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Dussarrat T, Nilo-Poyanco R, Moyano TC, Prigent S, Jeffers TL, Díaz FP, Decros G, Audi L, Sondervan VM, Shen B, Araus V, Rolin D, Shasha D, Coruzzi GM, Gibon Y, Latorre C, Pétriacq P, Gutiérrez RA. Phylogenetically diverse wild plant species use common biochemical strategies to thrive in the Atacama Desert. J Exp Bot 2024:erae117. [PMID: 38477678 DOI: 10.1093/jxb/erae117] [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] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Indexed: 03/14/2024]
Abstract
The best ideotypes are under mounting pressure due to increased aridity. Understanding the conserved molecular mechanisms that evolve in wild plants adapted to harsh environments is crucial in developing new strategies for agriculture. Yet our knowledge of such mechanisms in wild species is scant. We performed metabolic pathway reconstruction using transcriptome information from 32 Atacama and phylogenetically related species that do not live in Atacama (Sisters species). We analyzed reaction enrichment to understand the commonalities and differences of Atacama plants. To gain insights into the mechanisms that ensure survival, we compared expressed gene isoform numbers and gene expression patterns between the annotated biochemical reactions from 32 Atacama and Sister species. We found biochemical convergences characterized by reactions enriched in at least 50% of the Atacama species, pointing to potential advantages against drought and nitrogen starvation, for instance. These findings suggest that the adaptation in the Atacama Desert may result in part from shared genetic legacies governing the expression of key metabolic pathways to face harsh conditions. Enriched reactions corresponded to ubiquitous compounds common to extreme and agronomic species and were congruent with our previous metabolomic analyses. Convergent adaptive traits offer promising candidates for improving abiotic stress resilience in crop species.
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Affiliation(s)
- Thomas Dussarrat
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Av Libertador Bernardo O'Higgins 340, Santiago, Chile
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33140 Villenave d'Ornon, France
| | - Ricardo Nilo-Poyanco
- Universidad Mayor, Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Camino La Pirámide 5750, Huechuraba, Santiago, Chile
| | - Tomás C Moyano
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Av Libertador Bernardo O'Higgins 340, Santiago, Chile
| | - Sylvain Prigent
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33140 Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140 Villenave d'Ornon, France
| | - Tim L Jeffers
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, 10003, NY, USA
| | - Francisca P Díaz
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras, 3425, Ñuñoa, Santiago, Chile
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Av Libertador Bernardo O'Higgins 340, Santiago, Chile
- Instituto de Geografía, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Guillaume Decros
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33140 Villenave d'Ornon, France
| | - Lauren Audi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, 10003, NY, USA
| | - Veronica M Sondervan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, 10003, NY, USA
| | - Bingran Shen
- Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, 251 Mercer St, New York, 10012, USA
| | - Viviana Araus
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Av Libertador Bernardo O'Higgins 340, Santiago, Chile
| | - Dominique Rolin
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33140 Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140 Villenave d'Ornon, France
| | - Dennis Shasha
- Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, 251 Mercer St, New York, 10012, USA
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, 10003, NY, USA
| | - Yves Gibon
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33140 Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140 Villenave d'Ornon, France
| | - Claudio Latorre
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras, 3425, Ñuñoa, Santiago, Chile
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Av Libertador Bernardo O'Higgins 340, Santiago, Chile
| | - Pierre Pétriacq
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33140 Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140 Villenave d'Ornon, France
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Av Libertador Bernardo O'Higgins 340, Santiago, Chile
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras, 3425, Ñuñoa, Santiago, Chile
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Av Libertador Bernardo O'Higgins 340, Santiago, Chile
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Díaz FP, Dussarrat T, Carrasco-Puga G, Colombié S, Prigent S, Decros G, Bernillon S, Cassan C, Flandin A, Guerrero PC, Gibon Y, Rolin D, Cavieres LA, Pétriacq P, Latorre C, Gutiérrez RA. Ecological and metabolic implications of the nurse effect of Maihueniopsis camachoi in the Atacama Desert. New Phytol 2024; 241:1074-1087. [PMID: 37984856 DOI: 10.1111/nph.19415] [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: 07/06/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023]
Abstract
Plant-plant positive interactions are key drivers of community structure. Yet, the underlying molecular mechanisms of facilitation processes remain unexplored. We investigated the 'nursing' effect of Maihueniopsis camachoi, a cactus that thrives in the Atacama Desert between c. 2800 and 3800 m above sea level. We hypothesised that an important protective factor is thermal amelioration of less cold-tolerant species with a corresponding impact on molecular phenotypes. To test this hypothesis, we compared plant cover and temperatures within the cactus foliage with open areas and modelled the effect of temperatures on plant distribution. We combined eco-metabolomics and machine learning to test the molecular consequences of this association. Multiple species benefited from the interaction with M. camachoi. A conspicuous example was the extended distribution of Atriplex imbricata to colder elevations in association with M. camachoi (400 m higher as compared to plants in open areas). Metabolomics identified 93 biochemical markers predicting the interaction status of A. imbricata with 79% accuracy, independently of year. These findings place M. camachoi as a key species in Atacama plant communities, driving local biodiversity with an impact on molecular phenotypes of nursed species. Our results support the stress-gradient hypothesis and provide pioneer insights into the metabolic consequences of facilitation.
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Affiliation(s)
- Francisca P Díaz
- Instituto de Geografía, Pontificia Universidad Católica de Valparaíso, 2362807, Valparaíso, Chile
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
| | - Thomas Dussarrat
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
| | - Gabriela Carrasco-Puga
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
| | - Sophie Colombié
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Sylvain Prigent
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Guillaume Decros
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
| | - Stéphane Bernillon
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Cédric Cassan
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Amélie Flandin
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Pablo C Guerrero
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 7800003, Concepción, Chile
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos, 8331150, Santiago, Chile
| | - Yves Gibon
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Dominique Rolin
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Lohengrin A Cavieres
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 7800003, Concepción, Chile
| | - Pierre Pétriacq
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Claudio Latorre
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
| | - Rodrigo A Gutiérrez
- Institute of Ecology and Biodiversity, Chile (IEB), Las Palmeras 3425, Ñuñoa, 7800003, Santiago, Chile
- ANID Millennium Institute Center for Genome Regulation and ANID Millennium Institute for Integrative Biology (iBio), Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, 8331150, Santiago, Chile
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Araya M, Villarreal P, Moyano T, Santos ARO, Díaz FP, Bustos-Jarufe A, Urbina K, Del Pino JE, Groenewald M, Gutiérrez RA, Rosa CA, Cubillos FA. Nakazawaea atacamensis f.a., sp. nov. a novel nonconventional fermentative ascomycetous yeast species from the Atacama Desert. Yeast 2024; 41:52-63. [PMID: 38146767 DOI: 10.1002/yea.3920] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/29/2023] [Accepted: 12/09/2023] [Indexed: 12/27/2023] Open
Abstract
In this study, we describe Nakazawaea atacamensis f. a., sp. nov., a novel species obtained from Neltuma chilensis plant samples in Chile's hyperarid Atacama Desert. In total, three strains of N. atacamensis were obtained from independent N. chilensis samples (synonym Prosopis chilensis, Algarrobo). Two strains were obtained from bark samples, while the third strain was obtained from bark-exuded gum from another tree. The novel species was defined using molecular characteristics and subsequently characterized with respect to morphological, physiological, and biochemical properties. A neighbor-joining analysis using the sequences of the D1/D2 domains of the large subunit ribosomal RNA gene revealed that N. atacamensis clustered with Nakazawaea pomicola. The sequence of N. atacamensis differed from closely related species by 1.3%-5.2% in the D1/D2 domains. A phylogenomic analysis based on single-nucleotide polymorphism's data confirms that the novel species belongs to the genus Nakazawaea, where N. atacamensis clustered with N. peltata. Phenotypic comparisons demonstrated that N. atacamensis exhibited distinct carbon assimilation patterns compared to its related species. Genome sequencing of the strain ATA-11A-BT revealed a genome size of approximately 12.4 Mbp, similar to other Nakazawaea species, with 5116 protein-coding genes annotated using InterProScan. In addition, N. atacamensis exhibited the capacity to ferment synthetic wine must, representing a potential new yeast for mono or co-culture wine fermentations. This comprehensive study expands our understanding of the genus Nakazawaea and highlights the ecological and industrial potential of N. atacamensis in fermentation processes. The holotype of N. atacamensis sp. nov. is CBS 18375T . The Mycobank number is MB 849680.
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Affiliation(s)
- Macarena Araya
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Pablo Villarreal
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Tomás Moyano
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ana R O Santos
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Francisca P Díaz
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Instituto de Geografía, Facultad de Ciencias del Mar y Geografía, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Milenio de Ecología Histórica Aplicada para los Bosques Áridos (AFOREST), Santiago, Chile
| | | | - Kamila Urbina
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
| | - Javier E Del Pino
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | | | - Rodrigo A Gutiérrez
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Institute Center for Genome Regulation, Institute of Ecology and Biodiversity, Santiago, Chile
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Francisco A Cubillos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
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4
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Dussarrat T, Prigent S, Latorre C, Bernillon S, Flandin A, Díaz FP, Cassan C, Van Delft P, Jacob D, Varala K, Joubes J, Gibon Y, Rolin D, Gutiérrez RA, Pétriacq P. Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience. New Phytol 2022; 234:1614-1628. [PMID: 35288949 PMCID: PMC9324839 DOI: 10.1111/nph.18095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Current crop yield of the best ideotypes is stagnating and threatened by climate change. In this scenario, understanding wild plant adaptations in extreme ecosystems offers an opportunity to learn about new mechanisms for resilience. Previous studies have shown species specificity for metabolites involved in plant adaptation to harsh environments. Here, we combined multispecies ecological metabolomics and machine learning-based generalized linear model predictions to link the metabolome to the plant environment in a set of 24 species belonging to 14 families growing along an altitudinal gradient in the Atacama Desert. Thirty-nine common compounds predicted the plant environment with 79% accuracy, thus establishing the plant metabolome as an excellent integrative predictor of environmental fluctuations. These metabolites were independent of the species and validated both statistically and biologically using an independent dataset from a different sampling year. Thereafter, using multiblock predictive regressions, metabolites were linked to climatic and edaphic stressors such as freezing temperature, water deficit and high solar irradiance. These findings indicate that plants from different evolutionary trajectories use a generic metabolic toolkit to face extreme environments. These core metabolites, also present in agronomic species, provide a unique metabolic goldmine for improving crop performances under abiotic pressure.
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Affiliation(s)
- Thomas Dussarrat
- Departamento de Genética Molecular y MicrobiologíaPontificia Universidad Católica de ChileFONDAP Center for Genome Regulation and Millenium Institute for Integrative Biology (iBio)Av Libertador Bernardo O'Higgins 340SantiagoChile
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
| | - Sylvain Prigent
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Claudio Latorre
- Departamento de EcologíaPontificia Universidad Católica de ChileAv Libertador Bernardo O'Higgins 340SantiagoChile
- Institute of Ecology and Biodiversity (IEB)Las Palmeras3425ÑuñoaSantiagoChile
| | - Stéphane Bernillon
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Amélie Flandin
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Francisca P. Díaz
- Departamento de Genética Molecular y MicrobiologíaPontificia Universidad Católica de ChileFONDAP Center for Genome Regulation and Millenium Institute for Integrative Biology (iBio)Av Libertador Bernardo O'Higgins 340SantiagoChile
| | - Cédric Cassan
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Pierre Van Delft
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
- Laboratoire de Biogenèse Membranaire, CNRSUniv. Bordeaux, UMR 5200Villenave d'OrnonFrance
| | - Daniel Jacob
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Kranthi Varala
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteIN47907USA
- Center for Plant BiologyPurdue UniversityWest LafayetteIN47907USA
| | - Jérôme Joubes
- Laboratoire de Biogenèse Membranaire, CNRSUniv. Bordeaux, UMR 5200Villenave d'OrnonFrance
| | - Yves Gibon
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Dominique Rolin
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
| | - Rodrigo A. Gutiérrez
- Departamento de Genética Molecular y MicrobiologíaPontificia Universidad Católica de ChileFONDAP Center for Genome Regulation and Millenium Institute for Integrative Biology (iBio)Av Libertador Bernardo O'Higgins 340SantiagoChile
| | - Pierre Pétriacq
- Univ. BordeauxINRAEUMR1332 BFP, 33882Villenave d'OrnonFrance
- Bordeaux MetabolomeMetaboHUBPHENOME‐EMPHASIS33140Villenave d'OrnonFrance
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Santana-Sagredo F, Schulting RJ, Méndez-Quiros P, Vidal-Elgueta A, Uribe M, Loyola R, Maturana-Fernández A, Díaz FP, Latorre C, McRostie VB, Santoro CM, Mandakovic V, Harrod C, Lee-Thorp J. 'White gold' guano fertilizer drove agricultural intensification in the Atacama Desert from AD 1000. Nat Plants 2021; 7:152-158. [PMID: 33495555 DOI: 10.1038/s41477-020-00835-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
The archaeological record shows that large pre-Inca agricultural systems supported settlements for centuries around the ravines and oases of northern Chile's hyperarid Atacama Desert. This raises questions about how such productivity was achieved and sustained, and its social implications. Using isotopic data of well-preserved ancient plant remains from Atacama sites, we show a dramatic increase in crop nitrogen isotope values (δ15N) from around AD 1000. Maize was most affected, with δ15N values as high as +30‰, and human bone collagen following a similar trend; moreover, their carbon isotope values (δ13C) indicate a considerable increase in the consumption of maize at the same time. We attribute the shift to extremely high δ15N values-the highest in the world for archaeological plants-to the use of seabird guano to fertilize crops. Guano-'white gold' as it came to be called-thus sustained agricultural intensification, supporting a substantial population in an otherwise extreme environment.
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Affiliation(s)
- Francisca Santana-Sagredo
- Escuela de Antropología, Pontificia Universidad Católica de Chile, Santiago, Chile.
- Universidad de Antofagasta Stable Isotope Facility, Instituto Antofagasta, Universidad de Antofagasta, Angamos, Antofagasta, Chile.
- School of Archaeology, University of Oxford, Oxford, UK.
- Escuela de Antropología, Pontificia Universidad Católica de Chile, Santiago, Chile, Santiago, Chile.
| | | | - Pablo Méndez-Quiros
- Departamento de Prehistoria, Programa de Doctorado en Arqueología Prehistórica, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Ale Vidal-Elgueta
- Programa de Doctorado en Biología, mención Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mauricio Uribe
- Departamento de Antropología, Universidad de Chile, Santiago, Chile
| | - Rodrigo Loyola
- Instituto de Arqueología y Antropología (IIA), Universidad Católica del Norte (UCN), San Pedro de Atacama, Chile
- UMR 7055 Prehistoire et Technologie (PreTéch), Université Paris Ouest Nanterre La, Défense, France
| | | | - Francisca P Díaz
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudio Latorre
- Centro del Desierto de Atacama, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute of Ecology and Biodiversity, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Virginia B McRostie
- Escuela de Antropología, Pontificia Universidad Católica de Chile, Santiago, Chile
- Centro del Desierto de Atacama, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Valentina Mandakovic
- Programa de Magíster en Antropología, Departamento de Antropología, Universidad de Tarapacá, Arica, Chile
| | - Chris Harrod
- Universidad de Antofagasta Stable Isotope Facility, Instituto Antofagasta, Universidad de Antofagasta, Angamos, Antofagasta, Chile
- Núcleo Milenio INVASAL, Concepción, Chile
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
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6
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Díaz FP, Latorre C, Carrasco-Puga G, Wood JR, Wilmshurst JM, Soto DC, Cole TL, Gutiérrez RA. Multiscale climate change impacts on plant diversity in the Atacama Desert. Glob Chang Biol 2019; 25:1733-1745. [PMID: 30706600 DOI: 10.1111/gcb.14583] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 08/14/2018] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
Comprehending ecological dynamics requires not only knowledge of modern communities but also detailed reconstructions of ecosystem history. Ancient DNA (aDNA) metabarcoding allows biodiversity responses to major climatic change to be explored at different spatial and temporal scales. We extracted aDNA preserved in fossil rodent middens to reconstruct late Quaternary vegetation dynamics in the hyperarid Atacama Desert. By comparing our paleo-informed millennial record with contemporary observations of interannual variations in diversity, we show local plant communities behave differentially at different timescales. In the interannual (years to decades) time frame, only annual herbaceous expand and contract their distributional ranges (emerging from persistent seed banks) in response to precipitation, whereas perennials distribution appears to be extraordinarily resilient. In contrast, at longer timescales (thousands of years) many perennial species were displaced up to 1,000 m downslope during pluvial events. Given ongoing and future natural and anthropogenically induced climate change, our results not only provide baselines for vegetation in the Atacama Desert, but also help to inform how these and other high mountain plant communities may respond to fluctuations of climate in the future.
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Affiliation(s)
- Francisca P Díaz
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation & Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Claudio Latorre
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute of Ecology and Biodiversity (IEB), Ñuñoa, Santiago, Chile
| | - Gabriela Carrasco-Puga
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation & Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Jamie R Wood
- Manaaki Whenua - Landcare Research, Lincoln, New Zealand
| | - Janet M Wilmshurst
- Manaaki Whenua - Landcare Research, Lincoln, New Zealand
- School of Environment, The University of Auckland, Auckland, New Zealand
| | - Daniela C Soto
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation & Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Theresa L Cole
- Manaaki Whenua - Landcare Research, Lincoln, New Zealand
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation & Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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7
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Fredes I, Moreno S, Díaz FP, Gutiérrez RA. Nitrate signaling and the control of Arabidopsis growth and development. Curr Opin Plant Biol 2019; 47:112-118. [PMID: 30496968 DOI: 10.1016/j.pbi.2018.10.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/05/2018] [Accepted: 10/18/2018] [Indexed: 05/07/2023]
Abstract
Coordination between plant development and nutrient availability ensures a suitable supply of macromolecules for growth and developmental programs. Nitrate is an important source of nitrogen (N) that acts as a signal molecule to modulate gene expression, physiological, growth and developmental responses throughout the life of the plant. New key players in the nitrate signaling pathway have been described and knowledge of the molecular mechanics of how it impacts growth and developmental processes is increasing fast. Importantly, mechanisms for nitrate-control of growth and developmental processes have been proposed for both local as well as systemic responses. This article provides a synthesis of recent insights into molecular mechanisms by which nitrate impacts growth and development over Arabidopsis life-cycle.
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Affiliation(s)
- Isabel Fredes
- FONDAP Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile
| | - Sebastián Moreno
- FONDAP Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile
| | - Francisca P Díaz
- FONDAP Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile.
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8
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Wood JR, Díaz FP, Latorre C, Wilmshurst JM, Burge OR, Gutiérrez RA. Plant pathogen responses to Late Pleistocene and Holocene climate change in the central Atacama Desert, Chile. Sci Rep 2018; 8:17208. [PMID: 30464240 PMCID: PMC6249261 DOI: 10.1038/s41598-018-35299-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/01/2018] [Indexed: 01/17/2023] Open
Abstract
Future climate change has the potential to alter the distribution and prevalence of plant pathogens, which may have significant implications for both agricultural crops and natural plant communities. However, there are few long-term datasets against which modelled predictions of pathogen responses to climate change can be tested. Here, we use 18S metabarcoding of 28 rodent middens (solidified deposits of rodent coprolites and nesting material) from the Central Atacama, spanning the last ca. 49 ka, to provide the first long-term late Quaternary record of change in plant pathogen communities in response to changing climate. Plant pathogen richness was significantly greater in middens deposited during the Central Andean Pluvial Event (CAPE); a period of increased precipitation between 17.5–8.5 ka. Moreover, the occurrence frequency of Pucciniaceae (rust fungi) was significantly greater during the CAPE, and the highest relative abundances for five additional potentially pathogenic taxa also occurred during this period. The results demonstrate the promising potential for ancient DNA analysis of late Quaternary samples to reveal insights into how plant pathogens responded to past climatic and environmental change, which could help predict how pathogens may responded to future change.
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Affiliation(s)
- Jamie R Wood
- Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, 7640, New Zealand.
| | - Francisca P Díaz
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile. .,FONDAP Center for Genome Regulation & Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
| | - Claudio Latorre
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Alameda, 340, Santiago, Chile.,Institute of Ecology and Biodiversity (IEB), Las Palmeras, 3425, Ñuñoa, Santiago, Chile
| | - Janet M Wilmshurst
- Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, 7640, New Zealand.,School of Environment, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Olivia R Burge
- Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, 7640, New Zealand
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,FONDAP Center for Genome Regulation & Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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Díaz FP, Frugone M, Gutiérrez RA, Latorre C. Nitrogen cycling in an extreme hyperarid environment inferred from δ(15)N analyses of plants, soils and herbivore diet. Sci Rep 2016; 6:22226. [PMID: 26956399 PMCID: PMC4783660 DOI: 10.1038/srep22226] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/04/2016] [Indexed: 11/21/2022] Open
Abstract
Climate controls on the nitrogen cycle are suggested by the negative correlation between precipitation and δ15N values across different ecosystems. For arid ecosystems this is unclear, as water limitation among other factors can confound this relationship. We measured herbivore feces, foliar and soil δ15N and δ13C values and chemically characterized soils (pH and elemental composition) along an elevational/climatic gradient in the Atacama Desert, northern Chile. Although very positive δ15N values span the entire gradient, soil δ15N values show a positive correlation with aridity as expected. In contrast, foliar δ15N values and herbivore feces show a hump-shaped relationship with elevation, suggesting that plants are using a different N source, possibly of biotic origin. Thus at the extreme limits of plant life, biotic interactions may be just as important as abiotic processes, such as climate in explaining ecosystem δ15N values.
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Affiliation(s)
- Francisca P Díaz
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.,Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile.,FONDAP Center for Genome Regulation and Millennium Nucleus Center for Plant Systems and Synthetic Biology. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Matías Frugone
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.,Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Laboratorio Internacional de Cambio Global, LINCGlobal PUC-CSIC.,Instituto Pirenaico de Ecología, Montañana, España
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation and Millennium Nucleus Center for Plant Systems and Synthetic Biology. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Claudio Latorre
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.,Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile.,FONDAP Center for Genome Regulation and Millennium Nucleus Center for Plant Systems and Synthetic Biology. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.,Laboratorio Internacional de Cambio Global, LINCGlobal PUC-CSIC
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