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Dyson K, Nicolau AP, Tenneson K, Francesconi W, Daniels A, Andrich G, Caldas B, Castaño S, de Campos N, Dilger J, Guidotti V, Jaques I, McCullough IM, McDevitt AD, Molina L, Nekorchuk DM, Newberry T, Pereira CL, Perez J, Richards-Dimitrie T, Rivera O, Rodriguez B, Sales N, Tello J, Wespestad C, Zutta B, Saah D. Coupling remote sensing and eDNA to monitor environmental impact: A pilot to quantify the environmental benefits of sustainable agriculture in the Brazilian Amazon. PLoS One 2024; 19:e0289437. [PMID: 38354171 PMCID: PMC10866516 DOI: 10.1371/journal.pone.0289437] [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: 07/17/2023] [Accepted: 12/01/2023] [Indexed: 02/16/2024] Open
Abstract
Monitoring is essential to ensure that environmental goals are being achieved, including those of sustainable agriculture. Growing interest in environmental monitoring provides an opportunity to improve monitoring practices. Approaches that directly monitor land cover change and biodiversity annually by coupling the wall-to-wall coverage from remote sensing and the site-specific community composition from environmental DNA (eDNA) can provide timely, relevant results for parties interested in the success of sustainable agricultural practices. To ensure that the measured impacts are due to the environmental projects and not exogenous factors, sites where projects have been implemented should be benchmarked against counterfactuals (no project) and control (natural habitat) sites. Results can then be used to calculate diverse sets of indicators customized to monitor different projects. Here, we report on our experience developing and applying one such approach to assess the impact of shaded cocoa projects implemented by the Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA) near São Félix do Xingu, in Pará, Brazil. We used the Continuous Degradation Detection (CODED) and LandTrendr algorithms to create a remote sensing-based assessment of forest disturbance and regeneration, estimate carbon sequestration, and changes in essential habitats. We coupled these remote sensing methods with eDNA analyses using arthropod-targeted primers by collecting soil samples from intervention and counterfactual pasture field sites and a control secondary forest. We used a custom set of indicators from the pilot application of a coupled monitoring framework called TerraBio. Our results suggest that, due to IMAFLORA's shaded cocoa projects, over 400 acres were restored in the intervention area and the community composition of arthropods in shaded cocoa is closer to second-growth forests than that of pastures. In reviewing the coupled approach, we found multiple aspects worked well, and we conclude by presenting multiple lessons learned.
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Affiliation(s)
- Karen Dyson
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Andréa P. Nicolau
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Karis Tenneson
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Wendy Francesconi
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Amy Daniels
- United States Agency for International Development (USAID), Washington, DC, United States of America
| | - Giulia Andrich
- Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA), Piracicaba, Brazil
| | - Bernardo Caldas
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Silvia Castaño
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Nathanael de Campos
- Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA), Piracicaba, Brazil
| | - John Dilger
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Vinicius Guidotti
- Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA), Piracicaba, Brazil
| | - Iara Jaques
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Ian M. McCullough
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | | | - Luis Molina
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Dawn M. Nekorchuk
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Tom Newberry
- University of Salford, Salford, Manchester, United Kingdom
| | | | - Jorge Perez
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | | | - Ovidio Rivera
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Beatriz Rodriguez
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Naiara Sales
- University of Salford, Salford, Manchester, United Kingdom
| | - Jhon Tello
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Crystal Wespestad
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Brian Zutta
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - David Saah
- University of San Francisco, San Francisco, California, United States of America
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Guerrieri A, Carteron A, Bonin A, Marta S, Ambrosini R, Caccianiga M, Cantera I, Compostella C, Diolaiuti G, Fontaneto D, Gielly L, Gili F, Gobbi M, Poulenard J, Taberlet P, Zerboni A, Thuiller W, Ficetola GF. Metabarcoding data reveal vertical multitaxa variation in topsoil communities during the colonization of deglaciated forelands. Mol Ecol 2023; 32:6304-6319. [PMID: 35997629 DOI: 10.1111/mec.16669] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 07/21/2022] [Accepted: 08/15/2022] [Indexed: 11/27/2022]
Abstract
Ice-free areas are expanding worldwide due to dramatic glacier shrinkage and are undergoing rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. It has been proposed that the colonization dynamics of deglaciated terrains is different between surface and deep soils but that the heterogeneity between communities inhabiting surface and deep soils decreases through time. Nevertheless, tests of this hypothesis remain scarce, and it is unclear whether patterns are consistent among different taxonomic groups. Here, we used environmental DNA metabarcoding to test whether community diversity and composition of six groups (Eukaryota, Bacteria, Mycota, Collembola, Insecta, and Oligochaeta) differ between the surface (0-5 cm) and deeper (7.5-20 cm) soil at different stages of development and across five Alpine glaciers. Taxonomic diversity increased with time since glacier retreat and with soil evolution. The pattern was consistent across groups and soil depths. For Eukaryota and Mycota, alpha-diversity was highest at the surface. Time since glacier retreat explained more variation of community composition than depth. Beta-diversity between surface and deep layers decreased with time since glacier retreat, supporting the hypothesis that the first 20 cm of soil tends to homogenize through time. Several molecular operational taxonomic units of bacteria and fungi were significant indicators of specific depths and/or soil development stages, confirming the strong functional variation of microbial communities through time and depth. The complexity of community patterns highlights the importance of integrating information from multiple taxonomic groups to unravel community variation in response to ongoing global changes.
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Affiliation(s)
- Alessia Guerrieri
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Alexis Carteron
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Aurélie Bonin
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
- Argaly, Bâtiment CleanSpace, Sainte-Hélène-du-Lac, France
| | - Silvio Marta
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Roberto Ambrosini
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Marco Caccianiga
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Isabel Cantera
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Chiara Compostella
- Department of Earth Sciences, "A. Desio," Università degli Studi di Milano, Milan, Italy
| | - Guglielmina Diolaiuti
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | | | - Ludovic Gielly
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
| | - Fabrizio Gili
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Mauro Gobbi
- Research & Museum Collections Office, Climate and Ecology Unit, MUSE-Science Museum, Trento, Italy
| | | | - Pierre Taberlet
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | - Andrea Zerboni
- Department of Earth Sciences, "A. Desio," Università degli Studi di Milano, Milan, Italy
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
| | - Gentile Francesco Ficetola
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
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Philpott M, Liew ECY, van der Merwe MM, Mertin A, French K. The Influence of Cone Age and Urbanisation on the Diversity and Community Composition of Culturable Seed Fungal Endophytes within Native Australian Banksia ericifolia L.f. subsp. ericifolia. J Fungi (Basel) 2023; 9:706. [PMID: 37504695 PMCID: PMC10381327 DOI: 10.3390/jof9070706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Seed fungal endophytes play a crucial role in assisting the overall health and success of their host plant; however, little is known about the factors that influence the diversity and composition of these endophytes, particularly with respect to how they change over time and within urban environments. Using culturing techniques, morphological analyses, and Sanger sequencing, we identified the culturable seed fungal endophytes of Banksia ericifolia at two urban and two natural sites in Sydney, New South Wales, Australia. A total of 27 Operational Taxonomic Units were obtained from 1200 seeds. Older cones were found to contain, on average, more colonised endophytes than younger cones. Species richness was also significantly influenced by cone age, with older cones being more speciose. Between urban and natural sites, the overall community composition did not change, although species richness and diversity were greatest at urban sites. Understanding how these endophytes vary in time and space may help provide an insight into the transmission pathways used and the potential role they play within the development and survival of the seed. This knowledge may also be crucial for restoration purposes, especially regarding the need to consider endophyte viability in ex situ seed collection and storage in seed-banking practices.
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Affiliation(s)
- Merize Philpott
- Centre for Sustainable Ecosystems Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Edward C Y Liew
- Research Centre for Ecosystem Resilience, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW 2000, Australia
| | - Marlien M van der Merwe
- Research Centre for Ecosystem Resilience, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW 2000, Australia
| | - Allison Mertin
- Research Centre for Ecosystem Resilience, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW 2000, Australia
| | - Kristine French
- Centre for Sustainable Ecosystems Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
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Whitehead J, Roy J, Hempel S, Rillig MC. Soil microbial communities shift along an urban gradient in Berlin, Germany. Front Microbiol 2022; 13:972052. [PMID: 36033838 PMCID: PMC9412169 DOI: 10.3389/fmicb.2022.972052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
The microbial communities inhabiting urban soils determine the functioning of these soils, in regards to their ability to cycle nutrients and support plant communities. In an increasingly urbanized world these properties are of the utmost importance, and the microbial communities responsible are worthy of exploration. We used 53 grassland sites spread across Berlin to describe and explain the impacts of urbanity and other environmental parameters upon the diversity and community composition of four microbial groups. These groups were (i) the Fungi, with a separate dataset for (ii) the Glomeromycota, (iii) the Bacteria, and (iv) the protist phylum Cercozoa. We found that urbanity had distinct impacts on fungal richness, which tended to increase. Geographic distance between sites and soil chemistry, in addition to urbanity, drove microbial community composition, with site connectivity being important for Glomeromycotan communities, potentially due to plant host communities. Our findings suggest that many microbial species are well adapted to urban soils, as supported by an increase in diversity being a far more common result of urbanity than the reverse. However, we also found distinctly separate distributions of operational taxonomic unit (OTU)s from the same species, shedding doubt of the reliability of indicator species, and the use of taxonomy to draw conclusion on functionality. Our observational study employed an extensive set of sites across an urbanity gradient, in the region of the German capital, to produce a rich microbial dataset; as such it can serve as a blueprint for other such investigations.
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Affiliation(s)
- James Whitehead
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Julien Roy
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Stefan Hempel
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Matthias C. Rillig
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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SIMONS ARIELLEVI, CALDWELL STEVIE, FU MICHELLE, GALLEGOS JOSE, GATHERU MICHAEL, RICCARDELLI LAURA, TRUONG NHI, VIERA VALERIA. Constructing ecological indices for urban environments using species distribution models. Urban Ecosyst 2022. [DOI: 10.1007/s11252-022-01265-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
AbstractIn an increasingly urbanized world, there is a need to study urban areas as their own class of ecosystems as well as assess the impacts of anthropogenic impacts on biodiversity. However, collecting a sufficient number of species observations to estimate patterns of biodiversity in a city can be costly. Here we investigated the use of community science-based data on species occurrences, combined with species distribution models (SDMs), built using MaxEnt and remotely-sensed measures of the environment, to predict the distribution of a number of species across the urban environment of Los Angeles. By selecting species with the most accurate SDMs, and then summarizing these by class, we were able to produce two species richness models (SRMs) to predict biodiversity patterns for species in the class Aves and Magnoliopsida and how they respond to a variety of natural and anthropogenic environmental gradients.We found that species considered native to Los Angeles tend to have significantly more accurate SDMs than their non-native counterparts. For all species considered in this study we found environmental variables describing anthropogenic activities, such as housing density and alterations to land cover, tend to be more influential than natural factors, such as terrain and proximity to freshwater, in shaping SDMs. Using a random forest model we found our SRMs could account for approximately 54% and 62% of the predicted variation in species richness for species in the classes Aves and Magnoliopsida respectively. Using community science-based species occurrences, SRMs can be used to model patterns of urban biodiversity and assess the roles of environmental factors in shaping them.
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