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Muema EK, van Lill M, Venter SN, Chan WY, Claassens R, Steenkamp ET. Mesorhizobium salmacidum sp. nov. and Mesorhizobium argentiipisi sp. nov. are symbionts of the dry-land forage legumes Lessertia diffusa and Calobota sericea. Antonie Van Leeuwenhoek 2025; 118:54. [PMID: 39934476 PMCID: PMC11814006 DOI: 10.1007/s10482-025-02063-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Accepted: 01/30/2025] [Indexed: 02/13/2025]
Abstract
Legumes Lessertia diffusa and Calobota sericea, indigenous to South Africa, are commonly used as fodder crops with potential for sustainable livestock pasture production. Rhizobia were isolated from their root nodules grown in their respective soils from the Succulent Karoo biome (SKB) in South Africa, identified and characterized using a polyphasic approach. Sequence analysis of the 16S rRNA gene confirmed all isolates as Mesorhizobium members, which were categorized into two distinct lineages using five housekeeping protein-coding genes. Lineage I included 14 strains from both legumes, while Lineage II comprised a single isolate from C. sericea. Differences in phenotypic traits were observed between the lineages and corroborated by average nucleotide identity analyses. While all strains nodulated their original hosts, strains from C. sericea failed to effectively nodulate L. diffusa and vice versa. Phylogenetic analyses of nitrogen fixation (nifH) and nodulation (nodA, nodC) loci grouped all strains in a single clade, suggesting that unique symbiotic loci determine nodulation of these legumes. We designated Lineage I and II as Mesorhizobium salmacidum sp. nov. (Ld1326Ts; GCA_037179605.1Ts) and Mesorhizobium argentiipisi sp. nov. (Cs1330R2N1Ts; GCA_037179585.1Ts), using genome sequences as nomenclatural types according to the Nomenclatural Code for Prokaryotes using Sequence Data, thus avoiding complications with South Africa's biodiversity regulations. Identifying effective microsymbionts of L. diffusa and C. sericea is essential for conservation of Succulent Karoo Biome, where indigenous invasive species like Vachellia karroo and non-native Australian acacia species are present. Furthermore, targeted management practices using effective symbionts of the studied legumes can sustain the biome's socio-economic contribution through fodder provision.
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Affiliation(s)
- Esther K Muema
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.
- Department of Soil Science, Faculty of AgriSciences, Stellenbosch University, Matieland, South Africa.
| | - Melandré van Lill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Wai Yin Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Ricu Claassens
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
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Quiroga-Carmona M, Storz JF, D’Elía G. Elevational range extension of the Puna Mouse, Punomys (Cricetidae), with the first record of the genus from Chile. J Mammal 2023; 104:1144-1151. [PMID: 37800100 PMCID: PMC10550245 DOI: 10.1093/jmammal/gyad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/22/2023] [Indexed: 10/07/2023] Open
Abstract
We report an elevational record for the Andean sigmodontine Puna Mouse Punomys, which is also the first record of the genus in Chile. The record is based on a mummified specimen that we discovered at an elevation of 5,461 m (17,917 feet) in the caldera of Volcán Acamarachi, Región de Antofagasta, Chile. Results of a morphological assessment suggest that the specimen can be provisionally referred to the species P. lemminus. This new record also extends the known geographic distribution of the genus by 700 km to the south and brings the known Chilean mammal richness to a total of 170 living species and 88 genera. This finding highlights the need for increased survey efforts in more remote, high-elevation regions and demonstrates that there is still much to be learned about the mammal fauna of the Andean Altiplano.
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Affiliation(s)
- Marcial Quiroga-Carmona
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
- Colección de Mamíferos, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
| | - Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
- Colección de Mamíferos, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
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Humphries M, Benitez-Nelson N, Combrink X. Trace Metal Accumulation in Eggs of Wild Nile Crocodiles (Crocodylus niloticus) from Lake St Lucia, South Africa: Implications for Biomonitoring in a Global Biodiversity Hotspot. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 83:214-225. [PMID: 36171509 DOI: 10.1007/s00244-022-00960-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Nile crocodiles (Crocodylus niloticus) at Lake St Lucia, South Africa, have some of the highest blood lead (Pb) concentrations ever recorded in wildlife globally. Although exposure to Pb is known to pose major risks to wildlife reproductive success, potential impacts on crocodile reproduction at Lake St Lucia have yet to be examined. In this study, we investigated the accumulation of Pb and other trace metals (Al, V, Cr, Co, Cu, Ni, Zn and Cd) in eggs (n = 20) collected from five wild crocodile nests at Lake St Lucia. All metals analysed in this study were detected in egg contents, although concentrations varied considerably among nests and within clutches. Lead was detected in the contents of all eggs, but only at relatively low concentrations (43 ± 26 ng g-1 dry weight). Although sampling limitations commonly associated with wild population surveys prevent a complete assessment of exposure variability, our findings suggest maternal transfer may not be a significant depuration pathway for Pb and females possibly clear Pb through other mechanisms (e.g. sequestration into claws, bone and osteoderms). Metal concentrations in eggshells and shell membranes were poorly correlated with concentrations measured in egg content and thus do not provide viable non-lethal indicators for monitoring metal exposure in Nile crocodiles. Intra-clutch variability accounted for a considerable proportion of the total variance in egg content metal concentrations, suggesting the "one egg" sampling strategy often applied in reptile studies may not be an effective biomonitoring tool for wild crocodilian populations. Although maternally derived Pb does not appear to present widespread toxicological concern at Lake St Lucia, adverse effects of Pb exposure on other reproductive functions (e.g. spermatogenesis) cannot be discounted and warrant further investigation.
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Affiliation(s)
- Marc Humphries
- School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa.
| | - Noah Benitez-Nelson
- School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa
| | - Xander Combrink
- Department of Nature Conservation, Tshwane University of Technology, Pretoria, South Africa
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Ramírez-Castañeda V, Westeen EP, Frederick J, Amini S, Wait DR, Achmadi AS, Andayani N, Arida E, Arifin U, Bernal MA, Bonaccorso E, Bonachita Sanguila M, Brown RM, Che J, Condori FP, Hartiningtias D, Hiller AE, Iskandar DT, Jiménez RA, Khelifa R, Márquez R, Martínez-Fonseca JG, Parra JL, Peñalba JV, Pinto-García L, Razafindratsima OH, Ron SR, Souza S, Supriatna J, Bowie RCK, Cicero C, McGuire JA, Tarvin RD. A set of principles and practical suggestions for equitable fieldwork in biology. Proc Natl Acad Sci U S A 2022; 119:e2122667119. [PMID: 35972961 PMCID: PMC9407469 DOI: 10.1073/pnas.2122667119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Field biology is an area of research that involves working directly with living organisms in situ through a practice known as "fieldwork." Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of the core team members. However, existing power imbalances stemming from geopolitical history, discrimination, and professional position, among other factors, perpetuate inequities when conducting these research endeavors. After reflecting on our own research programs, we propose four general principles to guide equitable, inclusive, ethical, and safe practices in field biology: be collaborative, be respectful, be legal, and be safe. Although many biologists already structure their field programs around these principles or similar values, executing equitable research practices can prove challenging and requires careful consideration, especially by those in positions with relatively greater privilege. Based on experiences and input from a diverse group of global collaborators, we provide suggestions for action-oriented approaches to make field biology more equitable, with particular attention to how those with greater privilege can contribute. While we acknowledge that not all suggestions will be applicable to every institution or program, we hope that they will generate discussions and provide a baseline for training in proactive, equitable fieldwork practices.
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Affiliation(s)
- Valeria Ramírez-Castañeda
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Erin P. Westeen
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Environmental, Science, Policy, and Management, University of California, Berkeley, CA, 94720
| | - Jeffrey Frederick
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Sina Amini
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Daniel R. Wait
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Anang S. Achmadi
- Research Center for Applied Zoology, National Research and Innovation Agency, Jawa Barat 16911, Indonesia
| | - Noviar Andayani
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Kampus UI Depok, Depok 16424, Indonesia
- Research Center for Climate Change, Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Evy Arida
- Research Center for Applied Zoology, National Research and Innovation Agency, Jawa Barat 16911, Indonesia
| | - Umilaela Arifin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Centre for Taxonomy and Morphology, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg 20146 Germany
| | - Moisés A. Bernal
- Department of Biological Sciences, Auburn University, Auburn, AL 36849
| | - Elisa Bonaccorso
- Laboratorio de Biología Evolutiva, Colegio de Ciencias Biológicas y Ambientales e Instituto Biósfera, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Marites Bonachita Sanguila
- Biodiversity Informatics and Research Center, Father Saturnino Urios University, Butuan City 8600, Philippines
| | - Rafe M. Brown
- Biodiversity Institute, University of Kansas, Lawrence, KS 66044
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66044
| | - Jing Che
- State Key Laboratory of Genetic Resource and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
| | - F. Peter Condori
- Museo de Biodiversidad del Perú, Cusco 08003, Perú
- Museo de Historia Natural de la Universidad Nacional de San Antonio Abad del Cusco, Cusco 08002, Perú
| | | | - Anna E. Hiller
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Djoko T. Iskandar
- Basic Sciences Commision, Indonesian Academy of Sciences, Jakarta 10110, Indonesia
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Rosa Alicia Jiménez
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Escuela de Biología, Facultad de Ciencias Químicas y Farmacia, Universidad de San Carlos de Guatemala, Ciudad de Guatemala 01012, Guatemala
| | - Rassim Khelifa
- Institute for Resources, Environment and Sustainability, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Biology Department, Condordia University, Montreal, Quebec H4B 1R6, Canada
| | - Roberto Márquez
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Michigan Society of Fellows, University of Michigan, Ann Arbor, MI 48109
| | - José G. Martínez-Fonseca
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86011
- Nicaraguan Bat Conservation Program, Carazo, Nicaragua
| | - Juan L. Parra
- Grupo de Ecología y Evolución de Vertebrados, Instituto de Biología, Universidad de Antioquia, Medellín 050010, Colombia
| | - Joshua V. Peñalba
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin 10115, Germany
| | - Lina Pinto-García
- Centro Interdisciplinario de Estudios sobre el Desarrollo, Universidad de los Andes, Bogotá 111711, Colombia
- Institute for Science, Innovation and Society, University of Oxford, Oxford OX2 6PN, United Kingdom
| | - Onja H. Razafindratsima
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
- Mention Zoologie et Biodiversité Animale, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Santiago R. Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito 170525, Ecuador
| | - Sara Souza
- Environment, Health & Safety, University of California, Berkeley, CA 94720
| | - Jatna Supriatna
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Kampus UI Depok, Depok 16424, Indonesia
- Research Center for Climate Change, Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Rebecca D. Tarvin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
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