1
|
Guadalupe JJ, Pazmiño‐Vela M, Pozo G, Vernaza W, Ochoa‐Herrera V, Torres MDL, Torres AF. Metagenomic analysis of microbial consortia native to the Amazon, Highlands, and Galapagos regions of Ecuador with potential for wastewater remediation. Environ Microbiol Rep 2024; 16:e13272. [PMID: 38692845 PMCID: PMC11062868 DOI: 10.1111/1758-2229.13272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 04/06/2024] [Indexed: 05/03/2024]
Abstract
Native microbial consortia have been proposed for biological wastewater treatment, but their diversity and function remain poorly understood. This study investigated three native microalgae-bacteria consortia collected from the Amazon, Highlands, and Galapagos regions of Ecuador to assess their metagenomes and wastewater remediation potential. The consortia were evaluated for 12 days under light (LC) and continuous dark conditions (CDC) to measure their capacity for nutrient and organic matter removal from synthetic wastewater (SWW). Overall, all three consortia demonstrated higher nutrient removal efficiencies under LC than CDC, with the Amazon and Galapagos consortia outperforming the Highlands consortium in nutrient removal capabilities. Despite differences in α- and β-diversity, microbial species diversity within and between consortia did not directly correlate with their nutrient removal capabilities. However, all three consortia were enriched with core taxonomic groups associated with wastewater remediation activities. Our analyses further revealed higher abundances for nutrient removing microorganisms in the Amazon and Galapagos consortia compared with the Highland consortium. Finally, this study also uncovered the contribution of novel microbial groups that enhance wastewater bioremediation processes. These groups have not previously been reported as part of the core microbial groups commonly found in wastewater communities, thereby highlighting the potential of investigating microbial consortia isolated from ecosystems of megadiverse countries like Ecuador.
Collapse
Affiliation(s)
- Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida PampiteQuitoEcuador
| | - Miguel Pazmiño‐Vela
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida PampiteQuitoEcuador
| | - Gabriela Pozo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida PampiteQuitoEcuador
| | - Wendy Vernaza
- Colegio de Ciencias e IngenieríaUniversidad San Francisco de Quito USFQ, Diego de Robles y Vía InteroceánicaQuitoEcuador
| | - Valeria Ochoa‐Herrera
- Colegio de Ciencias e IngenieríaUniversidad San Francisco de Quito USFQ, Diego de Robles y Vía InteroceánicaQuitoEcuador
- Department of Environmental Sciences and Engineering, Gillings School of Global Public HealthUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida PampiteQuitoEcuador
| | - Andres F. Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida PampiteQuitoEcuador
| |
Collapse
|
2
|
Pozo G, Albuja-Quintana M, Larreátegui L, Gutiérrez B, Fuentes N, Alfonso-Cortés F, Torres MDL. First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies. G3 (Bethesda) 2024; 14:jkae014. [PMID: 38244218 PMCID: PMC10917520 DOI: 10.1093/g3journal/jkae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024]
Abstract
The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered [International union for conservation of nature (IUCN)]. It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are keys for the management of endangered species, but this requires a reference genome, which until now was unavailable for A. f. fusciceps. The present study reports the first whole-genome sequence and assembly of A. f. fusciceps generated using Oxford Nanopore long reads. DNA was extracted from a subadult male, and libraries were prepared for sequencing following the Ligation Sequencing Kit SQK-LSK112 workflow. Sequencing was performed using a MinION Mk1C sequencer. The sequencing reads were processed to generate a genome assembly. Two different assemblers were used to obtain draft genomes using raw reads, of which the Flye assembly was found to be superior. The final assembly has a total length of 2.63 Gb and contains 3,861 contigs, with an N50 of 7,560,531 bp. The assembly was analyzed for annotation completeness based on primate ortholog prediction using a high-resolution database, and was found to be 84.3% complete, with a low number of duplicated genes indicating a precise assembly. The annotation of the assembly predicted 31,417 protein-coding genes, comparable with other mammal assemblies. A reference genome for this critically endangered species will allow researchers to gain insight into the genetics of its populations and thus aid conservation and management efforts of this vulnerable species.
Collapse
Affiliation(s)
- Gabriela Pozo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
| | - Martina Albuja-Quintana
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
| | - Lizbeth Larreátegui
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
| | - Bernardo Gutiérrez
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Nathalia Fuentes
- Proyecto Washu/Fundación Naturaleza y Arte, Quito 170521, Ecuador
| | | | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
| |
Collapse
|
3
|
Altamirano-Ponce L, Dávila-Játiva M, Pozo G, Pozo MJ, Terán-Velástegui M, Cadena CD, Cisneros-Heredia DF, Torres MDL. First genetic insights of Gonatodescaudiscutatus (Reptilia, Gekkota) in the Galapagos Islands and mainland Ecuador. Biodivers Data J 2023; 11:e113396. [PMID: 38028240 PMCID: PMC10680088 DOI: 10.3897/bdj.11.e113396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
Studies on genetic variability amongst native and introduced species contribute to a better understanding of the genetic diversity of species along their autochthonous distribution and identify possible routes of introduction. Gonatodescaudiscutatus is a gecko native to western Ecuador and introduced to the Galapagos Islands. Despite being a successful species in human-modified habitats along its native and non-native ranges, neither the colonisation process nor the genetic diversity of this gecko is known. In this study, we analysed 55 individuals from 14 localities in western Ecuador and six localities in San Cristobal Island, Galapagos - the only island with a large, self-sustaining population. We amplified and analysed the genetic variability of two nuclear genes (Cmos and Rag2) and one mitochondrial gene (16S). Cmos and Rag2 sequences presented little to none genetic variability, while 16S allowed us to build a haplotype network. We identified nine haplotypes across mainland Ecuador, two of which are also present in Galapagos. Low genetic diversity between insular and continental populations suggests that the introduction of G.caudiscutatus on the Islands is relatively recent. Due to the widespread geographical distribution of mainland haplotypes, it was not possible to determine the source population of the introduction. This study represents the first exploration of the genetic diversity of Gonatodescaudiscutatus, utilising genetic tools to gain insights into its invasion history in the Galapagos.
Collapse
Affiliation(s)
- Lía Altamirano-Ponce
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología Terrestre, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología TerrestreQuitoEcuador
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalQuitoEcuador
| | - Mateo Dávila-Játiva
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología Terrestre, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología TerrestreQuitoEcuador
- Universidad San Francisco de Quito USFQ, extensión Galápagos GAIAS, Puerto Baquerizo Moreno, San Cristóbal, Galápagos, EcuadorUniversidad San Francisco de Quito USFQ, extensión Galápagos GAIAS, Puerto Baquerizo Moreno, San CristóbalGalápagosEcuador
- Universidad de los Andes, Departamento de Ciencias Biológicas, Laboratorio de Biología Evolutiva de Vertebrados, Bogotá, ColombiaUniversidad de los Andes, Departamento de Ciencias Biológicas, Laboratorio de Biología Evolutiva de VertebradosBogotáColombia
- Galápagos Science Center, Universidad San Francisco de Quito USFQ & University of North Carolina at Chapel Hill UNC, Galápagos, EcuadorGalápagos Science Center, Universidad San Francisco de Quito USFQ & University of North Carolina at Chapel Hill UNCGalápagosEcuador
| | - Gabriela Pozo
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalQuitoEcuador
| | - María José Pozo
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalQuitoEcuador
| | - Martín Terán-Velástegui
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalQuitoEcuador
| | - Carlos Daniel Cadena
- Universidad de los Andes, Departamento de Ciencias Biológicas, Laboratorio de Biología Evolutiva de Vertebrados, Bogotá, ColombiaUniversidad de los Andes, Departamento de Ciencias Biológicas, Laboratorio de Biología Evolutiva de VertebradosBogotáColombia
| | - Diego F. Cisneros-Heredia
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología Terrestre, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología TerrestreQuitoEcuador
- Universidad San Francisco de Quito USFQ, extensión Galápagos GAIAS, Puerto Baquerizo Moreno, San Cristóbal, Galápagos, EcuadorUniversidad San Francisco de Quito USFQ, extensión Galápagos GAIAS, Puerto Baquerizo Moreno, San CristóbalGalápagosEcuador
- Galápagos Science Center, Universidad San Francisco de Quito USFQ & University of North Carolina at Chapel Hill UNC, Galápagos, EcuadorGalápagos Science Center, Universidad San Francisco de Quito USFQ & University of North Carolina at Chapel Hill UNCGalápagosEcuador
| | - Maria de Lourdes Torres
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalQuitoEcuador
- Universidad San Francisco de Quito USFQ, extensión Galápagos GAIAS, Puerto Baquerizo Moreno, San Cristóbal, Galápagos, EcuadorUniversidad San Francisco de Quito USFQ, extensión Galápagos GAIAS, Puerto Baquerizo Moreno, San CristóbalGalápagosEcuador
- Galápagos Science Center, Universidad San Francisco de Quito USFQ & University of North Carolina at Chapel Hill UNC, Galápagos, EcuadorGalápagos Science Center, Universidad San Francisco de Quito USFQ & University of North Carolina at Chapel Hill UNCGalápagosEcuador
| |
Collapse
|
4
|
Chuctaya J, Shibatta OA, Encalada AC, Barragán KS, Torres MDL, Rojas E, Ochoa-Herrera V, Ferrer J. Rediscovery of Rhyacoglanis pulcher (Boulenger, 1887) (Siluriformes: Pseudopimelodidae), a rare rheophilic bumblebee catfish from Ecuadorian Amazon. PLoS One 2023; 18:e0287120. [PMID: 37437013 PMCID: PMC10337946 DOI: 10.1371/journal.pone.0287120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 05/30/2023] [Indexed: 07/14/2023] Open
Abstract
Rhyacoglanis pulcher is a rare Neotropical rheophilic bumblebee catfish known only from the type locality in the Cis-Andean Amazon region, Ecuador, and the type-species of the genus. So far, the three syntypes collected in 1880 were the only specimens unambiguously associated to the name R. pulcher available in scientific collections. Recently, a specimen was discovered in a fast-flowing stretch of the Villano river, a tributary of the Curaray river, Napo river basin, Ecuador, representing a new record after nearly 140 years. Here, we present this new record, identified by morphology, provide the DNA barcode sequence of the specimen, and propose why the species of Rhyacoglanis are scarce in zoological collections. Additionally, we discuss the intraspecific variation in the color pattern observed in R. pulcher.
Collapse
Affiliation(s)
- Junior Chuctaya
- Programa de Pós-Graduação em Biologia Animal, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- AQUAREC, Laboratorio de Biología y Genética Molecular, Instituto de Investigaciones de la Amazonia Peruana, Iquitos, Loreto, Peru
- Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Oscar Akio Shibatta
- Museu de Zoologia, Departamento de Biologia Animal e Vegetal, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Andrea C. Encalada
- Instituto BIOSFERA, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Karla S. Barragán
- Instituto BIOSFERA, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Maria de Lourdes Torres
- Instituto BIOSFERA, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
- Laboratorio Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Estefanía Rojas
- Instituto BIOSFERA, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Valeria Ochoa-Herrera
- Instituto BIOSFERA, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
- Escuela de Ingeniería, Ciencia y Tecnología, Universidad del Rosario, Bogotá, Colombia
| | - Juliano Ferrer
- Programa de Pós-Graduação em Biologia Animal, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| |
Collapse
|
5
|
Muñoz-Abril L, Torres MDL, Valle CA, Rubianes-Landázuri F, Galván-Magaña F, Canty SWJ, Terán MA, Brandt M, Chaves JA, Grewe PM. Lack of genetic differentiation in yellowfin tuna has conservation implications in the Eastern Pacific Ocean. PLoS One 2022; 17:e0272713. [PMID: 36040879 PMCID: PMC9426925 DOI: 10.1371/journal.pone.0272713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 07/25/2022] [Indexed: 11/19/2022] Open
Abstract
Yellowfin tuna, Thunnus albacares, is an important global fishery and of particular importance in the Eastern Pacific Ocean (EPO). According to the 2019 Inter-American Tropical Tuna Commission (IATTC) assessment, yellowfin tuna within the EPO is a single stock, and is being managed as one stock. However, previous studies indicate site fidelity, or limited home ranges, of yellowfin tuna which suggests the potential for multiple yellowfin tuna stocks within the EPO, which was supported by a population genetic study using microsatellites. If numerous stocks are present, management at the wrong spatial scales could cause the loss of minor yellowfin tuna populations in the EPO. In this study we used double digestion RADseq to assess the genetic structure of yellowfin tuna in the EPO. A total of 164 yellowfin tuna from Cabo San Lucas, México, and the Galápagos Islands and Santa Elena, Ecuador, were analysed using 18,011 single nucleotide polymorphisms. Limited genetic differentiation (FST = 0.00058–0.00328) observed among the sampling locations (México, Ecuador, Peru, and within Ecuador) is consistent with presence of a single yellowfin tuna population within the EPO. Our findings are consistent with the IATTC assessment and provide further evidence of the need for transboundary cooperation for the successful management of this important fishery throughout the EPO.
Collapse
Affiliation(s)
- Laia Muñoz-Abril
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito USFQ, Diego de Robles y Pampite, Quito, Ecuador
- Department of Marine Sciences, University of South Alabama, USA Drive North, Mobile, Alabama, United States of America
- * E-mail:
| | - Maria de Lourdes Torres
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito USFQ, Diego de Robles y Pampite, Quito, Ecuador
| | - Carlos A. Valle
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito USFQ, Diego de Robles y Pampite, Quito, Ecuador
| | - Francisco Rubianes-Landázuri
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito USFQ, Diego de Robles y Pampite, Quito, Ecuador
| | - Felipe Galván-Magaña
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, La Paz, México
| | - Steven W. J. Canty
- Smithsonian Marine Station Fort Pierce, Fort Pierce, Florida, United States of America
- Working Land and Seascapes, Smithsonian Institution, Washington, DC, United States of America
| | - Martin A. Terán
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito USFQ, Diego de Robles y Pampite, Quito, Ecuador
| | - Margarita Brandt
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito USFQ, Diego de Robles y Pampite, Quito, Ecuador
| | - Jaime A. Chaves
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito USFQ, Diego de Robles y Pampite, Quito, Ecuador
- Department of Biology, San Francisco State University, San Francisco, CA, United States of America
| | - Peter M. Grewe
- CSIRO Oceans & Atmosphere, Castray Esplanade, Hobart, Tasmania, Australia
| |
Collapse
|
6
|
Gulisano A, Alves S, Rodriguez D, Murillo A, van Dinter BJ, Torres AF, Gordillo-Romero M, Torres MDL, Neves-Martins J, Paulo MJ, Trindade LM. Diversity and Agronomic Performance of Lupinus mutabilis Germplasm in European and Andean Environments. Front Plant Sci 2022; 13:903661. [PMID: 35755685 PMCID: PMC9226751 DOI: 10.3389/fpls.2022.903661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/05/2022] [Indexed: 05/27/2023]
Abstract
The introduction of Lupinus mutabilis (Andean lupin) in Europe will provide a new source of protein and oil for plant-based diets and biomass for bio-based products, while contributing to the improvement of marginal soils. This study evaluates for the first time the phenotypic variability of a large panel of L. mutabilis accessions both in their native environment and over two cropping conditions in Europe (winter crop in the Mediterranean region and summer crop in North-Central Europe), paving the way for the selection of accessions adapted to specific environments. The panel of 225 accessions included both germplasm pools from the Andean region and breeding lines from Europe. Notably, we reported higher grain yield in Mediterranean winter-cropping conditions (18 g/plant) than in the native region (9 g/plant). Instead, North European summer-cropping conditions appear more suitable for biomass production (up to 2 kg/plant). The phenotypic evaluation of 16 agronomical traits revealed significant variation in the panel. Principal component analyses pointed out flowering time, yield, and architecture-related traits as the main factors explaining variation between accessions. The Peruvian material stands out among the top-yielding accessions in Europe, characterized by early lines with high grain yield (e.g., LIB065, LIB072, and LIB155). Bolivian and Ecuadorian materials appear more valuable for the selection of genotypes for Andean conditions and for biomass production in Europe. We also observed that flowering time in the different environments is influenced by temperature accumulation. Within the panel, it is possible to identify both early and late genotypes, characterized by different thermal thresholds (600°C-700°C and 1,000-1,200°C GDD, respectively). Indications on top-yielding and early/late accessions, heritability of morpho-physiological traits, and their associations with grain yield are reported and remain largely environmental specific, underlining the importance of selecting useful genetic resources for specific environments. Altogether, these results suggest that the studied panel holds the genetic potential for the adaptation of L. mutabilis to Europe and provide the basis for initiating a breeding program based on exploiting the variation described herein.
Collapse
Affiliation(s)
- Agata Gulisano
- Wageningen University and Research Plant Breeding, Wageningen University, Wageningen, Netherlands
| | - Sofia Alves
- DRAT, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Diego Rodriguez
- Instituto Nacional de Investigaciones Agropecuarias (INIAP), Estación Experimental Santa Catalina, Quito, Ecuador
| | - Angel Murillo
- Instituto Nacional de Investigaciones Agropecuarias (INIAP), Estación Experimental Santa Catalina, Quito, Ecuador
| | | | - Andres F. Torres
- Plant Biotechnology Laboratory, Universidad San Francisco de Quito, Quito, Ecuador
| | | | | | - João Neves-Martins
- DRAT, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Maria-João Paulo
- Wageningen University and Research Biometris, Wageningen Research, Wageningen, Netherlands
| | - Luisa M. Trindade
- Wageningen University and Research Plant Breeding, Wageningen University, Wageningen, Netherlands
| |
Collapse
|
7
|
Carranco AS, Romo D, de Lourdes Torres M, Wilhelm K, Sommer S, Gillingham MAF. Egg microbiota is the starting point of hatchling gut microbiota in the endangered yellow-spotted Amazon river turtle. Mol Ecol 2022; 31:3917-3933. [PMID: 35621392 DOI: 10.1111/mec.16548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/30/2022] [Accepted: 05/17/2022] [Indexed: 11/29/2022]
Abstract
Establishment and development of gut microbiota during vertebrates' early life are likely to be important predictors of health and fitness. Host-parental and host-environment interactions are essential to these processes. In oviparous reptiles whose nests represent a source of the parent's microbial inocula, the relative role of host-selection and stochastic environmental factors during gut microbial assemblage remains unknown. We sampled eggs incubated in artificial nests as well as hatchlings and juveniles (up to 30 days old) of the yellow-spotted Amazon river turtle (Podocnemis unifilis) developing in tubs filled with river water. We examined the relative role of the internal egg microbiota and the abiotic environment on hatchling and juvenile turtle's cloacal microbiota assemblages during the first 30 days of development. A mean of 71% of ASVs in hatched eggs could be traced to the nest environmental microbiota and in turn a mean of 77% of hatchlings' cloacal ASVs were traced to hatched eggs. Between day 5 and 20 of juvenile turtle's development, the river water environment plays a key role in the establishment of the gut microbiota (accounting for a mean of 13%-34.6% of cloacal ASVs) and strongly influences shifts in microbial diversity and abundance. After day 20, shifts in gut microbiota composition were mainly driven by host-selection processes. Therefore, colonization by environmental microbiota is key in the initial stages of establishing the host's gut microbiota which is subsequently shaped by host-selection processes. Our study provides a novel quantitative understanding of the host-environment interactions during gut microbial assemblage of oviparous reptiles.
Collapse
Affiliation(s)
- Ana Sofia Carranco
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - David Romo
- Tiputini Biodiversity Station, Universidad San Francisco de Quito, Cumbaya-, Quito, Ecuador
| | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Cumbaya-, Quito, Ecuador
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Mark A F Gillingham
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany.,Biodiversity Research Institute (CSIC, Oviedo University, Principality of Asturias), Campus of Mieres, University of Oviedo, 33600, Mieres, Spain
| |
Collapse
|
8
|
Carranco AS, Gillingham MAF, Wilhelm K, Torres MDL, Sommer S, Romo D. Transcending sea turtles: first report of hatching failure in eggs of an Amazonian freshwater turtle with symptoms of the fungal emerging disease fusariosis. Transbound Emerg Dis 2022; 69:e3282-e3288. [PMID: 35561152 DOI: 10.1111/tbed.14596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 11/30/2022]
Abstract
During the last few decades, fungal pathogens have caused devastating population declines across a broad range of taxa. A newly emerging fungal disease, sea turtle egg fusariosis, caused by members of the Fusarium solani species complex (FSSC), has been reported to be responsible for hatching failure in sea turtles worldwide. However, this has not been detected in fresh water turtle species. Here, using relocated clutches and artificial incubation, we report high hatching failure in eggs symptomatic of fusariosis in the yellow-spotted Amazon River turtle (Podocnemis unifilis) inhabiting a pristine environment in the Ecuadorian Amazon. In 2020, we screened 680 eggs of the yellow-spotted Amazon River turtle, relocated from wild nesting areas to artificial nests, for visual symptoms of fusariosis and to estimate hatchability despite infection. We selected 68 eggs sampled in 2019 to confirm Fusarium infection by PCR amplification of the TEF-1α gene and sequenced seven of those amplicons on an Illumina Miseq to assess FSSC membership. We observed fusariosis symptoms in 42% of the 680 eggs. The proportion of symptomatic eggs within nests was negatively linked to the proportion of eggs that hatched. Hatchability was 8% for symptomatic eggs compared with 72% of asymptomatic eggs. Through PCR testing, 58% of symptomatic and 8% of asymptomatic eggs sampled in 2019 tested positive for Fusarium spp., and sequencing revealed that nine sequence variants from three asymptomatic and four symptomatic eggs corresponded to F. keratoplasticum, F. solani, and F. falciforme, the three major FSSC pathogens reported in sea turtle egg fusariosis. Our study suggests that hatching failure in eggs linked to symptoms of fusariosis appears to be partially caused by Fusarium pathogens within FSSC in a freshwater turtle. Thus, fusariosis is more widespread among the Testudines than previously reported and is not limited to sea environments, findings of particular conservation concern. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Ana Sofia Carranco
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, 89069, Ulm, Germany
| | - Mark A F Gillingham
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, 89069, Ulm, Germany.,Biodiversity Research Institute (CSIC, Oviedo University, Principality of Asturias), Campus of Mieres, University of Oviedo, Mieres, 33600, Spain
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, 89069, Ulm, Germany
| | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, 89069, Ulm, Germany
| | - David Romo
- Tiputini Biodiversity Station, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| |
Collapse
|
9
|
Urquía D, Gutierrez B, Pozo G, Pozo MJ, Torres MDL. Origin and dispersion pathways of guava in the Galapagos Islands inferred through genetics and historical records. Ecol Evol 2021; 11:15111-15131. [PMID: 34765164 PMCID: PMC8571588 DOI: 10.1002/ece3.8193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/07/2021] [Accepted: 09/16/2021] [Indexed: 11/23/2022] Open
Abstract
Guava (Psidium guajava) is an aggressive invasive plant in the Galapagos Islands. Determining its provenance and genetic diversity could explain its adaptability and spread, and how this relates to past human activities. With this purpose, we analyzed 11 SSR markers in guava individuals from Isabela, Santa Cruz, San Cristobal, and Floreana islands in the Galapagos, as well as from mainland Ecuador. The mainland guava population appeared genetically differentiated from the Galapagos populations, with higher genetic diversity levels found in the former. We consistently found that the Central Highlands region of mainland Ecuador is one of the most likely origins of the Galapagos populations. Moreover, the guavas from Isabela and Floreana show a potential genetic input from southern mainland Ecuador, while the population from San Cristobal would be linked to the coastal mainland regions. Interestingly, the proposed origins for the Galapagos guava coincide with the first human settlings of the archipelago. Through approximate Bayesian computation, we propose a model where San Cristobal was the first island to be colonized by guava from the mainland, and then, it would have spread to Floreana and finally to Santa Cruz; Isabela would have been seeded from Floreana. An independent trajectory could also have contributed to the invasion of Floreana and Isabela. The pathway shown in our model agrees with the human colonization history of the different islands in the Galapagos. Our model, in conjunction with the clustering patterns of the individuals (based on genetic distances), suggests that guava introduction history in the Galapagos archipelago was driven by either a single event or a series of introduction events in rapid succession. We thus show that genetic analyses supported by historical sources can be used to track the arrival and spread of invasive species in novel habitats and the potential role of human activities in such processes.
Collapse
Affiliation(s)
- Diego Urquía
- Laboratorio de Biotecnología VegetalUniversidad San Francisco de Quito (USFQ)QuitoEcuador
| | - Bernardo Gutierrez
- Laboratorio de Biotecnología VegetalUniversidad San Francisco de Quito (USFQ)QuitoEcuador
- Department of ZoologyUniversity of OxfordOxfordUK
| | - Gabriela Pozo
- Laboratorio de Biotecnología VegetalUniversidad San Francisco de Quito (USFQ)QuitoEcuador
| | - Maria Jose Pozo
- Laboratorio de Biotecnología VegetalUniversidad San Francisco de Quito (USFQ)QuitoEcuador
| | - Maria de Lourdes Torres
- Laboratorio de Biotecnología VegetalUniversidad San Francisco de Quito (USFQ)QuitoEcuador
- Galapagos Science CenterUniversidad San Francisco de Quito and University of North Carolina at Chapel HillGalapagosEcuador
| |
Collapse
|
10
|
Vega-Polo P, Cobo MM, Argudo A, Gutierrez B, Rowntree J, Torres MDL. Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands. PLoS One 2020; 15:e0243420. [PMID: 33284832 PMCID: PMC7721170 DOI: 10.1371/journal.pone.0243420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/22/2020] [Indexed: 11/18/2022] Open
Abstract
The Ecuadorian páramo, a high altitude tundra-like ecosystem, is a unique source of various ecosystem services and distinct biodiversity. Anthropogenic activities are associated with its fragmentation, which alters ecological factors and directly threatens resident species. Vaccinium floribundum Kunth., commonly known as Andean blueberry or mortiño, is a wild shrub endemic to the Andean region and highly valued in Ecuador for its berries, which are widely used in food preparations and hold an important cultural value. Since it is a wild species, mortiño could be vulnerable to environmental changes, resulting in a reduction of the size and distribution of its populations. To evaluate the extent of these effects on the mortiño populations, we assessed the genetic diversity and population structure of the species along the Ecuadorian highlands. We designed and developed a set of 30 species-specific SSR (simple sequence repeats) markers and used 16 of these to characterize 100 mortiño individuals from 27 collection sites. Our results revealed a high degree of genetic diversity (HE = 0.73) for the Ecuadorian mortiño, and a population structure analyses suggested the existence of distinct genetic clusters present in the northern, central and southern highlands. A fourth, clearly differentiated cluster was also found and included individuals from locations at higher elevations. We suggest that the population structure of the species could be explained by an isolation-by-distance model and can be associated with the geological history of the Andean region. Our results suggest that elevation could also be a key factor in the differentiation of mortiño populations. This study provides an extensive overview of the species across its distribution range in Ecuador, contributing to a better understanding of its conservation status. These results can assist in the development of conservation programs for this valuable biological and cultural resource and for the páramo ecosystem as a whole.
Collapse
Affiliation(s)
- Pamela Vega-Polo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Maria Mercedes Cobo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Andrea Argudo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Bernardo Gutierrez
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jennifer Rowntree
- Department of Natural Sciences, Ecology and Environment Research Centre, Manchester Metropolitan University, Oxford, United Kingdom
| | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- * E-mail:
| |
Collapse
|
11
|
Abstract
We report the complete plastome sequences of an endemic and an unidentified species from the genus
Psidium in the Galápagos Islands (
P. galapageium and
Psidium sp. respectively).
Collapse
Affiliation(s)
- Bryan Reatini
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27514, USA
| | | | | | - Todd Vision
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27514, USA
| |
Collapse
|
12
|
Fiallos-Jurado J, Pollier J, Moses T, Arendt P, Barriga-Medina N, Morillo E, Arahana V, de Lourdes Torres M, Goossens A, Leon-Reyes A. Saponin determination, expression analysis and functional characterization of saponin biosynthetic genes in Chenopodium quinoa leaves. Plant Sci 2016; 250:188-197. [PMID: 27457995 DOI: 10.1016/j.plantsci.2016.05.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 05/17/2016] [Accepted: 05/19/2016] [Indexed: 05/09/2023]
Abstract
Quinoa (Chenopodium quinoa Willd.) is a highly nutritious pseudocereal with an outstanding protein, vitamin, mineral and nutraceutical content. The leaves, flowers and seed coat of quinoa contain triterpenoid saponins, which impart bitterness to the grain and make them unpalatable without postharvest removal of the saponins. In this study, we quantified saponin content in quinoa leaves from Ecuadorian sweet and bitter genotypes and assessed the expression of saponin biosynthetic genes in leaf samples elicited with methyl jasmonate. We found saponin accumulation in leaves after MeJA treatment in both ecotypes tested. As no reference genes were available to perform qPCR in quinoa, we mined publicly available RNA-Seq data for orthologs of 22 genes known to be stably expressed in Arabidopsis thaliana using geNorm, NormFinder and BestKeeper algorithms. The quinoa ortholog of At2g28390 (Monensin Sensitivity 1, MON1) was stably expressed and chosen as a suitable reference gene for qPCR analysis. Candidate saponin biosynthesis genes were screened in the quinoa RNA-Seq data and subsequent functional characterization in yeast led to the identification of CqbAS1, CqCYP716A78 and CqCYP716A79. These genes were found to be induced by MeJA, suggesting this phytohormone might also modulate saponin biosynthesis in quinoa leaves. Knowledge of the saponin biosynthesis and its regulation in quinoa may aid the further development of sweet cultivars that do not require postharvest processing.
Collapse
Affiliation(s)
- Jennifer Fiallos-Jurado
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agroempresas, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito, Campus Cumbayá, 17-1200-841 Quito, Ecuador; Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Campus Cumbayá, 17-1200-841 Quito, Ecuador
| | - Jacob Pollier
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Tessa Moses
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Philipp Arendt
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium; Inflammation Research Centre (IRC), VIB, 9052 Gent, Belgium; Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Noelia Barriga-Medina
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agroempresas, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito, Campus Cumbayá, 17-1200-841 Quito, Ecuador
| | - Eduardo Morillo
- Instituto Nacional de Investigaciones Agropecuarias (INIAP), Estación Experimental Santa Catalina, Quito, Ecuador
| | - Venancio Arahana
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Campus Cumbayá, 17-1200-841 Quito, Ecuador
| | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Campus Cumbayá, 17-1200-841 Quito, Ecuador
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agroempresas, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito, Campus Cumbayá, 17-1200-841 Quito, Ecuador.
| |
Collapse
|