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Scholz C, Jarquín-Díaz VH, Planillo A, Radchuk V, Scherer C, Schulze C, Ortmann S, Kramer-Schadt S, Heitlinger E. Host weight, seasonality and anthropogenic factors contribute to parasite community differences between urban and rural foxes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 936:173355. [PMID: 38796016 DOI: 10.1016/j.scitotenv.2024.173355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
Pathogens often occur at different prevalence along environmental gradients. This is of particular importance for gradients of anthropogenic impact such as rural-urban transitions presenting a changing interface between humans and wildlife. The assembly of parasite communities is affected by both the external environmental conditions and individual host characteristics. Hosts with low body weight (smaller individuals or animals with poor body condition) might be more susceptible to infection. Furthermore, parasites' mode of transmission might affect their occurrence: rural environments with better availability of intermediate hosts might favour trophic transmission, while urban environments, typically with dense definitive host populations, might favour direct transmission. We here study helminth communities (141 intestinal samples) within the red fox (Vulpes vulpes), a synanthropic host, using DNA metabarcoding of multiple marker genes. We analysed the effect of urbanisation, seasonality and host-intrinsic (weight, sex) variables on helminth communities. Helminth species richness increased in foxes with lower body weight and in winter and spring. Season and urbanisation, however, had strong effects on the community composition, i.e., on the identity of the detected species. Surprisingly, transmission in two-host life cycles (trophic transmission) was more pronounced in urban Berlin than in rural Brandenburg. This disagrees with the prevailing hypothesis that trophically transmitted helminths are less prevalent in urban areas than in rural areas. Generally, co-infestations with multiple helminths and high infection intensity are associated with lighter (younger, smaller or low body condition) animals. Both host-intrinsic traits and environmental drivers together shape parasite community composition and turnover along urban-rural gradients.
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Affiliation(s)
- Carolin Scholz
- Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany
| | - Víctor Hugo Jarquín-Díaz
- Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany; Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin (HU), Berlin, Germany; Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Aimara Planillo
- Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Viktoriia Radchuk
- Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany
| | - Cédric Scherer
- Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany
| | - Christoph Schulze
- Berlin-Brandenburg State Laboratory (LLBB), Frankfurt (Oder), Germany
| | - Sylvia Ortmann
- Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany
| | - Stephanie Kramer-Schadt
- Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany; Institute of Ecology, Technische Universität Berlin, Germany
| | - Emanuel Heitlinger
- Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany; Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin (HU), Berlin, Germany.
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Bonfim FCG, Galetti M, Benchimol M, Morante-Filho JC, Magioli M, Cazetta E. Land-use homogenization reduces the occurrence and diversity of frugivorous birds in a tropical biodiversity hotspot. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e2980. [PMID: 38725332 DOI: 10.1002/eap.2980] [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: 01/20/2023] [Revised: 01/04/2024] [Accepted: 03/08/2024] [Indexed: 06/04/2024]
Abstract
Understanding how human-modified landscapes maintain biodiversity and provide ecosystem services is crucial for establishing conservation practices. Given that responses to land-use are species-specific, it is crucial to understand how land-use changes may shape patterns of species diversity and persistence in human-modified landscapes. Here, we used a comprehensive data set on bird distribution from the Brazilian Atlantic Forest to understand how species richness and individual occurrences of frugivorous bird species responded to land-use spatial predictors and, subsequently, assess how ecological traits and phylogeny modulated these responses. Using Bayesian hierarchical modeling, we reveal that the richness of frugivorous birds was positively associated with the amount of native forest and negatively with both agriculture and pasture amount at the landscape scale. Conversely, the effect of these predictors on species occurrence and ecological traits was highly variable and presented a weak phylogenetic signal. Furthermore, land-use homogenization (i.e., the conversion of forest to pasture or agriculture) led to pervasive consequences for forest-dependent bird species, whereas several generalist species thrived in deforested areas, replacing those sensitive to habitat disturbances.
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Affiliation(s)
- Fernando César Gonçalves Bonfim
- Postgraduate Program in Ecology and Biodiversity Conservation, Applied Ecology and Conservation Lab, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Mauro Galetti
- Instituto de Biociências, Departamento de Biodiversidade, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Maíra Benchimol
- Postgraduate Program in Ecology and Biodiversity Conservation, Applied Ecology and Conservation Lab, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - José Carlos Morante-Filho
- Postgraduate Program in Ecology and Biodiversity Conservation, Applied Ecology and Conservation Lab, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Marcelo Magioli
- Instituto Pró-Carnívoros, Atibaia, Brazil
- Centro Nacional de Pesquisa e Conservação de Mamíferos Carnívoros (CENAP), Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Atibaia, Brazil
- Laboratório de Ecologia e Conservação (LAEC), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Eliana Cazetta
- Postgraduate Program in Ecology and Biodiversity Conservation, Applied Ecology and Conservation Lab, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
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3
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Ovaskainen O, Abrego N, Furneaux B, Hardwick B, Somervuo P, Palorinne I, Andrew NR, Babiy UV, Bao T, Bazzano G, Bondarchuk SN, Bonebrake TC, Brennan GL, Bret-Harte S, Bässler C, Cagnolo L, Cameron EK, Chapurlat E, Creer S, D'Acqui LP, de Vere N, Desprez-Loustau ML, Dongmo MAK, Dyrholm Jacobsen IB, Fisher BL, Flores de Jesus M, Gilbert GS, Griffith GW, Gritsuk AA, Gross A, Grudd H, Halme P, Hanna R, Hansen J, Hansen LH, Hegbe ADMT, Hill S, Hogg ID, Hultman J, Hyde KD, Hynson NA, Ivanova N, Karisto P, Kerdraon D, Knorre A, Krisai-Greilhuber I, Kurhinen J, Kuzmina M, Lecomte N, Lecomte E, Loaiza V, Lundin E, Meire A, Mešić A, Miettinen O, Monkhause N, Mortimer P, Müller J, Nilsson RH, Nonti PYC, Nordén J, Nordén B, Paz C, Pellikka P, Pereira D, Petch G, Pitkänen JM, Popa F, Potter C, Purhonen J, Pätsi S, Rafiq A, Raharinjanahary D, Rakos N, Rathnayaka AR, Raundrup K, Rebriev YA, Rikkinen J, Rogers HMK, Rogovsky A, Rozhkov Y, Runnel K, Saarto A, Savchenko A, Schlegel M, Schmidt NM, Seibold S, Skjøth C, Stengel E, Sutyrina SV, Syvänperä I, Tedersoo L, Timm J, Tipton L, Toju H, Uscka-Perzanowska M, van der Bank M, Herman van der Bank F, Vandenbrink B, Ventura S, Vignisson SR, Wang X, Weisser WW, Wijesinghe SN, Joseph Wright S, Yang C, Yorou NS, Young A, Yu DW, Zakharov EV, Hebert PDN, Roslin T. Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA. Sci Data 2024; 11:561. [PMID: 38816458 PMCID: PMC11139991 DOI: 10.1038/s41597-024-03410-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024] Open
Abstract
Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition.
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Affiliation(s)
- Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland.
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P. O. Box 65, 00014, Helsinki, Finland.
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, N-7491, Norway.
| | - Nerea Abrego
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, FI-00014, Helsinki, Finland
| | - Brendan Furneaux
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
| | - Bess Hardwick
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, FI-00014, Helsinki, Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P. O. Box 65, 00014, Helsinki, Finland
| | - Isabella Palorinne
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, FI-00014, Helsinki, Finland
| | - Nigel R Andrew
- Natural History Museum, Zoology, University of New England, Armidale, NSW, 2351, Australia
- Faculty of Science and Engineering, Southern Cross University, Northern Rivers, NSW, 2480, Australia
| | | | - Tan Bao
- Department of Biological Sciences, MacEwan University, 10, 700 - 104 Avenue, Edmonton, AB, T5J 2P2, Canada
| | - Gisela Bazzano
- Universidad Nacional de Còrdoba, Facultad de Ciencias Exactas Físicas y Naturales, Centro de Zoología Aplicada, Córdoba, Argentina
| | - Svetlana N Bondarchuk
- Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov, 44 Partizanskaya Str., Terney, Primorsky krai, 692150, Russia
| | - Timothy C Bonebrake
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Georgina L Brennan
- CSIC, Institute of Marine Sciences, Passeig Marítim de la Barceloneta, 37-49ES08003, Barcelona, Spain
| | | | - Claus Bässler
- Goethe-University Frankfurt, Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Conservation Biology, D- 60438, Frankfurt am Main, Germany
- Bavarian Forest National Park, Freyunger Str. 2, D-94481, Grafenau, Germany
- Ecology of Fungi, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstraße 30, 95440, Bayreuth, Germany
| | - Luciano Cagnolo
- Consejo de Investigaciones Científicas y Técnicas (CONICET), Instituto Multidisciplinario de Biología Vegetal, Córdoba, Argentina
| | - Erin K Cameron
- Department of Environmental Science, Saint Mary's University, 923 Robie St., Halifax, NS, B3H 3C3, Canada
| | - Elodie Chapurlat
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Simon Creer
- Molecular Ecology and Evolution at Bangor (MEEB), School of Environmental and Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd, Wales, LL57 2UW, UK
| | - Luigi P D'Acqui
- Research Institute on Terrestrial Ecosystems - IRET, National Research Council - CNR, Via Madonna del Piano n° 10, 50019, Sesto Fiorentino, Firenze, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Gothersgade 130, 1123, København K, Denmark
| | | | - Michel A K Dongmo
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
- International Institute of Tropical Agriculture (IITA), P.O. Box 2008 (Messa), Yaoundé, Cameroon
| | | | - Brian L Fisher
- Entomology, 55 Music Concourse Drive, California Academy of Sciences, San Francisco, CA, 94118, USA
- Madagascar Biodiversity Center, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, 101, Madagascar
| | | | - Gregory S Gilbert
- Environmental Studies Department, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA, 95065, USA
| | - Gareth W Griffith
- Department of Life Sciences, Aberystwyth University, Aberystwyth, Ceredigion, WALES SY23 3DD, UK
| | - Anna A Gritsuk
- Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov, 44 Partizanskaya Str., Terney, Primorsky krai, 692150, Russia
| | - Andrin Gross
- Research Unit Biodiversity and Conservation Biology, SwissFungi, Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Håkan Grudd
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Vetenskapens väg 38, SE-981 07, Abisko, Sweden
| | - Panu Halme
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
| | - Rachid Hanna
- Center for Tropical Research, Congo Basin Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
| | - Jannik Hansen
- Department of Ecoscience, Aarhus University, Dk-4000, Roskilde, Denmark
| | - Lars Holst Hansen
- Department of Ecoscience, Aarhus University, Dk-4000, Roskilde, Denmark
| | - Apollon D M T Hegbe
- Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, BP 123, Parakou, Republic of Benin
| | - Sarah Hill
- Natural History Museum, Zoology, University of New England, Armidale, NSW, 2351, Australia
| | - Ian D Hogg
- Canadian High Arctic Research Station, Polar Knowledge Canada, PO Box 2150, 1 Uvajuq Road, Cambridge Bay, Nunavut, X0B 0C0, Canada
- Department of Integrative Biology, College of Biological Science, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
- School of Science, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014, Helsinki, Finland
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Nicole A Hynson
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Natalia Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Nature Metrics North America Ltd., 590 Hanlon Creek Boulevard, Unit 11, Guelph, ON, N1C 0A1, Canada
| | - Petteri Karisto
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Plant Health, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Deirdre Kerdraon
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Anastasia Knorre
- Science Department, National Park Krasnoyarsk Stolby, 26a Kariernaya str., 660006, Krasnoyarsk, Russia
- Institute of Ecology and Geography, Siberian Federal University, 79 Svobodny pr., 660041, Krasnoyarsk, Russia
| | - Irmgard Krisai-Greilhuber
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Wien, Austria
| | - Juri Kurhinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P. O. Box 65, 00014, Helsinki, Finland
| | - Masha Kuzmina
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Nicolas Lecomte
- Centre d'études nordiques and Canada Research Chair in Polar and Boreal Ecology, Department of Biology, Pavillon Rémi-Rossignol, 18, Antonine-Maillet, Université de Moncton, Moncton, NB, E1A 3E9, Canada
| | - Erin Lecomte
- Centre d'études nordiques and Canada Research Chair in Polar and Boreal Ecology, Department of Biology, Pavillon Rémi-Rossignol, 18, Antonine-Maillet, Université de Moncton, Moncton, NB, E1A 3E9, Canada
| | - Viviana Loaiza
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
| | - Erik Lundin
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Vetenskapens väg 38, SE-981 07, Abisko, Sweden
| | - Alexander Meire
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Vetenskapens väg 38, SE-981 07, Abisko, Sweden
| | - Armin Mešić
- Laboratory for Biological Diversity, Rudjer Boskovic Institute, Bijenicka cesta 54, HR-10000, Zagreb, Croatia
| | - Otto Miettinen
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014, Helsinki, Finland
| | - Norman Monkhause
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Peter Mortimer
- Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology (Zoology III), Julius Maximilians University Würzburg, Rauhenebrach, Germany
- Bavarian Forest National Park, Grafenau, Germany
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 405 30, Göteborg, Sweden
| | - Puani Yannick C Nonti
- Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, BP 123, Parakou, Republic of Benin
| | - Jenni Nordén
- Norwegian Institute for Nature Research (NINA), Sognsveien 68, N-0855, Oslo, Norway
| | - Björn Nordén
- Norwegian Institute for Nature Research (NINA), Sognsveien 68, N-0855, Oslo, Norway
| | - Claudia Paz
- Department of Biodiversity, Institute of Biosciences, São Paulo State University, Av 24A 1515, Rio Claro, SP, 13506-900, Brazil
- Department of Entomology and Acarology, Laboratory of Pathology and Microbial Control, University of São Paulo, CEP 13418-900, Piracicaba, SP, Brazil
| | - Petri Pellikka
- Department of Geosciences and Geography, Faculty of Science, University of Helsinki, P.O. Box 64, 00014, Helsinki, Finland
- State Key Laboratory for Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, 430079, China
- Wangari Maathai Institute for Environmental and Peace Studies, University of Nairobi, P.O. Box 29053, 00625, Kangemi, Kenya
| | - Danilo Pereira
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
| | - Geoff Petch
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester, WR2 6AJ, UK
| | - Juha-Matti Pitkänen
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Flavius Popa
- Department of Ecosystem Monitoring, Research & Conservation, Black Forest National Park, Kniebisstraße 67, 77740, Bad Peterstal-Griesbach, Germany
| | - Caitlin Potter
- Department of Life Sciences, Aberystwyth University, Aberystwyth, Ceredigion, WALES SY23 3DD, UK
| | - Jenna Purhonen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
- School of Resource Wisdom, University of Jyväskylä, P.O. Box 35, FIN-40014, Jyväskylä, Finland
| | - Sanna Pätsi
- The Biodiversity Unit of the University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Abdullah Rafiq
- Molecular Ecology and Evolution at Bangor (MEEB), School of Environmental and Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd, Wales, LL57 2UW, UK
| | - Dimby Raharinjanahary
- Madagascar Biodiversity Center, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, 101, Madagascar
| | - Niklas Rakos
- Swedish Polar Research Secretariat, Abisko Scientific Research Station, Vetenskapens väg 38, SE-981 07, Abisko, Sweden
| | - Achala R Rathnayaka
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Katrine Raundrup
- Greenland Institute of Natural Resources, Kivioq 2, P.O. Box 570, 3900, Nuuk, Greenland
| | - Yury A Rebriev
- Southern Scientific Center of the Russian Academy of Sciences, 41 Chekhov ave., Rostov-on-Don, 344006, Russia
| | - Jouko Rikkinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P. O. Box 65, 00014, Helsinki, Finland
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014, Helsinki, Finland
| | - Hanna M K Rogers
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Andrey Rogovsky
- Science Department, National Park Krasnoyarsk Stolby, 26a Kariernaya str., 660006, Krasnoyarsk, Russia
| | - Yuri Rozhkov
- State Nature Reserve Olekminsky, Olekminsk, Russian Federation, Russia
| | - Kadri Runnel
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409, Tartu, Estonia
| | - Annika Saarto
- The Biodiversity Unit of the University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Anton Savchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409, Tartu, Estonia
| | - Markus Schlegel
- Research Unit Biodiversity and Conservation Biology, SwissFungi, Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Niels Martin Schmidt
- Department of Ecoscience, Aarhus University, Dk-4000, Roskilde, Denmark
- Arctic Research Center, Aarhus University, Dk-4000, Roskilde, Denmark
| | - Sebastian Seibold
- TUD Dresden University of Technology, Forest Zoology, Pienner Str. 7, 01737, Tharandt, Germany
- Technical University of Munich, Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - Carsten Skjøth
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester, WR2 6AJ, UK
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000, Roskilde, Denmark
| | - Elisa Stengel
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology (Zoology III), Julius Maximilians University Würzburg, Rauhenebrach, Germany
| | - Svetlana V Sutyrina
- Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov, 44 Partizanskaya Str., Terney, Primorsky krai, 692150, Russia
| | - Ilkka Syvänperä
- The Biodiversity Unit of the University of Turku, Kevontie 470, 99980, Utsjoki, Finland
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Jebidiah Timm
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA
| | - Laura Tipton
- School of Natural Science and Mathematics, Chaminade University of Honolulu, Honolulu, HI, USA
| | - Hirokazu Toju
- Laboratory of Ecosystems and Coevolution, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
- Center for Living Systems Information Science (CeLiSIS), Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | | | - Michelle van der Bank
- African Centre for DNA Barcoding (ACDB), University of Johannesburg, PO BOX 524, Auckland Park, 2006, South Africa
| | - F Herman van der Bank
- African Centre for DNA Barcoding (ACDB), University of Johannesburg, PO BOX 524, Auckland Park, 2006, South Africa
| | - Bryan Vandenbrink
- Canadian High Arctic Research Station, Polar Knowledge Canada, PO Box 2150, 1 Uvajuq Road, Cambridge Bay, Nunavut, X0B 0C0, Canada
| | - Stefano Ventura
- Research Institute on Terrestrial Ecosystems - IRET, National Research Council - CNR, Via Madonna del Piano n° 10, 50019, Sesto Fiorentino, Firenze, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Solvi R Vignisson
- Sudurnes Science and Learning Center, Garðvegi 1, 245, Sandgerði, Iceland
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wolfgang W Weisser
- Technical University of Munich, Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - Subodini N Wijesinghe
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Panama
| | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Nourou S Yorou
- Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, BP 123, Parakou, Republic of Benin
| | - Amanda Young
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Paul D N Hebert
- Canadian High Arctic Research Station, Polar Knowledge Canada, PO Box 2150, 1 Uvajuq Road, Cambridge Bay, Nunavut, X0B 0C0, Canada
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Tomas Roslin
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P. O. Box 65, 00014, Helsinki, Finland
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
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4
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Liu C, Van Meerbeek K. Predicting the responses of European grassland communities to climate and land cover change. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230335. [PMID: 38583469 PMCID: PMC10999271 DOI: 10.1098/rstb.2023.0335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/27/2024] [Indexed: 04/09/2024] Open
Abstract
European grasslands are among the most species-rich ecosystems on small spatial scales. However, human-induced activities like land use and climate change pose significant threats to this diversity. To explore how climate and land cover change will affect biodiversity and community composition in grassland ecosystems, we conducted joint species distribution models (SDMs) on the extensive vegetation-plot database sPlotOpen to project distributions of 1178 grassland species across Europe under current conditions and three future scenarios. We further compared model accuracy and computational efficiency between joint SDMs (JSDMs) and stacked SDMs, especially for rare species. Our results show that: (i) grassland communities in the mountain ranges are expected to suffer high rates of species loss, while those in western, northern and eastern Europe will experience substantial turnover; (ii) scaling anomalies were observed in the predicted species richness, reflecting regional differences in the dominant drivers of assembly processes; (iii) JSDMs did not outperform stacked SDMs in predictive power but demonstrated superior efficiency in model fitting and predicting; and (iv) incorporating co-occurrence datasets improved the model performance in predicting the distribution of rare species. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.
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Affiliation(s)
- Chang Liu
- Department of Earth and Environmental Sciences, KU Leuven, Leuven, Flanders 3001, Belgium
| | - Koenraad Van Meerbeek
- Department of Earth and Environmental Sciences, KU Leuven, Leuven, Flanders 3001, Belgium
- KU Leuven Plant Institute, Leuven, Flanders, Belgium
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5
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Parmentier T, Bonte D, De Laender F. A successional shift enhances stability in ant symbiont communities. Commun Biol 2024; 7:645. [PMID: 38802499 PMCID: PMC11130137 DOI: 10.1038/s42003-024-06305-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024] Open
Abstract
Throughout succession, communities undergo structural shifts, which can alter the relative abundances of species and how they interact. It is frequently asserted that these alterations beget stability, i.e. that succession selects for communities better able to resist perturbations. Yet, whether and how alterations of network structure affect stability during succession in complex communities is rarely studied in natural ecosystems. Here, we explore how network attributes influence stability of different successional stages of a natural network: symbiotic arthropod communities forming food webs inside red wood ant nests. We determined the abundance of 16 functional groups within the symbiont community across 51 host nests in the beginning and end stages of succession. Nest age was the main driver of the compositional shifts: symbiont communities in old nests contained more even species abundance distributions and a greater proportion of specialists. Based on the abundance data, we reconstructed interaction matrices and food webs of the symbiont community for each nest. We showed that the enhanced community evenness in old nests leads to an augmented food web stability in all but the largest symbiont communities. Overall, this study demonstrates that succession begets stability in a natural ecological network by making the community more even.
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Affiliation(s)
- Thomas Parmentier
- Terrestrial Ecology Unit, Department of Biology, University of Ghent, Ghent, Belgium.
- Research Unit of Environmental and Evolutionary Biology, naXys, ILEE, University of Namur, Namur, Belgium.
| | - Dries Bonte
- Terrestrial Ecology Unit, Department of Biology, University of Ghent, Ghent, Belgium
| | - Frederik De Laender
- Research Unit of Environmental and Evolutionary Biology, naXys, ILEE, University of Namur, Namur, Belgium
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6
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Larouche JD, Laumont CM, Trofimov A, Vincent K, Hesnard L, Brochu S, Côté C, Humeau JF, Bonneil É, Lanoix J, Durette C, Gendron P, Laverdure JP, Richie ER, Lemieux S, Thibault P, Perreault C. Transposable elements regulate thymus development and function. eLife 2024; 12:RP91037. [PMID: 38635416 PMCID: PMC11026094 DOI: 10.7554/elife.91037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Transposable elements (TEs) are repetitive sequences representing ~45% of the human and mouse genomes and are highly expressed by medullary thymic epithelial cells (mTECs). In this study, we investigated the role of TEs on T-cell development in the thymus. We performed multiomic analyses of TEs in human and mouse thymic cells to elucidate their role in T-cell development. We report that TE expression in the human thymus is high and shows extensive age- and cell lineage-related variations. TE expression correlates with multiple transcription factors in all cell types of the human thymus. Two cell types express particularly broad TE repertoires: mTECs and plasmacytoid dendritic cells (pDCs). In mTECs, transcriptomic data suggest that TEs interact with transcription factors essential for mTEC development and function (e.g., PAX1 and REL), and immunopeptidomic data showed that TEs generate MHC-I-associated peptides implicated in thymocyte education. Notably, AIRE, FEZF2, and CHD4 regulate small yet non-redundant sets of TEs in murine mTECs. Human thymic pDCs homogenously express large numbers of TEs that likely form dsRNA, which can activate innate immune receptors, potentially explaining why thymic pDCs constitutively secrete IFN ɑ/β. This study highlights the diversity of interactions between TEs and the adaptive immune system. TEs are genetic parasites, and the two thymic cell types most affected by TEs (mTEcs and pDCs) are essential to establishing central T-cell tolerance. Therefore, we propose that orchestrating TE expression in thymic cells is critical to prevent autoimmunity in vertebrates.
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Affiliation(s)
- Jean-David Larouche
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Medicine, Université de MontréalMontréalCanada
| | - Céline M Laumont
- Deeley Research Centre, BC CancerVictoriaCanada
- Department of Medical Genetics, University of British ColumbiaVancouverCanada
| | - Assya Trofimov
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Computer Science and Operations Research, Université de MontréalMontréalCanada
- Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Physics, University of WashingtonSeattleUnited States
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Leslie Hesnard
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Sylvie Brochu
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Caroline Côté
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Juliette F Humeau
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Joel Lanoix
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | | | - Ellen R Richie
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M.D. Anderson Cancer CenterHoustonUnited States
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Biochemistry and Molecular Medicine, Université de MontréalMontrealCanada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Chemistry, Université de MontréalMontréalCanada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Medicine, Université de MontréalMontréalCanada
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7
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Tennakoon S, Apan A, Maraseni T. Unravelling the impact of climate change on honey bees: An ensemble modelling approach to predict shifts in habitat suitability in Queensland, Australia. Ecol Evol 2024; 14:e11300. [PMID: 38638367 PMCID: PMC11024685 DOI: 10.1002/ece3.11300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 03/30/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024] Open
Abstract
Honey bees play a vital role in providing essential ecosystem services and contributing to global agriculture. However, the potential effect of climate change on honey bee distribution is still not well understood. This study aims to identify the most influential bioclimatic and environmental variables, assess their impact on honey bee distribution, and predict future distribution. An ensemble modelling approach using the biomod2 package in R was employed to develop three models: a climate-only model, an environment-only model, and a combined climate and environment model. By utilising bioclimatic data (radiation of the wettest and driest quarters and temperature seasonality) from 1990 to 2009, combined with observed honey bee presence and pseudo absence data, this model predicted suitable locations for honey bee apiaries for two future time spans: 2020-2039 and 2060-2079. The climate-only model exhibited a true skill statistic (TSS) value of 0.85, underscoring the pivotal role of radiation and temperature seasonality in shaping honey bee distribution. The environment-only model, incorporating proximity to floral resources, foliage projective cover, and elevation, demonstrated strong predictive performance, with a TSS of 0.88, emphasising the significance of environmental variables in determining habitat suitability for honey bees. The combined model had a higher TSS of 0.96, indicating that the combination of climate and environmental variables enhances the model's performance. By the 2020-2039 period, approximately 88% of highly suitable habitats for honey bees are projected to transition from their current state to become moderate (14.84%) to marginally suitable (13.46%) areas. Predictions for the 2060-2079 period reveal a concerning trend: 100% of highly suitable land transitions into moderately (0.54%), marginally (17.56%), or not suitable areas (81.9%) for honey bees. These results emphasise the critical need for targeted conservation efforts and the implementation of policies aimed at safeguarding honey bees and the vital apiary industry.
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Affiliation(s)
- Sarasie Tennakoon
- School of Surveying and Built EnvironmentUniversity of Southern QueenslandToowoombaQueenslandAustralia
| | - Armando Apan
- School of Surveying and Built EnvironmentUniversity of Southern QueenslandToowoombaQueenslandAustralia
- Institute of Environmental Science and MeteorologyUniversity of the Philippines DilimanQuezon CityPhilippines
| | - Tek Maraseni
- Institute for Life Sciences and the EnvironmentUniversity of Southern QueenslandToowoombaQueenslandAustralia
- Chinese Academy of SciencesNorthwest Institute of Eco‐Environment and ResourcesLanzhouChina
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8
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Daouti E, Neidel V, Carbonne B, Vašková H, Traugott M, Wallinger C, Bommarco R, Feit B, Bohan DA, Saska P, Skuhrovec J, Vasconcelos S, Petit S, van der Werf W, Jonsson M. Functional redundancy of weed seed predation is reduced by intensified agriculture. Ecol Lett 2024; 27:e14411. [PMID: 38577993 DOI: 10.1111/ele.14411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 01/19/2024] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
Intensified agriculture, a driver of biodiversity loss, can diminish ecosystem functions and their stability. Biodiversity can increase functional redundancy and is expected to stabilize ecosystem functions. Few studies, however, have explored how agricultural intensity affects functional redundancy and its link with ecosystem function stability. Here, within a continental-wide study, we assess how functional redundancy of seed predation is affected by agricultural intensity and landscape simplification. By combining carabid abundances with molecular gut content data, functional redundancy of seed predation was quantified for 65 weed genera across 60 fields in four European countries. Across weed genera, functional redundancy was reduced with high field management intensity and simplified crop rotations. Moreover, functional redundancy increased the spatial stability of weed seed predation at the field scale. We found that ecosystem functions are vulnerable to disturbances in intensively managed agroecosystems, providing empirical evidence of the importance of biodiversity for stable ecosystem functions across space.
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Affiliation(s)
- Eirini Daouti
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Veronika Neidel
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | | | - Hana Vašková
- Functional Diversity in Agro-Ecosystems, Crop Research Institute, Praha 6, Ruzyně, Czech Republic
| | - Michael Traugott
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Corinna Wallinger
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Riccardo Bommarco
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Benjamin Feit
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - David A Bohan
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne Franche-Comté, Dijon, France
| | - Pavel Saska
- Functional Diversity in Agro-Ecosystems, Crop Research Institute, Praha 6, Ruzyně, Czech Republic
| | - Jiří Skuhrovec
- Functional Diversity in Agro-Ecosystems, Crop Research Institute, Praha 6, Ruzyně, Czech Republic
| | - Sasha Vasconcelos
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sandrine Petit
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne Franche-Comté, Dijon, France
| | - Wopke van der Werf
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Mattias Jonsson
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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9
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Martini F, Kounnamas C, Goodale E, Mammides C. Examining the co-occurrences of human threats within terrestrial protected areas. AMBIO 2024; 53:592-603. [PMID: 38273093 PMCID: PMC10920590 DOI: 10.1007/s13280-023-01966-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/02/2023] [Accepted: 11/23/2023] [Indexed: 01/27/2024]
Abstract
Human threats to biodiversity are prevalent within protected areas (PAs), undermining their effectiveness in halting biodiversity loss. Certain threats tend to co-occur, resulting in amplified cumulative impact through synergistic effects. However, it remains unclear which threats are related the most. We analyzed a dataset of 71 human threats in 18 013 terrestrial PAs of the European Union's Natura 2000 network, using a Joint Species Distribution Modelling approach, to assess the threats' co-occurrence patterns and potential drivers. Overall, threats were more frequently correlated positively than negatively. Threats related to agriculture and urbanization were correlated strongly with most other threats. Approximately 70% of the variance in our model was explained by country-specific factors, indicating the importance of local drivers. Minimizing the negative impact of key threats can likely reduce the impact of related threats. However, more research is needed to understand better the relationships among threats and, importantly, their combined impact on biodiversity.
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Affiliation(s)
- Francesco Martini
- Botany Department, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland.
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic.
| | - Constantinos Kounnamas
- Nature Conservation Unit, Frederick University, 7, Yianni Frederickou Street, Pallouriotissa, 1036, Nicosia, Cyprus
| | - Eben Goodale
- Department of Health and Environmental Science, Xi'an Jiaotong Liverpool University, 8 Chongwen Road, Suzhou Industrial Park, Suzhou, 215123, Jiangsu, China
| | - Christos Mammides
- Nature Conservation Unit, Frederick University, 7, Yianni Frederickou Street, Pallouriotissa, 1036, Nicosia, Cyprus
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10
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Contos P, Murphy NP, Kayll ZJ, Morgan T, Vido JJ, Decker O, Gibb H. Rewilding soil and litter invertebrates and fungi increases decomposition rates and alters detritivore communities. Ecol Evol 2024; 14:e11128. [PMID: 38469050 PMCID: PMC10925487 DOI: 10.1002/ece3.11128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/16/2023] [Accepted: 02/28/2024] [Indexed: 03/13/2024] Open
Abstract
Habitat degradation and associated reductions in ecosystem functions can be reversed by reintroducing or 'rewilding' keystone species. Rewilding projects have historically targeted restoration of processes such as grazing regimes or top-down predation effects. Few projects focus on restoring decomposition efficiency, despite the pivotal role decomposition plays in global carbon sequestration and nutrient cycling. Here, we tested whether rewilding entire communities of detritivorous invertebrates and fungi can improve litter decomposition efficiency and restore detritivore communities during ecological restoration. Rewilding was conducted by transplanting leaf litter and soil, including associated invertebrate and fungal communities from species-rich remnant sites into species-poor, and geographically isolated, revegetated farmland sites in a temperate woodland region of southeastern Australia. We compared communities in sites under the following treatments: remnant (conservation area and source of litter transplant), rewilded revegetation (revegetated farmland site with litter transplant) and control revegetation (revegetated site, no transplant). In one 'before' and three 'after' sampling periods, we measured litter decomposition and the abundance and diversity of detritivorous invertebrates and fungi. We quantified the effect of detritivores on the rate of litter decomposition using piecewise Structural Equation Modelling. Decomposition was significantly faster in rewilding sites than in both control and remnant areas and was largely driven by a greater abundance of invertebrate detritivores. Similarly, the abundance of invertebrate detritivores in rewilding revegetation sites exceeded the level of remnant communities, whereas there was little difference between control and remnant sites. In contrast, rewilding did not increase saprotrophic fungi relative abundance/diversity and there was no strong relationship between decomposition and fungal diversity. Our findings suggest the relatively simple act of transplanting leaf litter and soil can increase functional efficiency during restoration and alter community composition. Our methods may prove important across a range of contexts where other restoration methods have failed to restore ecosystem processes to pre-degradation levels.
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Affiliation(s)
- Peter Contos
- Department of Environment and Genetics, Centre for Future Landscapes, School of Agriculture, Biomedicine, and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
| | - Nicholas P. Murphy
- Department of Environment and Genetics, Centre for Future Landscapes, School of Agriculture, Biomedicine, and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
| | - Zachary J. Kayll
- Department of Environment and Genetics, Centre for Future Landscapes, School of Agriculture, Biomedicine, and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
| | - Tamara Morgan
- Department of Environment and Genetics, Centre for Future Landscapes, School of Agriculture, Biomedicine, and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
| | - Joshua J. Vido
- Department of Environment and Genetics, Centre for Future Landscapes, School of Agriculture, Biomedicine, and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine, and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
| | - Orsi Decker
- Department of Environment and Genetics, Centre for Future Landscapes, School of Agriculture, Biomedicine, and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
- Bavarian Forest National ParkNature Conservation and ResearchGrafenauGermany
| | - Heloise Gibb
- Department of Environment and Genetics, Centre for Future Landscapes, School of Agriculture, Biomedicine, and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
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11
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Röder N, Stoll VS, Jupke JF, Kolbenschlag S, Bundschuh M, Theißinger K, Schwenk K. How non-target chironomid communities respond to mosquito control: Integrating DNA metabarcoding and joint species distribution modelling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169735. [PMID: 38163597 DOI: 10.1016/j.scitotenv.2023.169735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/26/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The conservation and management of riparian ecosystems rely on understanding the ecological consequences of anthropogenic stressors that impact natural communities. In this context, studies investigating the effects of anthropogenic stressors require reliable methods capable of mapping the relationships between taxa occurrence or abundance and environmental predictors within a spatio-temporal framework. Here, we present an integrative approach using DNA metabarcoding and Hierarchical Modelling of Species Communities (HMSC) to unravel the intricate dynamics and resilience of chironomid communities exposed to Bacillus thuringiensis var. israelensis (Bti). Chironomid emergence was sampled from a total of 12 floodplain pond mesocosms, half of which received Bti treatment, during a 16-week period spanning spring and summer of 2020. Subsequently, we determined the community compositions of chironomids and examined their genus-specific responses to the Bti treatment, considering their phylogenetic affiliations and ecological traits of the larvae. Additionally, we investigated the impact of the Bti treatment on the body size distribution of emerging chironomids. Our study revealed consistent responses to Bti among different chironomid genera, indicating that neither phylogenetic affiliations nor larval feeding strategies significantly contributed to the observed patterns. Both taxonomic and genetic diversity were positively correlated with the number of emerged individuals. Furthermore, our findings demonstrated Bti-related effects on chironomid body size distribution, which could have relevant implications for size-selective terrestrial predators. Hence, our study highlights the value of employing a combination of DNA metabarcoding and HMSC to unravel the complex dynamics of Bti-related non-target effects on chironomid communities. The insights gained from this integrated framework contribute to our understanding of the ecological consequences of anthropogenic stressors and provide a foundation for informed decision-making regarding the conservation and management of riparian ecosystems.
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Affiliation(s)
- Nina Röder
- iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany.
| | - V Sophie Stoll
- iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany
| | - Jonathan F Jupke
- iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany
| | - Sara Kolbenschlag
- iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany
| | - Mirco Bundschuh
- iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany; Department of Aquatic Science and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kathrin Theißinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Klaus Schwenk
- iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany; LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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12
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Wanghe K, Ahmad S, Zhou X, Tian F, Liu S, Zhou B, Nabi G, Wang G, Li K, Jian S, Jiang H, Chen S, Niu Y, Khan MI, Zhao K. Spatially explicit estimation of freshwater fish stock biomass with limited data: A case study of an endangered endemic fish on the Tibetan Plateau, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168717. [PMID: 38008312 DOI: 10.1016/j.scitotenv.2023.168717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 11/28/2023]
Abstract
Accurate evaluation of fish stock biomass is essential for effective conservation management and targeted species enhancement efforts. However, this remains challenging owing to limited data availability. Therefore, we present an integrated modeling framework combining catch per unit effort with ensemble species distribution modeling called CPUESDM, which explicitly assesses and validates the spatial distribution of stock biomass for freshwater fish species with limited data, applied to Herzensteinia microcephalus. The core algorithm incorporates the Leslie regression model, ensemble species distribution modeling, and exploratory spatial interpolation techniques. We found that H. microcephalus biomass in the Yangtze River source area yielded an initial estimate of 113.52 tons. Our validation results demonstrate high accuracy with a Cohen's kappa coefficient of 0.78 and root mean square error of 0.05. Furthermore, our spatially-explicit, global, absolute biomass density map effectively identified areas with high and low concentrations of biomass distribution centers. Additionally, this study offers access to the source code, example raw data, and a step-by-step instruction manual for other researchers using field data to explore the application of this model. Our findings can help inform for future conservation efforts around fish stock biomass estimation, especially for endangered species.
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Affiliation(s)
- Kunyuan Wanghe
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.
| | - Shahid Ahmad
- School of Ecology and Environment, Hainan University, Haikou, China; Wildlife and Ecosystem Research Lab, Department of Zoology, University of Chitral, Khyber Pakhtunkhwa, Pakistan
| | - Xin Zhou
- Qinghai University, Xining, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Sijia Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | | | - Ghulam Nabi
- Institute of Nature Conservation, Polish Academy of Sciences, Krakow, Poland
| | - Guojie Wang
- Qinghai Provincial Fishery Technology Extension Center, Xining, China
| | - Kemao Li
- Qinghai Provincial Fishery Technology Extension Center, Xining, China
| | - Shenglong Jian
- Qinghai Provincial Fishery Technology Extension Center, Xining, China
| | - Huamin Jiang
- The Rescues Center of Qinghai-Lake Naked Carp, Xining, China
| | - Shengxue Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Yimeng Niu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | | | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.
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13
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Lin L, Deng WD, Li JT, Kang B. Whether including exotic species alters conservation prioritization: a case study in the Min River in southeastern China. JOURNAL OF FISH BIOLOGY 2024; 104:450-462. [PMID: 36843140 DOI: 10.1111/jfb.15356] [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: 10/19/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Conservation practices from the perspective of functional diversity (FD) and conservation prioritization need to account for the impacts of exotic species in freshwater ecosystems. This work first simulated the influence of exotic species on the values of FD in a schemed mechanistic model, and then a practical case study of conservation prioritization was performed in the Min River, the largest river in southeastern China, to discuss whether including exotic species alters prioritization. The mechanistic model revealed that exotic species significantly altered the expected FD if the number of exotic species occupied 2% of the community. Joint species distribution modelling indicated that the highest FD occurred in the west, northwest and north upstreams of the Min River. Values of FD in 64.69% of the basin decreased after the exotic species were removed from calculation. Conservation prioritization with the Zonation software proved that if first the habitats of exotic species were removed during prioritization, 62.75% of the highest prioritized areas were shifted, average species representation of the endemic species was improved and mean conservation efficiency was increased by 7.53%. Existence of exotic species will significantly alter the metrics of biodiversity and the solution for conservation prioritization, and negatively weighting exotic species in the scope of conservation prioritization is suggested to better protect endemic species. This work advocates a thorough estimate of the impacts of exotic species on FD and conservation prioritization, providing complementary evidence for conservation biology and valuable implications for local freshwater fish conservation.
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Affiliation(s)
- Li Lin
- College of Fisheries, Ocean University of China, Qingdao, China
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, China
| | - Wei-De Deng
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung, Taiwan
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Jin-Tao Li
- College of Fisheries, Ocean University of China, Qingdao, China
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, China
| | - Bin Kang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, China
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14
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Dash NR, Al Bataineh MT, Alili R, Al Safar H, Alkhayyal N, Prifti E, Zucker JD, Belda E, Clément K. Functional alterations and predictive capacity of gut microbiome in type 2 diabetes. Sci Rep 2023; 13:22386. [PMID: 38104165 PMCID: PMC10725451 DOI: 10.1038/s41598-023-49679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023] Open
Abstract
The gut microbiome plays a significant role in the development of Type 2 Diabetes Mellitus (T2DM), but the functional mechanisms behind this association merit deeper investigation. Here, we used the nanopore sequencing technology for metagenomic analyses to compare the gut microbiome of individuals with T2DM from the United Arab Emirates (n = 40) with that of control (n = 44). DMM enterotyping of the cohort resulted concordantly with previous results, in three dominant groups Bacteroides (K1), Firmicutes (K2), and Prevotella (K3) lineages. The diversity analysis revealed a high level of diversity in the Firmicutes group (K2) both in terms of species richness and evenness (Wilcoxon rank-sum test, p value < 0.05 vs. K1 and K3 groups), consistent with the Ruminococcus enterotype described in Western populations. Additionally, functional enrichment analyses of KEGG modules showed significant differences in abundance between individuals with T2DM and controls (FDR < 0.05). These differences include modules associated with the degradation of amino acids, such as arginine, the degradation of urea as well as those associated with homoacetogenesis. Prediction analysis with the Predomics approach suggested potential biomarkers for T2DM, including a balance between a depletion of Enterococcus faecium and Blautia lineages with an enrichment of Absiella spp or Eubacterium limosum in T2DM individuals, highlighting the potential of metagenomic analysis in predicting predisposition to diabetic cardiomyopathy in T2DM patients.
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Affiliation(s)
- Nihar Ranjan Dash
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohammad T Al Bataineh
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, PO Box: 127788, Abu Dhabi, United Arab Emirates.
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, UAE.
| | - Rohia Alili
- INSERM, Nutrition and obesities: systemics approaches (NutriOmics), Sorbonne University, Paris, France
- Nutrition Department, Pitié-Salpêtrière Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Habiba Al Safar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, UAE
| | | | - Edi Prifti
- INSERM, Nutrition and obesities: systemics approaches (NutriOmics), Sorbonne University, Paris, France
- Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, IRD, Sorbonne Université, 93143, Bondy, France
| | - Jean-Daniel Zucker
- INSERM, Nutrition and obesities: systemics approaches (NutriOmics), Sorbonne University, Paris, France
- Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, IRD, Sorbonne Université, 93143, Bondy, France
| | - Eugeni Belda
- INSERM, Nutrition and obesities: systemics approaches (NutriOmics), Sorbonne University, Paris, France
- Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, IRD, Sorbonne Université, 93143, Bondy, France
| | - Karine Clément
- INSERM, Nutrition and obesities: systemics approaches (NutriOmics), Sorbonne University, Paris, France.
- Nutrition Department, Pitié-Salpêtrière Hospital, Assistance Publique Hôpitaux de Paris, Paris, France.
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15
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Mondal S, Lee MA, Weng JS, Osuka KE, Chen YK, Ray A. Seasonal distribution patterns of Scomberomorus commerson in the Taiwan Strait in relation to oceanographic conditions: An ensemble modeling approach. MARINE POLLUTION BULLETIN 2023; 197:115733. [PMID: 37925992 DOI: 10.1016/j.marpolbul.2023.115733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023]
Abstract
The decline in the stock of the narrow-barred Spanish mackerel in the Taiwan Strait has sparked interest in conservation efforts. To optimize conservation and restoration efforts, it is crucial to understand their habitat preference in response to changing environments. In this study, ensemble modeling was used to investigate the seasonal distribution patterns of Spanish mackerel. Winter was identified as the most productive season, followed by fall; productivity was the lowest in summer. Five single-algorithm models were developed, and on the basis of their performance, four were selected for inclusion in an ensemble species distribution model. The spatial distribution of Spanish mackerel was primarily along the latitudinal range 23°-25°N in spring and summer. However, in fall and winter, the geographical range increased toward the southern region. The findings of this study will contribute to the understanding of this specific species and the approach used in this study may be applicable to other fisheries stocks also.
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Affiliation(s)
- Sandipan Mondal
- Department of Environmental Biology Fisheries Science, National Taiwan Ocean University, Keelung 202, Taiwan; Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Ming-An Lee
- Department of Environmental Biology Fisheries Science, National Taiwan Ocean University, Keelung 202, Taiwan; Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202, Taiwan; Doctoral degree program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung 202, Taiwan.
| | - Jinn-Shing Weng
- Coastal and Offshore Resources Research Center of Fisheries Research Institute, Council of Agriculture Executive Yuan, Kaohsiung 80672, Taiwan
| | - Kennedy Edeye Osuka
- Department of Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Yu Kai Chen
- Coastal and Offshore Resources Research Center of Fisheries Research Institute, Council of Agriculture Executive Yuan, Kaohsiung 80672, Taiwan
| | - Aratrika Ray
- Department of Environmental Biology Fisheries Science, National Taiwan Ocean University, Keelung 202, Taiwan
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16
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Kampango A, Saleh F, Furu P, Konradsen F, Alifrangis M, Schiøler KL, Weldon CW. A protocol for evaluating the entomological impact of larval source reduction on mosquito vectors at hotel compounds in Zanzibar. PLoS One 2023; 18:e0294773. [PMID: 38011153 PMCID: PMC10681246 DOI: 10.1371/journal.pone.0294773] [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: 05/10/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
There is an increasing awareness of the association between tourism activity and risks of emerging mosquito-borne diseases (MBDs) worldwide. In previous studies we showed that hotels in Zanzibar may play an important role in maintaining residual foci of mosquito vectors populations of public health concern. These findings indicated larval sources removal (LSR) interventions may have a significant negative impact on vector communities. However, a thorough analysis of the response vector species to potential LSM strategies must be evaluated prior to implementation of a large-scale area-wide control campaign. Here we propose a protocol for evaluation of the impact of LSR against mosquito vectors at hotel settings in Zanzibar. This protocol is set to determine the efficacy of LSR in a randomized control partial cross-over experimental design with four hotel compounds representing the unit of randomization for allocation of interventions. However, the protocol can be applied to evaluate the impact of LRS in more than four sites. Proposed interventions are active removal of disposed containers, and installation of water dispenser to replace single use discarded plastic water bottles, which were identified as the most important source of mosquitoes studied hotels. The ideal time for allocating intervention to the intervention arms the dry season, when the mosquito abundance is predictably lower. The possible impact of interventions on mosquito occurrence and abundance risks is then evaluated throughout subsequent rainy and dry seasons. If an appreciable reduction in mosquito abundance and occurrence risks is observed during the trial period, intervention could be extended to the control arm to determine whether any potential reduction of mosquito density is reproducible. A rigorous evaluation of the proposed LRS interventions will inspire large scale trials and provide support for evidence-based mosquito management at hotel facilities in Zanzibar and similar settings.
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Affiliation(s)
- Ayubo Kampango
- Sector de Estudos de Vectores, Instituto Nacional de Saúde (INS), Vila de Marracuene, Província de Maputo, Mozambique
- Department of Zoology and Entomology, University of Pretoria (UP), Pretoria, South Africa
| | - Fatma Saleh
- Department of Allied Health Sciences, School of Health and Medical Sciences, The State University of Zanzibar, Zanzibar, Tanzania
| | - Peter Furu
- Global Health Section, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Konradsen
- Global Health Section, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Michael Alifrangis
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Karin L. Schiøler
- Global Health Section, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Christopher W. Weldon
- Department of Zoology and Entomology, University of Pretoria (UP), Pretoria, South Africa
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17
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Chen H, Zhang G, Ding G, Huang J, Zhang H, Vidal MC, Corlett RT, Liu C, An J. Interspecific Host Variation and Biotic Interactions Drive Pathogen Community Assembly in Chinese Bumblebees. INSECTS 2023; 14:887. [PMID: 37999086 PMCID: PMC10672019 DOI: 10.3390/insects14110887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
Bumblebees have been considered one of the most important pollinators on the planet. However, recent reports of bumblebee decline have raised concern about a significant threat to ecosystem stability. Infectious diseases caused by multiple pathogen infections have been increasingly recognized as an important mechanism behind this decline worldwide. Understanding the determining factors that influence the assembly and composition of pathogen communities among bumblebees can provide important implications for predicting infectious disease dynamics and making effective conservation policies. Here, we study the relative importance of biotic interactions versus interspecific host resistance in shaping the pathogen community composition of bumblebees in China. We first conducted a comprehensive survey of 13 pathogens from 22 bumblebee species across China. We then applied joint species distribution modeling to assess the determinants of pathogen community composition and examine the presence and strength of pathogen-pathogen associations. We found that host species explained most of the variations in pathogen occurrences and composition, suggesting that host specificity was the most important variable in predicting pathogen occurrences and community composition in bumblebees. Moreover, we detected both positive and negative associations among pathogens, indicating the role of competition and facilitation among pathogens in determining pathogen community assembly. Our research demonstrates the power of a pluralistic framework integrating field survey of bumblebee pathogens with community ecology frameworks to understand the underlying mechanisms of pathogen community assembly.
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Affiliation(s)
- Huanhuan Chen
- State Key Laboratory of Resource Insects, Key Laboratory of Insect-Pollinator Biology of Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.C.); (G.Z.); (G.D.); (J.H.); (H.Z.)
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Guangshuo Zhang
- State Key Laboratory of Resource Insects, Key Laboratory of Insect-Pollinator Biology of Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.C.); (G.Z.); (G.D.); (J.H.); (H.Z.)
| | - Guiling Ding
- State Key Laboratory of Resource Insects, Key Laboratory of Insect-Pollinator Biology of Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.C.); (G.Z.); (G.D.); (J.H.); (H.Z.)
| | - Jiaxing Huang
- State Key Laboratory of Resource Insects, Key Laboratory of Insect-Pollinator Biology of Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.C.); (G.Z.); (G.D.); (J.H.); (H.Z.)
| | - Hong Zhang
- State Key Laboratory of Resource Insects, Key Laboratory of Insect-Pollinator Biology of Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.C.); (G.Z.); (G.D.); (J.H.); (H.Z.)
| | - Mayra C. Vidal
- Biology Department, University of Massachusetts, Boston, MA 02125, USA;
| | - Richard T. Corlett
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China;
| | - Cong Liu
- Biology Department, University of Massachusetts, Boston, MA 02125, USA;
- Department of Organismic and Evolutional Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Jiandong An
- State Key Laboratory of Resource Insects, Key Laboratory of Insect-Pollinator Biology of Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.C.); (G.Z.); (G.D.); (J.H.); (H.Z.)
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18
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Eliason J, Rao A. Investigating Ecological Interactions in the Tumor Microenvironment using Joint Species Distribution Models for Point Patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567108. [PMID: 38014073 PMCID: PMC10680696 DOI: 10.1101/2023.11.14.567108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The tumor microenvironment (TME) is a complex and dynamic ecosystem that involves interactions between different cell types, such as cancer cells, immune cells, and stromal cells. These interactions can promote or inhibit tumor growth and affect response to therapy. Multitype Gibbs point process (MGPP) models are statistical models used to study the spatial distribution and interaction of different types of objects, such as the distribution of cell types in a tissue sample. Such models are potentially useful for investigating the spatial relationships between different cell types in the tumor microenvironment, but so far studies of the TME using cell-resolution imaging have been largely limited to spatial descriptive statistics. However, MGPP models have many advantages over descriptive statistics, such as uncertainty quantification, incorporation of multiple covariates and the ability to make predictions. In this paper, we describe and apply a previously developed MGPP method, the saturated pairwise interaction Gibbs point process model , to a publicly available multiplexed imaging dataset obtained from colorectal cancer patients. Importantly, we show how these methods can be used as joint species distribution models (JSDMs) to precisely frame and answer many relevant questions related to the ecology of the tumor microenvironment.
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19
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Epp Schmidt D, Maul JE, Yarwood SA. Quantitative Amplicon Sequencing Is Necessary to Identify Differential Taxa and Correlated Taxa Where Population Sizes Differ. MICROBIAL ECOLOGY 2023; 86:2790-2801. [PMID: 37563275 DOI: 10.1007/s00248-023-02273-z] [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: 05/12/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023]
Abstract
High-throughput, multiplexed-amplicon sequencing has become a core tool for understanding environmental microbiomes. As researchers have widely adopted sequencing, many open-source analysis pipelines have been developed to compare microbiomes using compositional analysis frameworks. However, there is increasing evidence that compositional analyses do not provide the information necessary to accurately interpret many community assembly processes. This is especially true when there are large gradients that drive distinct community assembly processes. Recently, sequencing has been combined with Q-PCR (among other sources of total quantitation) to generate "Quantitative Sequencing" (QSeq) data. QSeq more accurately estimates the true abundance of taxa, is a more reliable basis for inferring correlation, and, ultimately, can be more reliably related to environmental data to infer community assembly processes. In this paper, we use a combination of published data sets, synthesis, and empirical modeling to offer guidance for which contexts QSeq is advantageous. As little as 5% variation in total abundance among experimental groups resulted in more accurate inference by QSeq than compositional methods. Compositional methods for differential abundance and correlation unreliably detected patterns in abundance and covariance when there was greater than 20% variation in total abundance among experimental groups. Whether QSeq performs better for beta diversity analysis depends on the question being asked, and the analytic strategy (e.g., what distance metric is being used); for many questions and methods, QSeq and compositional analysis are equivalent for beta diversity analysis. QSeq is especially useful for taxon-specific analysis; QSeq transformation and analysis should be the default for answering taxon-specific questions of amplicon sequence data. Publicly available bioinformatics pipelines should incorporate support for QSeq transformation and analysis.
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Affiliation(s)
| | - Jude E Maul
- United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
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20
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Koziol A, Odriozola I, Leonard A, Eisenhofer R, San José C, Aizpurua O, Alberdi A. Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors. mBio 2023; 14:e0160623. [PMID: 37650630 PMCID: PMC10653949 DOI: 10.1128/mbio.01606-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE In our manuscript, we report the first interspecific comparative study about the plasticity of the gut microbiota. We conducted a captivity experiment that exposed wild-captured mammals to a series of environmental challenges over 45 days. We characterized their gut microbial communities using genome-resolved metagenomics and modeled how the taxonomic, phylogenetic, and functional microbial dynamics varied across a series of disturbances in both species. Our results indicate that the intrinsic properties (e.g., diversity and functional redundancy) of microbial communities coupled with physiological attributes (e.g., thermal plasticity) of hosts shape the taxonomic, phylogenetic, and functional response of gut microbiomes to environmental stressors, which might influence their contribution to the acclimation and adaptation capacity of animal hosts.
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Affiliation(s)
- Adam Koziol
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Iñaki Odriozola
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Aoife Leonard
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Raphael Eisenhofer
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Carlos San José
- Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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21
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Martínez-Vilalta J, García-Valdés R, Jump A, Vilà-Cabrera A, Mencuccini M. Accounting for trait variability and coordination in predictions of drought-induced range shifts in woody plants. THE NEW PHYTOLOGIST 2023; 240:23-40. [PMID: 37501525 DOI: 10.1111/nph.19138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/20/2023] [Indexed: 07/29/2023]
Abstract
Functional traits offer a promising avenue to improve predictions of species range shifts under climate change, which will entail warmer and often drier conditions. Although the conceptual foundation linking traits with plant performance and range shifts appears solid, the predictive ability of individual traits remains generally low. In this review, we address this apparent paradox, emphasizing examples of woody plants and traits associated with drought responses at the species' rear edge. Low predictive ability reflects the fact not only that range dynamics tend to be complex and multifactorial, as well as uncertainty in the identification of relevant traits and limited data availability, but also that trait effects are scale- and context-dependent. The latter results from the complex interactions among traits (e.g. compensatory effects) and between them and the environment (e.g. exposure), which ultimately determine persistence and colonization capacity. To confront this complexity, a more balanced coverage of the main functional dimensions involved (stress tolerance, resource use, regeneration and dispersal) is needed, and modelling approaches must be developed that explicitly account for: trait coordination in a hierarchical context; trait variability in space and time and its relationship with exposure; and the effect of biotic interactions in an ecological community context.
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Affiliation(s)
- Jordi Martínez-Vilalta
- CREAF, E08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
- Universitat Autònoma de Barcelona, E08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
| | - Raúl García-Valdés
- CREAF, E08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
- Forest Science and Technology Centre of Catalonia (CTFC), E25280, Solsona, Spain
- Department of Biology, Geology, Physics and Inorganic Chemistry, School of Experimental Sciences and Technology, Rey Juan Carlos University, E28933, Móstoles, Madrid, Spain
| | - Alistair Jump
- Biological and Environmental Sciences, University of Stirling, FK9 4LA, Stirling, UK
| | - Albert Vilà-Cabrera
- CREAF, E08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
- Biological and Environmental Sciences, University of Stirling, FK9 4LA, Stirling, UK
| | - Maurizio Mencuccini
- CREAF, E08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
- ICREA, Pg. Lluís Companys 23, E08010, Barcelona, Spain
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22
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Burner RC, Stephan JG, Drag L, Potterf M, Birkemoe T, Siitonen J, Müller J, Ovaskainen O, Sverdrup‐Thygeson A, Snäll T. Alternative measures of trait-niche relationships: A test on dispersal traits in saproxylic beetles. Ecol Evol 2023; 13:e10588. [PMID: 37869428 PMCID: PMC10585442 DOI: 10.1002/ece3.10588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/11/2023] [Accepted: 09/22/2023] [Indexed: 10/24/2023] Open
Abstract
Functional trait approaches are common in ecology, but a lack of clear hypotheses on how traits relate to environmental gradients (i.e., trait-niche relationships) often makes uncovering mechanisms difficult. Furthermore, measures of community functional structure differ in their implications, yet inferences are seldom compared among metrics. Community-weighted mean trait values (CWMs), a common measure, are largely driven by the most common species and thus do not reflect community-wide trait-niche relationships per se. Alternatively, trait-niche relationships can be estimated across a larger group of species using hierarchical joint species distribution models (JSDMs), quantified by a parameter Γ. We investigated how inferences about trait-niche relationships are affected by the choice of metric. Using deadwood-dependent (saproxylic) beetles in fragmented Finnish forests, we followed a protocol for investigating trait-niche relationships by (1) identifying environmental filters (climate, forest age, and deadwood volume), (2) relating these to an ecological function (dispersal ability), and (3) identifying traits related to this function (wing morphology). We tested 18 hypothesized dispersal relationships using both CWM and Γ estimates across these environmental gradients. CWMs were more likely than Γ to show support for trait-niche relationships. Up to 13% of species' realized niches were explained by dispersal traits, but the directions of effects were consistent with fewer than 11%-39% of our 18 trait-niche hypotheses (depending on the metric used). This highlights the difficulty in connecting morphological traits and ecological functions in insects, despite the clear conceptual link between landscape connectivity and flight-related traits. Caution is thus warranted in hypothesis development, particularly where apparent trait-function links are less clear. Inferences differ when CWMs versus Γ estimates are used, necessitating the choice of a metric that reflects study questions. CWMs help explain the effects of environmental gradients on community trait composition, whereas the effects of traits on species' niches are better estimated using hierarchical JSDMs.
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Affiliation(s)
- Ryan C. Burner
- U.S. Geological SurveyUpper Midwest Environmental Sciences CenterLa CrosseWisconsinUSA
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
| | - Jörg G. Stephan
- SLU Swedish Species Information CentreSwedish University of Agricultural SciencesUppsalaSweden
| | - Lukas Drag
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, BiocenterUniversity of WürzburgRauhenebrachGermany
- Institute of EntomologyBiology Centre of the Czech Academy of SciencesCeske BudejoviceCzech Republic
| | - Mária Potterf
- Department of Life Science SystemsTechnical University of MunichFreisingBavariaGermany
| | - Tone Birkemoe
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
| | - Juha Siitonen
- Natural Resources Institute Finland (Luke)HelsinkiFinland
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, BiocenterUniversity of WürzburgRauhenebrachGermany
- Bavarian Forest National ParkGrafenauGermany
| | - Otso Ovaskainen
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Department of Biology, Centre for Biodiversity DynamicsNorwegian University of Science and TechnologyTrondheimNorway
| | - Anne Sverdrup‐Thygeson
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
| | - Tord Snäll
- SLU Swedish Species Information CentreSwedish University of Agricultural SciencesUppsalaSweden
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23
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Jokinen M, Sallinen S, Jones MM, Sirén J, Guilbault E, Susi H, Laine AL. The first arriving virus shapes within-host viral diversity during natural epidemics. Proc Biol Sci 2023; 290:20231486. [PMID: 37700649 PMCID: PMC10498040 DOI: 10.1098/rspb.2023.1486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023] Open
Abstract
Viral diversity has been discovered across scales from host individuals to populations. However, the drivers of viral community assembly are still largely unknown. Within-host viral communities are formed through co-infections, where the interval between the arrival times of viruses may vary. Priority effects describe the timing and order in which species arrive in an environment, and how early colonizers impact subsequent community assembly. To study the effect of the first-arriving virus on subsequent infection patterns of five focal viruses, we set up a field experiment using naïve Plantago lanceolata plants as sentinels during a seasonal virus epidemic. Using joint species distribution modelling, we find both positive and negative effects of early season viral infection on late season viral colonization patterns. The direction of the effect depends on both the host genotype and which virus colonized the host early in the season. It is well established that co-occurring viruses may change the virulence and transmission of viral infections. However, our results show that priority effects may also play an important, previously unquantified role in viral community assembly. The assessment of these temporal dynamics within a community ecological framework will improve our ability to understand and predict viral diversity in natural systems.
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Affiliation(s)
- Maija Jokinen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland
| | - Suvi Sallinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
| | - Mirkka M. Jones
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
- Institute of Biotechnology, HiLIFE-Helsinki Institute of Life Science, University of Helsinki, PO Box 65, 00014, Finland
| | - Jukka Sirén
- Institute of Biotechnology, HiLIFE-Helsinki Institute of Life Science, University of Helsinki, PO Box 65, 00014, Finland
| | - Emy Guilbault
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
| | - Hanna Susi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
| | - Anna-Liisa Laine
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
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24
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Santangeli A, Weigel B, Antão LH, Kaarlejärvi E, Hällfors M, Lehikoinen A, Lindén A, Salemaa M, Tonteri T, Merilä P, Vuorio K, Ovaskainen O, Vanhatalo J, Roslin T, Saastamoinen M. Mixed effects of a national protected area network on terrestrial and freshwater biodiversity. Nat Commun 2023; 14:5426. [PMID: 37704608 PMCID: PMC10499833 DOI: 10.1038/s41467-023-41073-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023] Open
Abstract
Protected areas are considered fundamental to counter biodiversity loss. However, evidence for their effectiveness in averting local extinctions remains scarce and taxonomically biased. We employ a robust counterfactual multi-taxon approach to compare occupancy patterns of 638 species, including birds (150), mammals (23), plants (39) and phytoplankton (426) between protected and unprotected sites across four decades in Finland. We find mixed impacts of protected areas, with only a small proportion of species explicitly benefiting from protection-mainly through slower rates of decline inside protected areas. The benefits of protection are enhanced for larger protected areas and are traceable to when the sites were protected, but are mostly unrelated to species conservation status or traits (size, climatic niche and threat status). Our results suggest that the current protected area network can partly contribute to slow down declines in occupancy rates, but alone will not suffice to halt the biodiversity crisis. Efforts aimed at improving coverage, connectivity and management will be key to enhance the effectiveness of protected areas towards bending the curve of biodiversity loss.
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Affiliation(s)
- Andrea Santangeli
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
- Animal Demography and Ecology Unit, Institute for Mediterranean Studies (IMEDEA), CSIC-UIB, 07190, Esporles, Spain.
| | - Benjamin Weigel
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- INRAE, EABX, Cestas, France
| | - Laura H Antão
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Elina Kaarlejärvi
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Maria Hällfors
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Nature Solutions Unit, Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Aleksi Lehikoinen
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | - Maija Salemaa
- Natural Resources Institute (LUKE), Helsinki, Finland
| | - Tiina Tonteri
- Natural Resources Institute (LUKE), Helsinki, Finland
| | - Päivi Merilä
- Natural Resources Institute (LUKE), Helsinki, Finland
| | - Kristiina Vuorio
- Nature Solutions Unit, Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Otso Ovaskainen
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (Survontie 9C), FI-40014, Jyväskylä, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jarno Vanhatalo
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, Faculty of Science, University of Helsinki, Helsinki, Finland
| | - Tomas Roslin
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Spatial Foodweb Ecology Group, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Spatial Foodweb Ecology Group, Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marjo Saastamoinen
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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25
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Pantel JH, Becks L. Statistical methods to identify mechanisms in studies of eco-evolutionary dynamics. Trends Ecol Evol 2023; 38:760-772. [PMID: 37437547 DOI: 10.1016/j.tree.2023.03.011] [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: 08/18/2022] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 07/14/2023]
Abstract
While the reciprocal effects of ecological and evolutionary dynamics are increasingly recognized as an important driver for biodiversity, detection of such eco-evolutionary feedbacks, their underlying mechanisms, and their consequences remains challenging. Eco-evolutionary dynamics occur at different spatial and temporal scales and can leave signatures at different levels of organization (e.g., gene, protein, trait, community) that are often difficult to detect. Recent advances in statistical methods combined with alternative hypothesis testing provides a promising approach to identify potential eco-evolutionary drivers for observed data even in non-model systems that are not amenable to experimental manipulation. We discuss recent advances in eco-evolutionary modeling and statistical methods and discuss challenges for fitting mechanistic models to eco-evolutionary data.
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Affiliation(s)
- Jelena H Pantel
- Ecological Modelling, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 2, 45117 Essen, Germany.
| | - Lutz Becks
- University of Konstanz, Aquatic Ecology and Evolution, Limnological Institute University of Konstanz Mainaustraße 252 78464, Konstanz/Egg, Germany
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26
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Malchow AK, Hartig F, Reeg J, Kéry M, Zurell D. Demography-environment relationships improve mechanistic understanding of range dynamics under climate change. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220194. [PMID: 37246385 DOI: 10.1098/rstb.2022.0194] [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: 09/27/2022] [Accepted: 04/15/2023] [Indexed: 05/30/2023] Open
Abstract
Species respond to climate change with range and abundance dynamics. To better explain and predict them, we need a mechanistic understanding of how the underlying demographic processes are shaped by climatic conditions. Here, we aim to infer demography-climate relationships from distribution and abundance data. For this, we developed spatially explicit, process-based models for eight Swiss breeding bird populations. These jointly consider dispersal, population dynamics and the climate-dependence of three demographic processes-juvenile survival, adult survival and fecundity. The models were calibrated to 267 nationwide abundance time series in a Bayesian framework. The fitted models showed moderate to excellent goodness-of-fit and discriminatory power. The most influential climatic predictors for population performance were the mean breeding-season temperature and the total winter precipitation. Contemporary climate change benefitted the population trends of typical mountain birds leading to lower population losses or even slight increases, whereas lowland birds were adversely affected. Our results emphasize that generic process-based models embedded in a robust statistical framework can improve our predictions of range dynamics and may allow disentangling of the underlying processes. For future research, we advocate a stronger integration of experimental and empirical studies in order to gain more precise insights into the mechanisms by which climate affects populations. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.
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Affiliation(s)
- A-K Malchow
- Institute for Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - F Hartig
- Theoretical Ecology Lab, Faculty of Biology and Pre-Clinical Medicine, University of Regensburg, 93053 Regensburg, Germany
| | - J Reeg
- Institute for Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - M Kéry
- Swiss Ornithological Institute, 6204 Sempach, Switzerland
| | - D Zurell
- Institute for Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
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27
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Carvalho S, Shchepanik H, Aylagas E, Berumen ML, Costa FO, Costello MJ, Duarte S, Ferrario J, Floerl O, Heinle M, Katsanevakis S, Marchini A, Olenin S, Pearman JK, Peixoto RS, Rabaoui LJ, Ruiz G, Srėbalienė G, Therriault TW, Vieira PE, Zaiko A. Hurdles and opportunities in implementing marine biosecurity systems in data-poor regions. Bioscience 2023; 73:494-512. [PMID: 37560322 PMCID: PMC10408360 DOI: 10.1093/biosci/biad056] [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: 12/15/2022] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 08/11/2023] Open
Abstract
Managing marine nonindigenous species (mNIS) is challenging, because marine environments are highly connected, allowing the dispersal of species across large spatial scales, including geopolitical borders. Cross-border inconsistencies in biosecurity management can promote the spread of mNIS across geopolitical borders, and incursions often go unnoticed or unreported. Collaborative surveillance programs can enhance the early detection of mNIS, when response may still be possible, and can foster capacity building around a common threat. Regional or international databases curated for mNIS can inform local monitoring programs and can foster real-time information exchange on mNIS of concern. When combined, local species reference libraries, publicly available mNIS databases, and predictive modeling can facilitate the development of biosecurity programs in regions lacking baseline data. Biosecurity programs should be practical, feasible, cost-effective, mainly focused on prevention and early detection, and be built on the collaboration and coordination of government, nongovernment organizations, stakeholders, and local citizens for a rapid response.
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Affiliation(s)
- Susana Carvalho
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
| | - Hailey Shchepanik
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
| | - Eva Aylagas
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
- Red Sea Global, Riyadh 12382-6726, Saudi Arabia
| | - Michael L Berumen
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA) and Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | | | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Jasmine Ferrario
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | | | - Moritz Heinle
- Applied Research Center for Environment & Marine Studies, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
- International Centre for Water Resources and Global Change, Federal Institute of Hydrology, Koblenz, Germany
| | | | - Agnese Marchini
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Sergej Olenin
- Marine Research Institute, Klaipeda University, Lithuania
| | | | - Raquel S Peixoto
- King Abdullah University of Science and Technology, Red Sea Research Center, 23955-6900 Thuwal, Saudi Arabia
| | - Lotfi J Rabaoui
- Applied Research Center for Environment & Marine Studies, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
- National Center for Wildlife, Riyadh, Saudi Arabia
| | - Greg Ruiz
- Smithsonian Environmental Research Center, Edgewater, Maryland
| | | | | | - Pedro E Vieira
- Centre of Molecular and Environmental Biology (CBMA) and Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Anastasija Zaiko
- Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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28
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Weigel B, Graco-Roza C, Hultman J, Pajunen V, Teittinen A, Kuzmina M, Zakharov EV, Soininen J, Ovaskainen O. Local eukaryotic and bacterial stream community assembly is shaped by regional land use effects. ISME COMMUNICATIONS 2023; 3:65. [PMID: 37365224 PMCID: PMC10293236 DOI: 10.1038/s43705-023-00272-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023]
Abstract
With anticipated expansion of agricultural areas for food production and increasing intensity of pressures stemming from land-use, it is critical to better understand how species respond to land-use change. This is particularly true for microbial communities which provide key ecosystem functions and display fastest responses to environmental change. However, regional land-use effects on local environmental conditions are often neglected, and, hence, underestimated when investigating community responses. Here we show that the effects stemming from agricultural and forested land use are strongest reflected in water conductivity, pH and phosphorus concentration, shaping microbial communities and their assembly processes. Using a joint species distribution modelling framework with community data based on metabarcoding, we quantify the contribution of land-use types in determining local environmental variables and uncover the impact of both, land-use, and local environment, on microbial stream communities. We found that community assembly is closely linked to land-use type but that the local environment strongly mediates the effects of land-use, resulting in systematic variation of taxon responses to environmental conditions, depending on their domain (bacteria vs. eukaryote) and trophic mode (autotrophy vs. heterotrophy). Given that regional land-use type strongly shapes local environments, it is paramount to consider its key role in shaping local stream communities.
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Affiliation(s)
- Benjamin Weigel
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. 65, FI-00014, Helsinki, Finland.
- INRAE, EABX, 50 avenue de Verdun, 33612, Cestas, France.
| | - Caio Graco-Roza
- Laboratory of Ecology and Physiology of Phytoplankton, Department of Plant Biology, State University of Rio de Janeiro, Rua São Francisco Xavier 524, PHLC, Sala 511a, Rio de Janeiro, 20550-900, Brazil
- Department of Geosciences and Geography, University of Helsinki, PO, Box 64, FI-00014, Helsinki, Finland
| | - Jenni Hultman
- Soil Ecosystems, Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Virpi Pajunen
- Department of Geosciences and Geography, University of Helsinki, PO, Box 64, FI-00014, Helsinki, Finland
- Department of Built Environment, Aalto University, PO Box 11000, 00076 AALTO, Espoo, Finland
| | - Anette Teittinen
- Department of Geosciences and Geography, University of Helsinki, PO, Box 64, FI-00014, Helsinki, Finland
| | - Maria Kuzmina
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Janne Soininen
- Department of Geosciences and Geography, University of Helsinki, PO, Box 64, FI-00014, Helsinki, Finland
| | - Otso Ovaskainen
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. 65, FI-00014, Helsinki, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
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29
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Maioli F, Weigel B, Chiarabelli E, Manfredi C, Anibaldi A, Isailović I, Vrgoč N, Casini M. Influence of ecological traits on spatio-temporal dynamics of an elasmobranch community in a heavily exploited basin. Sci Rep 2023; 13:9596. [PMID: 37311785 DOI: 10.1038/s41598-023-36038-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/28/2023] [Indexed: 06/15/2023] Open
Abstract
Elasmobranchs, which include sharks and batoids, play critical roles in maintaining the integrity and stability of marine food webs. However, these cartilaginous fish are among the most threatened vertebrate lineages due to their widespread depletion. Consequently, understanding dynamics and predicting changes of elasmobranch communities are major research topics in conservation ecology. Here, we leverage long-term catch data from a standardized bottom trawl survey conducted from 1996 to 2019, to evaluate the spatio-temporal dynamics of the elasmobranch community in the heavily exploited Adriatic Sea, where these fish have historically been depleted. We use joint species distribution modeling to quantify the responses of the species to environmental variation while also including important traits such as species age at first maturity, reproductive mode, trophic level, and phylogenetic information. We present spatio-temporal changes in the species community and associated modification of the trait composition, highlighting strong spatial and depth-mediated patterning. We observed an overall increase in the abundance of the dominant elasmobranch species, except for spurdog, which has shown a continued decline. However, our results showed that the present community displays lower age at first maturity and a smaller fraction of viviparous species compared to the earlier observed community due to changes in species' relative abundance. The selected traits contributed considerably to explaining community patterns, suggesting that the integration of trait-based approaches in elasmobranch community analyses can aid efforts to conserve this important lineage of fish.
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Affiliation(s)
- Federico Maioli
- Department of Biological, Geological, and Environmental Sciences, Laboratory of Marine Biology and Fisheries, University of Bologna, 61032, Fano, Italy.
| | - Benjamin Weigel
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Programme, Research Centre for Ecological Change, University of Helsinki, 00100, Helsinki, Finland
- EABX, INRAE, 33612, Cestas, France
| | - Elettra Chiarabelli
- Department of Biological, Geological, and Environmental Sciences, Laboratory of Marine Biology and Fisheries, University of Bologna, 61032, Fano, Italy
- CoNISMa, 00196, Rome, Italy
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Chiara Manfredi
- Department of Biological, Geological, and Environmental Sciences, Laboratory of Marine Biology and Fisheries, University of Bologna, 61032, Fano, Italy
| | - Alessandra Anibaldi
- Department of Biological, Geological, and Environmental Sciences, Laboratory of Marine Biology and Fisheries, University of Bologna, 61032, Fano, Italy
- CoNISMa, 00196, Rome, Italy
| | - Igor Isailović
- Institute of Oceanography and Fisheries, 21000, Split, Croatia
| | - Nedo Vrgoč
- Institute of Oceanography and Fisheries, 21000, Split, Croatia
| | - Michele Casini
- Department of Biological, Geological, and Environmental Sciences, Laboratory of Marine Biology and Fisheries, University of Bologna, 61032, Fano, Italy.
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, 45330, Lysekil, Sweden.
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30
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Heylen DJA, Kumsa B, Kimbita E, Frank MN, Muhanguzi D, Jongejan F, Adehan SB, Toure A, Aboagye-Antwi F, Ogo NI, Juleff N, Crafford D, Fourie J, Labuchange M, Madder M. Tick-borne pathogens and body condition of cattle in smallholder rural livestock production systems in East and West Africa. Parasit Vectors 2023; 16:117. [PMID: 36998091 PMCID: PMC10064580 DOI: 10.1186/s13071-023-05709-0] [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: 11/28/2022] [Accepted: 02/18/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND The majority of the African population lives in rural areas where they heavily depend on crop and livestock production for their livelihoods. Given their socio-economic importance, we initiated a standardized multi-country (Benin, Burkina Faso, Ghana, Nigeria, Ethiopia Tanzania and Uganda) surveillance study to assess the current status of important tick-borne haemoparasites (TBHPs) of cattle. METHODS We assessed pathogen prevalences (Anaplasma marginale, Anaplasma centrale, Babesia bigemina, Babesia bovis, Ehrlichia ruminantium, and Theileria parva) in the blood of 6447 animals spread over fourteen districts (two districts per country). In addition, we screened for intrinsic (sex, weight, body condition) and extrinsic (husbandry, tick exposure) risk factors as predictors of infections with TBHPs. RESULTS There was a large macro-geographic variation observed in A. marginale, B. bigemina, B. bovis and E. ruminantium prevalences. Most correlated with the co-occurrence of their specific sets of vector-competent ticks. Highest numbers of infected cattle were found in Ghana and Benin, and lowest in Burkina Faso. While T. parva was seldomly found (Uganda only: 3.0%), A. marginale was found in each country with a prevalence of at least 40%. Babesia bovis infected individuals had lower body condition scores. Age (as estimated via body weight) was higher in A. marginale infected cattle, but was negatively correlated with B. bigemina and E. ruminantium prevalences. Ehrlichia ruminantium infection was more often found in males, and A. marginale more often in transhumance farming. High levels of co-infection, especially the combination A. marginale × B. bigemina, were observed in all countries, except for Uganda and Burkina Faso. Babesia bigemina was more or less often observed than expected by chance, when cattle were also co-infected with E. ruminantium or A. marginale, respectively. CONCLUSIONS Tick-borne pathogens of cattle are ubiquitous in African's smallholder cattle production systems. Our standardized study will help a wide range of stakeholders to provide recommendations for TBHP surveillance and prevention in cattle, especially for B. bovis which heavily impacts production and continues its spread over the African continent via the invasive Rhipicephalus microplus tick.
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Affiliation(s)
- Dieter J A Heylen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Wilrijk, Belgium.
- Eco-Epidemiology Group, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium.
| | - Bersissa Kumsa
- Department of Parasitology, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
| | - Elikira Kimbita
- Department of Veterinary Microbiology and Parasitology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, PO Box 3019, Morogoro, Tanzania
| | - Mwiine Nobert Frank
- Department of Bio-Molecular Resources and Bio-Laboratory Sciences (BBS), College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Dennis Muhanguzi
- Department of Bio-Molecular Resources and Bio-Laboratory Sciences (BBS), College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Frans Jongejan
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Safiou Bienvenu Adehan
- Zootechnical, Veterinary and Halieutic Research Laboratory (LRZVH), National Institute of Agricultural Research (INRAB), 01 BP 884, Cotonou, Benin
| | - Alassane Toure
- Université Nangui Abrogoua, UFR Sciences de La Nature, 02 Bp 801, Abidjan 02, Côte d'Ivoire
| | - Fred Aboagye-Antwi
- Department of Animal Biology and Conservation Science, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Legon-Accra, Ghana
| | - Ndudim Isaac Ogo
- National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | - Nick Juleff
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Dionne Crafford
- Clinvet International Pty (Ltd), 1479 Talmadge Hill South, Waverly, NY, 14892, USA
| | - Josephus Fourie
- Clinvet International Pty (Ltd), 1479 Talmadge Hill South, Waverly, NY, 14892, USA
| | | | - Maxime Madder
- Clinglobal, B03/04, The Tamarin Commercial Hub, Jacaranda Avenue, Tamarin, 90903, Mauritius
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31
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Ruiz L, Carrión-Paladines V, Vega M, López F, Benítez Á. Biological Crust Diversity Related to Elevation and Soil Properties at Local Scale in a Montane Scrub of Ecuador. J Fungi (Basel) 2023; 9:jof9030386. [PMID: 36983554 PMCID: PMC10058557 DOI: 10.3390/jof9030386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
The montane shrublands of southern Ecuador represent one of the least studied ecosystems, which in the last decade have been seriously threatened by increasing wildfires, deforestation, overgrazing, and conversion to forest plantations. Our main objective was to determine, at the local scale, the diversity of species composing the biological soil crust (BSC) at three elevations (2100, 2300, and 2500 m.a.s.l.) and their possible relationships with soil physical and chemical properties in montane shrublands. For this purpose, three monitoring plots of 100 m2 were established at each elevation, and within each plot, 20 subplots were established (180 subplots sampled in total). In addition, composite soil samples were collected at a depth of 0 to 10 cm, and some physical and biochemical parameters (e.g., bulk density, texture, pH, organic matter, soil organic carbon, total nitrogen, available phosphorus, and potassium) of the soil were analyzed. The results show 35 species (23 lichens, 10 bryophytes and 2 cyanobacteria) at three elevations with a bell-shaped or hump-shaped distribution pattern. This allowed us to point out that the species richness was higher at the intermediate elevations and that the composition showed significant differences in the three elevations related to soil factors. Elevation and soil drivers may help to better chose the more suitable biological soil crust (lichen-dominated and bryophyte-dominated BSC) for the management and conservation of the montane scrub of Ecuador, which is strongly threatened by human activities.
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Affiliation(s)
- Leslye Ruiz
- Carrera de Biología, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador
| | - Vinicio Carrión-Paladines
- Biodiversidad de Ecosistemas Tropicales-BIETROP, Herbario HUTPL, Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador
| | - Marlon Vega
- Carrera de Biología, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador
| | - Fausto López
- Carrera de Biología, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador
| | - Ángel Benítez
- Carrera de Biología, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador
- Biodiversidad de Ecosistemas Tropicales-BIETROP, Herbario HUTPL, Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador
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32
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Syme J, Kiszka JJ, Parra GJ. Habitat partitioning, co-occurrence patterns, and mixed-species group formation in sympatric delphinids. Sci Rep 2023; 13:3599. [PMID: 36869065 PMCID: PMC9984456 DOI: 10.1038/s41598-023-30694-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/28/2023] [Indexed: 03/05/2023] Open
Abstract
Numerous species have been reported to form mixed-species groups, however, little is known about the interplay between niche partitioning and mixed-species group formation. Furthermore, it is often unclear whether species come together by chance due to overlapping habitat preferences, by shared attraction to resources, or by attraction between them. We assessed habitat partitioning, co-occurrence patterns, and mixed-species group formation of sympatric Australian humpback (Sousa sahulensis) and Indo-Pacific bottlenose dolphins (Tursiops aduncus) around the North West Cape, Western Australia, with a joint species distribution model and temporal analyses of sighting data. Australian humpback dolphins preferred shallower and more nearshore waters than Indo-Pacific bottlenose dolphins, yet these species co-occurred more often than expected by chance given shared responses to environmental variables. Indo-Pacific bottlenose dolphins were sighted more often than Australian humpback dolphins during the afternoon, however, we did not find any temporal patterns in the occurrence of mixed-species groups. We propose that the positive association in the species' occurrence indicates the active formation of mixed-species groups. By evaluating habitat partitioning and co-occurrence patterns, this study provides direction for future work which should proceed to investigate the benefits that these species may gain from grouping with each other.
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Affiliation(s)
- Jonathan Syme
- Cetacean Ecology, Behaviour and Evolution Lab, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.
| | - Jeremy J Kiszka
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, FL, USA
| | - Guido J Parra
- Cetacean Ecology, Behaviour and Evolution Lab, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
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Suárez-Tangil BD, Rodríguez A. Environmental filtering drives the assembly of mammal communities in a heterogeneous Mediterranean region. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2801. [PMID: 36546604 DOI: 10.1002/eap.2801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/15/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Agricultural expansion and intensification are major drivers of global change. Quantifying the importance of different processes governing the assembly of local communities in agroecosystems is essential to guide the conservation effort allocated to enhancing habitat connectivity, improving habitat quality or managing species interactions. We used multiple detection methods to record the occurrence of medium-sized and large-sized mammals in three managed landscapes of a heterogeneous Mediterranean region. Then we used a joint species distribution model to evaluate the relative influence of dispersal limitation, environmental filtering, and interspecific interactions on the local assembly of mammal communities in 4-km2 plots. The partitioning of the explained variation in species occurrence was attributed on average 99% to environmental filters and 1% to dispersal filters. No role was attributed to biotic filters, in agreement with the scarce support for strong competition or other negative interactions found after a literature review. Four principal environmental factors explained on average 63% of variance in species occurrence and operated mainly at the landscape scale. The amount of shrub cover in the neighboring landscape was the most influential factor favoring mammal occurrence and accounted for nearly one-third of the total variance. The proportion of intensively managed croplands and proxies of human activity within landscape samples limited mammal presence. At the microhabitat scale (~80 m2 plots) the mean percentage area deprived of woody vegetation also had a negative effect. Functional traits such as body mass or social behavior accounted for a substantial fraction of the variation attributed to environmental factors. We concluded that multiscale environmental filtering governed local community assembly, whereas the role of dispersal limitation and interspecific interactions was negligible. Our results suggest that further removal of shrubland, the expansion of intensive agriculture, and the increase of human activity are expected to result in species losses. The fact that community integrity responds to a single type of ecological process simplifies practical recommendations. Management strategies should focus on the conservation and restoration of shrubland, adopting alternatives to intensive schemes of agricultural production, and minimizing recreational and other human activities in remnant natural habitats within agroecosystems or mosaic landscapes.
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Affiliation(s)
- Bruno D Suárez-Tangil
- Department of Conservation Biology, Estación Biológica de Doñana (EBD), CSIC, Sevilla, Spain
| | - Alejandro Rodríguez
- Department of Conservation Biology, Estación Biológica de Doñana (EBD), CSIC, Sevilla, Spain
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Riva F, Drapeau Picard AP, Larrivée M. Butterfly foraging is remarkably synchronous in an experimental tropical macrocosm. Biol Lett 2023; 19:20220555. [PMID: 36987612 PMCID: PMC10050915 DOI: 10.1098/rsbl.2022.0555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Diel patterns in foraging activity are dictated by a combination of abiotic, biotic and endogenous limits. Understanding these limits is important for insects because ectotherm taxa will respond more pronouncedly to ongoing climatic change, potentially affecting crucial ecosystem services. We leverage an experimental macrocosm, the Montreal Insectarium Grand Vivarium, to test the importance of endogenous mechanisms in determining temporal patterns in foraging activity of butterflies. Specifically, we assessed the degree of temporal niche partitioning among 24 butterfly species originating from the Earth's tropics within controlled environmental conditions. We found strong niche overlap, with the frequency of foraging events peaking around solar noon for 96% of the species assessed. Our models suggest that this result was not due to the extent of cloud cover, which affects radiational heating and thus limits body temperature in butterflies. Together, these findings suggest that an endogenous mechanism evolved to regulate the timing of butterfly foraging activity within suitable environmental conditions. Understanding similar mechanisms will be crucial to forecast the effects of climate change on insects, and thus on the many ecosystem services they provide.
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Affiliation(s)
- Federico Riva
- Montréal Insectarium - Space for Life, 4581, Rue Sherbrooke East, Montréal, Québec, Canada H1X 2B2
- Geomatics and Landscape Ecology Laboratory, Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6
| | | | - Maxim Larrivée
- Montréal Insectarium - Space for Life, 4581, Rue Sherbrooke East, Montréal, Québec, Canada H1X 2B2
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Contos P, Murphy NP, Gibb H. Whole-of-community invertebrate rewilding: Leaf litter transplants rapidly increase beetle diversity during restoration. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2779. [PMID: 36398530 DOI: 10.1002/eap.2779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/03/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Restoration of degraded areas is now a central tool in humanity's response to continued species-loss. However, restoration projects often report exceedingly slow or failed recolonization of fauna, especially dispersal-constrained groups such as invertebrates. Active interventions via reintroducing or "rewilding" invertebrates may assist recolonization and speed up restoration of communities toward a desired target. However, invertebrate rewilding is rarely implemented during ecological restoration. Here, we studied the efficacy of invertebrate rewilding as a means of reintroducing dispersal-constrained species and improving diversity and compositional similarities to remnant communities during restoration. Rewilding was conducted by transplanting leaf litter and soil, including associated communities of invertebrates from species rich remnant sites into species poor, and geographically isolated, revegetated farmland sites. We sampled pre- and post-rewilding invertebrate communities in remnant, rewilded revegetation, and control revegetation sites. We analyzed morphospecies richness, abundance, community composition, and modeled morphospecies traits (dispersal method/trophic guild) using a Hierarchical Modelling of Species Communities approach to determine which biological properties facilitated establishment. Beetle (Coleoptera) morphospecies richness increased rapidly in rewilded sites and was indistinguishable from remnant communities as early as 7 months post-rewilding. Beetle community similarity in the rewilding sites significantly deviated from the control sites 27 months post-rewilding, however remnant communities remained distinct over the study timeframe. Establishment success varied as other taxa did not respond as consistently as beetles within the study timeframe. Furthermore, there were no discernible shifts in dispersal traits in rewilded sites. However, predatory morphospecies were more likely to establish post-rewilding than other trophic groups. Our results demonstrate that the relatively simple act of transplanting leaf litter can result in comparatively large increases in morphospecies richness during restoration in a short timeframe. We advocate methodologies such as ours should be adopted more frequently to address failed community restoration as they are cost-effective and can be easily applied by practitioners in various restoration settings. However, further efficacy tests (e.g., varying the number of rewilding events) and longer study timeframes are needed to ensure effectiveness for a broader range of invertebrate taxa and ecosystems.
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Affiliation(s)
- Peter Contos
- Department of Environment and Genetics, and Centre for Future Landscapes, School of Agriculture, Biomedicine, and Environment, La Trobe University, Melbourne, Victoria, Australia
| | - Nicholas P Murphy
- Department of Environment and Genetics, and Centre for Future Landscapes, School of Agriculture, Biomedicine, and Environment, La Trobe University, Melbourne, Victoria, Australia
| | - Heloise Gibb
- Department of Environment and Genetics, and Centre for Future Landscapes, School of Agriculture, Biomedicine, and Environment, La Trobe University, Melbourne, Victoria, Australia
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Barrero A, Ovaskainen O, Traba J, Gómez‐Catasús J. Co‐occurrence patterns in a steppe bird community: insights into the role of dominance and competition. OIKOS 2023. [DOI: 10.1111/oik.09780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- Adrián Barrero
- Terrestrial Ecology Group, Dept of Ecology, Univ. Autónoma de Madrid (TEG-UAM) Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global, Univ. Autónoma de Madrid (CIBC‐UAM) Madrid Spain
| | - Otso Ovaskainen
- Dept of Biological and Environmental Science, Univ. of Jyväskylä Jyväskylä Finland
- Organismal and Evolutionary Biology Research Program, Univ. of Helsinki Helsinki Finland
| | - Juan Traba
- Terrestrial Ecology Group, Dept of Ecology, Univ. Autónoma de Madrid (TEG-UAM) Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global, Univ. Autónoma de Madrid (CIBC‐UAM) Madrid Spain
| | - Julia Gómez‐Catasús
- Terrestrial Ecology Group, Dept of Ecology, Univ. Autónoma de Madrid (TEG-UAM) Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global, Univ. Autónoma de Madrid (CIBC‐UAM) Madrid Spain
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37
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Weigel B, Kotamäki N, Malve O, Vuorio K, Ovaskainen O. Macrosystem community change in lake phytoplankton and its implications for diversity and function. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2023; 32:295-309. [PMID: 37081858 PMCID: PMC10107180 DOI: 10.1111/geb.13626] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 11/04/2022] [Accepted: 11/24/2022] [Indexed: 05/03/2023]
Abstract
Aim We use lake phytoplankton community data to quantify the spatio-temporal and scale-dependent impacts of eutrophication, land-use and climate change on species niches and community assembly processes while accounting for species traits and phylogenetic constraints. Location Finland. Time period 1977-2017. Major taxa Phytoplankton. Methods We use hierarchical modelling of species communities (HMSC) to model metacommunity trajectories at 853 lakes over four decades of environmental change, including a hierarchical spatial structure to account for scale-dependent processes. Using a "region of common profile" approach, we evaluate compositional changes of species communities and trait profiles and investigate their temporal development. Results We demonstrate the emergence of novel and widespread community composition clusters in previously more compositionally homogeneous communities, with cluster-specific community trait profiles, indicating functional differences. A strong phylogenetic signal of species responses to the environment implies similar responses among closely related taxa. Community cluster-specific species prevalence indicates lower taxonomic dispersion within the current dominant clusters compared with the historically dominant cluster and an overall higher prevalence of smaller species sizes within communities. Our findings denote profound spatio-temporal structuring of species co-occurrence patterns and highlight functional differences of lake phytoplankton communities. Main conclusions Diverging community trajectories have led to a nationwide reshuffling of lake phytoplankton communities. At regional and national scales, lakes are not single entities but metacommunity hubs in an interconnected waterscape. The assembly mechanisms of phytoplankton communities are strongly structured by spatio-temporal dynamics, which have led to novel community types, but only a minor part of this reshuffling could be linked to temporal environmental change.
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Affiliation(s)
- Benjamin Weigel
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | | | - Olli Malve
- Finnish Environment InstituteHelsinkiFinland
| | | | - Otso Ovaskainen
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and TechnologyTrondheimNorway
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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38
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Brian JI, Aldridge DC. Factors at multiple scales drive parasite community structure. J Anim Ecol 2023; 92:377-390. [PMID: 36421047 PMCID: PMC10098736 DOI: 10.1111/1365-2656.13853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022]
Abstract
Understanding how ecological communities are assembled remains a key goal of ecosystem ecology. Because communities are hierarchical, factors acting at multiple scales can contribute to patterns of community structure. Parasites provide a natural system to explore this idea, as they exist as discrete communities within host individuals, which are themselves part of a community and metacommunity. We aimed to understand the relative contribution of multi-scale drivers in parasite community assembly and assess how patterns at one level may mask those occurring at another. Specifically, we wanted to disentangle patterns caused by passive sampling from those determined by ecological drivers, and how these vary with scale. We applied a Markov Random Fields model and assessed measures of β-diversity and nestedness for 420 replicate parasite infracommunities (parasite assemblages in host individuals) across two freshwater mussel host species, three sites and two time periods, comparing our results to simulations from four different ecologically relevant null models. We showed that β-diversity between sites (explaining 25% of variation in parasite distribution) and host species (41%) is greater than expected, and β-diversity between individual hosts is smaller than expected, even after accounting for parasite prevalence and characteristics of host individuals. Furthermore, parasite communities were significantly less nested than expected once parasite prevalence and host characteristics were both accounted for, but more nested than expected otherwise, suggesting a degree of modularity at the within-host level that is masked if underlying host and parasite characteristics are not taken into account. The Markov Random Fields model provided evidence for possible competitive within-host parasite interactions, providing a mechanism for the observed infracommunity modularity. An integrative approach that examines factors at multiple scales is necessary to understand the composition of ecological communities. Furthermore, patterns at one level can alter the interpretation of ecologically important drivers at another if variation at higher scales is not accounted for.
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Affiliation(s)
- Joshua I Brian
- Aquatic Ecology Group, The David Attenborough Building, Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Geography, Bush House NE, King's College London, London, UK
| | - David C Aldridge
- Aquatic Ecology Group, The David Attenborough Building, Department of Zoology, University of Cambridge, Cambridge, UK
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Mondal S, Lee MA, Chen YK, Wang YC. Ensemble modeling of black pomfret ( Parastromateus niger) habitat in the Taiwan Strait based on oceanographic variables. PeerJ 2023; 11:e14990. [PMID: 36919168 PMCID: PMC10008307 DOI: 10.7717/peerj.14990] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/12/2023] [Indexed: 03/12/2023] Open
Abstract
The location, effort, number of captures, and time of fishing were all used in this study to assess the geographic distribution of Parastromateus niger in the Taiwan Strait. Other species distribution models performed worse than generalized linear models (GLMs) based on six oceanographic parameters. The sea surface temperature (SST) was between 26.5 °C and 29.5 °C, the sea surface chlorophyll (SSC) level was between 0.3-0.44 mg/m3, the sea surface salinity (SSS) was between 33.4 °C and 34.4 °C, the mixed layer depth was between 10 °C and 14 °C, the sea surface height was between 0.57 °C and 0.77 °C, and the eddy kinetic energy (EKE) was between 0.603 °C. According to the statistical findings, SST is merely a small effect compared to SSS, SSC level, and EKE in terms of impacting species distribution. By combining four effective single-algorithm models with no obvious bias, an ensemble habitat model was created. The ranges of 117°E-119°E and 22°N-24°N have the highest annual distributions of S.CPUE and nominal CPUE.
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Affiliation(s)
- Sandipan Mondal
- Environmental Biology & Fishery Science, National Taiwan Ocean University, Keelung, Taiwan.,Center of Excellence for Ocean Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Ming An Lee
- Environmental Biology & Fishery Science, National Taiwan Ocean University, Keelung, Taiwan.,Center of Excellence for Ocean Engineering, National Taiwan Ocean University, Keelung, Taiwan.,Doctoral Degree Program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung, Taiwan
| | - Yu-Kai Chen
- Coastal and Offshore Resource Research Center, Fisheries Research Institute, Council of Agriculture, Kaohsiung, Taiwan
| | - Yi-Chen Wang
- Environmental Biology & Fishery Science, National Taiwan Ocean University, Keelung, Taiwan.,Center of Excellence for Ocean Engineering, National Taiwan Ocean University, Keelung, Taiwan
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40
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Jurburg SD, Buscot F, Chatzinotas A, Chaudhari NM, Clark AT, Garbowski M, Grenié M, Hom EFY, Karakoç C, Marr S, Neumann S, Tarkka M, van Dam NM, Weinhold A, Heintz-Buschart A. The community ecology perspective of omics data. MICROBIOME 2022; 10:225. [PMID: 36510248 PMCID: PMC9746134 DOI: 10.1186/s40168-022-01423-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and β-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract.
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Affiliation(s)
- Stephanie D Jurburg
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Institute of Biology, Leipzig University, Leipzig, Germany.
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research- UFZ, Halle, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Narendrakumar M Chaudhari
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Adam T Clark
- Institute of Biology, University of Graz, Graz, Austria
| | - Magda Garbowski
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Botany, University of Wyoming, Wyoming, USA
| | - Matthias Grenié
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Erik F Y Hom
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, Oxford, Mississippi, USA
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Biology, Indiana University, Indiana, USA
| | - Susanne Marr
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle Wittenberg, Halle, Germany
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, Halle, Germany
| | - Steffen Neumann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, Halle, Germany
| | - Mika Tarkka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research- UFZ, Halle, Germany
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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Li Y, Fang Z, Yang F, Ji B, Li X, Wang S. Elevational changes in the bacterial community composition and potential functions in a Tibetan grassland. Front Microbiol 2022; 13:1028838. [DOI: 10.3389/fmicb.2022.1028838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022] Open
Abstract
In the Tibetan grasslands, the distribution patterns of the microbial community structure and function along elevation gradients have attracted considerable attention due to the wide distribution of mountain slopes, but the controlling factors of these patterns are still unclear. Here we investigated the taxonomy and potential functions of soil bacteria along an elevation gradient in a Tibetan mountainous grassland in 2 years, aiming to explore the elevation patterns of the bacterial structure and function and the underlying drivers. High-throughput sequencing and environment attribute measurements were conducted to survey the bacterial and environment characters. Furthermore, PICRUSt2 for prediction of bacterial functions, iCAMP for unraveling the drivers controlling community assembly, and HMSC for variance partitioning of bacterial community composition were used. Elevation did not significantly affect the bacterial diversity but changed their composition, driven by both deterministic and stochastic processes. In addition, elevation did not significantly affect the relative importance of deterministic and stochastic processes. Soil carbon, nitrogen, and temperature were important deterministic factors in driving bacterial community structure. The genus Solirubrobacter in Actinobacteriota was identified as most elevation discriminatory. Based on these observations, the bacterial community in the Tibetan mountainous grasslands was more controlled by edaphic factors than temperature, indicating their relative stability under climate change scenarios.
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42
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Eisen KE, Ma R, Raguso RA. Among- and within-population variation in morphology, rewards, and scent in a hawkmoth-pollinated plant. AMERICAN JOURNAL OF BOTANY 2022; 109:1794-1810. [PMID: 35762273 DOI: 10.1002/ajb2.16030] [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: 01/20/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Floral scent is a complex trait that mediates many plant-insect interactions, but our understanding of how floral scent variation evolves, either independently or in concert with other traits, remains limited. Assessing variation in floral scent at multiple levels of biological organization and comparing patterns of variation in scent to variation in other floral traits can contribute to our understanding of how scent variation evolves in nature. METHODS We used a greenhouse common garden experiment to investigate variation in floral scent at three scales-within plants, among plants, and among populations-and to determine whether scent, alone or in combination with morphology and rewards, contributes to population differentiation in Oenothera cespitosa subsp. marginata. Its range spans most of the biomes in the western United States, such that variation in both the abiotic and biotic environment could contribute to trait variation. RESULTS Multiple analytical approaches demonstrated substantial variation among and within populations in compound-specific and total floral scent measures. Overall, populations were differentiated in morphology and reward traits and in scent. Across populations, coupled patterns of variation in linalool, leucine-derived compounds, and hypanthium length are consistent with a long-tongued moth pollination syndrome. CONCLUSIONS The considerable variation in floral scent detected within populations suggests that, similar to other floral traits, variation in floral scent may have a heritable genetic component. Differences in patterns of population differentiation in floral scent and in morphology and rewards indicate that these traits may be shaped by different selective pressures.
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Affiliation(s)
- Katherine E Eisen
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Biology, Lund University, Lund, Sweden
| | - Rong Ma
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Robert A Raguso
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
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43
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Opedal ØH, Gross K, Chapurlat E, Parachnowitsch A, Joffard N, Sletvold N, Ovaskainen O, Friberg M. Measuring, comparing and interpreting phenotypic selection on floral scent. J Evol Biol 2022; 35:1432-1441. [PMID: 36177776 PMCID: PMC9828191 DOI: 10.1111/jeb.14103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 01/12/2023]
Abstract
Natural selection on floral scent composition is a key element of the hypothesis that pollinators and other floral visitors drive scent evolution. The measure of such selection is complicated by the high-dimensional nature of floral scent data and uncertainty about the cognitive processes involved in scent-mediated communication. We use dimension reduction through reduced-rank regression to jointly estimate a scent composite trait under selection and the strength of selection acting on this trait. To assess and compare variation in selection on scent across species, time and space, we reanalyse 22 datasets on six species from four previous studies. The results agreed qualitatively with previous analyses in terms of identifying populations and scent compounds subject to stronger selection but also allowed us to evaluate and compare the strength of selection on scent across studies. Doing so revealed that selection on floral scent was highly variable, and overall about as common and as strong as selection on other phenotypic traits involved in pollinator attraction or pollen transfer. These results are consistent with an important role of floral scent in pollinator attraction. Our approach should be useful for further studies of plant-animal communication and for studies of selection on other high-dimensional phenotypes. In particular, our approach will be useful for studies of pollinator-mediated selection on complex scent blends comprising many volatiles, and when no prior information on the physiological responses of pollinators to scent compounds is available.
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Affiliation(s)
| | - Karin Gross
- Department of Environment & BiodiversityParis Lodron University of SalzburgSalzburgAustria
| | - Elodie Chapurlat
- Plant Ecology and Evolution, Department of Ecology and Genetics, EBCUppsala UniversityUppsalaSweden,Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Amy Parachnowitsch
- Department of BiologyUniversity of New BrunswickFrederictonNew BrunswickCanada
| | - Nina Joffard
- University of Lille, UMR 8198 – Evo‐Eco‐PaleoLilleFrance
| | - Nina Sletvold
- Plant Ecology and Evolution, Department of Ecology and Genetics, EBCUppsala UniversityUppsalaSweden
| | - Otso Ovaskainen
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland,Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland,Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Magne Friberg
- Biodiversity Unit, Department of BiologyLund UniversityLundSweden
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Kidziński Ł, Hui FKC, Warton DI, Hastie T. Generalized Matrix Factorization: efficient algorithms for fitting generalized linear latent variable models to large data arrays. JOURNAL OF MACHINE LEARNING RESEARCH : JMLR 2022; 23:291. [PMID: 37102181 PMCID: PMC10129058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Unmeasured or latent variables are often the cause of correlations between multivariate measurements, which are studied in a variety of fields such as psychology, ecology, and medicine. For Gaussian measurements, there are classical tools such as factor analysis or principal component analysis with a well-established theory and fast algorithms. Generalized Linear Latent Variable models (GLLVMs) generalize such factor models to non-Gaussian responses. However, current algorithms for estimating model parameters in GLLVMs require intensive computation and do not scale to large datasets with thousands of observational units or responses. In this article, we propose a new approach for fitting GLLVMs to high-dimensional datasets, based on approximating the model using penalized quasi-likelihood and then using a Newton method and Fisher scoring to learn the model parameters. Computationally, our method is noticeably faster and more stable, enabling GLLVM fits to much larger matrices than previously possible. We apply our method on a dataset of 48,000 observational units with over 2,000 observed species in each unit and find that most of the variability can be explained with a handful of factors. We publish an easy-to-use implementation of our proposed fitting algorithm.
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Affiliation(s)
- Łukasz Kidziński
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Francis K C Hui
- Research School of Finance, Actuarial Studies and Statistics, The Australian National University, Canberra, ACT 2601, Australia
| | - David I Warton
- School of Mathematics and Statistics and Evolution & Ecology Research Centre, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Trevor Hastie
- Department of Statistics and Biomedical Data Science, Stanford University Stanford, CA 94305, USA
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45
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Liu X, Xu Q. Hydropeaking impacts on riverine plants downstream from the world's largest hydropower dam, the Three Gorges Dam. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157137. [PMID: 35803426 DOI: 10.1016/j.scitotenv.2022.157137] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Hydropeaking has become a global issue because of extensive hydropower dam construction worldwide. Yet, its ecological impacts on riverine ecosystems are not well studied. We explored the effects of hydropeaking on riverine plants, based on data from a ~300 km reach downstream of the world's largest hydropower dam, the Three Gorges Dam. We tested three hypotheses relating to hydropeaking impacts on species elevational distributions, assemblage structure and species-specific biomass patterns by generalized linear mixed modelling and joint species distribution modelling. We found that, first, hydropeaking greatly shaped species elevational ranges, leading to expansions of herbs to high elevations and shifting species dominance at low elevations. Secondly, we detected contrasting effects of hydropeaking on assemblage-level characteristics of herbs. The inundation induced by hydropeaking had strong effects on assemblage composition and biomass allocation, where more biomass was allocated to belowground part. Hydropeaking blurred the species richness-biomass relationship, although it had little effect on species richness or plot-level biomass. Thirdly, hydropeaking induced inundation was the most important covariate driving species biomass patterns of riverine plants, although complex species-specific effects were identified, and random effects were often large in fitted models. We concluded that hydropeaking likely acted as a major driver of plant community assembly in rivers with a hydropower dam. Conservation and restoration of riverine plants can benefit from the inclusion of water level management in operational schemes of hydropower dams, especially during the early life history stages.
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Affiliation(s)
- Xueqin Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China.
| | - Qiangqiang Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
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46
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Krawczyk AI, Röttjers S, Coimbra-Dores MJ, Heylen D, Fonville M, Takken W, Faust K, Sprong H. Tick microbial associations at the crossroad of horizontal and vertical transmission pathways. Parasit Vectors 2022; 15:380. [PMID: 36271430 PMCID: PMC9585727 DOI: 10.1186/s13071-022-05519-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbial communities can affect disease risk by interfering with the transmission or maintenance of pathogens in blood-feeding arthropods. Here, we investigated whether bacterial communities vary between Ixodes ricinus nymphs which were or were not infected with horizontally transmitted human pathogens. METHODS Ticks from eight forest sites were tested for the presence of Borrelia burgdorferi sensu lato, Babesia spp., Anaplasma phagocytophilum, and Neoehrlichia mikurensis by quantitative polymerase chain reaction (qPCR), and their microbiomes were determined by 16S rRNA amplicon sequencing. Tick bacterial communities clustered poorly by pathogen infection status but better by geography. As a second approach, we analysed variation in tick microorganism community structure (in terms of species co-infection) across space using hierarchical modelling of species communities. For that, we analysed almost 14,000 nymphs, which were tested for the presence of horizontally transmitted pathogens B. burgdorferi s.l., A. phagocytophilum, and N. mikurensis, and the vertically transmitted tick symbionts Rickettsia helvetica, Rickettsiella spp., Spiroplasma ixodetis, and Candidatus Midichloria mitochondrii. RESULTS With the exception of Rickettsiella spp., all microorganisms had either significant negative (R. helvetica and A. phagocytophilum) or positive (S. ixodetis, N. mikurensis, and B. burgdorferi s.l.) associations with M. mitochondrii. Two tick symbionts, R. helvetica and S. ixodetis, were negatively associated with each other. As expected, both B. burgdorferi s.l. and N. mikurensis had a significant positive association with each other and a negative association with A. phagocytophilum. Although these few specific associations do not appear to have a large effect on the entire microbiome composition, they can still be relevant for tick-borne pathogen dynamics. CONCLUSIONS Based on our results, we propose that M. mitochondrii alters the propensity of ticks to acquire or maintain horizontally acquired pathogens. The underlying mechanisms for some of these remarkable interactions are discussed herein and merit further investigation. Positive and negative associations between and within horizontally and vertically transmitted symbionts.
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Affiliation(s)
- Aleksandra Iwona Krawczyk
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3720 MA, Bilthoven, The Netherlands. .,Laboratory of Entomology, Wageningen University & Research, 6708PB, Wageningen, The Netherlands.
| | - Sam Röttjers
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Bacteriology, KU Leuven, Rega Institute for Medical Research, 3000, Leuven, Belgium
| | - Maria João Coimbra-Dores
- Centre for Environmental and Marine Studies (CESAM), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Dieter Heylen
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium.,Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Ln, Princeton, NJ, 08544, USA
| | - Manoj Fonville
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3720 MA, Bilthoven, The Netherlands
| | - Willem Takken
- Laboratory of Entomology, Wageningen University & Research, 6708PB, Wageningen, The Netherlands
| | - Karoline Faust
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Bacteriology, KU Leuven, Rega Institute for Medical Research, 3000, Leuven, Belgium
| | - Hein Sprong
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3720 MA, Bilthoven, The Netherlands.
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Mäenpää K, Wang S, Ilves M, El-Nezami H, Alenius H, Sinkko H, Karisola P. Skin microbiota of oxazolone-induced contact hypersensitivity mouse model. PLoS One 2022; 17:e0276071. [PMID: 36264944 PMCID: PMC9584374 DOI: 10.1371/journal.pone.0276071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/28/2022] [Indexed: 11/23/2022] Open
Abstract
Contact allergy is a common skin allergy, which can be studied utilising contact hypersensitivity (CHS) animal model. However, it is not clear, whether CHS is a suitable model to investigate skin microbiota interactions. We characterised the effect of contact dermatitis on the skin microbiota and studied the biological effects of oxazolone (OXA) -induced inflammation on skin thickness, immune cell numbers and changes of the microbiota in CHS mouse model (n = 72) for 28 days. Through 16S rRNA gene sequencing we defined the composition of bacterial communities and associations of bacteria with inflammation. We observed that the vehicle solution of acetone and olive oil induced bacterial community changes on day 1, and OXA-induced changes were observed mainly on day 7. Many of the notably enriched bacteria present in the OXA-challenged positive group represented the genus Faecalibaculum which were most likely derived from the cage environment. Additionally, skin inflammation correlated negatively with Streptococcus, which is considered a native skin bacterium, and positively with Muribacter muris, which is typical in oral environment. Skin inflammation favoured colonisation of cage-derived faecal bacteria, and additionally mouse grooming transferred oral bacteria on the skin. Due to the observed changes, we conclude that CHS model could be used for certain skin microbiome-related research set-ups. However, since vehicle exposure can alter the skin microbiome as such, future studies should include considerations such as careful control sampling and statistical tests to account for potential confounding factors.
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Affiliation(s)
- Kuunsäde Mäenpää
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Shuyuan Wang
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong
| | - Marit Ilves
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Hani El-Nezami
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong
| | - Harri Alenius
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
- Institute of Environmental Medicine (IMM), Karolinska Institutet, Stockholm, Sweden
| | - Hanna Sinkko
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Piia Karisola
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
- * E-mail:
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48
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Beyond Basic Diversity Estimates-Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data. Microorganisms 2022; 10:microorganisms10101961. [PMID: 36296237 PMCID: PMC9609705 DOI: 10.3390/microorganisms10101961] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022] Open
Abstract
Understanding microbial ecology through amplifying short read regions, typically 16S rRNA for prokaryotic species or 18S rRNA for eukaryotic species, remains a popular, economical choice. These methods provide relative abundances of key microbial taxa, which, depending on the experimental design, can be used to infer mechanistic ecological underpinnings. In this review, we discuss recent advancements in in situ analytical tools that have the power to elucidate ecological phenomena, unveil the metabolic potential of microbial communities, identify complex multidimensional interactions between species, and compare stability and complexity under different conditions. Additionally, we highlight methods that incorporate various modalities and additional information, which in combination with abundance data, can help us understand how microbial communities respond to change in a typical ecosystem. Whilst the field of microbial informatics continues to progress substantially, our emphasis is on popular methods that are applicable to a broad range of study designs. The application of these methods can increase our mechanistic understanding of the ongoing dynamics of complex microbial communities.
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Koziol A, Odriozola I, Nyholm L, Leonard A, San José C, Pauperio J, Ferreira C, Hansen AJ, Aizpurua O, Gilbert MTP, Alberdi A. Enriching captivity conditions with natural elements does not prevent the loss of wild‐like gut microbiota but shapes its compositional variation in two small mammals. Microbiologyopen 2022; 11:e1318. [PMCID: PMC9517064 DOI: 10.1002/mbo3.1318] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/08/2022] Open
Abstract
As continued growth in gut microbiota studies in captive and model animals elucidates the importance of their role in host biology, further pursuit of how to retain a wild‐like microbial community is becoming increasingly important to obtain representative results from captive animals. In this study, we assessed how the gut microbiota of two wild‐caught small mammals, namely Crocidura russula (Eulipotyphla, insectivore) and Apodemus sylvaticus (Rodentia, omnivore), changed when bringing them into captivity. We analyzed fecal samples of 15 A. sylvaticus and 21 C. russula, immediately after bringing them into captivity and 5 weeks later, spread over two housing treatments: a “natural” setup enriched with elements freshly collected from nature and a “laboratory” setup with sterile artificial elements. Through sequencing of the V3–V4 region of the 16S recombinant RNA gene, we found that the initial microbial diversity dropped during captivity in both species, regardless of treatment. Community composition underwent a change of similar magnitude in both species and under both treatments. However, we did observe that the temporal development of the gut microbiome took different trajectories (i.e., changed in different directions) under different treatments, particularly in C. russula, suggesting that C. russula may be more susceptible to environmental change. The results of this experiment do not support the use of microbially enriched environments to retain wild‐like microbial diversities and compositions, yet show that specific housing conditions can significantly affect the drift of microbial communities under captivity.
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Affiliation(s)
- Adam Koziol
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Iñaki Odriozola
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Lasse Nyholm
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Aoife Leonard
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Carlos San José
- Biodonostia Health Research Institute Donostia‐San Sebastian Spain
| | - Joana Pauperio
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado Universidade do Porto Vila do Conde Campus de Vairão Portugal
| | - Clara Ferreira
- Animal Ecology, Institute for Biochemistry and Biology University of Potsdam Potsdam Germany
| | - Anders J. Hansen
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - M. Thomas P. Gilbert
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
- University Museum, Norwegian University of Science and Technology Trondheim Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
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50
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Keppeler FW, Andrade MC, Trindade PAA, Sousa LM, Arantes CC, Winemiller KO, Jensen OP, Giarrizzo T. Early impacts of the largest Amazonian hydropower project on fish communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155951. [PMID: 35588808 DOI: 10.1016/j.scitotenv.2022.155951] [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: 03/17/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Hydropower is a threat to freshwater fishes. Despite a recent boom in dam construction, few studies have assessed their impact on mega-diverse tropical rivers. Using a before-after study design, we investigated the early impacts of the Belo Monte hydroelectric complex, the third-largest hydropower project in the world, on fishes of the Xingu River, a major clear-water tributary of the lower Amazon. We explored impacts across different river sectors (upstream, reservoir, reduced flow sector, and downstream) and spatial scales (individual sectors vs. all sectors combined) using joint species distribution models and different facets of diversity (taxonomic, functional, and phylogenetic). After 5 years of the Belo Monte operation, species richness declined ~12% in lentic and ~16% in lotic environments. Changes in abundance were of less magnitude (<4%). Effects were particularly negative for species of the families Serrasalmidae (mainly pacus), Anostomidae (headstanders), Auchenipteridae, and Pimelodidae (catfishes), whereas no taxonomic group consistently increased in richness or abundance. The reservoir and downstream sectors were the most impacted, with declines of ~24-29% in fish species richness, overall reductions in fish body size and trophic level, and a change in average body shape. Richness and abundance also declined in the reduced river flow, and changes in size, shape, and position of fins were observed. Relatively minor changes were found in the upstream sector. Variation in functional and phylogenetic diversity following river impoundment was subtle; however, across sectors, we found a reduction in functional divergence, indicating a decline in the abundance of species located near the extremities of community functional space. This may be the first sign of an environmental filtering process reducing functional diversity in the region. Greater changes in flow and habitats are expected as hydropower operations ramp up, and continued monitoring is warranted to understand the full scope and magnitude of ecological impacts.
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Affiliation(s)
- Friedrich W Keppeler
- Center for Limnology, University of Wisconsin-Madison, Madison, WI, USA; Núcleo de Ecologia Aquática e Pesca da Amazônia, Federal University of Pará, Belém, Pará, Brazil.
| | - Marcelo C Andrade
- Núcleo de Ecologia Aquática e Pesca da Amazônia, Federal University of Pará, Belém, Pará, Brazil
| | - Paulo A A Trindade
- Núcleo de Ecologia Aquática e Pesca da Amazônia, Federal University of Pará, Belém, Pará, Brazil
| | - Leandro M Sousa
- Laboratório de Ictiologia de Altamira, Federal University of Pará, Altamira, Pará, Brazil
| | - Caroline C Arantes
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
| | - Kirk O Winemiller
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
| | - Olaf P Jensen
- Center for Limnology, University of Wisconsin-Madison, Madison, WI, USA
| | - Tommaso Giarrizzo
- Núcleo de Ecologia Aquática e Pesca da Amazônia, Federal University of Pará, Belém, Pará, Brazil; Instituto de Ciências do Mar (LABOMAR), Federal University of Ceará, Fortaleza, Brazil
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