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Eberly JO, Hurd A, Oli D, Dyer AT, Seipel TF, Carr PM. Compositional profiling of the rhizosphere microbiome of Canada thistle reveals consistent patterns across the United States northern Great Plains. Sci Rep 2024; 14:18016. [PMID: 39097653 DOI: 10.1038/s41598-024-69082-3] [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: 03/14/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024] Open
Abstract
Canada thistle is a pervasive perennial weed, causing challenges to agricultural and natural ecosystems globally. Although research has focused on the phenology, genetics, and control of Canada thistle, little is known about the rhizosphere microbiome and the role plant-microbe interactions play in invasion success. This study investigated the rhizosphere microbiome of Canada thistle across diverse climates, soils, and crops in the U.S. northern Great Plains. Soil and rhizosphere samples were collected and bacterial 16S and fungal ITS2 sequencing were performed to characterize the core microbiome and identify potential factors contributing to invasion success. Amplicon sequencing revealed a stable core microbiome that was detected in the Canada thistle rhizosphere across all locations. The core microbiome was dominated by the bacterial phyla Actinobacteriota and Proteobacteria and fungal phyla Ascomycota and Basidiomycota. Differential abundance analysis showed rhizosphere fungal communities were enriched in pathogen-containing genera with a 1.7-fold greater abundance of Fusaria and a 2.6-fold greater abundance of Gibberella compared to bulk soil. Predictive functional profiling showed rhizosphere communities were enriched (p < 0.05, FDR corrected) in plant pathogen fungal guilds which represented 19% of the fungal community. The rhizosphere microbiome was similar in composition across environments, highlighting the stable association between Canada thistle and specific microbial taxa. This study characterized the core microbiome of Canada thistle, and the findings highlight plant-microbe interactions shaping invasive behavior. These findings are important for understanding the ecological impacts of plant invasion and soil-microbe ecological processes.
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Affiliation(s)
- Jed O Eberly
- Central Agricultural Research Center, Montana State University, Moccasin, MT, USA.
| | - Asa Hurd
- Central Agricultural Research Center, Montana State University, Moccasin, MT, USA
| | - Dipiza Oli
- Department of Plant Science and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Alan T Dyer
- Department of Plant Science and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Tim F Seipel
- Department of Land Resources and Environmental Science, Montana State University, Bozeman, MT, USA
| | - Patrick M Carr
- Central Agricultural Research Center, Montana State University, Moccasin, MT, USA
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2
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Tuong ZK, van der Merwe R, Canete PF, Roco JA. Computational estimation of clonal diversity in autoimmunity. Immunol Cell Biol 2024. [PMID: 39010261 DOI: 10.1111/imcb.12801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/17/2024]
Abstract
Diversity is the cornerstone of the adaptive immune system, crucial for its effectiveness against constantly evolving pathogens that pose threats to higher vertebrates. Accurately measuring and interpreting this diversity presents challenges for immunologists, as changes in diversity and clonotype composition can tip the balance between protective immunity and autoimmunity. In this review, we present the current methods commonly used to measure diversity from single-cell T-cell receptor and B-cell receptor sequencing. We also discuss two case studies where single-cell sequencing and diversity estimations have led to breakthroughs in autoimmune disease discovery and therapeutic innovation, and reflect upon the necessity and importance of accurately defining and measuring lymphocyte diversity in these contexts.
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Affiliation(s)
- Zewen Kelvin Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Rohan van der Merwe
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Pablo F Canete
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Jonathan A Roco
- Biological Data Science Institute, College of Science, The Australian National University, Canberra, ACT, Australia
- Clinical Hub for Interventional Research, College of Health & Medicine, The Australian National University, Canberra, ACT, Australia
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Kumar A, Kumar P, Patil M, Hussain S, Yadav R, Sharma S, Tokas D, Singh S, Singh AN. Disturbance and vegetational structure in an urban forest of Indian Siwaliks: an ecological assessment. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:691. [PMID: 38960930 DOI: 10.1007/s10661-024-12801-0] [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: 06/28/2023] [Accepted: 06/08/2024] [Indexed: 07/05/2024]
Abstract
Urban forests face multiple human-mediated pressures leading to compromised ecosystem structure and functioning. Therefore, understanding ecosystem structure in response to ongoing pressures is crucial for sustaining ecological integrity and human well-being. We aim to assess the disturbance and its effects on the vegetation structure of urban forests in Chandigarh using a combination of remote sensing techniques and vegetation surveys. The disturbance was evaluated as a change in NDVI (Normalised Difference Vegetation Index) from 2001 to 2021 by applying the BFAST (Breaks For Additive Season and Trend) algorithm to the MODIS satellite imagery data. A vegetation survey was conducted to compare the species composition, taxonomic and phylogenetic diversity as measures of forest vegetational structure. While signals of disturbance were evident, the changes in vegetation structure were not well established from our study. Further, this analysis indicated no significant differences in vegetation composition due to disturbance (F1,12 = 0.91, p = 0.575). However, the phylogenetic diversity was substantially lower for disturbed plots than undisturbed plots, though the taxonomic diversity was similar among the disturbed and undisturbed plots. Our results confirmed that disturbance effects are more prominent on the phylogenetic than taxonomic diversity. These findings can be considered early signals of disturbance and its impact on the vegetation structure of urban forests and contribute to the knowledge base on urban ecosystems. Our study has implications for facilitating evidence-based decision-making and the development of sustainable management strategies for urban forest ecosystems.
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Affiliation(s)
- Abhishek Kumar
- Soil Ecosystem and Restoration Ecology Lab, Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Pardeep Kumar
- Soil Ecosystem and Restoration Ecology Lab, Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Meenu Patil
- Soil Ecosystem and Restoration Ecology Lab, Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Sabir Hussain
- Soil Ecosystem and Restoration Ecology Lab, Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Rajni Yadav
- Soil Ecosystem and Restoration Ecology Lab, Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Sheenu Sharma
- Soil Ecosystem and Restoration Ecology Lab, Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Diksha Tokas
- Soil Ecosystem and Restoration Ecology Lab, Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Siril Singh
- Department of Environment Studies, Panjab University, Chandigarh, 160014, India
| | - Anand Narain Singh
- Soil Ecosystem and Restoration Ecology Lab, Department of Botany, Panjab University, Chandigarh, 160014, India.
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Zhuravleva EA, Shekhurdina SV, Laikova A, Kotova IB, Loiko NG, Popova NM, Kriukov E, Kovalev AA, Kovalev DA, Katraeva IV, Vivekanand V, Awasthi MK, Litti YV. Enhanced thermophilic high-solids anaerobic digestion of organic fraction of municipal solid waste with spatial separation from conductive materials in a single reactor volume. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 363:121434. [PMID: 38861886 DOI: 10.1016/j.jenvman.2024.121434] [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: 02/08/2024] [Revised: 05/22/2024] [Accepted: 06/07/2024] [Indexed: 06/13/2024]
Abstract
Despite benefits such as lower water and working volume requirements, thermophilic high solids anaerobic digestion (THSAD) often fails due to the rapid build-up of volatile fatty acids (VFAs) and the associated drop in pH. Use of conductive materials (CM) can promote THSAD through stimulation of direct interspecies electron transfer (DIET), while the need for their constant dosing due to poor separation from effluent impairs economic feasibility. This study used an approach of spatially separating magnetite and granular activated carbon (GAC) from the organic fraction of municipal solid waste (OFMSW) in a single reactor for THSAD. GAC and magnetite addition could both mitigate the severe inhibition of methanogenesis after VFAs build-up to ∼28-30 g/L, while negligible methane production was observed in the control group. The highest methane yield (286 mL CH4/g volatile solids (VS)) was achieved in magnetite-added reactors, while the highest maximum CH4 production rates (26.38 mL CH4/g VS/d) and lowest lag-phase (2.83 days) were obtained in GAC-added reactors. The enrichment of GAC and magnetite biofilms with various syntrophic and potentially electroactive microbial groups (Ruminiclostridium 1, Clostridia MBA03, Defluviitoga, Lentimicrobiaceae) in different relative abundances indicates the existence of specific preferences of these groups for the nature of CM. According to predicted basic metabolic functions, CM can enhance cellular processes and signals, lipid transport and metabolism, and methane metabolism, resulting in improved methane production. Rearrangement of metabolic pathways, formation of pili-like structures, enrichment of biofilms with electroactive groups and a significant improvement in THSAD performance was attributed to the enhancement of the DIET pathway. Promising results obtained in this work due to the spatial separation of the bulk OFMSW and CM can be useful for modeling larger-scale THSAD systems with better recovery of CM and cost-effectiveness.
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Affiliation(s)
- Elena A Zhuravleva
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2 117312 Moscow, Russia.
| | - Svetlana V Shekhurdina
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2 117312 Moscow, Russia.
| | - Aleksandra Laikova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2 117312 Moscow, Russia.
| | - Irina B Kotova
- Department of Biology, Lomonosov Moscow State University, Vorob'jovy gory, 119899 Moscow, Russia.
| | - Natalia G Loiko
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2 117312 Moscow, Russia.
| | - Nadezhda M Popova
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, 31, bld.4, Leninsky prospect, 119071 Moscow, Russia.
| | - Emil Kriukov
- Sechenov First Moscow State Medical University, 8-2 Trubetskaya str. 119435 Moscow, Russia.
| | - Andrey A Kovalev
- Federal Scientific Agroengineering Center VIM, 1st Institutsky proezd, 5,109428 Moscow, Russia.
| | - Dmitriy A Kovalev
- Federal Scientific Agroengineering Center VIM, 1st Institutsky proezd, 5,109428 Moscow, Russia.
| | - Inna V Katraeva
- Department of Water Supply, Sanitation, Engineering Ecology and Chemistry, Nizhny Novgorod State University of Architecture and Civil Engineering, Nizhny Novgorod, 603000, Russia.
| | - Vivekanand Vivekanand
- Centre for Energy and Environment, Malaviya National Institute of Technology Jaipur, Jaipur, 302017, Rajasthan, India.
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environmental, Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi, 71200, China.
| | - Yuriy V Litti
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2 117312 Moscow, Russia.
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Wellenbeck A, Fehrmann L, Feilhauer H, Schmidtlein S, Misof B, Hein N. Discriminating woody species assemblages from National Forest Inventory data based on phylogeny in Georgia. Ecol Evol 2024; 14:e11569. [PMID: 39045499 PMCID: PMC11264350 DOI: 10.1002/ece3.11569] [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: 03/04/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 07/25/2024] Open
Abstract
Classifications of forest vegetation types and characterization of related species assemblages are important analytical tools for mapping and diversity monitoring of forest communities. The discrimination of forest communities is often based on β-diversity, which can be quantified via numerous indices to derive compositional dissimilarity between samples. This study aims to evaluate the applicability of unsupervised classification for National Forest Inventory data from Georgia by comparing two cluster hierarchies. We calculated the mean basal area per hectare for each woody species across 1059 plot observations and quantified interspecies distances for all 87 species. Following an unspuervised cluster analysis, we compared the results derived from the species-neutral dissimilarity (Bray-Curtis) with those based on the Discriminating Avalanche dissimilarity, which incorporates interspecies phylogenetic variation. Incorporating genetic variation in the dissimilarity quantification resulted in a more nuanced discrimination of woody species assemblages and increased cluster coherence. Favorable statistics include the total number of clusters (23 vs. 20), mean distance within clusters (0.773 vs. 0.343), and within sum of squares (344.13 vs. 112.92). Clusters derived from dissimilarities that account for genetic variation showed a more robust alignment with biogeographical units, such as elevation and known habitats. We demonstrate that the applicability of unsupervised classification of species assemblages to large-scale forest inventory data strongly depends on the underlying quantification of dissimilarity. Our results indicate that by incorporating phylogenetic variation, a more precise classification aligned with biogeographic units is attained. This supports the concept that the genetic signal of species assemblages reflects biogeographical patterns and facilitates more precise analyses for mapping, monitoring, and management of forest diversity.
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Affiliation(s)
- Alexander Wellenbeck
- Systematic ZoologyUniversity of BonnBonnGermany
- Forest Inventory and Remote SensingUniversity of GöttingenGöttingenGermany
| | - Lutz Fehrmann
- Forest Inventory and Remote SensingUniversity of GöttingenGöttingenGermany
| | - Hannes Feilhauer
- Remote Sensing Centre for Earth System Research (RSC4Earth)Leipzig UniversityLeipzigGermany
| | - Sebastian Schmidtlein
- Institute of Geography and GeoecologyKarlsruhe Institute of Technology (KIT)KarlsruheGermany
| | - Bernhard Misof
- Systematic ZoologyUniversity of BonnBonnGermany
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)Museum KoenigBonnGermany
| | - Nils Hein
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)Museum KoenigBonnGermany
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Drake VA, Hao Z, Wang H. Monitoring insect numbers and biodiversity with a vertical-beam entomological radar. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230117. [PMID: 38705193 PMCID: PMC11070261 DOI: 10.1098/rstb.2023.0117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/06/2024] [Indexed: 05/07/2024] Open
Abstract
Concerns about perceived widespread declines in insect numbers have led to recognition of a requirement for long-term monitoring of insect biodiversity. Here we examine whether an existing, radar-based, insect monitoring system developed for research on insect migration could be adapted to this role. The radar detects individual larger (greater than 10 mg) insects flying at heights of 150-2550 m and estimates their size and mass. It operates automatically and almost continuously through both day and night. Accumulation of data over a 'half-month' (approx. 15 days) averages out weather effects and broadens the source area of the wind-borne observation sample. Insect counts are scaled or interpolated to compensate for missed observations; adjustment for variation of detectability with range and insect size is also possible. Size distributions for individual days and nights exhibit distinct peaks, representing different insect types, and Simpson and Shannon-Wiener indices of biodiversity are calculated from these. Half-month count, biomass and index statistics exhibit variations associated with the annual cycle and year to year changes that can be attributed to drought and periods of high rainfall. While species-based biodiversity measures cannot be provided, the radar's capacity to estimate insect biomass over a wide area indicates utility for tracking insect population sizes. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- V. Alistair Drake
- School of Science, The University of New South Wales, Canberra, ACT 2610, Australia
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia
| | - Zhenhua Hao
- School of Science, The University of New South Wales, Canberra, ACT 2610, Australia
- Australian Bureau of Agricultural and Resource Economics and Science, Australian Government, Canberra, ACT 2601, Australia
| | - Haikou Wang
- Australian Plague Locust Commission, Department of Agriculture, Fisheries and Forestry, Australian Government, Canberra, ACT 2601, Australia
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Michl K, David C, Dumont B, Mårtensson LMD, Rasche F, Berg G, Cernava T. Determining the footprint of breeding in the seed microbiome of a perennial cereal. ENVIRONMENTAL MICROBIOME 2024; 19:40. [PMID: 38886863 PMCID: PMC11184768 DOI: 10.1186/s40793-024-00584-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Seed endophytes have a significant impact on plant health and fitness. They can be inherited and passed on to the next plant generation. However, the impact of breeding on their composition in seeds is less understood. Here, we studied the indigenous seed microbiome of a recently domesticated perennial grain crop (Intermediate wheatgrass, Thinopyrum intermedium L.) that promises great potential for harnessing microorganisms to enhance crop performance by a multiphasic approach, including amplicon and strain libraries, as well as molecular and physiological assays. RESULTS Intermediate wheatgrass seeds harvested from four field sites in Europe over three consecutive years were dominated by Proteobacteria (88%), followed by Firmicutes (10%). Pantoea was the most abundant genus and Pantoea agglomerans was identified as the only core taxon present in all samples. While bacterial diversity and species richness were similar across all accessions, the relative abundance varied especially in terms of low abundant and rare taxa. Seeds from four different breeding cycles (TLI C3, C5, C704, C801) showed significant differences in bacterial community composition and abundance. We found a decrease in the relative abundance of the functional genes nirK and nifH as well as a drop in bacterial diversity and richness. This was associated with a loss of amplicon sequence variants (ASVs) in Actinobacteria, Alphaproteobacteria, and Bacilli, which could be partially compensated in offspring seeds, which have been cultivated at a new site. Interestingly, only a subset assigned to potentially beneficial bacteria, e.g. Pantoea, Kosakonia, and Pseudomonas, was transmitted to the next plant generation or shared with offspring seeds. CONCLUSION Overall, this study advances our understanding of the assembly and transmission of endophytic seed microorganisms in perennial intermediate wheatgrass and highlights the importance of considering the plant microbiome in future breeding programs.
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Affiliation(s)
- Kristina Michl
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Christophe David
- Department of Agroecosystems, Environment and Production, ISARA, 23 rue Jean Baldassini, Lyon Cedex 07, 69364, France
| | - Benjamin Dumont
- Plant Sciences Axis, Crop Science lab, ULiege - Gembloux Agro-Bio Tech, Gembloux, B- 5030, Belgium
| | | | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, 70593, Stuttgart, Germany
- International Institute of Tropical Agriculture, P.O. Box 30772-00100, Nairobi, Kenya
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
- Leibnitz-Institute for Agricultural Engineering, 14469, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria.
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO171BJ, UK.
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Tiffeau-Mayer A. Unbiased estimation of sampling variance for Simpson's diversity index. Phys Rev E 2024; 109:064411. [PMID: 39020976 DOI: 10.1103/physreve.109.064411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 06/03/2024] [Indexed: 07/20/2024]
Abstract
Quantification of measurement uncertainty is crucial for robust scientific inference, yet accurate estimates of this uncertainty remain elusive for ecological measures of diversity. Here, we address this longstanding challenge by deriving a closed-form unbiased estimator for the sampling variance of Simpson's diversity index. In numerical tests the estimator consistently outperforms existing approaches, particularly for applications in which species richness exceeds sample size. We apply the estimator to quantify biodiversity loss in marine ecosystems and to demonstrate ligand-dependent contributions of T-cell-receptor chains to specificity, illustrating its versatility across fields. The novel estimator provides researchers with a reliable method for comparing diversity between samples, essential for quantifying biodiversity trends and making informed conservation decisions.
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Medina-Espinoza EF, Juen L, Calvão LB, Arellano Cruz G. Variations in the Odonata Assemblages: How Do the Dry Season and Water Bodies Influence Them? NEOTROPICAL ENTOMOLOGY 2024; 53:630-640. [PMID: 38656590 DOI: 10.1007/s13744-024-01153-6] [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: 10/12/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
Diverse abiotic and biotic factors drive the ecological variation of communities across spatial and temporal dimensions. Within the Amazonian landscape, various freshwater environments exhibit distinct physicochemical characteristics. Thus, our study delved into the fluctuations of Odonata assemblages amidst distinct water bodies within Amazonia, encompassing two distinct climatic seasons. Comparative analysis was conducted on Odonata species diversity and assemblage composition across a blackwater pond, a lake, and a stream, spanning the initiation and culmination of the dry season in the southwestern Amazon region in Peru. Our methodology involved capturing adult Odonata using entomological nets on three separate occasions between 11:00 and 14:00 h for each water body in May (beginning of the dry season) and October (end of the dry season) of 2018. We also evaluated the influence of temperature, precipitation, and percent cloud cover on the abundance and richness of adult Odonata. Species richness and composition differed among the three water bodies in both periods of the dry season. No effect of the dry season periods on species richness and abundance was observed. However, except in the oxbow lake, the more abundant species were substituted to the end of the dry season. Our study highlights the influence of water body types on Odonata species diversity and composition. The effects of the sampling period during the dry season may not be immediately apparent in conventional diversity metrics, such as species richness and abundance. Instead, its effects manifest predominantly in the relative abundance of the species that compose these assemblages.
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Affiliation(s)
- Emmy Fiorella Medina-Espinoza
- Depto de Entomología, Museo de Historia Natural, Univ Nacional Mayor de San Marcos, Lima, Lima, Peru.
- Programa de Pós-Graduação Em Zoologia, Univ Federal Do Pará, Belém, Pará, Brazil.
- Lab de Ecologia E Conservação (LABECO), Univ Federal Do Pará, Belém, Pará, Brazil.
| | - Leandro Juen
- Programa de Pós-Graduação Em Zoologia, Univ Federal Do Pará, Belém, Pará, Brazil
- Lab de Ecologia E Conservação (LABECO), Univ Federal Do Pará, Belém, Pará, Brazil
| | - Lenize Batista Calvão
- Programa de Pós-Graduação Em Zoologia, Univ Federal Do Pará, Belém, Pará, Brazil
- Lab de Ecologia E Conservação (LABECO), Univ Federal Do Pará, Belém, Pará, Brazil
| | - Germán Arellano Cruz
- Lab de Ecología de Artrópodos (LEA), Univ Nacional Agraria La Molina, Lima, Lima, Perú
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Hovestadt T, Poethke HJ, Müller J, Mitesser O. Species Diversity and Habitat Fragmentation Per Se: The Influence of Local Extinctions and Species Clustering. Am Nat 2024; 203:655-667. [PMID: 38781529 DOI: 10.1086/729620] [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] [Indexed: 05/25/2024]
Abstract
AbstractAnthropogenic fragmentation of habitat is considered to be a critical factor contributing to the decline of species. However, a general consensus on the degree to which habitat loss and what has been called "habitat fragmentation per se" contribute to the loss of species diversity has not yet emerged. For empirical and theoretical reasons the topic has recently attracted renewed attention, thus reviving the "single large or several small" (SLOSS) debate. To study the effect of fragmentation per se, we use a spatially explicit and continuous, competitively neutral simulation model with immigration from a regional pool. The model accounts for the influence of ecological drift and intrafragment species clustering (due to limited dispersal) on local (plot) and global (landscape) diversity. We find that fragmentation increases global diversity but decreases local diversity, prominently so if fragments become more isolated. Cluster formation is a key mechanism reducing local diversity. By adding external disturbance events that lead to the occasional extinction of entire communities in habitat fragments, we show that the combined effect of such extinctions and cluster formation can create nonlinear interactive effects of fragmentation and fragment isolation on diversity patterns. We conclude that while in most cases fragmentation will decrease local and increase landscape diversity, universal predictions concerning the SLOSS debate should be taken with care.
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Liu Y, Wang X, Zeng D, Wang H, Ma Y, Zhao X, Guan Z, Ning Z, Qu L. Temporal variation in production performance, biochemical and oxidative stress markers, and gut microbiota in Pekin ducks during the late growth stage. Poult Sci 2024; 103:103894. [PMID: 39013293 DOI: 10.1016/j.psj.2024.103894] [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: 03/24/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 07/18/2024] Open
Abstract
In the late growth stage of commercial Pekin ducks, a significant increase in feed intake and a decline in body weight gain have been observed, leading to impaired feed conversion efficiency. To address this issue, we investigated alterations in production performance, blood biochemical indices, ileum tissue architecture, and microbial community structure in Pekin ducks. The primary objective was to provide robust data supporting the improvement of meat duck production efficiency during the late growth stage (28-42-days-old). Forty 28-day-old Pekin ducks were randomly assigned to 8 replicates, with five ducks per replicate. The rearing period lasted 14 days, with feed and water provided ad libitum. Our findings indicated a significant increase in Pekin duck body and heart weights with advancing age (P < 0.05). Moreover, serum antioxidant enzyme and high-density lipoprotein concentrations significantly increased, whereas triglyceride levels decreased (P < 0.05). Notably, the height of the ileal villi was significantly reduced (P < 0.05). The microbial community structure of the ileum exhibited significant changes as ducks aged, accompanied by a substantial increase in microbial flora diversity, particularly with the formation of more tightly connected microbial network modules. Time-dependent enrichment was observed in microbial gene functions related to energy metabolism pathways. At the genus level, Sphingomonas and Subdoligranulum have emerged as crucial players in microbial differential functional pathways and network formation. These bacteria likely serve as the key driving factors in the dynamic microbial changes that occur in Pekin ducks over time. Overall, our findings suggest a potential decline in the absorption function of the small intestine and fat deposition performance of Pekin ducks during later growth stages, which may be attributed to the maturation and proliferation of the gut microbial community.
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Affiliation(s)
- Yuchen Liu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xintong Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Dan Zeng
- Huayu Agricultural Science and Technology Co., Ltd., Handan, China
| | - Haiyan Wang
- Technical Center of Hohhot Customs, Huhhot, Inner Mongolia, China
| | - Ying Ma
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiurong Zhao
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zi Guan
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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12
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Del Pino Herrera A, Ferrall-Fairbanks MC. A war on many fronts: cross disciplinary approaches for novel cancer treatment strategies. Front Genet 2024; 15:1383676. [PMID: 38873108 PMCID: PMC11169904 DOI: 10.3389/fgene.2024.1383676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/26/2024] [Indexed: 06/15/2024] Open
Abstract
Cancer is a disease characterized by uncontrolled cellular growth where cancer cells take advantage of surrounding cellular populations to obtain resources and promote invasion. Carcinomas are the most common type of cancer accounting for almost 90% of cancer cases. One of the major subtypes of carcinomas are adenocarcinomas, which originate from glandular cells that line certain internal organs. Cancers such as breast, prostate, lung, pancreas, colon, esophageal, kidney are often adenocarcinomas. Current treatment strategies include surgery, chemotherapy, radiation, targeted therapy, and more recently immunotherapy. However, patients with adenocarcinomas often develop resistance or recur after the first line of treatment. Understanding how networks of tumor cells interact with each other and the tumor microenvironment is crucial to avoid recurrence, resistance, and high-dose therapy toxicities. In this review, we explore how mathematical modeling tools from different disciplines can aid in the development of effective and personalized cancer treatment strategies. Here, we describe how concepts from the disciplines of ecology and evolution, economics, and control engineering have been applied to mathematically model cancer dynamics and enhance treatment strategies.
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Affiliation(s)
- Adriana Del Pino Herrera
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States
| | - Meghan C. Ferrall-Fairbanks
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States
- University of Florida Health Cancer Center, University of Florida, Gainesville, FL, United States
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13
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van Heule M, El-Sheikh Ali H, Monteiro HF, Scoggin K, Fedorka C, Weimer BC, Ball B, Daels P, Dini P. Characterization of the equine placental microbial population during nocardioform placentitis. Theriogenology 2024; 225:172-179. [PMID: 38810343 DOI: 10.1016/j.theriogenology.2024.05.025] [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: 02/02/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 05/31/2024]
Abstract
Nocardioform placentitis is a poorly understood disease of equine late gestation. The presence of nocardioform, filamentous branching gram-positive bacteria, has been linked to the disease, with Crossiella equi, Amycolatopsis spp., and Streptomyces spp. being the most frequently identified bacteria. However, these bacteria are not found in all clinical cases in addition to being isolated from healthy, normal postpartum placentas. To better understand this form of placentitis, we analyzed the microbial composition in the equine placenta (chorioallantois) of both healthy postpartum (control; n = 11) and nocardioform-affected samples (n = 22) using 16S rDNA sequencing. We found a lower Shannon index in nocardioform samples, a higher Chao1 index in nocardioform samples, and a difference in beta diversity between control and nocardioform samples (p < 0.05), suggesting the presence of dysbiosis during the disease. In the majority of the NP samples (77 %), one of the following genera-Amycolatopsis, Crossiella, Lentzea, an unidentified member of the Pseudonocardiaceae family, Mycobacterium, or Enterococcus -represented over 70 % of the relative abundance. Overall, the data suggest that a broader spectrum of potential opportunistic pathogens could be involved in nocardioform placentitis, extending beyond the traditionally recognized bacteria, resulting in a similar histomorphological profile.
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Affiliation(s)
- Machteld van Heule
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA; Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, University of Ghent, Merelbeke, 9800, Belgium
| | - Hossam El-Sheikh Ali
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40503, USA
| | - Hugo Fernando Monteiro
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Kirsten Scoggin
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40503, USA
| | - Carleigh Fedorka
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40503, USA
| | - Bart C Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Barry Ball
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40503, USA
| | - Peter Daels
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, University of Ghent, Merelbeke, 9800, Belgium
| | - Pouya Dini
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA.
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14
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Roch FF, Dzieciol M, Quijada NM, Alteio LV, Mester PJ, Selberherr E. Microbial community structure of plant-based meat alternatives. NPJ Sci Food 2024; 8:27. [PMID: 38740858 DOI: 10.1038/s41538-024-00269-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
A reduction in animal-based diets has driven market demand for alternative meat products, currently raising a new generation of plant-based meat alternatives (PBMAs). It remains unclear whether these substitutes are a short-lived trend or become established in the long term. Over the last few years, the trend of increasing sales and diversifying product range has continued, but publication activities in this field are currently limited mainly to market research and food technology topics. As their popularity increases, questions emerge about the safety and nutritional risks of these novel products. Even though all the examined products must be heated before consumption, consumers lack experience with this type of product and thus further research into product safety, is desirable. To consider these issues, we examined 32 PBMAs from Austrian supermarkets. Based on 16S rRNA gene amplicon sequencing, the majority of the products were dominated by lactic acid bacteria (either Leuconostoc or Latilactobacillus), and generally had low alpha diversity. Pseudomonadota (like Pseudomonas and Shewanella) dominated the other part of the products. In addition to LABs, a high diversity of different Bacillus, but also some Enterobacteriaceae and potentially pathogenic species were isolated with the culturing approach. We assume that especially the dominance of heterofermentative LABs has high relevance for the product stability and quality with the potential to increase shelf life of the products. The number of isolated Enterobacteriaceae and potential pathogens were low, but they still demonstrated that these products are suitable for their presence.
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Affiliation(s)
- Franz-Ferdinand Roch
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Monika Dzieciol
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Narciso M Quijada
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185, Villamayor (Salamanca), Spain
| | - Lauren V Alteio
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, 3430, Tulln, Austria
| | - Patrick-Julian Mester
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Evelyne Selberherr
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria.
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15
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Mejia P, Urbieta GL, Xavier BDS, Castro IJD, DE Toledo JJ, Graciolli G, Viana Dias LA, Carvalho WD. Seasonal variation and host sex affect bat-bat fly interaction networks in the Amazonian savannahs. Integr Zool 2024; 19:400-416. [PMID: 37553290 DOI: 10.1111/1749-4877.12756] [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: 08/10/2023]
Abstract
Bats are the second-most diverse group of mammals in the world, and bat flies are their main parasites. However, significant knowledge gaps remain regarding these antagonistic interactions, especially since diverse factors such as seasonality and host sex can affect their network structures. Here, we explore the influence of such factors by comparing species richness and composition of bat flies on host bats, as well as specialization and modularity of bat-bat fly interaction networks between seasons and adult host sexes. We captured bats and collected their ectoparasitic flies at 10 sampling sites in the savannahs of Amapá State, northeastern region of the Brazilian Amazon. Despite female bats being more parasitized and recording greater bat fly species richness in the wet season, neither relationship was statistically significant. The pooled network could be divided into 15 compartments with 54 links, and all subnetworks comprised >12 compartments. The total number of links ranged from 27 to 48 (for the dry and wet seasons, respectively), and female and male subnetworks had 44 and 41 links, respectively. Connectance values were very low for the pooled network and for all subnetworks. Our results revealed higher bat fly species richness and abundance in the wet season, whereas specialization and modularity were higher in the dry season. Moreover, the subnetwork for female bats displayed higher specialization and modularity than the male subnetwork. Therefore, both seasonality and host sex contribute in different ways to bat-bat fly network structure. Future studies should consider these factors when evaluating bat-bat fly interaction networks.
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Affiliation(s)
- Paulo Mejia
- Programa de Pós-Graduação em Biodiversidade Tropical, Universidade Federal do Amapá (UNIFAP), Macapá AP, Brazil
| | - Gustavo Lima Urbieta
- Programa de Pós-Graduação em Biodiversidade Tropical, Universidade Federal do Amapá (UNIFAP), Macapá AP, Brazil
| | - Bruna da Silva Xavier
- Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Isaí Jorge de Castro
- Laboratório de Mamíferos, Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA), Macapá AP, Brazil
| | - José Júlio DE Toledo
- Programa de Pós-Graduação em Biodiversidade Tropical, Universidade Federal do Amapá (UNIFAP), Macapá AP, Brazil
| | - Gustavo Graciolli
- Programa de Pós-Graduação em Biologia Animal, Laboratório de Sistemática, Ecologia e Evolução (LSEE), Instituto de Biociências, Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, MT, Brazil
| | - Lucio André Viana Dias
- Programa de Pós-Graduação em Biodiversidade Tropical, Universidade Federal do Amapá (UNIFAP), Macapá AP, Brazil
| | - William Douglas Carvalho
- Programa de Pós-Graduação em Biodiversidade Tropical, Universidade Federal do Amapá (UNIFAP), Macapá AP, Brazil
- Terrestrial Ecology Group (TEG-UAM), Departamento de Ecología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
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16
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Peng Z, Qian X, Liu Y, Li X, Gao H, An Y, Qi J, Jiang L, Zhang Y, Chen S, Pan H, Chen B, Liang C, van der Heijden MGA, Wei G, Jiao S. Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally. Nat Commun 2024; 15:3624. [PMID: 38684659 PMCID: PMC11058813 DOI: 10.1038/s41467-024-47348-8] [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: 09/16/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Agriculture contributes to a decline in local species diversity and to above- and below-ground biotic homogenization. Here, we conduct a continental survey using 1185 soil samples and compare microbial communities from natural ecosystems (forest, grassland, and wetland) with converted agricultural land. We combine our continental survey results with a global meta-analysis of available sequencing data that cover more than 2400 samples across six continents. Our combined results demonstrate that land conversion to agricultural land results in taxonomic and functional homogenization of soil bacteria, mainly driven by the increase in the geographic ranges of taxa in croplands. We find that 20% of phylotypes are decreased and 23% are increased by land conversion, with croplands enriched in Chloroflexi, Gemmatimonadota, Planctomycetota, Myxcoccota and Latescibacterota. Although there is no significant difference in functional composition between natural ecosystems and agricultural land, functional genes involved in nitrogen fixation, phosphorus mineralization and transportation are depleted in cropland. Our results provide a global insight into the consequences of land-use change on soil microbial taxonomic and functional diversity.
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Affiliation(s)
- Ziheng Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yu Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Xiaomeng Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Hang Gao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yining An
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Jiejun Qi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Lan Jiang
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yiran Zhang
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Shi Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Haibo Pan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Beibei Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Chunling Liang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China.
| | - Shuo Jiao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China.
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17
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Gols R, Barden A, Ozden Ö. A comparison of butterfly communities in irrigated and non-irrigated Mediterranean farmlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171247. [PMID: 38423333 DOI: 10.1016/j.scitotenv.2024.171247] [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: 10/24/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024]
Abstract
Irrigation is considered a form of agricultural intensification and is of significant importance in arid and semi-arid regions, such as those in the Mediterranean basin. This region differs substantially from temperate ones, in terms of climate, land-use policies and types of agricultural systems. Therefore, how biodiversity is affected by agricultural intensification may also differ substantially from countries in north-western Europe. We investigated the effect of irrigation on butterfly diversity and abundance at two different spatial scales in an agricultural region in northern Cyprus, an area representative of typical lowland agricultural practices of the Eastern Mediterranean. We investigated how local field-scale management (irrigated vs rain-fed) and the proportion of irrigated land at a larger scale of 0.25 km2 affected the abundance and diversity of butterflies and herbaceous plant species. Butterflies and herbaceous plants were surveyed in field boundaries adjacent to agricultural fields located in paired plots that had contrasting levels of irrigation. Butterflies in the field boundaries along agricultural fields were strongly positively affected by irrigation in the adjacent fields both in terms of abundance and species diversity, whereas the effect of irrigation at the larger scale of the 0.25-km2 plot was less prominent. Species composition of butterflies and plants did not correlate. However, plant abundance and alpha diversity of the vegetation in the field boundaries correlated with both abundance and alpha diversity of the butterflies when the abundance of plants was relatively low, in particular, when grasses were omitted from the data set. Crop species associated with irrigated fields contributed to the observed patterns. Comparing the results of this study with those reported for temperate regions in northwestern Europe reveals that the effectiveness of management schemes on biodiversity depend on biogeographical region, highlighting the risk of making broad assumption on the effectiveness of management strategies on biodiversity.
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Affiliation(s)
- Rieta Gols
- Laboratory of Entomology, Wageningen University & Research, Wageningen, the Netherlands.
| | | | - Özge Ozden
- Department of Landscape Architecture, Faculty of Agriculture, Near East University, Nicosia, Cyprus
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18
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Pushpavathi D, Krishnamurthy YL. Study on endolichenic fungal assemblage in Parmotrema and Heterodermia lichens of Shivamoga, Karnataka. Mol Biol Rep 2024; 51:549. [PMID: 38642168 DOI: 10.1007/s11033-024-09497-3] [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: 02/08/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Lichen is a symbiotic association of algae and fungi, recognized as a self-sustaining ecosystem that constitutes an indeterminant number of bacteria, actinomycetes, fungi, and protozoa. We evaluated the endolichenic fungal assemblage given the dearth of knowledge on endolichenic fungi (ELFs), particularly from part of the Central Western Ghats, Karnataka, and conducted a phylogenetic analysis of xylariaceous fungi, the most diversified group of fungi using ITS and ITS+Tub2 gene set. RESULTS Out of 17 lichen thalli collected from 5 ecoregions, 42 morphospecies recovered, belong to the class Sordariomycetes, Eurotiomycetes, Dothideomycetes, Leotiomycetes, Saccharomycetes. About 19 and 13 ELF genera have been reported from Parmotrema and Heterodermia thallus. Among the ecoregions EC2 showing highest species diversity (Parmotrema (1-D) = 0.9382, (H) = 2.865, Fisher-α = 8.429, Heterodermia (1-D) = 0.8038, H = 1.894, F-α = 4.57) followed the EC3 and EC1. Xylariales are the predominant colonizer reported from at least one thallus from four ecoregions. The morphotypes ELFX04, ELFX05, ELFX08 and ELFX13 show the highest BLAST similarity (> 99%) with Xylaria psidii, X. feejeensis, X. berteri and Hypoxylon fragiforme respectively. Species delimitation and phylogenetic position reveal the closest relation of Xylariaceous ELFs with plant endophytes. CONCLUSIONS The observation highlights that the deciduous forest harness a high number of endolichenic fungi, a dominant portion of these fungi are non-sporulating and still exist as cryptic. Overall, 8 ELF species recognized based on phylogenetic analysis, including the two newly reported fungi ELFX03 and ELFX06 which are suspected to be new species based on the present evidence. The study proved, that the lichen being rich source to establish fungal diversity and finding new species. Successful amplification of most phylogenetic markers like RPB2, building of comprehensive taxonomic databases and application of multi-omics data are further needed to understand the complex nature of lichen-fungal symbiosis.
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Affiliation(s)
- D Pushpavathi
- Department of PG Studies and Research in Applied Botany, Kuvempu University, Jnanasahyadri, Shankaraghatta, Karnataka, 577451, India
| | - Y L Krishnamurthy
- Department of PG Studies and Research in Applied Botany, Kuvempu University, Jnanasahyadri, Shankaraghatta, Karnataka, 577451, India.
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19
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Ahern A, Hughes DF. Citizen science initiatives document biodiversity baselines at an urban lake. PeerJ 2024; 12:e17209. [PMID: 38646485 PMCID: PMC11032101 DOI: 10.7717/peerj.17209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/18/2024] [Indexed: 04/23/2024] Open
Abstract
Changes to biodiversity from urbanization are occurring worldwide, and baseline data is vital to document the magnitude and direction of these alterations. We set out to document the biodiversity of an urban lake in Eastern Iowa that was devoid of baseline data prior to a renovation project that will convert the site into a major area for human recreation. Throughout the course of one year, we studied the biodiversity at Cedar Lake utilizing the citizen-science application iNaturalist coupled with semi-structured BioBlitz events, which we compared to previous opportunistic observations at the site. From a semi-structured approach to document biodiversity with citizen science, our analyses revealed more diverse community metrics over a shorter period compared to more than a decade of prior observations.
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Affiliation(s)
- Alyssah Ahern
- Department of Biology, Coe College, Cedar Rapids, IA, United States of America
| | - Daniel F. Hughes
- Department of Biology, Coe College, Cedar Rapids, IA, United States of America
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20
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van Klink R, Bowler DE, Gongalsky KB, Shen M, Swengel SR, Chase JM. Disproportionate declines of formerly abundant species underlie insect loss. Nature 2024; 628:359-364. [PMID: 38123681 PMCID: PMC11006610 DOI: 10.1038/s41586-023-06861-4] [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: 06/02/2022] [Accepted: 11/10/2023] [Indexed: 12/23/2023]
Abstract
Studies have reported widespread declines in terrestrial insect abundances in recent years1-4, but trends in other biodiversity metrics are less clear-cut5-7. Here we examined long-term trends in 923 terrestrial insect assemblages monitored in 106 studies, and found concomitant declines in abundance and species richness. For studies that were resolved to species level (551 sites in 57 studies), we observed a decline in the number of initially abundant species through time, but not in the number of very rare species. At the population level, we found that species that were most abundant at the start of the time series showed the strongest average declines (corrected for regression-to-the-mean effects). Rarer species were, on average, also declining, but these were offset by increases of other species. Our results suggest that the observed decreases in total insect abundance2 can mostly be explained by widespread declines of formerly abundant species. This counters the common narrative that biodiversity loss is mostly characterized by declines of rare species8,9. Although our results suggest that fundamental changes are occurring in insect assemblages, it is important to recognize that they represent only trends from those locations for which sufficient long-term data are available. Nevertheless, given the importance of abundant species in ecosystems10, their general declines are likely to have broad repercussions for food webs and ecosystem functioning.
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Affiliation(s)
- Roel van Klink
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Department of Computer Science, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.
| | - Diana E Bowler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- Department of Ecosystem Services, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
- UK Centre for Ecology & Hydrology, Crowmarsh Gifford, UK
| | - Konstantin B Gongalsky
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russian Federation
| | - Minghua Shen
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Computer Science, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | | | - Jonathan M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Computer Science, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
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21
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Kibria MK, Ali MA, Yaseen M, Khan IA, Bhat MA, Islam MA, Mahumud RA, Mollah MNH. Discovery of Bacterial Key Genes from 16S rRNA-Seq Profiles That Are Associated with the Complications of SARS-CoV-2 Infections and Provide Therapeutic Indications. Pharmaceuticals (Basel) 2024; 17:432. [PMID: 38675393 PMCID: PMC11053588 DOI: 10.3390/ph17040432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
SARS-CoV-2 infections, commonly referred to as COVID-19, remain a critical risk to both human life and global economies. Particularly, COVID-19 patients with weak immunity may suffer from different complications due to the bacterial co-infections/super-infections/secondary infections. Therefore, different variants of alternative antibacterial therapeutic agents are required to inhibit those infection-causing drug-resistant pathogenic bacteria. This study attempted to explore these bacterial pathogens and their inhibitors by using integrated statistical and bioinformatics approaches. By analyzing bacterial 16S rRNA sequence profiles, at first, we detected five bacterial genera and taxa (Bacteroides, Parabacteroides, Prevotella Clostridium, Atopobium, and Peptostreptococcus) based on differentially abundant bacteria between SARS-CoV-2 infection and control samples that are significantly enriched in 23 metabolic pathways. A total of 183 bacterial genes were found in the enriched pathways. Then, the top-ranked 10 bacterial genes (accB, ftsB, glyQ, hldD, lpxC, lptD, mlaA, ppsA, ppc, and tamB) were selected as the pathogenic bacterial key genes (bKGs) by their protein-protein interaction (PPI) network analysis. Then, we detected bKG-guided top-ranked eight drug molecules (Bemcentinib, Ledipasvir, Velpatasvir, Tirilazad, Acetyldigitoxin, Entreatinib, Digitoxin, and Elbasvir) by molecular docking. Finally, the binding stability of the top-ranked three drug molecules (Bemcentinib, Ledipasvir, and Velpatasvir) against three receptors (hldD, mlaA, and lptD) was investigated by computing their binding free energies with molecular dynamic (MD) simulation-based MM-PBSA techniques, respectively, and was found to be stable. Therefore, the findings of this study could be useful resources for developing a proper treatment plan against bacterial co-/super-/secondary-infection in SARS-CoV-2 infections.
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Affiliation(s)
- Md. Kaderi Kibria
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Statistics, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Chemistry, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Imran Ahmad Khan
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11421, Saudi Arabia;
| | - Md. Ariful Islam
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
| | - Rashidul Alam Mahumud
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
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22
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Sohaib H, Fays M, Khatib A, Rivière J, El Aouad N, Desoignies N. Contribution to the characterization of the seed endophyte microbiome of Argania spinosa across geographical locations in Central Morocco using metagenomic approaches. Front Microbiol 2024; 15:1310395. [PMID: 38601940 PMCID: PMC11005822 DOI: 10.3389/fmicb.2024.1310395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/08/2024] [Indexed: 04/12/2024] Open
Abstract
Microbial endophytes are microorganisms that live inside plants, and some of them play important yet understudied roles in plant health, growth, and adaptation to environmental conditions. Their diversity within plants has traditionally been underestimated due to the limitations of culture-dependent techniques. Metagenomic profiling provides a culture-independent approach to characterize entire microbial communities. The argan tree (Argania spinosa) is ecologically and economically important in Morocco, yet its seed endophyte microbiome remains unexplored. This study aimed to compare the bacterial and fungal endophyte communities associated with argan seeds collected from six sites across Morocco using Illumina MiSeq sequencing of the 16S rRNA gene and ITS regions, respectively. Bacterial DNA was extracted from surface-sterilized seeds and amplified using universal primers, while fungal DNA was isolated directly from seeds. Bioinformatics analysis of sequencing data identified taxonomic profiles at the phylum to genus levels. The results indicated that bacterial communities were dominated by the genus Rhodoligotrophos, while fungal communities exhibited varying degrees of dominance between Ascomycota and Basidiomycota depending on site, with Penicillium being the most abundant overall. Distinct site-specific profiles were observed, with Pseudomonas, Bacillus, and Aspergillus present across multiple locations. Alpha diversity indices revealed variation in endophyte richness between seed sources. In conclusion, this first exploration of the argan seed endophyte microbiome demonstrated environmental influence on community structure. While facing limitations due to small sample sizes and lack of ecological metadata, it provides a foundation for future mechanistic investigations into how specific endophyte-host interactions shape argan adaptation across Morocco's diverse landscapes.
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Affiliation(s)
- Hourfane Sohaib
- Laboratory of Life and Health Sciences, Faculty of Medicine and Pharmacy of Tangier, University Abdelmalek Essaâdi, Tetouan, Morocco
| | - Morgan Fays
- Phytopathology, Microbial and Molecular Farming Lab, Centre D’Etudes et Recherche Appliquée-Haute Ecole Provinciale du Hainaut Condorcet, Ath, Belgium
| | - Abderrezzak Khatib
- Laboratory of Life and Health Sciences, Faculty of Medicine and Pharmacy of Tangier, University Abdelmalek Essaâdi, Tetouan, Morocco
| | - John Rivière
- Laboratory of Biotechnology and Applied Biology, Haute Ecole Provinciale de Hainaut-Condorcet, Ath, Hainaut, Belgium
| | - Noureddine El Aouad
- Laboratory of Life and Health Sciences, Faculty of Medicine and Pharmacy of Tangier, University Abdelmalek Essaâdi, Tetouan, Morocco
| | - Nicolas Desoignies
- Phytopathology, Microbial and Molecular Farming Lab, Centre D’Etudes et Recherche Appliquée-Haute Ecole Provinciale du Hainaut Condorcet, Ath, Belgium
- University of Liege - Gembloux Agro-Bio Tech, TERRA - Teaching and Research Center, Plant Sciences Axis, Gembloux, Belgium
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23
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Bouilloud M, Galan M, Pradel J, Loiseau A, Ferrero J, Gallet R, Roche B, Charbonnel N. Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota. Anim Microbiome 2024; 6:16. [PMID: 38528597 DOI: 10.1186/s42523-024-00301-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.
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Affiliation(s)
- Marie Bouilloud
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France.
- Centre de Biologie pour la Gestion des Populations, 750 Avenue Agropolis, 34988, Montferrier sur Lez, France.
| | - Maxime Galan
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Julien Pradel
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Anne Loiseau
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Julien Ferrero
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Romain Gallet
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Benjamin Roche
- MIVEGEC, IRD, CNRS, Univ Montpellier, Montpellier, France
| | - Nathalie Charbonnel
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
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24
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Liu B, Yao J, Xu Y, Huang J, Ding Y, Zang R. Latitudinal variation and driving factors of above-ground carbon proportion of large trees in old-growth forests across China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170586. [PMID: 38301777 DOI: 10.1016/j.scitotenv.2024.170586] [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: 09/04/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
Large trees play a vital role in forest carbon stocks, dominating the distribution of community biomass. However, climate change and deforestation are reducing large trees globally, resulting in regional differences in their contribution to carbon stocks. Here, we examined the latitudinal change pattern and drivers of large trees' contributions to stand carbon stocks. Above-ground carbon storage was calculated for 530 plots in old-growth forests across China. Linear regression was used to calculate latitudinal variation in the proportion of above-ground carbon in large trees (i.e., AGC proportion). Variance partitioning and multiple linear regression were used to calculate the relative importance of species diversity, stand structure, functional traits, and environmental factors to AGC proportion. The study found that AGC proportion decreased with increasing latitude, averaging at 64.44 %. Stand structure, particularly the coefficient of variation of DBH, was identified as the key drivers of the AGC proportion. The number of common species (Hill's 1D) had no direct effect on the AGC proportion, while wood density, maximum tree height, and leaf nitrogen-to‑phosphorus ratio showed negative effects. The mass-ratio effects on AGC proportion were stronger than diversity effects. Climate variables primarily affected the AGC proportion through stand variables. These results indicate that simultaneously managing high diversity and AGC proportion may pose challenges. Moreover, considering the substantial contribution of large trees to carbon stocks, their storage capacity and sensitivity to environmental changes exert significant control over forest carbon cycles. Therefore, preserving and enhancing the carbon sink function of old-growth forests in the face of climate change and disturbance may depend primarily on protecting existing large trees and soon-to-be large-diameter trees.
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Affiliation(s)
- Bin Liu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jie Yao
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yue Xu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jihong Huang
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yi Ding
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Runguo Zang
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
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25
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Leigh RJ, Corrigan A, Murphy RA, Taylor-Pickard J, Moran CA, Walsh F. Yeast mannan rich fraction positively influences microbiome uniformity, productivity associated taxa, and lay performance. Anim Microbiome 2024; 6:9. [PMID: 38438939 PMCID: PMC10913240 DOI: 10.1186/s42523-024-00295-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/11/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Alternatives to antibiotic as growth promoters in agriculture, such as supplemental prebiotics, are required to maintain healthy and high performing animals without directly contributing to antimicrobial resistance bioburden. While the gut microbiota of broiler hens has been well established and successfully correlated to performance, to our knowledge, a study has yet to be completed on the effect of prebiotic supplementation on correlating the mature laying hen productivity and microbiota. This study focused on establishing the impact of a yeast derived prebiotic, mannan rich fraction (MRF), on the cecal microbiota of late laying hens. This study benefitted from large sample sizes so intra- and intergroup variation effects could be statistically accounted for. RESULTS Taxonomic richness was significantly greater at all taxonomic ranks and taxonomic evenness was significantly lower for all taxonomic ranks in MRF-supplemented birds (P < 0.005). Use of principal coordinate analyses and principal component analyses found significant variation between treatment groups. When assessed for compositional uniformity (an indicator of flock health), microbiota in MRF-supplemented birds was more uniform than control birds at the species level. From a food safety and animal welfare perspective, Campylobacter jejuni was significantly lower in abundance in MRF-supplemented birds. In this study, species associated with high weight gain (an anticorrelator of performance in laying hens) were significantly lower in abundance in laying hens while health-correlated butyrate and propionate producing species were significantly greater in abundance in MRF-supplemented birds. CONCLUSIONS The use of prebiotics may be a key factor in controlling the microbiota balance limiting agri-food chain pathogen persistence and in promoting uniformity. In previous studies, increased α- and β-diversity indices were determinants of pathogen mitigation and performance. MRF-supplemented birds in this study established greater α- and β-diversity indices in post-peak laying hens, greater compositional uniformity across samples, a lower pathogenic bioburden and a greater abundance of correlators of performance.
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Affiliation(s)
- Robert J Leigh
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| | | | | | | | - Colm A Moran
- Alltech SARL, Rue Charles Amand, 14500, Vire, France
| | - Fiona Walsh
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
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26
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Peña-Álvarez V, Baragaño D, Prosenkov A, Gallego JR, Peláez AI. Assessment of co-contaminated soil amended by graphene oxide: Effects on pollutants, microbial communities and soil health. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 272:116015. [PMID: 38290314 DOI: 10.1016/j.ecoenv.2024.116015] [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: 08/31/2023] [Revised: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 02/01/2024]
Abstract
Graphene oxide (GOx) is a nanomaterial with demonstrated capacity to remove metals from water. However, its effects on organic pollutants and metal(loid)s present in polluted soils when used for remediation purposes have not been extensively addressed. Likewise, few studies describe the effects of GOx on edaphic properties and soil biology. In this context, here we assessed the potential of GOx for remediating polluted soil focusing also on different unexplored effects of GOx in soil. To achieve this, we treated soil contaminated with concurrent inorganic (As and metals) and organic pollution (TPH and PAHs), using GOx alone and in combination with nutrients (N and P sources). In both cases increased availability of As and Zn was observed after 90 days, whereas Cu and Hg availability was reduced and the availability of Pb and the concentration of organic pollutants were not significantly affected. The application of GOx on the soil induced a significant and rapid change (within 1 week) in microbial populations, leading to a transient reduction in biodiversity, consistent with the alteration of several soil properties. Concurrently, the combination with nutrients exhibited a distinct behaviour, manifesting a more pronounced and persistent shift in microbial populations without a decrease in biodiversity. On the basis of these findings, GOx emerges as a versatile amendment for soil remediation approaches.
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Affiliation(s)
- V Peña-Álvarez
- Area of Microbiology, Department of Functional Biology and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Spain; Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Spain
| | - D Baragaño
- School of Mines and Energy Engineering, University of Cantabria, Blvr. Ronda Rufino Peón 254, 39300 Torrelavega, Cantabria, Spain.
| | - A Prosenkov
- Area of Microbiology, Department of Functional Biology and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Spain; Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Spain
| | - J R Gallego
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, Campus of Mieres, University of Oviedo, Mieres, Spain
| | - A I Peláez
- Area of Microbiology, Department of Functional Biology and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Spain; Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Spain
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27
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Battisti C. Changes in bird assemblages following an outdoor music festival: A BACI (before-after-control-impact) monitoring from central Italy. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 344:123384. [PMID: 38242304 DOI: 10.1016/j.envpol.2024.123384] [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: 11/15/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
An assessment of the short-term effects of an outdoor music festival (Jova Beach Party event; July 2019; central Italy) on bird assemblages has been carried out, adopting a BACI (Before-After-Control-Impact) survey design, and using the point counts method both in the impact site (Impact, I; where the concert was held) and in comparable Control site (C). In the I site, data have been stratified both for urban (U) and agro-mosaic (M) habitats. When comparing before and after the music event, in IU site, the species richness and the Hill diversity index decreased, differently from CU where species richness a species abundance increased. Diversity profiles highlighted the impoverishment of bird assemblages after the event, but only in the Impact urban habitats. After the musical event, individual rarefaction curves for richness were lower in IU after the concert, while, differently in CU curves are higher. These data suggest an impact in bird assemblages limited to the urban site, due to the stress mainly induced by high intensity noise pollution. Musical events may disrupt the structure of synanthropic bird assemblages, inducing a dispersal of individuals towards the surrounding landscape. Starling (Sturnus vulgaris) appeared a particularly sensitive bird. However, further efforts are necessary to study the effects of these events at species level.
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Affiliation(s)
- Corrado Battisti
- "Torre Flavia" LTER (Long Term Ecological Research) Station, Città Metropolitana di Roma Capitale, Servizio Aree Protette - Parchi Regionali, Viale G. Ribotta 41, 00144, Roma, Italy.
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28
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Sweeney CJ, Kaushik R, Bottoms M. Considerations for the inclusion of metabarcoding data in the plant protection product risk assessment of the soil microbiome. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2024; 20:337-358. [PMID: 37452668 DOI: 10.1002/ieam.4812] [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: 03/28/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
There is increasing interest in further developing the plant protection product (PPP) environmental risk assessment, particularly within the European Union, to include the assessment of soil microbial community composition, as measured by metabarcoding approaches. However, to date, there has been little discussion as to how this could be implemented in a standardized, reliable, and robust manner suitable for regulatory decision-making. Introduction of metabarcoding-based assessments of the soil microbiome into the PPP risk assessment would represent a significant increase in the degree of complexity of the data that needs to be processed and analyzed in comparison to the existing risk assessment on in-soil organisms. The bioinformatics procedures to process DNA sequences into community compositional data sets currently lack standardization, while little information exists on how these data should be used to generate regulatory endpoints and the ways in which these endpoints should be interpreted. Through a thorough and critical review, we explore these challenges. We conclude that currently, we do not have a sufficient degree of standardization or understanding of the required bioinformatics and data analysis procedures to consider their use in an environmental risk assessment context. However, we highlight critical knowledge gaps and the further research required to understand whether metabarcoding-based assessments of the soil microbiome can be utilized in a statistically and ecologically relevant manner within a PPP risk assessment. Only once these challenges are addressed can we consider if and how we should use metabarcoding as a tool for regulatory decision-making to assess and monitor ecotoxicological effects on soil microorganisms within an environmental risk assessment of PPPs. Integr Environ Assess Manag 2024;20:337-358. © 2023 SETAC.
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Affiliation(s)
- Christopher J Sweeney
- Syngenta, Jealott's Hill International Research Centre Bracknell, Bracknell, Berkshire, UK
| | - Rishabh Kaushik
- Syngenta, Jealott's Hill International Research Centre Bracknell, Bracknell, Berkshire, UK
| | - Melanie Bottoms
- Syngenta, Jealott's Hill International Research Centre Bracknell, Bracknell, Berkshire, UK
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29
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Gress TD, Rosenberg NA. Mathematical constraints on a family of biodiversity measures via connections with Rényi entropy. Biosystems 2024; 237:105153. [PMID: 38417692 DOI: 10.1016/j.biosystems.2024.105153] [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: 09/14/2023] [Revised: 01/24/2024] [Accepted: 02/09/2024] [Indexed: 03/01/2024]
Abstract
The Hill numbers are statistics for biodiversity measurement in ecological studies, closely related to the Rényi and Shannon entropies from information theory. Recent developments in the mathematics of diversity in the setting of population genetics have produced mathematical constraints that characterize how standard measures depend on the highest-frequency class in a discrete probability distribution. Here, we apply these constraints to diversity statistics in ecology, focusing on the Hill numbers and the Rényi and Shannon entropies. The mathematical bounds can shift perspectives on the diversities of communities, in that when upper and lower bounds on Hill numbers are evaluated in a classic butterfly example, Hill numbers that are initially larger in one community switch positions-so that associated normalized Hill numbers are instead smaller than those of the other community. The new bounds hence add to the tools available for interpreting a commonly used family of statistics for ecological data.
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Affiliation(s)
- Theodore D Gress
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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30
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Felappi JF, Sommer JH, Falkenberg T, Terlau W, Kötter T. Urban park qualities driving visitors mental well-being and wildlife conservation in a Neotropical megacity. Sci Rep 2024; 14:4856. [PMID: 38418539 PMCID: PMC10902329 DOI: 10.1038/s41598-024-55357-2] [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: 07/27/2023] [Accepted: 02/22/2024] [Indexed: 03/01/2024] Open
Abstract
Green infrastructure has been widely recognized for the benefits to human health and biodiversity conservation. However, knowledge of the qualities and requirements of such spaces and structures for the effective delivery of the range of ecosystem services expected is still limited, as well as the identification of trade-offs between services. In this study, we apply the One Health approach in the context of green spaces to investigate how urban park characteristics affect human mental health and wildlife support outcomes and identify synergies and trade-offs between these dimensions. Here we show that perceived restorativeness of park users varies significantly across sites and is mainly affected by safety and naturalness perceptions. In turn, these perceptions are driven by objective indicators of quality, such as maintenance of facilities and vegetation structure, and subjective estimations of biodiversity levels. The presence of water bodies benefited both mental health and wildlife. However, high tree canopy coverage provided greater restoration potential whereas a certain level of habitat heterogeneity was important to support a wider range of bird species requirements. To reconcile human and wildlife needs in green spaces, cities should strategically implement a heterogeneous green infrastructure network that considers trade-offs and maximizes synergies between these dimensions.
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Affiliation(s)
| | - Jan Henning Sommer
- Center for Development Research, University of Bonn, Genscherallee 3, 53113, Bonn, Germany
| | - Timo Falkenberg
- Center for Development Research, University of Bonn, Genscherallee 3, 53113, Bonn, Germany
- GeoHealth Centre, Institute for Hygiene and Public Health, University of Bonn, Venusberg Campus 1, 53105, Bonn, Germany
| | - Wiltrud Terlau
- International Centre for Sustainable Development, Bonn-Rhein-Sieg University of Applied Sciences, Grantham-Allee 20, 53757, Sankt Augustin, Germany
| | - Theo Kötter
- Urban Planning and Land Management Group, Institute of Geodesy and Geo-Information, University of Bonn, Nussallee 1, 53115, Bonn, Germany
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31
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Meng L, Li Y, Chen L, Sui M, Zhang G, Liu Q, Chen D, Wu Y, Yang Z, Chen S, Yang R, Zang L. Variations in species diversity patterns and community assembly rules among vegetation types in the karst landscape. FRONTIERS IN PLANT SCIENCE 2024; 15:1338596. [PMID: 38455729 PMCID: PMC10917898 DOI: 10.3389/fpls.2024.1338596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024]
Abstract
The various vegetation types in the karst landscape have been considered the results of heterogeneous habitats. However, the lack of a comprehensive understanding of regional biodiversity patterns and the underlying ecological processes limits further research on ecological management. This study established forest dynamic plots (FDPs) of the dominant vegetation types (shrubland, SL; mixed tree and shrub forest, MTSF; coniferous forest, CF; coniferous broadleaf mixed forest, CBMF; and broadleaf forest, BF) in the karst landscape and quantified the species diversity patterns and potential ecological processes. The results showed that in terms of diversity patterns, the evenness and species richness of the CF community were significantly lower than other vegetation types, while the BF community had the highest species richness. The other three vegetation types showed no significant variation in species richness and evenness. However, when controlling the number of individuals of FDPs, the rarefied species richness showed significant differences and ranked as BF > SL > MTSF > CBMF > CF, highlighting the importance of considering the impacts of abundance. Additionally, the community assembly of climax communities (CF or BF) was dominated by stochastic processes such as species dispersal or species formation, whereas deterministic processes (habitat filtering) dominated the secondary forests (SL, MTSF, and CBMF). These findings proved that community assembly differs mainly between the climax community and other communities. Hence, it is crucial to consider the biodiversity and of the potential underlying ecological processes together when studying regional ecology and management, particularly in heterogeneous ecosystems.
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Affiliation(s)
- Longchenxi Meng
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, China
| | - Yong Li
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, China
| | - Luyao Chen
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, China
| | - Mingzhen Sui
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, China
- Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, National Forestry and Grassland Administration, Libo, China
| | - Guangqi Zhang
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, China
- Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, National Forestry and Grassland Administration, Libo, China
| | - Qingfu Liu
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, China
- Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, National Forestry and Grassland Administration, Libo, China
| | - Danmei Chen
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, China
- Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, National Forestry and Grassland Administration, Libo, China
| | - Yuhang Wu
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, China
| | - Zeyu Yang
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, China
| | - Shiren Chen
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, China
| | - Rui Yang
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, China
| | - Lipeng Zang
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, China
- Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, National Forestry and Grassland Administration, Libo, China
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Onyekwelu JC, Agbelade AD, Stimm B, Mosandl R. Role of sacred groves in southwestern Nigeria in biodiversity conservation, biomass and carbon storage. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:269. [PMID: 38358544 DOI: 10.1007/s10661-024-12407-6] [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: 10/31/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024]
Abstract
Sacred groves are remnants of primary forests with rich biological diversity, protected by indigenous communities. Their role in carbon sequestration and provision of other ecosystem services is being recognized. We investigated four sacred groves (Idanre Hills, Igbo-Olodumare, Ogun-Onire, and Osun-Osogbo) in southwestern Nigeria for biodiversity conservation, biomass production, and carbon storage. A total of 32 temporary sample plots of 800 m2 each were laid across all the sacred groves. Within each plot, all trees with dbh greater or equal to 10 cm were identified, and their diameters and heights measured. Saplings and seedlings were assessed within 100 m2 and 25 m2 sub-plots, respectively. Non-destructive methods were employed in estimating volume, biomass production, and carbon storage. Shannon-Wiener diversity index, Margalef index, and tree species richness in the four groves ranged from 2.63-3.55, 5.64-10.02, and 41-85, respectively, and differed significantly. The four groves were sanctuaries for many indigenous tree species of immense social, religious, ecological, and socio-economic importance. The high densities of seedling and sapling, together with the inverted-J tree diameter distributions, are indications of active regeneration and healthy ecosystem. Mean volume was high (range 244.99 to 343.08 m3 ha-1). The biomass (range 87.8 to 231.85 t ha-1) and carbon stock (range 43.9 to 115.9 t ha-1) of the groves revealed their potentials for climate change mitigation through atmospheric CO2 sequestration. Thus, besides being an effective biodiversity conservation method, sacred groves are important carbon sink. This calls for further conservation of sacred groves to serve as long-term carbon storage mechanism.
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Affiliation(s)
- Jonathan C Onyekwelu
- Department of Forestry and Wood Technology, Federal University of Technology, P.M.B. 704, Akure, Nigeria.
| | - Aladesanmi D Agbelade
- Department of Forest Resources and Wildlife Management, Ekiti State University, P.M.B. 5363, Ado Ekiti, Nigeria
| | - Bernd Stimm
- Technical University of Munich, Hans-Carl-Von- Carlowitz-Platz 2 D, 85354, Freising, Germany
| | - Reinhard Mosandl
- Technical University of Munich, Hans-Carl-Von- Carlowitz-Platz 2 D, 85354, Freising, Germany
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Reeves DB, Rigau DN, Romero A, Zhang H, Simonetti FR, Varriale J, Hoh R, Zhang L, Smith KN, Montaner LJ, Rubin LH, Gange SJ, Roan NR, Tien PC, Margolick JB, Peluso MJ, Deeks SG, Schiffer JT, Siliciano JD, Siliciano RF, Antar AAR. Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.13.24302704. [PMID: 38405967 PMCID: PMC10888981 DOI: 10.1101/2024.02.13.24302704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The latent reservoir of HIV persists for decades in people living with HIV (PWH) on antiretroviral therapy (ART). To determine if persistence arises from the natural dynamics of memory CD4+ T cells harboring HIV, we compared the clonal dynamics of HIV proviruses to that of memory CD4+ T cell receptors (TCRβ) from the same PWH and from HIV-seronegative people. We show that clonal dominance of HIV proviruses and antigen-specific CD4+ T cells are similar but that the field's understanding of the persistence of the less clonally dominant reservoir is significantly limited by undersampling. We demonstrate that increasing reservoir clonality over time and differential decay of intact and defective proviruses cannot be explained by mCD4+ T cell kinetics alone. Finally, we develop a stochastic model of TCRβ and proviruses that recapitulates experimental observations and suggests that HIV-specific negative selection mediates approximately 6% of intact and 2% of defective proviral clearance. Thus, HIV persistence is mostly, but not entirely, driven by natural mCD4+ T cell kinetics.
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34
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Balashova D, van Schaik BDC, Stratigopoulou M, Guikema JEJ, Caniels TG, Claireaux M, van Gils MJ, Musters A, Anang DC, de Vries N, Greiff V, van Kampen AHC. Systematic evaluation of B-cell clonal family inference approaches. BMC Immunol 2024; 25:13. [PMID: 38331731 DOI: 10.1186/s12865-024-00600-8] [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: 04/21/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
The reconstruction of clonal families (CFs) in B-cell receptor (BCR) repertoire analysis is a crucial step to understand the adaptive immune system and how it responds to antigens. The BCR repertoire of an individual is formed throughout life and is diverse due to several factors such as gene recombination and somatic hypermutation. The use of Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) using next generation sequencing enabled the generation of full BCR repertoires that also include rare CFs. The reconstruction of CFs from AIRR-seq data is challenging and several approaches have been developed to solve this problem. Currently, most methods use the heavy chain (HC) only, as it is more variable than the light chain (LC). CF reconstruction options include the definition of appropriate sequence similarity measures, the use of shared mutations among sequences, and the possibility of reconstruction without preliminary clustering based on V- and J-gene annotation. In this study, we aimed to systematically evaluate different approaches for CF reconstruction and to determine their impact on various outcome measures such as the number of CFs derived, the size of the CFs, and the accuracy of the reconstruction. The methods were compared to each other and to a method that groups sequences based on identical junction sequences and another method that only determines subclones. We found that after accounting for data set variability, in particular sequencing depth and mutation load, the reconstruction approach has an impact on part of the outcome measures, including the number of CFs. Simulations indicate that unique junctions and subclones should not be used as substitutes for CF and that more complex methods do not outperform simpler methods. Also, we conclude that different approaches differ in their ability to correctly reconstruct CFs when not considering the LC and to identify shared CFs. The results showed the effect of different approaches on the reconstruction of CFs and highlighted the importance of choosing an appropriate method.
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Affiliation(s)
- Daria Balashova
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Barbera D C van Schaik
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Maria Stratigopoulou
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, Netherlands
| | - Jeroen E J Guikema
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Pathology, Lymphoma and Myeloma Center Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Tom G Caniels
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Mathieu Claireaux
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Marit J van Gils
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Anne Musters
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Dornatien C Anang
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Niek de Vries
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Antoine H C van Kampen
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands.
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands.
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands.
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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Larson DL, Pennarola N, Leone JB, Larson JL. Fewer bowl traps and more hand netting can increase effective number of bee species and reduce excessive captures. Ecol Evol 2024; 14:e11036. [PMID: 38414567 PMCID: PMC10897529 DOI: 10.1002/ece3.11036] [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: 08/11/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/29/2024] Open
Abstract
Reports increasingly point to substantial declines in wild bee abundance and diversity, yet there is uncertainty about how best to measure these attributes in wild bee populations. Two commonly used methods are passive trapping with bee bowls or active netting of bees on flowers, but each of these has drawbacks. Comparing the outcomes of the two methods is complicated by their uncomparable units of effort. The abundance distribution of bee species is also typically highly skewed, making it difficult to accurately assess diversity when rarer species are unlikely to be caught. The effective number of species, or Hill numbers, provides a way forward by basing the response metric on the number of equally abundant species. Our goal is to compare the effective number of bee species captured between hand netting and bowl trapping in wheatgrass prairie in South Dakota and tallgrass prairie in Minnesota, USA. Species overlap between the two methods ranged from ~40% to ~60%. Emphasis placed on rare species was important, so that 95% confidence limits overlapped between the two methods for species richness but netting exceeded trapping for Shannon's and Simpson's diversities. Netting always captured more bee species with fewer bee individuals than trapping. In most cases, the number of bees captured in bowl traps indicated substantial over-sampling, with little increase in bee species detected. Correlations between bee and floral abundance, richness, and diversity differed between netted and trapped samples. We conclude that netting and trapping together produce a more complete account of species richness, but shifting sampling emphasis from trapping to netting will result in fewer bees, but more bee species captured. Due to the different relationships between bee and floral diversities that depended on sampling method, it is unwise to compare habitat associations determined by netting with those determined by trapping.
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Affiliation(s)
- Diane L Larson
- U.S. Geological Survey, Northern Prairie Wildlife Research Center St. Paul Minnesota USA
| | - Nora Pennarola
- U.S. Fish and Wildlife Service Bloomington Minnesota USA
| | - Julia B Leone
- Friends of the Mississippi River St. Paul Minnesota USA
| | - Jennifer L Larson
- USDA Forest Service, Forest Health Protection St. Paul Minnesota USA
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36
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Wei G, Liang Y, Zhang G, Zhang Z, Zhang Y, Chen S, Dong L. Influence of sampling location and processing on the assembly and network of Polygoni Multiflori Radix surface microbiome. Int J Food Microbiol 2024; 410:110442. [PMID: 37984213 DOI: 10.1016/j.ijfoodmicro.2023.110442] [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: 08/25/2022] [Revised: 08/24/2023] [Accepted: 10/07/2023] [Indexed: 11/22/2023]
Abstract
The raw and processed roots of Polygonum multiflorum Thunb is a popular traditional Chinese medicine. However, Polygoni Multiflori Radix is easily contaminated by toxigenic fungi and mycotoxins during harvesting, processing, and transportation, thereby posing a health risk for consumers. This study aims to investigate the presence of fungi on the surface of raw and processed Polygoni Multiflori Radix collected from four producing areas using high-throughput sequencing. Results showed that the phyla Ascomycota and Basidiomycota, the genera Xeromyces, Cystofilobasidium, Eurotium, and Aspergillus were the dominant fungus, and significant differences are presented in four areas and two processed products. Three potential mycotoxin-producing fungi were detected, namely Trichosporon cutaneum, Aspergillus restrictus, and Fusarium oxysporum. The α-diversity and network complexity showed significant differences in four areas. Chao 1 and Shannon were highest in Yunnan (YN), then incrementally decreased from SC (Sichuan) to AH (Anhui) and GD (Guangdong) areas. Meanwhile, α-diversity was also strongly influenced by processing. Chao 1 and Shannon indices were higher in the raw group, however, the network complexity and connectivity were higher in the processed group. In conclusion, the assembly and network of the surface microbiome on Polygoni Multiflori Radix were influenced by sampling location and processing. This work provides details on the surface microbiome of Polygoni Multiflori Radix samples, which could ensure the drug and consumers' safety.
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Affiliation(s)
- Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Yichuan Liang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Zhaoyu Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Yongqing Zhang
- Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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37
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Zhou W, Li X. Fish diversity and selection of taxa for conservation in the Salween and Irrawaddy Rivers, Southeast Asia. Sci Rep 2024; 14:2393. [PMID: 38287045 PMCID: PMC10825156 DOI: 10.1038/s41598-024-51205-5] [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: 08/19/2023] [Accepted: 01/02/2024] [Indexed: 01/31/2024] Open
Abstract
Species diversity indices provide quantitative data for understanding the variations and trends in fish species diversity, as well as information on species richness and evenness. However, these diversity indices do not reflect differences in specific taxa, which can be of importance as key conservation targets, especially during the planning and construction of protected areas. In this study, simultaneously combining our improved traditional fish fauna analysis (TFFA) with the value of fish fauna presence (VFFP) methods, we studied fish diversity in the Salween and Irrawaddy basins. The results of the TFFA reflected the families (subfamilies) and genera that constitute the main body of fish diversity in the river basins. The results of the VFFP assessment showed which families (subfamilies) and genera were representative of certain characteristics in the basins. The VFFP scores of genera could be used as indicator indices and as priority taxa in the planning and construction of fish resource reserves. In this paper, we propose for the first time that the role and status of monotypic genera (genera comprising only a single species) in the conservation of fish diversity should not be ignored, and they should rather be a priority for protection.
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Affiliation(s)
- W Zhou
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, 300 Bailongsi Road, Kunming, 650224, Yunnan, China.
| | - X Li
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, 300 Bailongsi Road, Kunming, 650224, Yunnan, China
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Alfaro-Lucas JM, Martin D, Michel LN, Laes A, Cathalot C, Fuchs S, Sarrazin J. Fluid chemistry alters faunal trophodynamics but not composition on the deep-sea Capelinhos hydrothermal edifice (Lucky Strike vent field, Mid-Atlantic Ridge). Sci Rep 2024; 14:1940. [PMID: 38253666 PMCID: PMC10803789 DOI: 10.1038/s41598-024-52186-1] [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: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
The recently discovered deep-sea Capelinhos hydrothermal edifice, ~ 1.5 km of the main Lucky Strike (LS) vent field (northern Mid-Atlantic Ridge), contrasts with the other LS edifices in having poorly-altered end-member hydrothermal fluids with low pH and chlorine, and high metal concentrations. Capelinhos unique chemistry and location offer the opportunity to test the effects of local abiotic filters on faunal community structure while avoiding the often-correlated influence of dispersal limitation and depth. In this paper, we characterize for the first time the distribution patterns of the Capelinhos faunal communities, and analyze the benthic invertebrates (> 250 µm) inhabiting diffusive-flow areas and their trophic structures (δ13C, δ15N and δ34S). We hypothesized that faunal communities would differ from those of the nearest LS vent edifices, showing an impoverished species subset due to the potential toxicity of the chemical environment. Conversely, our results show that: (1) community distribution resembles that of other LS edifices, with assemblages visually dominated by shrimps (close to high-temperature focused-fluid areas) and mussels (at low-temperature diffuse flow areas); (2) most species from diffuse flow areas are well-known LS inhabitants, including the bed-forming and chemosymbiotic mussel Bathymodiolus azoricus and (3) communities are as diverse as those of the most diverse LS edifices. On the contrary, stable isotopes suggest different trophodynamics at Capelinhos. The high δ15N and, especially, δ13C and δ34S values suggest an important role of methane oxidation (i.e., methanotrophy), rather than the sulfide oxidation (i.e., thiotrophy) that predominates at most LS edifices. Our results indicate that Capelinhos shows unique environmental conditions, trophic structure and trophodynamics, yet similar fauna, compared to other LS edifices, which suggest a great environmental and trophic plasticity of the vent faunal communities at the LS.
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Affiliation(s)
- Joan M Alfaro-Lucas
- Univ Brest, Ifremer, CNRS, Unité BEEP, 29280, Plouzané, France.
- Department of Biology, University of Victoria, Victoria, BC, Canada.
| | - Daniel Martin
- Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
| | - Loïc N Michel
- Univ Brest, Ifremer, CNRS, Unité BEEP, 29280, Plouzané, France
- Université de Liège, Liège, Belgium
| | - Agathe Laes
- Univ Brest, Ifremer, CNRS, Unité BEEP, 29280, Plouzané, France
| | - Cécile Cathalot
- Univ Brest, Ifremer, CNRS, Unité BEEP, 29280, Plouzané, France
| | - Sandra Fuchs
- Univ Brest, Ifremer, CNRS, Unité BEEP, 29280, Plouzané, France
| | - Jozée Sarrazin
- Univ Brest, Ifremer, CNRS, Unité BEEP, 29280, Plouzané, France
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Papazlatani C, Garbeva P, Huerta Lwanga E. Effect of microplastic pollution on the gut microbiome of anecic and endogeic earthworms. FEMS Microbiol Lett 2024; 371:fnae040. [PMID: 38849299 PMCID: PMC11232513 DOI: 10.1093/femsle/fnae040] [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: 12/18/2023] [Revised: 04/19/2024] [Accepted: 06/06/2024] [Indexed: 06/09/2024] Open
Abstract
Microplastic (MP) pollution constitutes an emerging type of pollution threatening both aquatic and terrestrial ecosystems. The impact on aquatic ecosystems has been extensively studied, but the effect on terrestrial ecosystems and their inhabitants is mostly underexplored. In this study, we explored the effect of MP pollution on gut bacterial microbiome of endogeic (Aporrectodea caliginosa) and anecic (Lumbricus terrestris) earthworms. The experiments were performed in sandy soil with 0.2% of low-density polyethylene MPs (LDPE MPs). We observed that the endogeic earthworms had 100% survival, while anecic earthworms survived 25 days in the control (i.e. in absence of MPs) and 21 days in the treatment with LDPE MPs. The main driver of shifts in the diversity and composition of the bacterial communities in the gut of tested earthworms was the lifestyle of the worms, followed by the presence of MPs. The bacterial microbiome diversity was significantly different among the two types of earthworms, and the highest bacterial diversity was found in the gut of the endogeic earthworms. The effect of MPs on gut bacterial microbiome was clearly observed in the changes in the relative abundance of several phyla and families of the bacterial communities in both types of earthworms, although it was most evident in the anecic earthworms. The Actinobacteriota, Proteobacteria, and Firmicutes were the main groups enhanced in the MP treatments, suggesting enrichment of the bacterial communities with potential plastic degraders.
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Affiliation(s)
- Christina Papazlatani
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Esperanza Huerta Lwanga
- Soil Physics and Land Management Group, Wageningen University and Research, PO Box 47, 6708 PB Wageningen, The Netherlands
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40
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Li M, Masri S, Chiu CH, Sun Y, Wu J. Mapping wild vascular plant species diversity in urban areas in California using crowdsourcing data by regression kriging: Examining socioeconomic disparities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166995. [PMID: 37717761 PMCID: PMC10947671 DOI: 10.1016/j.scitotenv.2023.166995] [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: 06/01/2023] [Revised: 09/09/2023] [Accepted: 09/09/2023] [Indexed: 09/19/2023]
Abstract
Biodiversity is crucial for human health, but previous methods of measuring biodiversity require intensive resources and have other limitations. Crowdsourced datasets from citizen scientists offer a cost-effective solution for characterizing biodiversity on a large spatial scale. This study has two aims: 1) to generate fine-resolution plant species diversity maps in California urban areas using crowdsourced data and extrapolation methods; and 2) to examine their associations with sociodemographic factors and identify subpopulations with low biodiversity exposure. We used iNaturalist observations from 2019 to 2022 to calculate species diversity metrics by exploring the sampling completeness in a 5 × 5-km2 grid and then computing species diversity metrics for grid cells with at least 80 % sample completeness (841 out of 4755 grid cells). A generalized additive model with ordinary kriging (GAM OK) provided moderately reliable estimates, with correlations of 0.64-0.66 between observed and extrapolated metrics, relative mean absolute errors of 21 %-23 %, and relative root mean squared errors of 27 %-30 % for grid cells with ≥80 % sample completeness from 10-fold cross-validation. GAM OK was further applied to extrapolate species diversity metrics from saturated grid cells (N = 841) to the remaining grid cells with <80 % sample completeness (N = 3914) and generate diversity maps that cover the grid. Further, generalized linear mixed models were used to examine the associations between species diversity and sociodemographic indicators at census tract level. The wild vascular plant species diversity metrics were inversely associated with neighborhood socioeconomic status (i.e., unemployment, linguistic isolation, educational attainment, and poverty rate). Minority populations (i.e., African American, Asian American, and Hispanic) and children had significantly lower diversity exposure in their neighborhoods. Crowdsourcing data offers a cost-effective solution for characterizing large-scale biodiversity in urban areas.
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Affiliation(s)
- Mengyi Li
- Department of Disease Prevention, Program in Public Health, University of California, Irvine, CA, USA
| | - Shahir Masri
- Department of Environmental and Occupational Health, Program in Public Health, University of California, Irvine, CA, USA
| | - Chun-Huo Chiu
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yi Sun
- Department of Environmental and Occupational Health, Program in Public Health, University of California, Irvine, CA, USA; Institute of Medical Information, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jun Wu
- Department of Environmental and Occupational Health, Program in Public Health, University of California, Irvine, CA, USA.
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41
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Sharma G, Zee PC, Zea L, Curtis PD. Whole genome-scale assessment of gene fitness of Novosphingobium aromaticavorans during spaceflight. BMC Genomics 2023; 24:782. [PMID: 38102595 PMCID: PMC10725011 DOI: 10.1186/s12864-023-09799-z] [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: 08/11/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023] Open
Abstract
In microgravity, bacteria undergo intriguing physiological adaptations. There have been few attempts to assess global bacterial physiological responses to microgravity, with most studies only focusing on a handful of individual systems. This study assessed the fitness of each gene in the genome of the aromatic compound-degrading Alphaproteobacterium Novosphingobium aromaticavorans during growth in spaceflight. This was accomplished using Comparative TnSeq, which involves culturing the same saturating transposon mutagenized library under two different conditions. To assess gene fitness, a novel comparative TnSeq analytical tool was developed, named TnDivA, that is particularly useful in leveraging biological replicates. In this approach, transposon diversity is represented numerically using a modified Shannon diversity index, which was then converted into effective transposon density. This transformation accounts for variability in read distribution between samples, such as cases where reads were dominated by only a few transposon inserts. Effective density values were analyzed using multiple statistical methods, including log2-fold change, least-squares regression analysis, and Welch's t-test. The results obtained across applied statistical methods show a difference in the number of significant genes identified. However, the functional categories of genes important to growth in microgravity showed similar patterns. Lipid metabolism and transport, energy production, transcription, translation, and secondary metabolite biosynthesis and transport were shown to have high fitness during spaceflight. This suggests that core metabolic processes, including lipid and secondary metabolism, play an important role adapting to stress and promoting growth in microgravity.
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Affiliation(s)
- Gayatri Sharma
- Department of Biology, University of Mississippi, 402 Shoemaker Hall, University, MS, 38677, USA
| | - Peter C Zee
- Department of Biology, University of Mississippi, 402 Shoemaker Hall, University, MS, 38677, USA
| | - Luis Zea
- Aerospace Engineering Sciences, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Patrick D Curtis
- Department of Biology, University of Mississippi, 402 Shoemaker Hall, University, MS, 38677, USA.
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42
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Thomas MC, Waugh G, Vanwonterghem I, Webster NS, Rinke C, Fisher R, Luter HM, Negri AP. Protecting the invisible: Establishing guideline values for copper toxicity to marine microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166658. [PMID: 37659522 DOI: 10.1016/j.scitotenv.2023.166658] [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: 07/11/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Understanding the rapid responses of marine microbiomes to environmental disturbances is paramount for supporting early assessments of harm to high-value ecosystems, such as coral reefs. Yet, management guidelines aimed at protecting aquatic life from environmental pollution remain exclusively defined for organisms at higher trophic levels. In this study, 16S rRNA gene amplicon sequencing was applied in conjunction with propidium monoazide for cell-viability assessment as a sensitive tool to determine taxon- and community-level changes in a seawater microbial community under copper (Cu) exposure. Bayesian model averaging was used to establish concentration-response relationships to evaluate the effects of copper on microbial composition, diversity, and richness for the purpose of estimating microbiome Hazard Concentration (mHCx) values. Predicted mHC5 values at which a 5 % change in microbial composition, diversity, and richness occurred were 1.05, 0.72, and 0.38 μg Cu L-1, respectively. Threshold indicator taxa analysis was applied across the copper concentrations to identify taxon-specific change points for decreasing taxa. These change points were then used to generate a Prokaryotic Sensitivity Distribution (PSD), from which mHCxdec values were derived for copper, suitable for the protection of 99, 95, 90, and 80 % of the marine microbiome. The mHC5dec guideline value of 0.61 μg Cu L-1, protective of 95 % of the marine microbial community, was lower than the equivalent Australian water quality guideline value based on eukaryotic organisms at higher trophic levels. This suggests that marine microbial communities might be more vulnerable, highlighting potential insufficiencies in their protection against copper pollution. The mHCx values proposed here provide approaches to quantitatively assess the effects of contaminants on microbial communities towards the inclusion of prokaryotes in future water quality guidelines.
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Affiliation(s)
- Marie C Thomas
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia; Australian Institute of Marine Science, Townsville, QLD 4810, Australia; AIMS@JCU, Division of Research and Innovation, James Cook University, Townsville, QLD 4811, Australia.
| | - Gretel Waugh
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia; Australian Institute of Marine Science, Townsville, QLD 4810, Australia; AIMS@JCU, Division of Research and Innovation, James Cook University, Townsville, QLD 4811, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia; Australian Institute of Marine Science, Townsville, QLD 4810, Australia; Australian Antarctic Division, Hobart, TAS 7050, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Rebecca Fisher
- Australian Institute of Marine Science Crawley, Crawley, WA, Australia
| | - Heidi M Luter
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia; AIMS@JCU, Division of Research and Innovation, James Cook University, Townsville, QLD 4811, Australia
| | - Andrew P Negri
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia; AIMS@JCU, Division of Research and Innovation, James Cook University, Townsville, QLD 4811, Australia
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Limoges A, Ribeiro S, Van Nieuwenhove N, Jackson R, Juggins S, Crosta X, Weckström K. Marine diatoms record Late Holocene regime shifts in the Pikialasorsuaq ecosystem. GLOBAL CHANGE BIOLOGY 2023; 29:6503-6516. [PMID: 37772765 DOI: 10.1111/gcb.16958] [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: 05/21/2023] [Revised: 08/10/2023] [Accepted: 09/12/2023] [Indexed: 09/30/2023]
Abstract
The Pikialasorsuaq (North Water polynya) is an area of local and global cultural and ecological significance. However, over the last decades, the region has been subject to rapid warming, and in some recent years, the seasonal ice arch that has historically defined the polynya's northern boundary has failed to form. Both factors are deemed to alter the polynya's ecosystem functioning. To understand how climate-induced changes to the Pikialasorsuaq impact the basis of the marine food web, we explored diatom community-level responses to changing conditions, from a sediment core spanning the last 3800 years. Four metrics were used: total diatom concentrations, taxonomic composition, mean size, and diversity. Generalized additive model statistics highlight significant changes at ca. 2400, 2050, 1550, 1200, and 130 cal years BP, all coeval with known transitions between colder and warmer intervals of the Late Holocene, and regime shifts in the Pikialasorsuaq. Notably, a weaker/contracted polynya during the Roman Warm Period and Medieval Climate Anomaly caused the diatom community to reorganize via shifts in species composition, with the presence of larger taxa but lower diversity, and significantly reduced export production. This study underlines the high sensitivity of primary producers to changes in the polynya dynamics and illustrates that the strong pulse of early spring cryopelagic diatoms that makes the Pikialasorsuaq exceptionally productive may be jeopardized by rapid warming and associated Nares Strait ice arch destabilization. Future alterations to the phenology of primary producers may disproportionately impact higher trophic levels and keystone species in this region, with implications for Indigenous Peoples and global diversity.
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Affiliation(s)
- Audrey Limoges
- Department of Earth Sciences, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Sofia Ribeiro
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Nicolas Van Nieuwenhove
- Department of Earth Sciences, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Rebecca Jackson
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
- Globe Institute, Copenhagen University, Copenhagen, Denmark
| | - Stephen Juggins
- School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK
| | - Xavier Crosta
- CNRS, EPHE, UMR 5805 EPOC, Université de Bordeaux, Pessac Cedex, France
| | - Kaarina Weckström
- Ecosystems and Environment Research Programme (ECRU), University of Helsinki, Helsinki, Finland
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Hardison SB, McGlathery KJ, Castorani MCN. Effects of seagrass restoration on coastal fish abundance and diversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14147. [PMID: 37424354 DOI: 10.1111/cobi.14147] [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: 10/04/2022] [Revised: 05/01/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
Restoration is accelerating to reverse global declines of key habitats and recover lost ecosystem functions, particularly in coastal ecosystems. However, there is high uncertainty about the long-term capacity of restored ecosystems to provide habitat and increase biodiversity and the degree to which these ecosystem services are mediated by spatial and temporal environmental variability. We addressed these gaps by sampling fishes biannually for 5-7 years (2012-2018) at 16 sites inside and outside a rapidly expanding restored seagrass meadow in coastal Virginia (USA). Despite substantial among-year variation in abundance and species composition, seine catches in restored seagrass beds were consistently larger (6.4 times more fish, p < 0.001) and more speciose (2.6 times greater species richness, p < 0.001; 3.1 times greater Hill-Shannon diversity, p = 0.03) than seine catches in adjacent unvegetated areas. Catches were particularly larger during summer than autumn (p < 0.01). Structural equation modeling revealed that depth and water residence time interacted to control seagrass presence, leading to higher fish abundance and richness in shallow, well-flushed areas that supported seagrass. Together, our results indicate that seagrass restoration yields large and consistent benefits for many coastal fishes, but that restoration and its benefits are sensitive to the dynamic seascapes in which restoration is conducted. Consideration of how seascape-scale environmental variability affects the success of habitat restoration and subsequent ecosystem function will improve restoration outcomes and the provisioning of ecosystem services.
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Affiliation(s)
- Sean B Hardison
- Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Karen J McGlathery
- Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Max C N Castorani
- Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia, USA
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Leclercq N, Marshall L, Weekers T, Basu P, Benda D, Bevk D, Bhattacharya R, Bogusch P, Bontšutšnaja A, Bortolotti L, Cabirol N, Calderón-Uraga E, Carvalho R, Castro S, Chatterjee S, De La Cruz Alquicira M, de Miranda JR, Dirilgen T, Dorchin A, Dorji K, Drepper B, Flaminio S, Gailis J, Galloni M, Gaspar H, Gikungu MW, Hatteland BA, Hinojosa-Diaz I, Hostinská L, Howlett BG, Hung KLJ, Hutchinson L, Jesus RO, Karklina N, Khan MS, Loureiro J, Men X, Molenberg JM, Mudri-Stojnić S, Nikolic P, Normandin E, Osterman J, Ouyang F, Oygarden AS, Ozolina-Pole L, Ozols N, Parra Saldivar A, Paxton RJ, Pitts-Singer T, Poveda K, Prendergast K, Quaranta M, Read SFJ, Reinhardt S, Rojas-Oropeza M, Ruiz C, Rundlöf M, Sade A, Sandberg C, Sgolastra F, Shah SF, Shebl MA, Soon V, Stanley DA, Straka J, Theodorou P, Tobajas E, Vaca-Uribe JL, Vera A, Villagra CA, Williams MK, Wolowski M, Wood TJ, Yan Z, Zhang Q, Vereecken NJ. Global taxonomic, functional, and phylogenetic diversity of bees in apple orchards. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:165933. [PMID: 37536603 DOI: 10.1016/j.scitotenv.2023.165933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 07/27/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
An essential prerequisite to safeguard pollinator species is characterisation of the multifaceted diversity of crop pollinators and identification of the drivers of pollinator community changes across biogeographical gradients. The extent to which intensive agriculture is associated with the homogenisation of biological communities at large spatial scales remains poorly understood. In this study, we investigated diversity drivers for 644 bee species/morphospecies in 177 commercial apple orchards across 33 countries and four global biogeographical biomes. Our findings reveal significant taxonomic dissimilarity among biogeographical zones. Interestingly, despite this dissimilarity, species from different zones share similar higher-level phylogenetic groups and similar ecological and behavioural traits (i.e. functional traits), likely due to habitat filtering caused by perennial monoculture systems managed intensively for crop production. Honey bee species dominated orchard communities, while other managed/manageable and wild species were collected in lower numbers. Moreover, the presence of herbaceous, uncultivated open areas and organic management practices were associated with increased wild bee diversity. Overall, our study sheds light on the importance of large-scale analyses contributing to the emerging fields of functional and phylogenetic diversity, which can be related to ecosystem function to promote biodiversity as a key asset in agroecosystems in the face of global change pressures.
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Affiliation(s)
- N Leclercq
- Agroecology Lab, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/02, B-1050 Brussels, Belgium.
| | - L Marshall
- Agroecology Lab, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/02, B-1050 Brussels, Belgium; Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, Netherlands
| | - T Weekers
- Agroecology Lab, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/02, B-1050 Brussels, Belgium
| | - P Basu
- Centre for Pollination Studies, University of Calcutta, Kolkata, India
| | - D Benda
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic; Department of Entomology, National Museum, Prague, Czech Republic
| | - D Bevk
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
| | - R Bhattacharya
- Centre for Pollination Studies, University of Calcutta, Kolkata, India
| | - P Bogusch
- Department of Biology, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - A Bontšutšnaja
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - L Bortolotti
- CREA Research Centre for Agriculture and Environment, Bologna, Italy
| | - N Cabirol
- Department of Ecology and Natural Resources, Faculty of Science, UNAM, México City, Mexico
| | - E Calderón-Uraga
- Department of Ecology and Natural Resources, Faculty of Science, UNAM, México City, Mexico
| | - R Carvalho
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - S Castro
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - S Chatterjee
- Centre for Pollination Studies, University of Calcutta, Kolkata, India
| | - M De La Cruz Alquicira
- Department of Ecology and Natural Resources, Faculty of Science, UNAM, México City, Mexico
| | - J R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, 750 05, Sweden
| | - T Dirilgen
- School of Agriculture and Food Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - A Dorchin
- Laboratory of Zoology, Université de Mons, Mons, Belgium; The Steinhardt Museum of Natural History, Tel Aviv University, 69978 Tel Aviv, Israel; Department of Entomology, Royal Museum for Central Africa, Tervuren, Belgium
| | - K Dorji
- College of Natural Resources, Royal University of Bhutan, Punakha, Bhutan
| | - B Drepper
- Division of Forest, Nature and Landscape, University of Leuven, Leuven, Belgium
| | - S Flaminio
- CREA Research Centre for Agriculture and Environment, Bologna, Italy; Laboratory of Zoology, Université de Mons, Mons, Belgium
| | - J Gailis
- Institute for Plant Protection Research Agrihorts, Latvia University of Life Sciences and Technologies, Jelgava, Latvia
| | - M Galloni
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - H Gaspar
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - M W Gikungu
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - B A Hatteland
- Division for Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Aas, Norway; Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - I Hinojosa-Diaz
- Department of Zoology, Institute of Biology, UNAM, México City, Mexico
| | - L Hostinská
- Department of Biology, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - B G Howlett
- The New Zealand Institute for Plant & Food Research Limited, Lincoln, Canterbury, New Zealand
| | - K-L J Hung
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; Oklahoma Biological Survey, University of Oklahoma, Norman, OK 73019, USA
| | - L Hutchinson
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - R O Jesus
- Graduate Program in Ecology, State University of Campinas, Campinas, São Paulo, Brazil
| | - N Karklina
- Institute for Plant Protection Research Agrihorts, Latvia University of Life Sciences and Technologies, Jelgava, Latvia
| | - M S Khan
- Department of Entomology, University of Agriculture, Peshawar, Pakistan
| | - J Loureiro
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - X Men
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Plant Virology,Jinan 250100, China
| | - J-M Molenberg
- Agroecology Lab, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/02, B-1050 Brussels, Belgium
| | - S Mudri-Stojnić
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - P Nikolic
- Faculty of Agriculture, University of Banja Luka, Banja Luka, Bosnia and Herzegovina
| | - E Normandin
- Centre sur la biodiversité, Département des sciences biologiques, Université de Montréal, QC, Québec H1X 2B2, Canada
| | - J Osterman
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany; Nature Conservation and Landscape Ecology, University of Freiburg, Tennenbacherstrasse 4, 79106, Freiburg im Breisgau, Germany
| | - F Ouyang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - A S Oygarden
- Department of Natural Sciences and Environmental Health, University of South-Eastern Norway, Bø, Norway
| | - L Ozolina-Pole
- Institute for Plant Protection Research Agrihorts, Latvia University of Life Sciences and Technologies, Jelgava, Latvia
| | - N Ozols
- Institute for Plant Protection Research Agrihorts, Latvia University of Life Sciences and Technologies, Jelgava, Latvia
| | - A Parra Saldivar
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación (UMCE), Santiago, Chile
| | - R J Paxton
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
| | - T Pitts-Singer
- USDA Agricultural Research Service, Pollinating Insects Research Unit, Logan, UT 84322, USA
| | - K Poveda
- Department of Entomology, Cornell University, 4126 Comstock Hall, Ithaca, NY 14853, USA
| | - K Prendergast
- Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - M Quaranta
- CREA Research Centre for Agriculture and Environment, Bologna, Italy
| | - S F J Read
- The New Zealand Institute for Plant & Food Research Limited, Lincoln, Canterbury, New Zealand
| | - S Reinhardt
- Department of Natural Sciences and Environmental Health, University of South-Eastern Norway, Bø, Norway
| | - M Rojas-Oropeza
- Department of Ecology and Natural Resources, Faculty of Science, UNAM, México City, Mexico
| | - C Ruiz
- Departamento Biología Animal, Edafología y Geología, Facultad de Ciencias, Universidad de La Laguna, La Laguna, 38206, Tenerife, Spain
| | - M Rundlöf
- Department of Biology, Lund University, Lund, Sweden
| | - A Sade
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905 Haifa, Israel
| | - C Sandberg
- Department of Biology, Lund University, Lund, Sweden; Calluna AB, Husargatan 3, Malmö, 211 28, Sweden
| | - F Sgolastra
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - S F Shah
- Department of Entomology, University of Agriculture, Peshawar, Pakistan
| | - M A Shebl
- Department of Plant Protection, Faculty of Agriculture, Suez Canal University, Ismailia 41522, Egypt
| | - V Soon
- Natural History Museum and Botanical Garden, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - D A Stanley
- School of Agriculture and Food Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - J Straka
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - P Theodorou
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
| | - E Tobajas
- Department of Biology, Lund University, Lund, Sweden; Department of Animal Biology, University of Salamanca, Campus Miguel de Unamuno, Salamanca, 37007, Spain
| | - J L Vaca-Uribe
- Laboratorio de Investigaciones en Abejas LABUN, Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá,111321, Colombia
| | - A Vera
- Departamento de Biología, Universidad Metropolitana de Ciencias de la Educación (UMCE), Santiago, Chile
| | - C A Villagra
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación (UMCE), Santiago, Chile
| | - M-K Williams
- Department of Biology, Utah State University, Logan, UT 84322, USA
| | - M Wolowski
- Institute of Natural Sciences, Federal University of Alfenas, Alfenas, Minas Gerais, Brazil
| | - T J Wood
- Laboratory of Zoology, Université de Mons, Mons, Belgium
| | - Z Yan
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Q Zhang
- Beijing Biodiversity Conservation Research Center/Beijing Milu Ecological Research Center, Beijing 100076, China
| | - N J Vereecken
- Agroecology Lab, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/02, B-1050 Brussels, Belgium
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Mathewos M, Sisay A, Berhanu Y. Grazing intensity effects on rangeland condition and tree diversity in Afar, northeastern Ethiopia. Heliyon 2023; 9:e22133. [PMID: 38045209 PMCID: PMC10692821 DOI: 10.1016/j.heliyon.2023.e22133] [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: 06/05/2023] [Revised: 10/27/2023] [Accepted: 11/05/2023] [Indexed: 12/05/2023] Open
Abstract
This study assessed the effects of different grazing pressures (light, moderate and heavy) on rangeland condition and woody species diversity in northeastern Ethiopia. Rangeland condition was analyzed using common protocols for the assessment of semi-arid rangelands. A total of 4 grasses, 5 herbs, 1 sedge and 14 tree and/or shrub species were identified. Results show that grazing intensity had detrimental effects on condition of the rangeland, and caused undesirable changes in herbaceous species composition. The contribution of undesirable plants to herbaceous aboveground biomass was particularly high (40 %) compared to the 30 % contributed by highly desirable species. Nearly all measures of range condition were negatively affected by grazing. Grass composition, number of seedlings and age distribution, basal and litter cover, soil erosion and compaction decreased significantly as grazing intensity increased. Species richness and diversity (Hill numbers) of woody plants were reduced significantly by grazing. The overall condition of the rangeland was generally poor. The pastoralists perceived that recurring droughts, heavy continuous grazing and inappropriate management interventions, and bush encroachment were the main contributing factors that led to overgrazing and rangeland deterioration in the area. In conclusion, our study shows that livestock grazing in northeastern Ethiopia degrade range condition and woody vegetation, and its effects are sever under moderate and heavy grazing. Management measures such as resting of the rangelands preferably with stock exclusions for 6-12 months or protecting heavily degraded or sensitive areas from livestock activity and reseeding may be the viable options to mitigate declines in range conditions.
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Affiliation(s)
- Mengeste Mathewos
- School of Animal and Range Sciences, Hawassa University, P.O. Box. 05, Hawassa, Ethiopia
| | - Amsalu Sisay
- School of Animal and Range Sciences, Hawassa University, P.O. Box. 05, Hawassa, Ethiopia
| | - Yonas Berhanu
- School of Animal and Range Sciences, Hawassa University, P.O. Box. 05, Hawassa, Ethiopia
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47
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Aspin TWH, Khamis K, Matthews TJ, Williams GMD, Windsor FM, Woodward G, Ledger ME. Extra terrestrials: drought creates niche space for rare invertebrates in a large-scale and long-term field experiment. Biol Lett 2023; 19:20230381. [PMID: 37935369 PMCID: PMC10645067 DOI: 10.1098/rsbl.2023.0381] [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: 08/23/2023] [Accepted: 10/17/2023] [Indexed: 11/09/2023] Open
Abstract
Freshwater habitats are drying more frequently and for longer under the combined pressures of climate change and overabstraction. Unsurprisingly, many aquatic species decline or become locally extinct as their benthic habitat is lost during stream droughts, but less is known about the potential 'winners': those terrestrial species that may exploit emerging niches in drying riverbeds. In particular, we do not know how these transient ecotones will respond as droughts become more extreme in the future. To find out we used a large-scale, long-term mesocosm experiment spanning a wide gradient of drought intensity, from permanent flows to full streambed dewatering, and analysed terrestrial invertebrate community assembly after 1 year. Droughts that caused stream fragmentation gave rise to the most diverse terrestrial invertebrate assemblages, including 10 species with UK conservation designations, and high species turnover between experimental channels. Droughts that caused streambed dewatering produced lower terrestrial invertebrate richness, suggesting that the persistence of instream pools may benefit these taxa as well as aquatic biota. Particularly intense droughts may therefore yield relatively few 'winners' among either aquatic or terrestrial species, indicating that the threat to riverine biodiversity from future drought intensification could be more pervasive than widely acknowledged.
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Affiliation(s)
- Thomas W. H. Aspin
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Environment Agency, Bristol, UK
| | - Kieran Khamis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Thomas J. Matthews
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Birmingham Institute of Forest Research, University of Birmingham, Birmingham B15 2TT, UK
- CE3C – Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group / CHANGE – Global Change and Sustainability Institute and Universidade dos Açores – Faculty of Agricultural Sciences and Environment, PT-9700-042, Angra do Heroísmo, Açores, Portugal
| | - Gavin M. D. Williams
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | | | - Guy Woodward
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, UK
| | - Mark E. Ledger
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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48
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Cantu-Jungles TM, Hamaker BR. Tuning Expectations to Reality: Don't Expect Increased Gut Microbiota Diversity with Dietary Fiber. J Nutr 2023; 153:3156-3163. [PMID: 37690780 DOI: 10.1016/j.tjnut.2023.09.001] [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: 08/01/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023] Open
Abstract
Dietary approaches, particularly those including fiber supplementation, can be used to promote health benefits by shaping gut microbial communities. Whereas community diversity measures, such as richness and evenness, are often used in microbial ecology to make sense of these complex and vast microbial ecosystems, it is less clear how these concepts apply when dietary fiber supplementation is given. In this perspective, we summarize and demonstrate how factors including experimental approach, number of bacteria sharing a dietary fiber, and initial relative abundances of bacteria that use a fiber can significantly affect diversity outcomes in fiber fermentation studies. We also show that a reduction in alpha diversity is possible, and perhaps expected, for most approaches that use fermentable fibers to beneficially shape the gut microbial community while still achieving health-related improvements.
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Affiliation(s)
- Thaisa M Cantu-Jungles
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, United States.
| | - Bruce R Hamaker
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, United States
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49
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González-Varo JP, Albrecht J, Arroyo JM, Bueno RS, Burgos T, Escribano-Ávila G, Farwig N, García D, Illera JC, Jordano P, Kurek P, Rösner S, Virgós E, Sutherland WJ. Frugivore-mediated seed dispersal in fragmented landscapes: Compositional and functional turnover from forest to matrix. Proc Natl Acad Sci U S A 2023; 120:e2302440120. [PMID: 37871198 PMCID: PMC10622928 DOI: 10.1073/pnas.2302440120] [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: 02/17/2023] [Accepted: 09/01/2023] [Indexed: 10/25/2023] Open
Abstract
Seed dispersal by frugivores is a fundamental function for plant community dynamics in fragmented landscapes, where forest remnants are typically embedded in a matrix of anthropogenic habitats. Frugivores can mediate both connectivity among forest remnants and plant colonization of the matrix. However, it remains poorly understood how frugivore communities change from forest to matrix due to the loss or replacement of species with traits that are less advantageous in open habitats and whether such changes ultimately influence the composition and traits of dispersed plants via species interactions. Here, we close this gap by using a unique dataset of seed-dispersal networks that were sampled in forest patches and adjacent matrix habitats of seven fragmented landscapes across Europe. We found a similar diversity of frugivores, plants, and interactions contributing to seed dispersal in forest and matrix, but a high turnover (replacement) in all these components. The turnover of dispersed seeds was smaller than that of frugivore communities because different frugivore species provided complementary seed dispersal in forest and matrix. Importantly, the turnover involved functional changes toward larger and more mobile frugivores in the matrix, which dispersed taller, larger-seeded plants with later fruiting periods. Our study provides a trait-based understanding of frugivore-mediated seed dispersal through fragmented landscapes, uncovering nonrandom shifts that can have cascading consequences for the composition of regenerating plant communities. Our findings also highlight the importance of forest remnants and frugivore faunas for ecosystem resilience, demonstrating a high potential for passive forest restoration of unmanaged lands in the matrix.
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Affiliation(s)
- Juan P. González-Varo
- Departamento de Biología, Instituto de Investigación Vitivinícola y Agroalimentaria, Universidad de Cádiz, Puerto Real11510, Spain
| | - Jörg Albrecht
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main60325, Germany
| | - Juan M. Arroyo
- Integrative Ecology Group, Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Sevilla41092, Spain
| | - Rafael S. Bueno
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo90128, Italy
| | - Tamara Burgos
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid28933, Spain
| | - Gema Escribano-Ávila
- Biodiversity, Ecology and Evolution Department, Complutense University Madrid, Madrid28040, Spain
| | - Nina Farwig
- Conservation Ecology, Department of Biology, Philipps-Universität Marburg, Marburg35032, Germany
| | - Daniel García
- Biodiversity Research Institute (University of Oviedo – Consejo Superior de Investigaciones Científicas – Principado de Asturias), Mieres33600, Spain
| | - Juan C. Illera
- Biodiversity Research Institute (University of Oviedo – Consejo Superior de Investigaciones Científicas – Principado de Asturias), Mieres33600, Spain
| | - Pedro Jordano
- Integrative Ecology Group, Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Sevilla41092, Spain
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Sevilla41012, Spain
| | - Przemysław Kurek
- Department of Plant Ecology and Environmental Protection, Adam Mickiewicz University, Poznań61-712, Poland
| | - Sascha Rösner
- Conservation Ecology, Department of Biology, Philipps-Universität Marburg, Marburg35032, Germany
| | - Emilio Virgós
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid28933, Spain
| | - William J. Sutherland
- Conservation Science Group, Department of Zoology, University of Cambridge, CambridgeCB2 3QZ, United Kingdom
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50
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Martens HR, Laage K, Eickmanns M, Drexler A, Heinsohn V, Wegner N, Muster C, Diekmann M, Seeber E, Kreyling J, Michalik P, Tanneberger F. Paludiculture can support biodiversity conservation in rewetted fen peatlands. Sci Rep 2023; 13:18091. [PMID: 37872150 PMCID: PMC10593922 DOI: 10.1038/s41598-023-44481-0] [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: 07/17/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023] Open
Abstract
Paludiculture, the productive use of wet or rewetted peatlands, offers an option for continued land use by farmers after rewetting formerly drained peatlands, while reducing the greenhouse gas emissions from peat soils. Biodiversity conservation may benefit, but research on how biodiversity responds to paludiculture is scarce. We conducted a multi-taxon study investigating vegetation, breeding bird and arthropod diversity at six rewetted fen sites dominated by Carex or Typha species. Sites were either unharvested, low- or high-intensity managed, and were located in Mecklenburg-Vorpommern in northeastern Germany. Biodiversity was estimated across the range of Hill numbers using the iNEXT package, and species were checked for Red List status. Here we show that paludiculture sites can provide biodiversity value even while not reflecting historic fen conditions; managed sites had high plant diversity, as well as Red Listed arthropods and breeding birds. Our study demonstrates that paludiculture has the potential to provide valuable habitat for species even while productive management of the land continues.
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Affiliation(s)
| | - K Laage
- University of Greifswald, Greifswald, Germany
| | - M Eickmanns
- University of Greifswald, Greifswald, Germany
| | - A Drexler
- University of Greifswald, Greifswald, Germany
| | - V Heinsohn
- University of Greifswald, Greifswald, Germany
| | - N Wegner
- University of Greifswald, Greifswald, Germany
| | - C Muster
- University of Greifswald, Greifswald, Germany
| | | | - E Seeber
- University of Greifswald, Greifswald, Germany
| | - J Kreyling
- University of Greifswald, Greifswald, Germany
| | - P Michalik
- University of Greifswald, Greifswald, Germany
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