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Luo T, Li L, Wang Q, Liu W, Guo J, Yan Y, Chris N, Zhou Y, Zhao J. The changes in zoological publication rates and focal subdisciplines between 1960 and 2022. Integr Zool 2024. [PMID: 39075983 DOI: 10.1111/1749-4877.12883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Since ancient times, zoology, as the branch of biology dealing with animals, has been a cornerstone of natural science and has developed substantially over the last century. We conducted a bibliometric analysis using structural topic modeling (STM) to determine changes in the representation of principal zoological subdisciplines in the literature between 1960 and 2022. We collated a corpus of 217 414 articles from 88 top-ranked zoology journals and identified three main fields: (i) ecology, (ii) evolution, and (iii) applied research. Within these, we identified 10 major subdisciplines. The number of studies published per year grew from 118 in 1960 to 6635 in 2022. Macroscale-related subdisciplines increased while classical and traditional subdisciplines decreased. Mammals (34.4%) and insects (18.1%) were the dominant taxa covered, followed by birds (15.2%) and fish (8.0%). Research on mammals, insects, and fish involved a broad range of subdisciplines, whereas studies of birds focused on ecological subdisciplines. Most publications were from the United States, followed by the United Kingdom, Germany, Canada, Australia, China, and Japan, with two developing countries, China and South Africa among the top 15 countries. There were different subdiscipline biases between countries, and the gross domestic product of each country correlated positively with its publication output (R2 = 0.681). We discuss our findings in the context of advances in technological innovations and computing power, as well as the emergence of ecology as a formal sister discipline, driven by changing environmental pressures and societal values. We caution that valuable publications from traditional zoological fields must not be completely supplanted by more contemporary topics and increasingly sophisticated analyses.
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Affiliation(s)
- Tianbao Luo
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang, China
| | - Liyu Li
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang, China
| | - Qian Wang
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang, China
| | - Wentong Liu
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang, China
| | - Jinyu Guo
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang, China
| | - Yimei Yan
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang, China
| | - Newman Chris
- Wildlife Conservation Research Unit, Department of Biology, University of Oxford, Oxford, UK
| | - Youbing Zhou
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang, China
- Hubei International Scientific and Technological Cooperation Center of Ecological Conservation and Management in Three Gorges Area, China Three Gorges University, Yichang, China
| | - Jin Zhao
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang, China
- Hubei International Scientific and Technological Cooperation Center of Ecological Conservation and Management in Three Gorges Area, China Three Gorges University, Yichang, China
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Meng J, Xu F, Yang H, Li X, Zhao P. Exploring microbiome and plankton responses and interactions in the mangrove ecosystem through eDNA and network analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172581. [PMID: 38641112 DOI: 10.1016/j.scitotenv.2024.172581] [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: 01/09/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 04/21/2024]
Abstract
The comprehensive analysis of multiple biological communities is essential for assessing diversities within mangrove ecosystems, yet such studies are infrequent. Environmental DNA (eDNA) facilitates the simultaneous exploration of organisms across various levels within a single ecosystem. In this investigation, 16S rRNA, cytochrome C oxidase I (COI), and Mito-fish primers were employed to characterize the microbiome, eukaryotic plankton, and fish communities, along with their intricate interactions, across 24 samples from three Chinese mangrove reservoirs. The resulting dataset encompasses 3779 taxonomic groups (genus level), spanning from the microbiome to vertebrates. Diversity analysis unveiled a higher level of stability in the microbiome community compared to plankton, underscoring the superior site-specificity of plankton. The association analysis revealed that biodiversity was primarily affected by temperature, turbidity, and fluorescent dissolved organic matter (fDOM). Notably, the physicochemical factors, turbidity, and fDOM had a more pronounced impact on the microbiome than on plankton, explaining their distinct sensitivities to site-specific conditions. Network analysis constructed 15 biological interaction subnetworks representing various community connections. The most connected genera in each subnetwork, highly responsive to different environmental factors, could serve as potential indicators of distinct ecosystem states. In summary, our findings represent the first comparison of the response sensitivities of different communities and the construction of their interaction networks in mangrove environments. These results contribute valuable insights into marine ecosystem dynamics and the role of environmental factors in shaping biodiversity.
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Affiliation(s)
- Jie Meng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Fei Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Wuhan, China
| | - Haijie Yang
- School of Marine Science and Engineering, Hainan University, Haikou 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Xiaoxu Li
- School of Marine Science and Engineering, Hainan University, Haikou 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Peng Zhao
- School of Marine Science and Engineering, Hainan University, Haikou 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
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Weber S, Stothut M, Mahla L, Kripp A, Hirschler L, Lenz N, Junker A, Künzel S, Krehenwinkel H. Plant-derived environmental DNA complements diversity estimates from traditional arthropod monitoring methods but outperforms them detecting plant-arthropod interactions. Mol Ecol Resour 2024; 24:e13900. [PMID: 38010630 DOI: 10.1111/1755-0998.13900] [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: 06/10/2023] [Revised: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 11/29/2023]
Abstract
Our limited knowledge about the ecological drivers of global arthropod decline highlights the urgent need for more effective biodiversity monitoring approaches. Monitoring of arthropods is commonly performed using passive trapping devices, which reliably recover diverse communities, but provide little ecological information on the sampled taxa. Especially the manifold interactions of arthropods with plants are barely understood. A promising strategy to overcome this shortfall is environmental DNA (eDNA) metabarcoding from plant material on which arthropods leave DNA traces through direct or indirect interactions. However, the accuracy of this approach has not been sufficiently tested. In four experiments, we exhaustively test the comparative performance of plant-derived eDNA from surface washes of plants and homogenized plant material against traditional monitoring approaches. We show that the recovered communities of plant-derived eDNA and traditional approaches only partly overlap, with eDNA recovering various additional taxa. This suggests eDNA as a useful complementary tool to traditional monitoring. Despite the differences in recovered taxa, estimates of community α- and β-diversity between both approaches are well correlated, highlighting the utility of eDNA as a broad scale tool for community monitoring. Last, eDNA outperforms traditional approaches in the recovery of plant-specific arthropod communities. Unlike traditional monitoring, eDNA revealed fine-scale community differentiation between individual plants and even within plant compartments. Especially specialized herbivores are better recovered with eDNA. Our results highlight the value of plant-derived eDNA analysis for large-scale biodiversity assessments that include information about community-level interactions.
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Affiliation(s)
- Sven Weber
- Department of Biogeography, Trier University, Trier, Germany
| | - Manuel Stothut
- Department of Biogeography, Trier University, Trier, Germany
| | - Lisa Mahla
- Department of Biogeography, Trier University, Trier, Germany
| | - Alanah Kripp
- iES Landau, Institute for Environmental Sciences, University of Kaiserslautern-Landau, Landau in der Pfalz, Germany
| | - Lena Hirschler
- Department of Biogeography, Trier University, Trier, Germany
| | - Nina Lenz
- Department of Biogeography, Trier University, Trier, Germany
| | - Anneke Junker
- Department of Biogeography, Trier University, Trier, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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Eisenhauer N, Ochoa-Hueso R, Huang Y, Barry KE, Gebler A, Guerra CA, Hines J, Jochum M, Andraczek K, Bucher SF, Buscot F, Ciobanu M, Chen H, Junker R, Lange M, Lehmann A, Rillig M, Römermann C, Ulrich J, Weigelt A, Schmidt A, Türke M. Ecosystem consequences of invertebrate decline. Curr Biol 2023; 33:4538-4547.e5. [PMID: 37757832 DOI: 10.1016/j.cub.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/21/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]
Abstract
Human activities cause substantial changes in biodiversity.1,2 Despite ongoing concern about the implications of invertebrate decline,3,4,5,6,7 few empirical studies have examined the ecosystem consequences of invertebrate biomass loss. Here, we test the responses of six ecosystem services informed by 30 above- and belowground ecosystem variables to three levels of aboveground (i.e., vegetation associated) invertebrate community biomass (100%, 36%, and 0% of ambient biomass) in experimental grassland mesocosms in a controlled Ecotron facility. In line with recent reports on invertebrate biomass loss over the last decade, our 36% biomass treatment also represented a decrease in invertebrate abundance (-70%) and richness (-44%). Moreover, we simulated the pronounced change in invertebrate biomass and turnover in community composition across the season. We found that the loss of invertebrate biomass decreases ecosystem multifunctionality, including two critical ecosystem services, aboveground pest control and belowground decomposition, while harvested plant biomass increases, likely because less energy was channeled up the food chain. Moreover, communities and ecosystem functions become decoupled with a lower biomass of invertebrates. Our study shows that invertebrate loss threatens the integrity of grasslands by decoupling ecosystem processes and decreasing ecosystem-service supply.
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Affiliation(s)
- Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany.
| | - Raúl Ochoa-Hueso
- Department of Biology, IVAGRO, University of Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Campus Del Rio San Pedro, 11510 Puerto Real, Cádiz, Spain; Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, the Netherlands
| | - Yuanyuan Huang
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
| | - Kathryn E Barry
- Ecology and Biodiversity; Department of Environmental Biology, Faculty of Science, Utrecht University Padualaan, 8 3584 CH Utrecht, the Netherlands
| | - Alban Gebler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
| | - Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
| | - Jes Hines
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
| | - Malte Jochum
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
| | - Karl Andraczek
- Systematic Botany and Functional Biodiversity, Leipzig University, Johannisallee 21, 04103 Leipzig, Germany
| | - Solveig Franziska Bucher
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Ecology and Evolution, Plant Biodiversity Group, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - Marcel Ciobanu
- Institute of Biological Research, Branch of the National Institute of Research and Development for Biological Sciences, 48 Republicii Street, 400015 Cluj-Napoca, Romania
| | - Hongmei Chen
- Systematic Botany and Functional Biodiversity, Leipzig University, Johannisallee 21, 04103 Leipzig, Germany; Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Robert Junker
- Evolutionary Ecology of Plants, Department of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Markus Lange
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Anika Lehmann
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research, Altensteinstr. 6, 14195 Berlin, Germany
| | - Matthias Rillig
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research, Altensteinstr. 6, 14195 Berlin, Germany
| | - Christine Römermann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Ecology and Evolution, Plant Biodiversity Group, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Josephine Ulrich
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Ecology and Evolution, Plant Biodiversity Group, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Alexandra Weigelt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Systematic Botany and Functional Biodiversity, Leipzig University, Johannisallee 21, 04103 Leipzig, Germany
| | - Anja Schmidt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany; Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - Manfred Türke
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biological and Medical Imaging, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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Krehenwinkel H, Weber S, Künzel S, Kennedy SR. The bug in a teacup-monitoring arthropod-plant associations with environmental DNA from dried plant material. Biol Lett 2022; 18:20220091. [PMID: 35702982 PMCID: PMC9198770 DOI: 10.1098/rsbl.2022.0091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Environmental DNA analysis (eDNA) has revolutionized the field of biomonitoring in the past years. Various sources have been shown to contain eDNA of diverse organisms, for example, water, soil, gut content and plant surfaces. Here we show that dried plant material is a highly promising source for arthropod community eDNA. We designed a metabarcoding assay to enrich diverse arthropod communities while preventing amplification of plant DNA. Using this assay, we analysed various commercially produced teas and herbs. These samples recovered ecologically and taxonomically diverse arthropod communities, a total of over a thousand species in more than 20 orders, many of them specific to their host plant and its geographical origin. Atypically for eDNA, arthropod DNA in dried plants shows very high temporal stability, opening up plant archives as a source for historical arthropod eDNA. Considering these results, dried plant material appears excellently suited as a novel tool to monitor arthropods and arthropod–plant interactions, detect agricultural pests and identify the geographical origin of imported plant material. The simplicity of our approach and the ability to detect highly diverse arthropod communities from all over the world in tea bags also highlights its utility for outreach purposes and to raise awareness about biodiversity.
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Affiliation(s)
| | | | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Ploen, Germany
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