Biología

URI permanente para esta colecciónhttps://hdl.handle.net/10669/273

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Primer registro del Albatros de Salvin (Thalassarche salvini) y nuevos registros del Albatros de Galápagos (Phoebastria irrorata) en Costa Rica
(2024-07-17) Chacón Arias, Sergio
La información de presencia de albatros (Diomedeidae) y aves oceánicas en aguas de Costa Rica en general es limitada. Aquí documento el primer registro de la especie Thalassarche salvini (Albatros de Salvin) para Costa Rica. Además, reporto 18 nuevos registros de Phoebastria irrorata (Albatros de Galápagos) en aguas costarricenses del 2015 al 2023, con lo que se actualiza el estado de conocimiento de la presencia de esta especie en el país.
Criminalización de la investigación en biodiversidad
(2021-11-05) Rojas Jiménez, Keilor Osvaldo; Karremans Lok, Adam Philip
Los científicos costarricenses queremos generar y compartir conocimiento. Sin embargo, los que trabajamos en biodiversidad nos vemos cada vez más agobiados por la creciente burocracia y el afán de control de la Comisión para la Gestión de la Biodiversidad (CONAGEBio). En lugar de articular con los diferentes sectores la gestión integral de la biodiversidad, para su conservación y uso sostenible, el ente se volvió un inquisidor de la investigación de las universidades públicas, desincentivando la generación de conocimiento e intimidando a los académicos costarricenses.
Que no le den zopilote por colibrí
(2024-03-05) Karremans Lok, Adam Philip
Comentario sobre pertinencia de propuesta de colibrí como símbolo nacional.
Fungal conservation through a private initiative: the Mushroom Research Centre (MRC) in Thailand
(2004-07-12) Rojas Alvarado, Carlos Alonso; Stephenson, Steven L.
The conservation of fungi is an integral part of ecosystem conservation. The Mushroom Research Centre's strategic approach to fungal conservation offers valuable insights. Located in northern Thailand, this institution has emerged as a research and training hub for mycologists across Asia, providing them with practical knowledge and skills. Its influence has not been limited to the region, making it a compelling case study for the potential impact of private conservation initiatives.
Group vocal composition and decision- making during roost finding in Spix’s disk- winged bats
(2024) Sagot, Maria; Rose, Nicole
Theoretical work suggests that having many informed individuals within social groups can promote efficient resource location. However, it may also give rise to group fragmentation if members fail to reach consensus on their direction of movement. In this study, we investigate whether the number of informed individuals, exemplified by bats emitting calls from different roosts, influences group cohesion in Spix’s disk-winged bats (Thyroptera tricolor). Additionally, we explore the role of signal reliability, quantified through signalling rates, in group consensus on where to roost. These bats use contact calls to announce the location of a roost site and recruit conspecifics. The groups they form exhibit high levels of cohesion and consist of both vocal and non-vocal bats, with vocal behaviour being consistent over time. Our findings revealed that an increase in the number of roosts broadcasting calls is strongly associated with the likelihood of groups fragmenting among multiple roosts. Additionally, we found that a majority of group members enter the roost with higher calling rates. This phenomenon can mitigate the risk of group fragmentation, as bats emitting more calls may contribute to greater group consensus on roosting locations, thereby reducing the likelihood of individuals separating and enhancing overall group cohesion. Our results highlight the potential costs of having too many information producers for group coordination, despite their established role in finding critical resources.
Distinct orchid mycorrhizal fungal communities among co-occurring Vanilla species in Costa Rica: root substrate and population-based segregation
(2024-04-26) Wong, Shan; Kaur, Jaspreet; Kumar, Pankaj; Karremans Lok, Adam Philip; Sharma, Jyotsna
Despite being the second largest family of flowering plants, orchids represent community structure variation in plant- microbial associations, contributes to niche partitioning in metacommunity assemblages. Yet, mycorrhizal communities and interactions remain unknown for orchids that are highly specialized or even obligated in their associations with their mycorrhizal partners. In this study, we sought to compare orchid mycorrhizal fungal (OMF) communities of three co- occurring hemiepiphytic Vanilla species (V. hartii, V. pompona, and V. trigonocarpa) in tropical forests of Costa Rica by addressing the identity of their OMF communities across species, root types, and populations, using high-throughput sequencing. Sequencing the nuclear ribosomal internal transcribed spacer (nrITS) yielded 299 fungal Operational Taxo- nomic Units (OTUs) from 193 root samples. We showed distinct segregation in the putative OMF (pOMF) communities of the three coexisting Vanilla hosts. We also found that mycorrhizal communities associated with the rare V. hartii var- ied among populations. Furthermore, we identified Tulasnellaceae and Ceratobasidiaceae as dominant pOMF families in terrestrial roots of the three Vanilla species. In contrast, the epiphytic roots were mainly dominated by OTUs belonging to the Atractiellales and Serendipitaceae. Furthermore, the pOMF communities differed significantly across populations of the widespread V. trigonocarpa and showed patterns of distance decay in similarity. This is the first report of differ- ent pOMF communities detected in roots of wild co-occurring Vanilla species using high-throughput sequencing, which provides evidence that three coexisting Vanilla species and their root types exhibited pOMF niche partitioning, and that the rare and widespread Vanilla hosts displayed diverse mycorrhizal preferences.
Global consortium for the classification of fungi and fungus-like taxa
(Mushroom Research Foundation, 2023) Hyde, Kevin David; Abdel Wahan, Mohamed A.; Abdollahzadeh, Jafar; Abeywickrama, Pranami D.; Absalan, Sahar; Afshari, Naghmeh; Ainsworth, A. Martyn; Akulov, Olexander Yu; Aleoshin, Vladimir V.; Al Sadi, Abdullah Mohammed; Alvarado, Pablo; Da Costa Peixoto Alves, Artur Jorge; Alves da Silva, Genivaldo; Amalfi, Mario; Amira, Yacoub; Amuhenage, Tharindu Bhagya; Anderson, Jennifer L. ; Antonín, Vladimír; Aouali, S. ; Aptroot, André; Apurillo, Carlo Chris; De Araújo, João Paulo Machado; Ariyawansa, Hiran Anjana; Armand, Alireza; Arumugam, Elangovan; Asghari, Raheleh; Assis, Daniele Magna Azevedo de; Atienza Tamarit, María Violeta; Avasthi, Shubhi; Azevedo, Egídia; Bahkali, Ali Hassan Abdulrahman; Bakhshi, Mounes; Banihashemi, Zia; Bao, Dan Feng; Baral, Hans Otto; Barata, Marcela; Barbosa, Flávia Rodrigues; Barbosa, Renan do Nascimento; Barreto, Robert Weingart; Baschien, Christiane; Belamesiatseva, Dasha B.; Bennet, Reuel Matignas; Bera, Ishika; Pereira Bezerra, Jadson Diogo; Bezerra, José Luiz; Bhat, Darbhe Jayarama; Bhunjun, Chitrabhanu Sharma; Bianchinotti, María Virginia; Błaszkowski, Janusz; Blondelle, Aimée; Boekhout, Teun; Bonito, Gregory; Boonmee, Saranyaphat; Boonyuen, Nattawut; Bregant, Carlo; Buchanan, Peter K.; Bundhun, Digvijayini; Burgaud, Gaëtan; Burgess, Treena; Buyck, Bart; Cabarroi Hernández, Milay; Cáceres, Marcela Eugênia da Silva; Caeiro, Maria Filomena; Cai, Lei; Cai, M. F.; Calabon, Mark Seasat; Calaça, Francisco Júnior Simões; Callalli Chancahuaña, Mario; Câmara, ‪Marcos Paz Saraiva; Cano Lira, José Francisco; Cantillo, Taimy; Cao, Bin; Carlavilla, Juan Ramón Díaz; Carvalho Alves, Anabela; Castañeda Ruiz, Rafael Felipe; Castlebury, Lisa A.; Castro Jauregui, Óscar; Catania, Myriam del Valle; Cavalcanti Andrade, Laise de Holanda; Cazabonne, Jonathan; Cedeño Sánchez, Marjorie L.; Chaharmiri Dokhaharani, Samaneh; Chaiwan, Napalai; Chakraborty, Nilanjan; Chaverri Echandi, Priscila; Cheewangkoon, Ratchadawan; Chen, C.; Chen, Chi Yu ; Chen, Ko Hsuan; Chen, J.; Chen, Qian; Chen, Wan Hao; Chen, Yan Peng; Thilini Chethana, Kandawatte Wedaralalage; Coleine, Claudia; Condé, Thiago Oliveira; Corazon Guivin, Mike Anderson; Cortés Pérez, Alonso; Costa de Rezende, Diogo Henrique; Courtecuisse, Régis; Crouch, Jo Anne; Crous, Pedro W. ; Cui, Bao Kai; Cui, Yang Yang; Alves da Silva, Danielle Karla ; Alves da Silva, Gladstone; Da Silva, Iolanda Ramalho; Ferreira da Silva, Rejane Maria ; Da Silva Santos, Ana Carla; Dai, Dong Qin; Dai, Yu Cheng; Damm, Ulrike; Darmostuk, Valerii; Daroodi, Zoha; Das, Kanad; Das, Kallol; Davoodian, Naveed; Davydov, Evgeny Alexandrovich; Dayarathne, Monika C.; Decock, Cony ; De Groot, Michiel D. ; De Kesel, André ; Dela Cruz, Thomas Edison; De Lange, Ruben; Delgado, Gregorio P.; Denchev, Cvetomir M. ; Denchev, Teodor T. ; Oliveira, Neiva Tinti ; De Silva, Nimali Indeewari; De Souza, Francisco Adriano ; Dentinger, Bryn; Devadatha, Bandarupalli ; Dianese, José Carmine; Dima, Bálint; Diniz, Athaline G.; Dissanayake, Asha Janadaree; Dissanayake, Lakmali S. ; Dogan, Hasan Huseyin; Doilom, Ming Kwan; Dolatabadi, Somayeh; Dong, Wei; Dong, Zhang Yong; Alves dos Santos, Lidiane; Drechsler Santos, Elisandro Ricardo; Du, Tian Ye; Dubey, Manish Kumar; Dutta, Arun Kumar ; Egidi, Eleonora ; Elliott, Todd F.; Elshahed, Mostafa S.; Erdoğdu, Makbule; Ertz, Damien; Etayo Salazar, Javier Ángel; Evans, Harry C. ; Fan, Xin Lei; Fan, Yu Guang; Fedosova, Anna G.; Fell, Jack W.; Rodrigues Fernandes, Isabel; Firmino, André Luiz; Oliveira Fiuza, Patrícia; Flakus, Adam; Fragoso de Souza, Carlos Alberto; Frisvad, Jens Christian; Fryar, Sally C. ; Gabaldón, Toni ; Gajanayake, Achala Jeevani ; Galindo, L. J.; Gannibal, P. B.; García, D.; García Sandoval, S. R.; Garrido Benavent, I.; Garzoli, L.; Gautam, A. K.; Ge, Z. W.; Gené, D. J.; Gentekaki, E.; Ghobad Nejhad, M.; Giachini, A. J.; Gibertoni, T. B.; Góes Neto, A.; Gomdola, D.; Gomes de Farias, A. R.; Gorjón, S. P.; Goto, B. T.; Granados Montero, María del Milagro; Griffith, G. W.; Groenewald, J. Z.; Groenewald, M.; Grossart, H. P.; Gueidan, C.; Gunarathne, A.; Gunaseelan, S.; Gusmão, L. F. P.; Gutierrez, A. C.; Guzmán Dávalos, L.; Haelewaters, D.; Halling, R.; Han, Y. F.; Hapuarachchi, K. K.; Harder, C. B.; Harrington, T. C.; Hattori, T.; He, M. Q.; He, S.; He, S. H.; Healy, R.; Herández Restrepo, M.; Heredia, G.; Hodge, K. T.; Holgado Rojas, M.; Hongsanan, S.; Horak, E.; Hosoya, T.; Houbraken, J.; Huang, S. K.; Huanraluek, N.; Hur, J. S.; Hurdeal, V. G.; Hustad, V. P.; Iotti, M.; Iturriaga, T.; Jafar, E.; Janik, P.; Jayalal, R. G. U.; Jayasiri, S. C.; Jayawardena, R. S.; Jeewon, R.; Jerônimo, G. H.; Jesus, A. L.; Jin, J.; Johnston, P. R.; Jones, E. B. G.; Joshi, Y.; Justo, A.; Kaishian, P.; Kakishima, M.; Kaliyaperumal, M.; Kang, G. P.; Kang, J. C.; Karimi, O.; Karpov, S. A.; Karunarathna, S. C.; Kaufmann, M.; Kemler, M.; Kezo, K.; Khyaju, S.; Kirchmair, M.; Kirk, P. M.; Kitaura, M. J.; Klawonn, I.; Kolarik, M.; Kong, A.; Kuhar, F.; Kukwa, M.; Kumar, S.; Kušan, I.; Lado, C.; Larsson, K. H.; Latha, K. P. D.; Lee, H. B.; Leonardi, M.; Leontyev, D. L.; Lestari, A. S.; Li, C. J. Y.; Li, D. W.; Li, H.; Li, H. Y.; Li, L.; Li, Q. R.; Li, W. L.; Li, Y.; Li, Y. C.; Liao, C. F.; Liimatainen, K.; Lim, Y. W.; Lin, C. G.; Linaldeddu, B. T.; Linde, C. C.; Linn, M. M.; Liu, F.; Liu, J. K.; Liu, N. G.; Liu, S.; Liu, S. L.; Liu, X. F.; Liu, X. Y.; Liu, X. Z.; Liu, Z. B.; Lu, L.; Lu, Y. Z.; Luangharn, T.; Luangsaard, J. J.; Lumbsch, H. T.; Lumyong, S.; Luo, L.; Luo, M.; Luo, Z. L.; Ma, J.; Machado, A. R.; Madagammana, A. D.; Madrid, H.; Magurno, F.; Magyar, D.; Mahadevan, N.; Maharachchikumbura, S. S. N.; Maimaiti, Y.; Malosso, E.; Manamgoda, D. S.; Manawasinghe, I. S.; Mapook, A.; Marasinghe, D. S.; Mardones Hidalgo, Melissa; Marin Felix, Y.; Márquez, R.; Masigol, H.; Matočec, N.; May, T.; McKenzie, E. H. C.; Meiras Ottoni, A.; Melo, R. F. R.; Mendes, A. R. L.; Mendieta, S.; Meng, Q. F.; Menkis, A.; Menolli Jr, N.; Mešić, A.; Meza Calvo, J. G.; Mikhailov, K. V.; Miller, S. L.; Moncada, B.; Moncalvo, J. M.; Monteiro, J. S.; Monteiro, M.; Mora Montes, H. M.; Moreau, P. A.; Mueller, G. M.; Mukhopadyay, S.; Murugadoss, R.; Nagy, L. G.; Najafiniya, M.; Nanayakkara, C. M.; Nascimento, C. C.; Nei, Y.; Neves, M. A.; Neuhauser, S.; Niego, A. G. T.; Nilsson, R. H.; Niskanen, T.; Niveiro, N.; Noorabadi, M. T.; Noordeloos, M. E.; Norphanphoun, C.; Nuñez Otaño, N. B.; O’Donnell, R. P.; Oehl, F.; Olariaga, I.; Orlando, F. P.; Pang, K. L.; Papp, V.; Pawłowska, J.; Peintner, U.; Pem, D.; Pereira, O. L.; Perera, R. H.; Perez Moreno, J.; Perez Ortega, S.; Péter, G.; Phillips, A. J. L.; Phonemany, M.; Phukhamsakda, C.; Phutthacharoen, K.; Piepenbring, M.; Pires Zottarelli, C. L. A. ; Poinar, G.; Pošta, A.; Prieto, M.; Promputtha, I.; Quandt, C. A.; Radek, R.; Rahnama, K.; Raj, K. N. A.; Rajeshkumar, K. C.; Rämä, T.; Rambold, G.; Ramírez Cruz, V.; Rasconi, S.; Rathnayaka, A. R.; Raza, M.; Ren, G. C.; Robledo, G. L.; Rodriguez Flakus, P.; Ronikier, A.; Rossi, W.; Ryberg, M.; Ryvarden, L. R.; Salvador Montoya, C. A.; Samant, B.; Samarakoon, B. C.; Samarakoon, M. C.; Sánchez Castro, I.; Sánchez García, M.; Sandoval Denis, M.; Santiago, A. L. C. M. A.; Santamaria, B.; Santos, A. C. S.; Sarma, V. V.; Savchenko, A.; Savchenko, K.; Saxena, R. K.; Scholler, M.; Schoutteten, N.; Seifollahi, E.; Selbmann, L.; Selcuk, F.; Senanayake, I. C.; Shabashova, T. G.; Shen, H. W.; Shen, Y. M.; SilvaFilho, A. G. S.; Simmons, D. R.; Singh, R.; Sir, E. B.; Song, Chang-Ge ; Souza Motta, C. M.; Sruthi, O. P.; Stadler, M.; Stchigel, A. M.; Stemler, J.; Stephenson, S. L.; Strassert, J. F. H.; Su, H. L.; Su, L.; Suetrong, S.; Sulistyo, B.; Sun, Y. F.; Sun, Y. R.; Svantesson, Sten; Sysouphanthong, P.; Takamatsu, S.; Tan, T. H.; Tanaka, K.; Tang, A. M. C.; Tang, X.; Tanney, J. B.; Tavakol, N. M.; Taylor, J. E.; Taylor, P. W. J.; Tedersoo, L.; Tennakoon, D. S.; Thamodini, G. K.; Thines, M.; Thiyagaraja, V.; Thongklang, N.; Tiago, P. V.; Tian, Q.; Tian, W. H.; Tibell, L.; Tibell, S.; Tibpromma, S.; Tkalčec, Z.; Tomšovský, M.; Toome Heller, M.; Torruella, G.; Tsurykau, A.; Udayanga, D.; Ulukapi, M.; Untereiner, W. A.; Uzunov, B. A.; Valle, L. G.; Van Caenegem, W.; Van den Wyngaert, S.; Van Vooren, N.; Velez. P.; Verma, R. K.; Vieira, L. C.; Vieira, W. A. S.; Vizzini, A.; Walker, A.; Walker, A. K.; Wanasinghe, D. N.; Wang, C. G.; Wang, K.; Wang, S. X.; Wang, X. Y.; Wang, Y.; Wannasawang, N.; Wartchow, F.; Wei, D. P.; Wei, X. L.; White, J. F.; Wijayawardene, N. N.; Wijesinghe, S. N.; Wijesundara, D. S. A.; Wisitrassameewong, K.; Worthy, F. R.; Wu, F.; Wu, G.; Wu, H. X.; Wu, N.; Wu, W. P.; Wurzbacher, C.; Xiao, Y. P.; Xiong, Y. R.; Xu, L. J.; Xu, R.; Xu, R. F.; Xu, R. J.; Xu, T. M.; Yakovchenko, L.; Yan, J. Y.; Yang, H.; Yang, J.; Yang, Z. L.; Yang, Y. H.; Yapa, N.; Yasanthika, E.; Youssef, N. H.; Yu, F. M.; Yu, Q.; Yu, Y. X.; Yu, Z. F.; Yuan, H. S.; Yuan, Y.; Yurkov, A.; Zafari, D.; Zamora, J. C.; Zare, R.; Zeng, M.; Zeng, N. K.; Zeng, X. Y.; Zhang, F.; Zhang, H.; Zhang, J. F.; Zhang, J. Y.; Zhang, Q. Y.; Zhang, S. N.; Zhang, W.; Zhang, Y.; Zhang, Y. X.; Zhao, C. L.; Zhao, H.; Zhao, Q.; Zhao, R. L.; Zhou, L. W.; Zhou, M.; Zhurbenko, M. P.; Zin, H. H.; Zucconi, L.
Sarcoglottis woodsonii (Orchidaceae: Spiranthinae)—rediscovered in Costa Rica after 80 years, with a preliminary survey on aquatic and other wetland orchids
(2024-06-30) Acuña Castillo, Rafael; Blanco Coto, Mario Alberto; Artavia Solís, Miguel; Jiménez Vargas, José Esteban
Orchidaceae, a highly diverse family of angiosperms, exhibits remarkable ecological and morphological adaptations, with most of its species being epiphytic or terrestrial. Nonetheless, their occurrence in aquatic and wetland habitats in the tropics is relatively uncommon, with only a few species adapted to these environments. Consequently, our current understanding of orchids inhabiting wetland ecosystems is limited. This research focuses on Sarcoglottis woodsonii, an aquatic orchid species exclusively found in palustrine wetlands of southern Central America. Previously considered endemic to western Panama, our recent collections (the first since 1940) extend its known distribution to include southern Costa Rica. We provide an updated description, a modern illustration, a conservation assessment based on IUCN criteria, and novel ecological data that shed light on its aquatic habit. With this recent discovery, the number of known Sarcoglottis species in Costa Rica stands at six. We provide a preliminary survey of reported wetland and aquatic orchid species from the Neotropics and give novel definitions for both wetland and aquatic plants. We also present an inventory of the vascular plant species found in the Cañas Gordas/Valle Azul wetland in Costa Rica, where S. woodsonii occurs. This study enhances our understanding of orchid diversity in wetland ecosystems and emphasizes
Ethnomycology, bioprospection, and uses of mushrooms in Costa Rica
(2023) Rojas Alvarado, Carlos Alonso; Arroyo Trejos, Ignacio; Doss, Robin G.
Habits relating to the use of mushrooms tend to classify human populations into either “mycophilic” or “mycophobic.” This dialectical approach to mushroom use cannot be used in Costa Rica because the systematic documentation of mycological resources has not been constructed on the basis of such theoretical arguments. Based on the evidence gathered from human populations in Costa Rica, it could be said that both indigenous and non-indigenous groups are at best “myco-indifferent” in the sense that they use mushrooms as a food resource, but their use is neither widespread nor culturally relevant. There are about 152 species of edible mushrooms in Costa Rica, from which about 10 are excellent culinary choices, 16 have been reported to have medicinal properties and no threatened species have been determined. The conservation of habitats where these species occur is vital to their population health and, in general, the Costa Rican people seem to be aware of this fact. The deep insertion of the sustainable development goals agenda into Costa Rica’s research and development investment plans has opened up many possibilities for the use of fungi in human-related activities. In the last decade, such planning has generated a series of studies of potential use, mainly within the Costa Rican academia, which have helped to consolidate the idea that mycological resources could be relevant for Costa Rica’s development. The current attitude towards the future of bioprospecting approaches and the use of mushrooms in Costa Rica is positive. Although mycology is a relatively recent discipline of academic activity in this country, the integration of fungi in initiatives with human impact has been slowly but steadily increasing over the last decades and can be expected to continue in a similar manner.
A decade of submersible observations revealed temporal trends in elasmobranchs in a remote island of the Eastern Tropical Pacific Ocean
(2024) Espinoza Mendiola, Mario; Quesada Pérez, Fabio; Madrigal Mora, Sergio; Naranjo Elizondo, Beatriz; Clarke, Tayler McLellan; Cortes Núñez, Jorge
No-take marine protected areas (MPAs) can mitigate the effects of overfishing, climate change and habitat degradation, which are leading causes of an unprecedented global biodiversity crisis. However, assessing the effectiveness of MPAs, especially in remote oceanic islands, can be logistically challenging and often restricted to relatively shallow and accessible environments. Here, we used a long-term dataset (2010-2019) collected by the DeepSee submersible of the Undersea Hunter Group that operates in Isla del Coco National Park, Costa Rica, to (1) determine the frequency of occurrence of elasmobranch species at two depth intervals (50-100 m; 300-400 m), and (2) investigate temporal trends in the occurrence of common elasmobranch species between 2010 and 2019, as well as potential drivers of the observed changes. Overall, we observed 17 elasmobranch species, 15 of which were recorded on shallow dives (50-100 m) and 11 on deep dives (300-400 m). We found a decreasing trend in the probability of occurrence of Carcharhinus falciformis over time (2010-2019), while other species (e.g. Taeniurops meyeni, Sphyrna lewini, Carcharhinus galapagensis, Triaenodon obesus, and Galeocerdo cuvier) showed an increasing trend. Our study suggests that some species like S. lewini may be shifting their distributions towards deeper waters in response to ocean warming but may also be sensitive to low oxygen levels at greater depths. These findings highlight the need for regional 3D environmental information and long-term deepwater surveys to understand the extent of shark and ray population declines in the ETP and other regions, as most fishery-independent surveys from data-poor countries have been limited to relatively shallow waters.
Seagrasses in the Eastern Tropical Pacific: species, distribution, ecology, blue carbon, and threats
(2024-07) Samper Villarreal, Jimena
Eastern Tropical Pacific (ETP) seagrasses are composed of three genera and four species: Halophila baillonii, Halodule beaudettei, Halodule wrightii, and Ruppia maritima. These are colonizing seagrass species and meadows in the ETP can be ephemeral. Current seagrass distribution in this region remains unknown, with verified extant presence at a limited number of locations and mapping heavily reliant on historical reports. Suitable environmental conditions for seagrasses in the ETP consist of sheltered bays <10 m depth with fine sediment, 19-35 salinity, 26-32C temperature, and water transparency of up to 10 m Secchi depth. In this region, seagrass organic carbon (OC) biomass pools (<0.2 Mg ha-1) have been reported from three locations, while sediment bulk density (<1.4 g mL-1) and OC (<24 Mg ha-1) have been reported from eight locations, all found on the Pacific coast of Costa Rica. Recent blue carbon reports from the ETP have not been included in global assessments to date. OC sequestration and sediment accumulation rates are currently unknown. Seagrasses provide key ecosystem services yet they are also threatened by anthropogenic and natural stressors. Seagrasses have already disappeared from two locations within the ETP, with restoration efforts currently underway on the northern Pacific coast of Costa Rica. This overview of our current understanding of seagrasses in the ETP and their services highlights the need for further research in this understudied region.
El genoma plastidial de la planta holoparásita prosopanche costaricensis: reducción del plastoma en la familia hydnoraceae
(2024) Obando Coronado, Mariel Paola; Albertazzi Castro, Federico
Desde el descubrimiento del síndrome de reducción parasitaria en los plastomas de plantas parásitas, los esfuerzos de investigación se han enfocado en describir cómo ocurre esta pérdida durante la transición hacia la vida heterótrofa. La familia Hydnoraceae, es uno de los 12 linajes de angiospermas holoparásitos que se han investigado para generar modelos de reducción. Los miembros de este linaje han sufrido una increíble reducción morfológica y es el segundo linaje parásito más antiguo, con un parasitismo que evolucionó hace aproximadamente ~ 55 Ma. Hydnoraceae contiene con dos géneros, Hydnora con ocho especies aceptadas en África y Prosopanche con seis especies aceptadas en América del Sur y una en América Central. De estas especies, se han ensamblado los plastomas de siete especies de Hydnora y tres de Prosopanche, y en esta investigación se ensambló el plastoma completo, de la única especie conocida de esta familia originario de América central, Prosopanche costaricensis. El ensamblaje del plastoma resultó ser un proceso difícil, lo que demuestra grandes desafíos asociados a la secuenciación y ensamblaje de plastomas inusuales, debido a sus características particulares de reducción de genoma. Así, el ensamblaje de estos plastomas requiere el uso de múltiples técnicas bioinformáticas y moleculares para ser exitoso. La obtención el plastoma de esta especie aportó evidencia crucial para apoyar el modelo de reducción plastidial desarrollado en el linaje Hydnoraceae. La estructura del plastoma de P. costaricensis es consistente con las de otras especies de la familia y coincidió con las características género. Este presentó la pérdida total de genes fotosintéticos y la retención de solo 27 genes esenciales, un bajo contenido GC (19.9%), una alta cantidad de sustituciones de nucleótidos en sus genes, y un tamaño que ronda los 29 mil pares de bases (28 705 pb). Además, presenta repeticiones directas (RD) contraídas (330 pb) y genes pseudogenizados. Las RD contraídas, las fuerzas de selección reducidas en los genes, la falta de genes fotosintéticos, la retención de genes esenciales, el tamaño disminuido y la presencia de genes pseudogenizados (ycf2 y trnI-AAU), corroboran resultados similares en genomas tanto de la misma familia como de otras plantas holoparásitas. Tras perder todos los genes fotosintéticos, estas especies han empezado a perder genes esenciales mediante procesos de degeneración y conversión en pseudogenes. Esto respalda la hipótesis de que los plastomas de esta familia se encuentran probablemente en el final de la segunda etapa o el inicio de la tercera del modelo de reducción planteado. Además, apoya la existencia de repeticiones directas reducidas, presentando dos estructuras diferentes en el género, una con 3 estructuras codificantes (5’ ycf2, trnI, y 5’ rpl2) y otra con solo dos (trnI, y 5’ rpl2). Adicionalmente, el genoma plastidial de P. costaricensis proporción nueva evidencia para confirmar que esta y P. americana son especies diferentes. Finalmente, los análisis filogenéticos revelaron que P. costaricensis y P. panguanensis son especies hermanas lo que concuerda con el hecho de que ambas son las únicas dos especies del género que habitan en bosques húmedos, además refuerza el hecho de que Prosopanche y Hydnora son géneros hermanos y por último posiciona a la familia como hermana del clado de los Piperales.
Características clínicas del paciente que debuta con cáncer de próstata metastásico en el Hospital San Juan de Dios durante el periodo comprendido entre 2019 y 2022
(2024) Dennise Monge Cedeño; Allan Ramos Esquivel
Introducción : Los datos epidemiológicos sobre el cáncer de próstata en Costa Rica son escasos y se desconoce el patrón de comportamiento en el estadio clínico castrato sensible metastásico. El objetivo del estudio fue analizar las características clínicas, epidemiológicas y la efectividad del tratamiento de la población con esta patología en el Hospital San Juan de Dios durante el año 2019 al 2022. Métodos: Este estudio fue unicéntrico, observacional, retrospectivo y de cohorte en el que se analizaron los expedientes clínicos de los pacientes que debutaron con cáncer de próstata metastásico castrato sensible dentro del periodo 2019 al 2022. Resultados: De la población analizada (n=758), 71 pacientes (9%) presentaron diagnóstico de cáncer de próstata metastásico castrato sensible; 41 de ellos (57%) con un alto volumen de enfermedad. Como tratamiento, 36 pacientes (50,7%) recibieron terapia anti androgénica en monoterapia. De los pacientes que recibieron terapia combinada en dupleta, 28 (39,4%) recibieron docetaxel, 6 (8,5%) asociaron el uso de abiraterona y solo 1 (1,41%) recibió enzalutamida. El grupo observado tuvo una mediana de progresión a la castrato resistencia de 23,3 meses (95% IC: 17,4-28,3) y una mediana de supervivencia general no alcanzada. Aquellos que recibieron terapia combinada tuvieron una supervivencia libre de progresión de 25,3 meses comparado a 17,8 meses en el grupo de monoterapia (HR: 0,74; 95% IC: 0,44- 1,36 p=0,43). La tasa de supervivencia global al año fue de 65,8% para el grupo que recibió deprivación androgénica sola vs 72,7% en la terapia combinada (p=0,41). Conclusión: Este estudio representa el primer análisis descriptivo realizado en Costa Rica que explora las características clínicas de los pacientes con cáncer de próstata metastásico sensible a la castración, así como los patrones de progresión y las tendencias de tratamiento en esta población. Además, se evaluó la supervivencia global según el medicamento administrado.
Determinación de áreas prioritarias actuales y futuras para la conservación de seis especies de aves en peligro de extinción en Costa Rica usando Modelos de Distribución de Especies
(2024) Villegas Retana, Sergio Armando; Ávalos Rodríguez, Gerardo
Las especies en peligro de extinción son prioritarias en las acciones de conservación. En Costa Rica se conocen 935 especies de aves, de las cuales siete se encuentran en peligro de extinción y tres están en peligro crítico de extinción. Determinar sus posibles distribuciones actuales y futuras mediante Modelos de Nicho Ecológico (MNE) es un paso crucial para identificar las áreas prioritarias para su conservación. En este estudio determiné las áreas prioritarias actuales y futuras para la conservación en Costa Rica de seis especies de aves en peligro de extinción (Amazilia boucardi, Habia atrimaxillaris, Cephalopterus glabricollis, Carpodectes antoniae, Amazona auropalliata y Ara ambiguus) usando MNE. Para esto, recopilé 1230 registros georreferenciados de Global Biodiversity Information Facility y de eBird de todas las especies. Utilicé al menos siete variables bioclimáticas por especie obtenidas de WorldClim, y para los escenarios de cambio climático usé las Trayectorias de Concentración Representativas (RCP), proyectadas bajo los escenarios RCP 2.6, 4.5, 6 y 8.5, para los periodos 2030s, 2050s y 2070s. Para predecir el área de hábitat potencialmente adecuado de cada especie, desarrollé MNEs utilizando un algoritmo de Máxima Entropía. Utilicé la Tasa de Omisión Media (OR) y el Área bajo la curva de respuesta (AUC) para seleccionar los modelos óptimos. Estos modelos fueron posteriormente proyectados a condiciones futuras. A partir de dichas predicciones determiné el Área Adecuada Real (AAR) y la parte de la predicción que se encuentra en Áreas Silvestres Protegida (ASP) considerando los datos de ocurrencia, los polígonos de distribución de las especies de la Unión Internacional para la Conservación de la Naturaleza y la preferencia de hábitat de cada especie. Los resultados muestran un aumento generalizado en el Área Potencial (AP) en el futuro para la mayoría de las especies. En promedio para el presente, el AAR para las especies varió entre 6% y 77%, y el ASP entre 3% y 42% del AP total estimada por los modelos. En el futuro el AAR varió entre 3% y 77%, y el ASP entre 1% y 40%. Las proyecciones muestran que para la mayoría de las especies la mayor parte del AP corresponde al AAR y que en el futuro podría haber un aumento en su rango de distribución. La idoneidad de estos sitios va a depender de la disponibilidad de recursos, conectividad y presencia de zonas boscosas. Este estudio representa un primer paso enfocado en el manejo y la toma de decisiones para la conservación estas seis especies. Los resultados deben integrarse con otros enfoques más allá de modelos correlativos, que permitan validar y refinar los resultados con estudios de campo. Los modelos MNE son útiles para orientar los esfuerzos de investigación y seleccionar áreas prioritarias para la sobrevivencia de las aves.
A metabolomic platform to identify and quantify polyphenols in coffee and related species using liquid chromatography mass spectrometry
(2023) Castro Moretti, Fernanda R.; Cocuron, Jean Christophe; Castillo González, Humberto; Escudero Leyva, Efraín; Chaverri Echandi, Priscila; Guerreiro Filho, Oliveiro; Slot, Jason C.; Alonso, Ana Paula
Introduction: Products of plant secondary metabolism, such as phenolic compounds, flavonoids, alkaloids, and hormones, play an important role in plant growth, development, stress resistance. The plant family Rubiaceae is extremely diverse and abundant in Central America and contains several economically important genera, e.g. Coffea and other medicinal plants. These are known for the production of bioactive polyphenols (e.g. caffeine and quinine), which have had major impacts on human society. The overall goal of this study was to develop a high-throughput workflow to identify and quantify plant polyphenols. Methods: First, a method was optimized to extract over 40 families of phytochemicals. Then, a high-throughput metabolomic platform has been developed to identify and quantify 184 polyphenols in 15 min. Results: The current metabolomics study of secondary metabolites was conducted on leaves from one commercial coffee variety and two wild species that also belong to the Rubiaceae family. Global profiling was performed using liquid chromatography high-resolution time-of-flight mass spectrometry. Features whose abundance was significantly different between coffee species were discriminated using statistical analysis and annotated using spectral databases. The identified features were validated by commercially available standards using our newly developed liquid chromatography tandem mass spectrometry method. Discussion: Caffeine, trigonelline and theobromine were highly abundant in coffee leaves, as expected. Interestingly, wild Rubiaceae leaves had a higher diversity of phytochemicals in comparison to commercial coffee: defenserelated molecules, such as phenylpropanoids (e.g., cinnamic acid), the terpenoid gibberellic acid, and the monolignol sinapaldehyde were found more abundantly in wild Rubiaceae leaves.
Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma
(2023) Scott, Kelsey; Konkel, Zachary; Gluck Thaler, Emile; Valero David, Guillermo E.; Farinas Simmt, Coralie; Grootmyers, Django; Chaverri Echandi, Priscila; Slot, Jason
Trichoderma is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like Trichoderma, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight Trichoderma genomes representing the full breadth of environmental Trichoderma’s diverse lifestyles and nutritional modes. We generated four new Trichoderma endophyticum genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic Trichoderma genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken in consideration, no particular class of metabolic gene cluster was independently associated with the Trichoderma endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic Trichoderma genomes. Most genomic differences between Trichoderma lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that Trichoderma genomes maybe particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to Trichoderma.
Out of the blue: the independent activity of sulfur‑oxidizers and diatoms mediate the sudden color shift of a tropical river
(2023-01-19) Arce Rodríguez, Alejandro; Libby Hernández, Eduardo; Castellón Elizondo, Erick; Avendaño Vega, Roberto; Cambronero Heinrichs, Juan Carlos; Vargas Montero, Maribelle; Pieper, Dietmar H.; Bertilsson, Stefan; Chavarría Vargas, Max; Puente Sánchez, Fernando
Río Celeste (“Sky-Blue River”) is a river located in the Tenorio National Park (Costa Rica) that has become an important hotspot for eco-tourism due to its striking sky-blue color. A previous study indicated that this color is not caused by dissolved chemical species, but by formation of light-scattering aluminosilicate particles at the mixing point of two colorless streams, the acidic Quebrada Agria and the neutral Río Buenavista. We now present microbiological information on Río Celeste and its two tributaries, as well as a more detailed characterization of the particles that occur at the mixing point. Our results overturn the previous belief that the light scattering particles are formed by the aggregation of smaller particles coming from Río Buenavista, and rather point to chemical formation of hydroxyaluminosilicate colloids when Quebrada Agria is partially neutralized by Río Buenavista, which also contributes silica to the reaction. The process is mediated by the activities of different microorganisms in both streams. In Quebrada Agria, sulfur-oxidizing bacteria generate an acidic environment, which in turn cause dissolution and mobilization of aluminum and other metals. In Río Buenavista, the growth of diatoms transforms dissolved silicon into colloidal biogenic forms which may facilitate particle precipitation. We show how the sky-blue color of Río Celeste arises from the tight interaction between chemical and biological processes, in what constitutes a textbook example of emergent behavior in environmental microbiology.
Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440
(2023-01-22) Avendaño Vega, Roberto; Muñoz Montero, Said; Rojas Gätjens, Diego; Fuentes Schweizer, Paola; Vieto Fonseca, Sofía; Montenegro, Rafael; Salvador, Manuel; Frew, Rufus; Kim, Juhyun; Chavarría Vargas, Max; Jiménez Ramírez, José Ignacio
The soil bacterium Pseudomonas putida KT2440 has been shown to produce selenium nanoparticles aerobically from selenite; however, the molecular actors involved in this process are unknown. Here, through a combination of genetic and analytical techniques, we report the first insights into selenite metabolism in this bacterium. Our results suggest that the reduction of selenite occurs through an interconnected metabolic network involving central metabolic reactions, sulphur metabolism, and the response to oxidative stress. Genes such as sucA, D2HGDH and PP_3148 revealed that the 2-ketoglutarate and glutamate metabolism is important to convert selenite into selenium. On the other hand, mutations affecting the activity of the sulphite reductase decreased the bacteria's ability to transform selenite. Other genes related to sulphur metabolism (ssuEF, sfnCE, sqrR, sqr and pdo2) and stress response (gqr, lsfA, ahpCF and sadI) were also identified as involved in selenite transformation. Interestingly, suppression of genes sqrR, sqr and pdo2 resulted in the production of selenium nanoparticles at a higher rate than the wild-type strain, which is of biotechnological interest. The data provided in this study brings us closer to understanding the metabolism of selenium in bacteria and offers new targets for the development of biotechnological tools for the production of selenium nanoparticles.
The endophytobiome of wild Rubiaceae as a source of antagonistic fungi against the American Leaf Spot of coffee (Mycena citricolor)
(2023) Escudero Leyva, Efraín; Granados Montero, María del Milagro; Orozco Ortiz, Cristofer; Araya Valverde, Emanuel; Alvarado Picado, Eduardo; Chaves Fallas, José Miguel; Aldrich Wolfe, Laura; Chaverri Echandi, Priscila
Aims: The American leaf spot, caused by Mycena citricolor, is an important disease of coffee (Coffea arabica), mostly in Central America. Currently, there are limited pathogen control alternatives that are environment friendly and economically accessible. The use of fungi isolated from the plant endomycobiota in their native habitats is on the rise because studies show their great potential for biological control. To begin to generate a green alternative to control M. citricolor, the objectives of the present study were to (i) collect, identify, screen (in vitro and in planta), and select endophytic fungi from wild Rubiaceae collected in old-growth forests of Costa Rica; (ii) confrm endophytic colonization in coffee plantlets; (iii) evaluate the effects of the endophytes on plantlet development; and (iv) corroborate the antagonistic ability in planta. Methods and results: Through in vitro and in planta antagonism assays, we found that out of the selected isolates (i.e. Daldinia eschscholzii GU11N, Nectria pseudotrichia GUHN1, Purpureocillium aff. lilacinum CT24, Sarocladium aff. kiliense CT25, Trichoderma rifaii CT5, T. aff. crassum G1C, T. aff. atroviride G7T, T. aff. strigosellum GU12, and Xylaria multiplex GU14T), Trichoderma spp. produced the highest growth inhibition percentages in vitro. Trichoderma isolates CT5 and G1C were then tested in planta using Coffea arabica cv. caturra plantlets. Endophytic colonization was verifed, followed by in planta growth promotion and antagonism assays. Conclusions: Results show that Trichoderma isolates CT5 and G1C have potential for plant growth promotion and antagonism against Mycena citricolor, reducing incidence and severity, and preventing plant mortality. Signifcance and Impact of Study The results of this study increase knowledge on the potential use of poorly studied species of endophytic fungi that are not only capable of reducing the impacts of phytopathogens, but also improve plant growth, aiding in the transition to organic agriculture.
Differences in fungal communities in the fur of two- and three-toed sloths revealed by ITS metabarcoding
(2023-02-27) Rojas Gätjens, Diego; Avey Arroyo, Judy; Chaverri Echandi, Priscila; Rojas Jiménez, Keilor Osvaldo; Chavarría Vargas, Max
Sloths have dense fur on which insects, algae, bacteria and fungi coexist. Previous studies using cultivation-dependent methods and 18S rRNA sequencing revealed that the fungal communities in their furs comprise members of the phyla Ascomycota and Basidiomycota. In this note, we increase the resolution and knowledge of the mycobiome inhabiting the fur of the two- (Choloepus hoffmanni) and three-toed (Bradypus variegatus) sloths. Targeted amplicon metagenomic analysis of ITS2 nrDNA sequences obtained from 10 individuals of each species inhabiting the same site revealed significant differences in the structure of their fungal communities and also in the alpha-diversity estimators. The results suggest a specialization by host species and that the host effect is stronger than that of sex, age and animal weight. Capnodiales were the dominant order in sloths’ fur and Cladosporium and Neodevriesia were the most abundant genera in Bradypus and Choloepus, respectively. The fungal communities suggest that the green algae that inhabit the fur of sloths possibly live lichenized with Ascomycota fungal species. The data shown in this note offer a more detailed view of the fungal content in the fur of these extraordinary animals and could help explain other mutualistic relationships in this complex ecosystem.

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