Dr. Manuel Gea González, Ciudad de México, México

April 30, 2019
PDF
https://doi.org/10.21083/ibol.v9i1.5475

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