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Quezada-Romegialli C, Quiroga-Carmona M, D’Elía G, Harrod C, Storz JF. Diet of Andean leaf-eared mice ( Phyllotis) living at extreme elevations on Atacama volcanoes: insights from metagenomics, DNA metabarcoding, and stable isotopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604871. [PMID: 39091768 PMCID: PMC11291156 DOI: 10.1101/2024.07.23.604871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
On the flanks of >6000 m Andean volcanoes that tower over the Atacama Desert, leaf-eared mice (Phyllotis vaccarum) live at extreme elevations that surpass known vegetation limits. What the mice eat in these barren, hyperarid environments has been the subject of much speculation. According to the arthropod fallout hypothesis, sustenance is provided by windblown insects that accumulate in snowdrifts ('aolian deposits'). It is also possible that mice feed on saxicolous lichen or forms of cryptic vegetation that have yet to be discovered at such high elevations. We tested hypotheses about the diet of mice living at extreme elevations on Atacama volcanoes by combining metagenomic and DNA metabarcoding analyses of gut contents with stable-isotope analyses of mouse tissues. Genomic analyses of contents of the gastrointestinal tract of a live-captured mouse from the 6739 m summit of Volcán Llullaillaco revealed evidence for an opportunistic but purely herbivorous diet, including lichens. Although we found no evidence of animal DNA in gut contents of the summit mouse, stable isotope data indicate that mice native to elevations at or near vegetation limits (~5100 m) include a larger fraction of animal prey in their diet than mice from lower elevations. Some plant species detected in the gut contents of the summit mouse are known to exist at lower elevations at the base of the volcano and in the surrounding Altiplano, suggesting that such plants may occur at higher elevations beneath the snowpack or in other cryptic microhabitats.
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Affiliation(s)
- Claudio Quezada-Romegialli
- Plataforma de Monitoreo Genómico y Ambiental, Departamento de Química, Facultad de Ciencias, Universidad de Tarapacá, Arica, Chile
| | - Marcial Quiroga-Carmona
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Colección de Mamíferos, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, Valdivia, Chile
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Colección de Mamíferos, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, Valdivia, Chile
| | - Chris Harrod
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
- Núcleo Milenio de Salmónidos Invasores Australes, INVASAL, Concepción, Chile
- Scottish Centre for Ecology and the Natural Environment, School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
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Becklin KM, Betancourt JL, Braasch J, Dézerald O, Díaz FP, González AL, Harbert R, Holmgren CA, Hornsby AD, Latorre C, Matocq MD, Smith FA. New uses for ancient middens: bridging ecological and evolutionary perspectives. Trends Ecol Evol 2024; 39:479-493. [PMID: 38553315 DOI: 10.1016/j.tree.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/30/2023] [Accepted: 12/08/2023] [Indexed: 05/12/2024]
Abstract
Rodent middens provide a fine-scale spatiotemporal record of plant and animal communities over the late Quaternary. In the Americas, middens have offered insight into biotic responses to past environmental changes and historical factors influencing the distribution and diversity of species. However, few studies have used middens to investigate genetic or ecosystem level responses. Integrating midden studies with neoecology and experimental evolution can help address these gaps and test mechanisms underlying eco-evolutionary patterns across biological and spatiotemporal scales. Fully realizing the potential of middens to answer cross-cutting ecological and evolutionary questions and inform conservation goals in the Anthropocene will require a collaborative research community to exploit existing midden archives and mount new campaigns to leverage midden records globally.
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Affiliation(s)
- Katie M Becklin
- Biology Department, Syracuse University, Syracuse, NY 13244, USA.
| | - Julio L Betancourt
- US Geological Survey, Science and Decisions Center, Reston, VA 20192, USA
| | - Joseph Braasch
- Department of Biology, Rutgers University, Camden, NJ 08103, USA; Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08103, USA
| | - Olivier Dézerald
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
| | - Francisca P Díaz
- Instituto de Geografía, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile; Institute of Ecology and Biodiversity (IEB), Santiago, Chile; Millennium Nucleus of Applied Historical Ecology for Arid Forests (AFOREST), Santiago, Chile
| | - Angélica L González
- Department of Biology, Rutgers University, Camden, NJ 08103, USA; Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08103, USA
| | - Robert Harbert
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Camille A Holmgren
- Department of Geosciences, SUNY Buffalo State University, Buffalo, NY 14222, USA
| | - Angela D Hornsby
- Philip L. Wright Zoological Museum, Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Claudio Latorre
- Institute of Ecology and Biodiversity (IEB), Santiago, Chile; Centro UC Desierto de Atacama, Pontificia Universidad Católica de Chile, Santiago, Chile; Department of Ecology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marjorie D Matocq
- Program in Ecology, Evolution, and Conservation Biology, Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV 89557, USA
| | - Felisa A Smith
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
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Pezo-Lanfranco L, Mut P, Chávez J, Fossile T, Colonese AC, Fernandes R. South American Archaeological Isotopic Database, a regional-scale multi-isotope data compendium for research. Sci Data 2024; 11:336. [PMID: 38575659 PMCID: PMC10995213 DOI: 10.1038/s41597-024-03148-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
The South American Archaeological Isotopic Database (SAAID) is a comprehensive open-access resource that aggregates all available bioarchaeological stable and radiogenic isotope measurements, encompassing data from human individuals, animals, and plants across South America. Resulting from a collaborative effort of scholars who work with stable isotopes in this region, SAAID contains 53,781 isotopic measurements across 24,507 entries from individuals/specimens spanning over 12,000 years. SAAID includes valuable contextual information on archaeological samples and respective sites, such as chronology, geographical region, biome, and spatial coordinates, biological details like estimated sex and age for human individuals, and taxonomic description for fauna and flora. SAAID is hosted at the PACHAMAMA community within the Pandora data platform and the CORA repository to facilitate easy access. Because of its rich data structure, SAAID is particularly well-suited for conducting spatiotemporal meta-analyses. It serves as a valuable tool for addressing a variety of research topics, including the spread, adoption, and consumption intensification of food items, paleo-environmental reconstruction, as well as the exploration of mobility patterns across extensive geographic regions.
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Affiliation(s)
- Luis Pezo-Lanfranco
- Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
- Department of Prehistory, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
| | - Patricia Mut
- Departamento de Antropología Biológica, Universidad de la República, Montevideo, Uruguay
| | - Juan Chávez
- Department of Anthropology, University of California, Riverside, USA
- Observatorio de Patrimonio Cultural y Arqueológico - Instituto de Investigaciones Antropológicas y Arqueológicas, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Thiago Fossile
- Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Department of Prehistory, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - André Carlo Colonese
- Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Department of Prehistory, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ricardo Fernandes
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany.
- Faculty of Archaeology, University of Warsaw, Warsaw, Poland.
- Arne Faculty of Arts, Masaryk University, Brno, Czech Republic.
- Climate Change and History Research Initiative, Princeton University, Princeton, USA.
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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. THE NEW PHYTOLOGIST 2024; 241:1074-1087. [PMID: 37984856 DOI: 10.1111/nph.19415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Mandakovic D, Aguado-Norese C, García-Jiménez B, Hodar C, Maldonado JE, Gaete A, Latorre M, Wilkinson MD, Gutiérrez RA, Cavieres LA, Medina J, Cambiazo V, Gonzalez M. Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert. ENVIRONMENTAL MICROBIOME 2023; 18:24. [PMID: 36978149 PMCID: PMC10052861 DOI: 10.1186/s40793-023-00486-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Soil microorganisms are in constant interaction with plants, and these interactions shape the composition of soil bacterial communities by modifying their environment. However, little is known about the relationship between microorganisms and native plants present in extreme environments that are not affected by human intervention. Using high-throughput sequencing in combination with random forest and co-occurrence network analyses, we compared soil bacterial communities inhabiting the rhizosphere surrounding soil (RSS) and the corresponding bulk soil (BS) of 21 native plant species organized into three vegetation belts along the altitudinal gradient (2400-4500 m a.s.l.) of the Talabre-Lejía transect (TLT) in the slopes of the Andes in the Atacama Desert. We assessed how each plant community influenced the taxa, potential functions, and ecological interactions of the soil bacterial communities in this extreme natural ecosystem. We tested the ability of the stress gradient hypothesis, which predicts that positive species interactions become increasingly important as stressful conditions increase, to explain the interactions among members of TLT soil microbial communities. RESULTS Our comparison of RSS and BS compartments along the TLT provided evidence of plant-specific microbial community composition in the RSS and showed that bacterial communities modify their ecological interactions, in particular, their positive:negative connection ratios in the presence of plant roots at each vegetation belt. We also identified the taxa driving the transition of the BS to the RSS, which appear to be indicators of key host-microbial relationships in the rhizosphere of plants in response to different abiotic conditions. Finally, the potential functions of the bacterial communities also diverge between the BS and the RSS compartments, particularly in the extreme and harshest belts of the TLT. CONCLUSIONS In this study, we identified taxa of bacterial communities that establish species-specific relationships with native plants and showed that over a gradient of changing abiotic conditions, these relationships may also be plant community specific. These findings also reveal that the interactions among members of the soil microbial communities do not support the stress gradient hypothesis. However, through the RSS compartment, each plant community appears to moderate the abiotic stress gradient and increase the efficiency of the soil microbial community, suggesting that positive interactions may be context dependent.
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Affiliation(s)
- Dinka Mandakovic
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, Chile
| | - Constanza Aguado-Norese
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Beatriz García-Jiménez
- Center for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM)/Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-CSIC, Madrid, Spain
- Present Address: Biome Makers Inc., West Sacramento, CA USA
| | - Christian Hodar
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Jonathan E. Maldonado
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, 9170022 Santiago, Chile
| | - Alexis Gaete
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Laboratorio de Bioingeniería, Instituto de Ciencias de La Ingeniería, Universidad de O’Higgins, Rancagua, Chile
| | - Mark D. Wilkinson
- Center for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM)/Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-CSIC, Madrid, Spain
| | - Rodrigo A. Gutiérrez
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Instituto de Biología Integrativa, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Lohengrin A. Cavieres
- Instituto de Ecología y Biodiversidad (IEB), 4070386 Concepción, Chile
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Joaquín Medina
- Center for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM)/Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-CSIC, Madrid, Spain
| | - Verónica Cambiazo
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Mauricio Gonzalez
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
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Liu X, Luo Z, Wang T, Su Q. Climatic and edaphic controls over soil δ15N in temperate grassland of northern China: A PLS-PATH analysis. PLoS One 2022; 17:e0265795. [PMID: 36315521 PMCID: PMC9621419 DOI: 10.1371/journal.pone.0265795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 10/07/2022] [Indexed: 01/24/2023] Open
Abstract
Identifying the impact path of climate and soil factors on soil δ15N is very crucial for better understanding the N turnover in soils and the integrated information about ecosystem N cycling. Many studies have showed that climate and soil variables influence the change of soil δ15N. However, most of the existing studies focused on the overall impact of factor on soil δ15N, without distinguishing between the direct and indirect effect. Although scholars have studied the relationships among temperature, precipitation, soil N, soil pH, and soil δ15N rather than estimating all the causal relationships simultaneously. To answer the above-mentioned questions, a regional-scale soil collection was conducted across a temperate grassland in northern China. Meanwhile, a PLS-PATH analysis was utilized to evaluate the direct and indirect effects of various factors on soil δ15N and to explore the causal relationships among variables. The results showed that along the transect, mean annual precipitation (MAP) and mean annual temperature (MAT) directly and significantly reduced soil δ15N, and indirectly affected soil δ15N through their effects on soil pH, soil clay, soil N and soil C/N. Soil C/N ratio has a significant direct impact on soil δ15N with a negative correlation. Soil clay, soil N content, and soil pH have a total positive effect on soil δ15N, but the total positive impact of soil pH is very weak because it has a negative indirect impact on soil δ15N by affecting soil clay, soil N and soil C/N ratio. The total influence is, in order, MAP > MAT > soil C/N > soil clay > soil N > soil pH (in absolute value). The above results will provide valuable information about ecosystem N cycle in temperate grassland of northern China.
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Affiliation(s)
- Xianzhao Liu
- School of Earth Science and space information Engineering, Hunan University of Science and Technology, Xiangtan, Hunan, China
- * E-mail:
| | - Zhengying Luo
- School of Earth Science and space information Engineering, Hunan University of Science and Technology, Xiangtan, Hunan, China
| | - Tianhao Wang
- School of Earth Science and space information Engineering, Hunan University of Science and Technology, Xiangtan, Hunan, China
| | - Qing Su
- School of Life and Health Science, Hunan University of Science and Technology, Xiangtan, Hunan, China
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Maldonado JE, Gaete A, Mandakovic D, Aguado-Norese C, Aguilar M, Gutiérrez RA, González M. Partners to survive: Hoffmannseggia doellii root-associated microbiome at the Atacama Desert. THE NEW PHYTOLOGIST 2022; 234:2126-2139. [PMID: 35274744 DOI: 10.1111/nph.18080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
The discovery and characterization of plant species adapted to extreme environmental conditions have become increasingly important. Hoffmannseggia doellii is a perennial herb endemic to the Chilean Atacama Desert that grows in the western Andes between 2800 and 3600 m above sea level. Its growing habitat is characterized by high radiation and low water and nutrient availability. Under these conditions, H. doellii can grow, reproduce, and develop an edible tuberous root. We characterized the H. doellii soil-associated microbiomes to understand the biotic factors that could influence their surprising ability to survive. We found an increased number of observed species and higher phylogenetic diversity of bacteria and fungi on H. doellii root soils compared with bare soil (BS) along different sites and to soil microbiomes of other plant species. Also, the H. doellii-associated microbiome had a higher incidence of overall positive interactions and fungal within-kingdom interactions than their corresponding BS network. These findings suggest a microbial diversity soil modulation mechanism that may be a characteristic of highly tolerant plants to diverse and extreme environments. Furthermore, since H. doellii is related to important cultivated crops, our results create an opportunity for future studies on climate change adaptation of crop plants.
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Affiliation(s)
- Jonathan E Maldonado
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Departamento de Genética Molecular y Microbiología, ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 7500565, Chile
- Laboratorio de Multiómica Vegetal y Bioinformática, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile
| | - Alexis Gaete
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, 7830490, Chile
| | - Dinka Mandakovic
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, 8580745, Chile
| | - Constanza Aguado-Norese
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, 7830490, Chile
| | - Melissa Aguilar
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Departamento de Genética Molecular y Microbiología, ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 7500565, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Departamento de Genética Molecular y Microbiología, ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 7500565, Chile
| | - Mauricio González
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, 7830490, Chile
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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. THE NEW PHYTOLOGIST 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] [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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9
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Chibowski P, Brzeziński M, Suska-Malawska M, Zub K. Diet/Hair and Diet/Faeces Trophic Discrimination Factors for Stable Carbon and Nitrogen Isotopes, and Hair Regrowth in the Yellow-Necked Mouse and Bank Vole. ANN ZOOL FENN 2022. [DOI: 10.5735/086.059.0115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Piotr Chibowski
- Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, PL-02-089 Warsaw, Poland
| | - Marcin Brzeziński
- Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, PL-02-089 Warsaw, Poland
| | - Małgorzata Suska-Malawska
- Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, PL-02-089 Warsaw, Poland
| | - Karol Zub
- Mammal Research Institute, Polish Academy of Sciences, Stoczek 1, PL-17-230 Białowieża, Poland
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10
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Plant ecological genomics at the limits of life in the Atacama Desert. Proc Natl Acad Sci U S A 2021; 118:2101177118. [PMID: 34725254 DOI: 10.1073/pnas.2101177118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 12/26/2022] Open
Abstract
The Atacama Desert in Chile-hyperarid and with high-ultraviolet irradiance levels-is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre-Lejía transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environmental conditions. We characterized climate, soil, plant, and soil-microbe diversity at 22 sites (every 100 m of altitude) along the TLT over a 10-y period. We quantified drought, nutrient deficiencies, large diurnal temperature oscillations, and pH gradients that define three distinct vegetational belts along the altitudinal cline. We deep-sequenced transcriptomes of 32 dominant plant species spanning the major plant clades, and assessed soil microbes by metabarcoding sequencing. The top-expressed genes in the 32 Atacama species are enriched in stress responses, metabolism, and energy production. Moreover, their root-associated soils are enriched in growth-promoting bacteria, including nitrogen fixers. To identify genes associated with plant adaptation to harsh environments, we compared 32 Atacama species with the 32 closest sequenced species, comprising 70 taxa and 1,686,950 proteins. To perform phylogenomic reconstruction, we concatenated 15,972 ortholog groups into a supermatrix of 8,599,764 amino acids. Using two codon-based methods, we identified 265 candidate positively selected genes (PSGs) in the Atacama plants, 64% of which are located in Pfam domains, supporting their functional relevance. For 59/184 PSGs with an Arabidopsis ortholog, we uncovered functional evidence linking them to plant resilience. As some Atacama plants are closely related to staple crops, these candidate PSGs are a "genetic goldmine" to engineer crop resilience to face climate change.
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11
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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. NATURE 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] [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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12
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Escobedo VM, Rios RS, Alcayaga-Olivares Y, Gianoli E. Disturbance reinforces community assembly processes differentially across spatial scales. ANNALS OF BOTANY 2021; 127:175-189. [PMID: 32880645 PMCID: PMC7789110 DOI: 10.1093/aob/mcaa162] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS There is a paucity of empirical research and a lack of predictive models concerning the interplay between spatial scale and disturbance as they affect the structure and assembly of plant communities. We proposed and tested a trait dispersion-based conceptual model hypothesizing that disturbance reinforces assembly processes differentially across spatial scales. Disturbance would reinforce functional divergence at the small scale (neighbourhood), would not affect functional dispersion at the intermediate scale (patch) and would reinforce functional convergence at the large scale (site). We also evaluated functional and species richness of native and exotic plants to infer underlying processes. Native and exotic species richness were expected to increase and decrease with disturbance, respectively, at the neighbourhood scale, and to show similar associations with disturbance at the patch (concave) and site (negative) scales. METHODS In an arid shrubland, we estimated species richness and functional dispersion and richness within 1 m2 quadrats (neighbourhood) nested within 100 m2 plots (patch) along a small-scale natural disturbance gradient caused by an endemic fossorial rodent. Data for the site scale (2500 m2 plots) were taken from a previous study. We also tested the conceptual model through a quantitative literature review and a meta-analysis. KEY RESULTS As spatial scale increased, disturbance sequentially promoted functional divergence, random trait dispersion and functional convergence. Functional richness was unaffected by disturbance across spatial scales. Disturbance favoured natives over exotics at the neighbourhood scale, while both decreased under high disturbance at the patch and site scales. CONCLUSIONS The results supported the hypothesis that disturbance reinforces assembly processes differentially across scales and hampers plant invasion. The quantitative literature review and the meta-analysis supported most of the model predictions.
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Affiliation(s)
- Víctor M Escobedo
- Departamento de Biología, Universidad de La Serena, Casilla La Serena, Chile
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Rodrigo S Rios
- Departamento de Biología, Universidad de La Serena, Casilla La Serena, Chile
- Instituto Multidisciplinario de Investigación en Ciencia y Tecnología, Universidad de La Serena, Chile
| | | | - Ernesto Gianoli
- Departamento de Biología, Universidad de La Serena, Casilla La Serena, Chile
- Departamento de Botánica, Universidad de Concepción, Casilla Concepción, Chile
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13
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Gaete A, Mandakovic D, González M. Isolation and Identification of Soil Bacteria from Extreme Environments of Chile and Their Plant Beneficial Characteristics. Microorganisms 2020; 8:microorganisms8081213. [PMID: 32785053 PMCID: PMC7466141 DOI: 10.3390/microorganisms8081213] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 12/15/2022] Open
Abstract
The isolation of soil bacteria from extreme environments represents a major challenge, but also an opportunity to characterize the metabolic potential of soil bacteria that could promote the growth of plants inhabiting these harsh conditions. The aim of this study was to isolate and identify bacteria from two Chilean desert environments and characterize the beneficial traits for plants through a biochemical approach. By means of different culture strategies, we obtained 39 bacterial soil isolates from the Coppermine Peninsula (Antarctica) and 32 from Lejía Lake shore soil (Atacama Desert). The results obtained from the taxonomic classification and phylogenetic analysis based on 16S rDNA sequences indicated that the isolates belonged to four phyla (Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes), and that the most represented genus at both sites was Pseudomonas. Regarding biochemical characterization, all strains displayed in vitro PGP capabilities, but these were in different proportions that grouped them according to their site of origin. This study contributes with microbial isolates from natural extreme environments with biotechnological potentials in improving plant growth under cold stress.
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Affiliation(s)
- Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, El Libano 5524, 7810000 Santiago, Chile;
- Center for Genome Regulation, El Libano 5524, Santiago 7810000, Chile
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile. Santa Rosa 11315, 8820808 Santiago, Chile
| | - Dinka Mandakovic
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Camino La Pirámide 5750, 8320000 Santiago, Chile;
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LGIB). Instituto de Nutrición y Tecnología de los Alimento, Universidad de Chile. El Líbano 5524, 7810000 Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, El Libano 5524, 7810000 Santiago, Chile;
- Center for Genome Regulation, El Libano 5524, Santiago 7810000, Chile
- Correspondence:
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14
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Araus V, Swift J, Alvarez JM, Henry A, Coruzzi GM. A balancing act: how plants integrate nitrogen and water signals. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4442-4451. [PMID: 31990028 PMCID: PMC7382378 DOI: 10.1093/jxb/eraa054] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/24/2020] [Indexed: 05/03/2023]
Abstract
Nitrogen (N) and water (W) are crucial inputs for plant survival as well as costly resources for agriculture. Given their importance, the molecular mechanisms that plants rely on to signal changes in either N or W status have been under intense scrutiny. However, how plants sense and respond to the combination of N and W signals at the molecular level has received scant attention. The purpose of this review is to shed light on what is currently known about how plant responses to N are impacted by W status. We review classic studies which detail how N and W combinations have both synergistic and antagonistic effects on key plant traits, such as root architecture and stomatal aperture. Recent molecular studies of N and W interactions show that mutations in genes involved in N metabolism affect drought responses, and vice versa. Specifically, perturbing key N signaling genes may lead to changes in drought-responsive gene expression programs, which is supported by a meta-analysis we conduct on available transcriptomic data. Additionally, we cite studies that show how combinatorial transcriptional responses to N and W status might drive crop phenotypes. Through these insights, we suggest research strategies that could help to develop crops adapted to marginal soils depleted in both N and W, an important task in the face of climate change.
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Affiliation(s)
- Viviana Araus
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Joseph Swift
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Jose M Alvarez
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Amelia Henry
- International Rice Research Institute, Metro Manila, Philippines
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
- Correspondence:
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15
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Szpak P, Valenzuela D. Camelid husbandry in the Atacama Desert? A stable isotope study of camelid bone collagen and textiles from the Lluta and Camarones Valleys, northern Chile. PLoS One 2020; 15:e0228332. [PMID: 32160199 PMCID: PMC7065742 DOI: 10.1371/journal.pone.0228332] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 01/13/2020] [Indexed: 11/19/2022] Open
Abstract
Management of camelids in the coastal valleys of the Andes has generated much debate in recent years. Zooarchaeological and isotopic studies have demonstrated that in the coastal valleys of northern and southern Peru there were locally maintained camelid herds. Because of the hyperarid conditions of the northern coast of Chile, this region has been assumed to be unsuitable for the raising of camelids. In this study we report stable carbon and nitrogen isotopic compositions of camelid bone collagen and textiles made from camelid fiber from Late Intermediate Period (LIP) and Late Horizon (LH) occupations in northern Chilean river valleys. The camelid bone collagen isotopic compositions are consistent with these animals originating in the highlands, although there is a significant difference in the camelids dating to the LIP and LH, possibly because of changes made to distribution and exchange networks by the Inca in the LH. There were no differences between the isotopic compositions of the camelid fibers sampled from textiles in the LIP and LH, suggesting that either the production of camelid fiber was unchanged by the Inca or the changes that were made do not present visible isotopic evidence. Several camelid fiber samples from both the LIP and LH present very high δ13C and δ15N values, comparable to human hair samples from one site (Huancarane) in the Camarones Valley. These data suggest that people in the northern valleys of Chile may have kept small numbers of animals specifically for fiber production. Overall, however, the vast majority of the textile samples have isotopic compositions that are consistent with an origin in the highlands. These data suggest that the hyperarid coastal river valleys of northern Chile did not support substantial camelid herds as has been interpreted for northern Peru.
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Affiliation(s)
- Paul Szpak
- Department of Anthropology, Trent University, Peterborough, Ontario, Canada
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16
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Fernández-Martínez MÁ, dos Santos Severino R, Moreno-Paz M, Gallardo-Carreño I, Blanco Y, Warren-Rhodes K, García-Villadangos M, Ruiz-Bermejo M, Barberán A, Wettergreen D, Cabrol N, Parro V. Prokaryotic Community Structure and Metabolisms in Shallow Subsurface of Atacama Desert Playas and Alluvial Fans After Heavy Rains: Repairing and Preparing for Next Dry Period. Front Microbiol 2019; 10:1641. [PMID: 31396176 PMCID: PMC6668633 DOI: 10.3389/fmicb.2019.01641] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/02/2019] [Indexed: 11/13/2022] Open
Abstract
The Atacama Desert, the oldest and driest desert on Earth, displays significant rains only once per decade. To investigate how microbial communities take advantage of these sporadic wet events, we carried out a geomicrobiological study a few days after a heavy rain event in 2015. Different physicochemical and microbial community analyses were conducted on samples collected from playas and an alluvial fan from surface, 10, 20, 50, and 80 cm depth. Gravimetric moisture content peaks were measured in 10 and 20 cm depth samples (from 1.65 to 4.1% w/w maximum values) while, in general, main anions such as chloride, nitrate, and sulfate concentrations increased with depth, with maximum values of 13-1,125; 168-10,109; and 9,904-30,952 ppm, respectively. Small organic anions such as formate and acetate had maximum concentrations from 2.61 to 3.44 ppm and 6.73 to 28.75 ppm, respectively. Microbial diversity inferred from DNA analysis showed Actinobacteria and Alphaproteobacteria as the most abundant and widespread bacterial taxa among the samples, followed by Chloroflexi and Firmicutes at specific sites. Archaea were mainly dominated by Nitrososphaerales, Methanobacteria, with the detection of other groups such as Halobacteria. Metaproteomics showed a high and even distribution of proteins involved in primary metabolic processes such as energy production and biosynthetic pathways, and a limited but remarkable presence of proteins related to resistance to environmental stressors such as radiation, oxidation, or desiccation. The results indicated that extra humidity in the system allows the microbial community to repair, and prepare for the upcoming hyperarid period. Additionally, it supplies biomarkers to the medium whose preservation potential could be high under strong desiccation conditions and relevant for planetary exploration.
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Affiliation(s)
| | | | | | | | | | - Kimberley Warren-Rhodes
- Carl Sagan Center, SETI Institute, Mountain View, CA, United States
- NASA Ames Research Center, Moffett Field, Mountain View, CA, United States
| | | | | | - Albert Barberán
- Department of Soil, Water, and Environmental Science, University of Arizona, Tucson, AZ, United States
| | - David Wettergreen
- Carnegie Mellon University, Robotics Institute, Pittsburgh, PA, United States
| | - Nathalie Cabrol
- Carl Sagan Center, SETI Institute, Mountain View, CA, United States
- NASA Ames Research Center, Moffett Field, Mountain View, CA, United States
| | - Víctor Parro
- Centro de Astrobiología (CAB, CSIC-INTA), Madrid, Spain
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17
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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. GLOBAL CHANGE BIOLOGY 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] [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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Maza F, Maldonado J, Vásquez-Dean J, Mandakovic D, Gaete A, Cambiazo V, González M. Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability. Front Bioeng Biotechnol 2019; 7:10. [PMID: 30805333 PMCID: PMC6371850 DOI: 10.3389/fbioe.2019.00010] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/16/2019] [Indexed: 11/13/2022] Open
Abstract
The Atacama Desert is a highly complex, extreme ecosystem which harbors microorganisms remarkable for their biotechnological potential. Here, a soil bacterial prospection was carried out in the high Altiplano region of the Atacama Desert (>3,800 m above sea level; m a.s.l.), where direct anthropogenic interference is minimal. We studied: (1) soil bacterial community composition using high-throughput sequencing of the 16S rRNA gene and (2) bacterial culturability, by using a soil extract medium (SEM) under a factorial design of three factors: temperature (15 and 30°C), nutrient content (high and low nutrient disposal) and oxygen availability (presence and absence). A total of 4,775 OTUs were identified and a total of 101 isolates were selected for 16S rRNA sequencing, 82 of them corresponded to unique or non-redundant sequences. To expand our view of the Altiplano landscape and to obtain a better representation of its microbiome, we complemented our Operational Taxonomic Units (OTUs) and isolate collection with data from other previous data from our group and obtained a merged set of OTUs and isolates that we used to perform our study. Taxonomic comparisons between culturable microbiota and metabarcoding data showed an overrepresentation of the phylum Firmicutes (44% of isolates vs. 2% of OTUs) and an underrepresentation of Proteobacteria (8% of isolates vs. 36% of OTUs). Within the Next Generation Sequencing (NGS) results, 33% of the OTUs were unknown up to genus, revealing an important proportion of putative new species in this environment. Biochemical characterization and analysis extracted from the literature indicated that an important number of our isolates had biotechnological potential. Also, by comparing our results with similar studies on other deserts, the Altiplano highland was most similar to a cold arid desert. In summary, our study contributes to expand the knowledge of soil bacterial communities in the Atacama Desert and complements the pipeline to isolate selective bacteria that could represent new potential biotechnological resources.
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Affiliation(s)
- Felipe Maza
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
| | - Javiera Vásquez-Dean
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Dinka Mandakovic
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
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Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils. Sci Rep 2019; 9:1042. [PMID: 30705356 PMCID: PMC6355873 DOI: 10.1038/s41598-018-37776-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 12/12/2018] [Indexed: 12/23/2022] Open
Abstract
The rhizosphere is considered the primary place for soil microbiome differentiation and plays a key role in plant survival, especially for those subjected to environmental stress. Using high-throughput sequencing of the 16S rRNA gene, we analyzed and compared soil bacterial communities associated to four of the most abundant high altitude native plant species of the Chilean Andean grasslands. We examined three soil compartments: the rhizosphere (bacteria firmly attached to the roots), the rhizosphere-surrounding soil (bacteria loosely attached to the roots) and the bulk soil (plant-free soil). The rhizosphere microbiome was in all cases the least diverse, exposing that the bulk soil was a more complex environment. Taxonomic analysis revealed an abrupt change between the rhizosphere and the rest of the non-rhizospheric soils. Thus, while rhizobacterial communities were enriched in Proteobacteria (mainly Alphaproteobacteria), Actinobacteria (mostly Blastocatellia) dominated in bulk soils. Finally, we detected certain taxonomic rhizosphere signatures, which could be attributed to a particular genotype. Overall, our results indicate that the thin layer of soil surrounding the roots constitute a distinctive soil environment. This study contributes to expand the knowledge about soil bacterial communities in the Chilean highlands and takes the first step to understand the processes that might lead to the rhizosphere differentiation in that area.
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Isotopic evidence for oligotrophication of terrestrial ecosystems. Nat Ecol Evol 2018; 2:1735-1744. [DOI: 10.1038/s41559-018-0694-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/12/2018] [Indexed: 11/09/2022]
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Wu L, Liu X, Fang Y, Hou S, Xu L, Wang X, Fu P. Nitrogen cycling in the soil-plant system along a series of coral islands affected by seabirds in the South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:166-175. [PMID: 29426138 DOI: 10.1016/j.scitotenv.2018.01.213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/11/2018] [Accepted: 01/21/2018] [Indexed: 06/08/2023]
Abstract
The nitrogen (N) utilization strategy of plants has become a topic of interest within the field of phytoecology. However, few studies have considered N cycling on coral island ecosystems from the perspective of their evolution. The aim of this study was to test the impacts of biological transport by seabirds, on the sources and uses of N by plants, and pathways of N cycling in soil-plant ecosystems on coral islands. A series of eight coral islands were investigated, five of which were affected to a varying extent by seabirds. The total phosphorus (TP) concentration from avian sources and the δ15N values of total nitrogen (TN) and inorganic nitrogen (IN: NH4+-N, and NO3--N), δ18O of NO3--O, in soils were determined, as well as proxies in plant leaves of two dominant plant species, including TN, the carbon/nitrogen ratio (C/N), and δ13C and δ15N values. The results show that, with an increase of TP, the TN and IN content, and δ15N values in soils all increased. Plant C/N and δ15N values decreased and increased, respectively, as the soil N content increased. When the TN content of the soil was low, the δ15N value in plant leaves was similar to that in soil NO3-, but was much lower than that in soil NH4+. When the soil TN content was high, the δ15N values were similar. Both plants and soil were probably N-limited prior to seabird colonization, with the N source on the barren coral islands originating primarily from atmospheric deposition. With seabird guano input and subsequent pedogenesis, the source of N switched to guano. Under these conditions, most of the N utilized by plants originated from NH4+, while nitrate is dominant for non-seabirds islands. Seabird activities have played a key role in the N dynamics of soil-plant ecosystems at coral islands.
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Affiliation(s)
- Libin Wu
- Institute of Polar Environment, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, Anhui 230026, PR China; Anhui Province Key Laboratory of Polar Environment and Global Change, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Xiaodong Liu
- Institute of Polar Environment, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, Anhui 230026, PR China; Anhui Province Key Laboratory of Polar Environment and Global Change, University of Science and Technology of China, Hefei, Anhui 230026, PR China.
| | - Yunting Fang
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China
| | - Shengjie Hou
- LAPC, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, PR China
| | - Liqiang Xu
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, PR China
| | - Xueying Wang
- Institute of Polar Environment, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, Anhui 230026, PR China; Anhui Province Key Laboratory of Polar Environment and Global Change, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Pingqing Fu
- Institute of Surface-Earth System Science, Tianjin University, Tianjin 300072, PR China
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Namib Desert primary productivity is driven by cryptic microbial community N-fixation. Sci Rep 2018; 8:6921. [PMID: 29720684 PMCID: PMC5932006 DOI: 10.1038/s41598-018-25078-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/09/2018] [Indexed: 12/03/2022] Open
Abstract
Carbon exchange in drylands is typically low, but during significant rainfall events (wet anomalies) drylands act as a C sink. During these anomalies the limitation on C uptake switches from water to nitrogen. In the Namib Desert of southern Africa, the N inventory in soil organic matter available for mineralisation is insufficient to support the observed increase in primary productivity. The C4 grasses that flourish after rainfall events are not capable of N fixation, and so there is no clear mechanism for adequate N fixation in dryland ecosystems to support rapid C uptake. Here we demonstrate that N fixation by photoautotrophic hypolithic communities forms the basis for the N budget for plant productivity events in the Namib Desert. Stable N isotope (δ15N) values of Namib Desert hypolithic biomass, and surface and subsurface soils were measured over 3 years across dune and gravel plain biotopes. Hypoliths showed significantly higher biomass and lower δ15N values than soil organic matter. The δ15N values of hypoliths approach the theoretical values for nitrogen fixation. Our results are strongly indicative that hypolithic communities are the foundation of productivity after rain events in the Namib Desert and are likely to play similar roles in other arid environments.
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Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience. Sci Rep 2018; 8:5875. [PMID: 29651160 PMCID: PMC5897386 DOI: 10.1038/s41598-018-23931-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/09/2018] [Indexed: 11/09/2022] Open
Abstract
Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks representing bacterial soil communities from two different sections of a pH, temperature and humidity gradient occurring along a western slope of the Andes in the Atacama Desert. In doing so, a topological graph alignment of co-occurrence networks was used to determine the impact of a shift in environmental variables on OTUs taxonomic composition and their relationships. We observed that a fraction of association patterns identified in the co-occurrence networks are persistent despite large environmental variation. This apparent resilience seems to be due to: (1) a proportion of OTUs that persist across the gradient and maintain similar association patterns within the community and (2) bacterial community ecological rearrangements, where an important fraction of the OTUs come to fill the ecological roles of other OTUs in the other network. Actually, potential functional features suggest a fundamental role of persistent OTUs along the soil gradient involving nitrogen fixation. Our results allow identifying factors that induce changes in microbial assemblage configuration, altering specific bacterial soil functions and interactions within the microbial communities in natural environments.
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Wood JR, Perry GLW, Wilmshurst JM. Using palaeoecology to determine baseline ecological requirements and interaction networks for de‐extinction candidate species. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12773] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jamie R. Wood
- Long‐term Ecology Lab Landcare Research PO Box 69040 Lincoln7640 New Zealand
| | - George L. W. Perry
- School of Environment The University of Auckland Private Bag 92019 Auckland1142 New Zealand
| | - Janet M. Wilmshurst
- Long‐term Ecology Lab Landcare Research PO Box 69040 Lincoln7640 New Zealand
- School of Environment The University of Auckland Private Bag 92019 Auckland1142 New Zealand
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