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Zettlemoyer MA, Munck S, Poschlod P, Rosbakh S. Subtle changes in plant diversity in the Bavarian Alps over the past eight decades. Ecol Evol 2024; 14:e70035. [PMID: 39224160 PMCID: PMC11366975 DOI: 10.1002/ece3.70035] [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: 05/19/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 09/04/2024] Open
Abstract
Historical resurveys represent a unique opportunity to analyze vegetation dynamics over longer timescales than is typically achievable. Leveraging the oldest historical dataset of vegetation change in the Bavarian Alps, Germany, we address how environmental conditions, vegetation composition, and functional diversity in the calcareous grasslands of the Schachen region have changed across different elevational ranges over an 83-year timeframe. We document changes in regional average temperature and precipitation. We use indicator values (IV) for species' ecological preferences and their palatability to grazers to infer local conditions (temperature, soil moisture/fertility, and grazing regime). We further estimate changes in temporal beta-diversity and functional trait community composition between historical (1936) and contemporary (2019) surveys in two elevational (subalpine and alpine) belts. Both subalpine and alpine sites became drier; subalpine sites also became warmer with more palatable plants. Species occurrence and abundance in the Schachen region has not changed substantially over time despite changing macroclimate and local environmental conditions under anthropogenic change. Yet these grasslands have experienced several "invisible" changes in functional composition over the past 80 years. As the Schachen has become drier, species with traits related to drought tolerance and animal-based dispersal have increased in dominance. Specifically, in alpine sites, community-weighted means revealed that with low fecundity, higher potential for endo- and epizoochory (seed dispersal via animal gut and fur, respectively), higher foliar frost tolerance, and deeper dormancy increased in dominance. Similar trends were found for increasing dominance of low fecundity, epizoochorous species in subalpine sites. Vegetation data from resurveying historical plots in combination with changes in local conditions, classic biodiversity indices, and functional trait indices can provide more holistic insights into changes in the environment and potential impacts of those environmental changes on long-term plant community and functional diversity.
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Affiliation(s)
| | - Svenja Munck
- Department of Ecology and Conservation BiologyUniversitat RegensburgRegensburgGermany
| | - Peter Poschlod
- Department of Ecology and Conservation BiologyUniversitat RegensburgRegensburgGermany
| | - Sergey Rosbakh
- Department of Ecology and Conservation BiologyUniversitat RegensburgRegensburgGermany
- Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
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2
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Fan X, Meng L, Wang Y, Zang L. Stochastic process drives the dissimilarity in biodiversity patterns between Pinus kwangtungensis coniferous forest and evergreen deciduous broad-leaved mixed forest in karst area. PeerJ 2024; 12:e17899. [PMID: 39224826 PMCID: PMC11368079 DOI: 10.7717/peerj.17899] [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: 01/23/2024] [Accepted: 07/20/2024] [Indexed: 09/04/2024] Open
Abstract
Pinus kwangtungensis is an endangered evergreen conifer tree species, and its in situ conservation has been considered one of the most critical issues. However, relative protection is limited by the lack of understanding of its community structure and underlying assembly processes. To study how the species diversity and assembly processes of Pinus kwangtungensis coniferous forest (CF) differed with regional climax community, this study established a series forest dynamic plots both in CF and evergreen deciduous broadleaved mixed forest (EDBM). By performing comparison analysis and PER-SIMPER approaches, we quantified the differences in species diversity and community assembly rules. The results showed that the species α-diversity of CF differed greatly from the EDBM both in species richness and evenness. In addition, the stochastic process acted a more important role in determining species composition, indicating the uncertainty in presence of species. The soil phosphorus and changeable calcium content were the main factors driving the differences in biodiversity, which the importance of soil nutrient factors in driving species composition. Our study highlighted that we should consider the community structure and ecological process when conducting conservation of Pinus kwangtungensis.
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Affiliation(s)
- Xingying Fan
- School of Medicine and Health Management, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Longchenxi Meng
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, Guizhou Province, China
| | - Yeheng Wang
- Zibo Real Estate Registration Center, Zibo, Shandong Province, China
| | - Lipeng Zang
- Research Center of Forest Ecology, College of Forestry, Guizhou University, Guiyang, Guizhou Province, China
- Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, Libo, Guizhou Province, China
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3
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Fenichel EP, Dean MF, Schmitz OJ. The path to scientifically sound biodiversity valuation in the context of the Global Biodiversity Framework. Proc Natl Acad Sci U S A 2024; 121:e2319077121. [PMID: 39141347 PMCID: PMC11348291 DOI: 10.1073/pnas.2319077121] [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: 08/15/2024] Open
Abstract
Successful implementation of the Kunming-Montreal Global Biodiversity Framework requires identifying a process for measuring and valuing changes in biodiversity that build on the recognition that economics and valuation must play a key role in "halting and reversing" biodiversity loss. Here, we discuss considerations for a practical path to valuing changes in biodiversity. Framing changes in the value of biodiversity as a summary of changes in certain natural assets enables leveraging existing approaches and international standards associated with environmental-economic accounting. We discuss why an approach that builds from individual species, evolutionary groups, or functional groups into a practical, hierarchical statistical classification system is better than the development of any one biodiversity index. We merge techniques from ecology and other natural sciences, national and environmental-economic accounting, and economics, which are all on the cusp of making measurement of the change in the value of biodiversity possible. The focus should be on scaling and integrating these approaches. The path forward appears to begin with imperfect but useful measures, grounded in robust concepts, while establishing ambition to further scale-up measurements-just like the past evolution of many other official statistical series.
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Affiliation(s)
- Eli P. Fenichel
- Yale University, Yale School of the Environment, New Haven, CT06511
| | - Monica F. Dean
- University of Southern California, USC Dornsife College of Letters, Arts, and Science, Public Exchange, Los Angeles, CA90089-0376
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4
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Groh C, Siriwardena GM, McMahon BJ. Diversity in Irish and British avifauna assemblages: What can variation in diversity profiles reveal about the forces that drive assemblage composition and structure? Ecol Evol 2024; 14:e70143. [PMID: 39139914 PMCID: PMC11319734 DOI: 10.1002/ece3.70143] [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: 03/11/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/15/2024] Open
Abstract
Ireland and Britain are two islands located at Europe's westernmost edge, both of which act as the final breeding outposts for many bird species within their European ranges. Despite their similar geographic locations and geological histories, Ireland and Britain host different breeding avifauna assemblages. Diversity profiles, which can serve as more robust alternatives to classic diversity indices, were employed in this study to explore disparities in the two islands' breeding avifauna assemblages. Variations in assemblages were explored, along with their potential drivers, through analyses at three levels: island-scale breeding bird assemblage compositions, island-scale diversity profiles considering 49 common breeding species, and habitat-specific diversity profiles considering assemblages in east/central Irish farmland and East Anglian farmland. Analysis of the two islands' breeding avifauna assemblages revealed that the Irish assemblage is a complete subset of the British assemblage. Analyses of Irish and British assemblages at both an island scale and a habitat scale revealed patterns linking land use to trends within the two islands' avifauna assemblages. Irish assemblages contained greater proportions of insectivorous farmland species by abundance, while British assemblages contained greater proportions of seed-eating farmland species; both trends appeared to be related to structural differences in agricultural land use on the two islands. The British and East Anglian assemblages exhibited higher diversity across all analyses, which appeared to be driven by the assemblages' higher relative abundances of species that were most genetically distinct. This study highlights the ability of diversity profiles to impart more information than classic diversity indices by incorporating species similarity data.
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Affiliation(s)
- Camille Groh
- UCD School of Agriculture and Food ScienceUniversity College DublinDublinIreland
| | | | - Barry J. McMahon
- UCD School of Agriculture and Food ScienceUniversity College DublinDublinIreland
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5
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Dai Z, Zhang N, Wang F, Li Y, Peng J, Xiang T, Zhao X, Yang S, Cao W. Loss of microbial functional diversity following Spartina alterniflora invasion reduces the potential of carbon sequestration and nitrogen removal in mangrove sediments-from a gene perspective. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121569. [PMID: 38914045 DOI: 10.1016/j.jenvman.2024.121569] [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: 03/24/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/26/2024]
Abstract
Mangrove ecosystems play an important role in carbon (C) sequestration and nitrogen (N) removal. Although Spartina alterniflora has successively invaded native mangrove habitats during the preceding two decades, the effects of this invasion on the microbial functional potential involved in nutrient cycling remain unclear. In this study, metagenomic sequencing was used to investigate microbial C and N cycling in sediments derived from S. alterniflora and three native mangrove species (Kandelia obovata, Avicennia marina, and Aegiceras corniculatum). Greater differences in functional profiles of C and N cycling-related genes were observed between S. alterniflora and mangrove sediments than between different mangrove sediments. Functional diversity was lower in S. alterniflora sediments than in native mangrove sediments. The growth of Thaumarchaeota and Proteobacteria, was enhanced due to their resilience to diversity loss, while the growth of oligotrophs, such as Chloroflexi and Firmicutes, was inhibited in S. alterniflora sediments. Compared to mangrove sediments, the abundance of genes involved in C fixation and methane production was lower in S. alterniflora sediments. However, S. alterniflora significantly increased the gene abundance of pmo which controlled the oxidation process of CH4 to carbon dioxide. Additionally, genes involved in nitrification were enriched, whereas genes involved in N reduction processes, such as denitrification and dissimilatory nitrate reduction to ammonium, N immobilization, and N mineralization, were depleted in S. alterniflora sediments compared to mangrove sediments. Partial least squares regression models demonstrated that the decrease in soil organic C and increase in pH after S. alterniflora invasion induced the loss of microbial functional diversity, which was the main driver of changes in the abundances of genes involved in C and N cycling. Overall, our findings indicate that S. alterniflora invasion modifies the microbial functional profile of nutrient cycling in native mangrove ecosystems and potentially weakens the capacity of mangroves to sequester carbon and remove nitrogen.
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Affiliation(s)
- Zetao Dai
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Ning Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Feifei Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yujie Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jiarui Peng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Tao Xiang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xiaoyu Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Shengchang Yang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Wenzhi Cao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China.
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6
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Gorman T, Kindermann G, Healy K, Morley TR. Variation in ecological scorecards and their potential for wider use. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:722. [PMID: 38985399 PMCID: PMC11236852 DOI: 10.1007/s10661-024-12845-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/22/2024] [Indexed: 07/11/2024]
Abstract
Ecological monitoring is a vital tool to help us assess habitat condition and understand the mechanism(s) for habitat change. Yet many countries struggle to meet their monitoring requirements in part due to the high assessment workload. Rapid ecological assessment methods may have an important role to play in this regard. Following their success within several European habitats (e.g., semi-natural grasslands), they are now being developed for additional habitats such as heathlands, peatlands, and other agri-associated areas. Whilst some rapid assessments using ecological scorecards have been shown to be accurate compared to traditional ecological monitoring, less is known about the functionality of these scorecards in heterogenous landscapes. In this study, we selected four existing scorecards to test alongside a prototype. We assessed how these different scorecards measured habitat condition on the same heathland sites. We found that the choice of metrics, their score weighting, and the thresholds used for categorical scores cause scorecards to assess the same site with substantial variation (37%). Vegetation metrics were the primary cause of score variation, with vegetation structure and positive indicator species being the leading causes. Our study indicates that whilst current scorecards may be representative of project-specific goals, they may not be suitable for wider monitoring uses in their current form. Ecological scorecards have great potential to drastically increase the extent of monitoring, but caution is needed before adapting existing scorecards beyond the purposes from which they were designed.
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Affiliation(s)
- Thomas Gorman
- Discipline of Geography, and the Ryan Institute, University of Galway, Galway, Ireland.
| | - Gesche Kindermann
- Earth and Life Sciences, School of Natural Sciences, and the Ryan Institute, University of Galway, Galway, Ireland
| | - Kevin Healy
- Earth and Life Sciences, School of Natural Sciences, and the Ryan Institute, University of Galway, Galway, Ireland
| | - Terry R Morley
- Discipline of Geography, and the Ryan Institute, University of Galway, Galway, Ireland
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7
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Peraza-Escarrá R, Armenteros M, Fernández-Garcés R, Gracia A. Taxonomic, phylogenetic, and functional diversity of mollusk death assemblages in coral reef and seagrass sediments from two shallow gulfs in Western Cuban Archipelago. PLoS One 2024; 19:e0303539. [PMID: 38743730 PMCID: PMC11093297 DOI: 10.1371/journal.pone.0303539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 04/25/2024] [Indexed: 05/16/2024] Open
Abstract
Mollusk death assemblages are formed by shell remnants deposited in the surficial mixed layer of the seabed. Diversity patterns in tropical marine habitats still are understudied; therefore, we aimed to investigate the taxonomic, phylogenetic, and functional diversity of mollusk death assemblages at regional and local scales in coral reef sands and seagrass meadows. We collected sediment samples at 11 sites within two shallow gulfs in the Northwestern Caribbean Sea and Southeastern Gulf of Mexico. All the shells were counted and identified to species level and classified into biological traits. We identified 7113 individuals belonging to 393 species (290 gastropods, 94 bivalves, and nine scaphopods). Diversity and assemblage structure showed many similarities between gulfs given their geological and biogeographical commonalities. Reef sands had higher richness than seagrasses likely because of a more favorable balance productivity-disturbance. Reef sands were dominated by epifaunal herbivores likely feeding on microphytobenthos and bysally attached bivalves adapted to intense hydrodynamic regime. In seagrass meadows, suspension feeders dominated in exposed sites and chemosynthetic infaunal bivalves dominated where oxygen replenishment was limited. Time averaging of death assemblages was likely in the order of 100 years, with stronger effects in reef sands compared to seagrass meadows. Our research provides evidence of the high taxonomic, phylogenetic, and functional diversity of mollusk death assemblages in tropical coastal sediments as result of the influence of scale-related processes and habitat type. Our study highlights the convenience of including phylogenetic and functional traits, as well as dead shells, for a more complete assessment of mollusk biodiversity.
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Affiliation(s)
- Rosely Peraza-Escarrá
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maickel Armenteros
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Adolfo Gracia
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
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8
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Lu S, Cheng D, Yao H, Wen Y, Yu Y, Li H, Wang J, Sun B. Cascade Microbial Metabolism of Ferulic Acid In Vitro Fermented by the Human Fecal Inoculum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:9807-9817. [PMID: 38602350 DOI: 10.1021/acs.jafc.3c09782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Ferulic acid (FA), predominantly existing in most cereals, can modulate the gut microbiome, but the influences of its metabolites on the microbial population and FA-transforming microorganisms are still unclear. In this study, FA and its potential phenolic metabolites were fermented in vitro for 24 h with the human fecal inoculum. A comparable short chain fatty acid (SCFA) production trend was observed in the presence and absence of substrates, suggesting limited contribution of FA mechanism to SCFA formation. Dihydroferulic acid, 3-(3,4-dihydroxyphenyl)propionic acid, and 3-(3-hydroxyphenyl)propionic acid were ascertained to be successive metabolites of FA, by tracking the intermediate variation. FA remarkably promoted the absolute abundances of total bacteria, while different metabolites affected bacterial growth of selective genera. Specific genera were identified as quantitatively correlating to the content of FA and its metabolites. Ultimately, FA-mediated gut microbiota modulation involves both the action of metabolizing microbes and the regulation effects of metabolites on bacterial growth.
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Affiliation(s)
- Shiyi Lu
- Key Laboratory of Geriatric Nutrition and Health (Ministry of Education), Beijing Technology and Business University (BTBU), 11 Fucheng Road, Beijing 100048, China
| | - Danyang Cheng
- Key Laboratory of Geriatric Nutrition and Health (Ministry of Education), Beijing Technology and Business University (BTBU), 11 Fucheng Road, Beijing 100048, China
| | - Hong Yao
- Department of Food Science and Engineering, Jinan University, Guangzhou 510632, China
| | - Yangyang Wen
- College of Chemistry and Materials Engineering, Beijing Technology and Business University (BTBU), 11 Fucheng Road, Beijing 100048, China
| | - Yonghui Yu
- Key Laboratory of Geriatric Nutrition and Health (Ministry of Education), Beijing Technology and Business University (BTBU), 11 Fucheng Road, Beijing 100048, China
| | - Hongyan Li
- Key Laboratory of Geriatric Nutrition and Health (Ministry of Education), Beijing Technology and Business University (BTBU), 11 Fucheng Road, Beijing 100048, China
| | - Jing Wang
- Key Laboratory of Geriatric Nutrition and Health (Ministry of Education), Beijing Technology and Business University (BTBU), 11 Fucheng Road, Beijing 100048, China
| | - Baoguo Sun
- Key Laboratory of Geriatric Nutrition and Health (Ministry of Education), Beijing Technology and Business University (BTBU), 11 Fucheng Road, Beijing 100048, China
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9
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Zhang Y, Datry T, Zhang Q, Wang X, Xiang X, Gong Z, Cai Y. Effects of different hydrological conditions on the taxonomic structure and functional traits of mollusk communities in a large floodplain wetland. Ecol Evol 2024; 14:e11466. [PMID: 38803609 PMCID: PMC11128460 DOI: 10.1002/ece3.11466] [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: 12/30/2023] [Revised: 03/13/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Floodplain wetlands are critical to the conservation of aquatic biodiversity and the ecological integrity of river networks. However, increasing drought severity and frequency caused by climate change can reduce floodplain wetlands' resistance and recovery capacities. Mollusks, which are common inhabitants of floodplain wetlands, are among the most vulnerable species to drought. However, the response of mollusk communities to drought has received little attention. Here, we investigated how the structure and functional traits of mollusk communities changed in response to varying hydrological conditions, including a flash drought (FD) in the Poyang Lake floodplain wetland. Our findings showed that FD strongly reduced mollusk abundance and biomass, decreased both α- and β-diversity, and resulted in the extinction of bivalve taxa. A sudden shift in community trait structure was discovered due to the extinction of many species. These traits, which include deposit feeding, crawling, scraping, aerial respiration, and dormancy, help mollusks survive in FD and tolerate completely dry out of their Changhuchi habitat. Finally, we discovered that dissolved oxygen was an important controlling variable for mollusk communities during drought. Our findings provide a scientific basis for the management and conservation of floodplain wetland biodiversity in the context of increasing drought frequency and intensity.
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Affiliation(s)
- Yao Zhang
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
- School of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐Founded by Anhui Province and Ministry of EducationWuhuChina
- Poyang Lake Wetland Research Station, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesJiujiangChina
| | - Thibault Datry
- INRAE, UR RiverLy, Centre de Lyon‐VilleurbanneVilleurbanne CedexFrance
| | - Qingji Zhang
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
- INRAE, UR RiverLy, Centre de Lyon‐VilleurbanneVilleurbanne CedexFrance
- School of Geography and Ocean ScienceNanjing UniversityNanjingChina
| | - Xiaolong Wang
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
- Poyang Lake Wetland Research Station, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesJiujiangChina
| | - Xianling Xiang
- School of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐Founded by Anhui Province and Ministry of EducationWuhuChina
| | - Zhijun Gong
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐Founded by Anhui Province and Ministry of EducationWuhuChina
| | - Yongjiu Cai
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐Founded by Anhui Province and Ministry of EducationWuhuChina
- Poyang Lake Wetland Research Station, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesJiujiangChina
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10
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Di Lorenzo T, Tabilio Di Camillo A, Mori E, Viviano A, Mazza G, Pontalti A, Rogora M, Fiasca B, Di Cicco M, Galassi DMP. Effects of a beaver dam on the benthic copepod assemblage of a Mediterranean river. Sci Rep 2024; 14:8956. [PMID: 38637569 PMCID: PMC11026539 DOI: 10.1038/s41598-024-59456-y] [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: 02/16/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
As known "ecosystem engineers", beavers influence river hydrology, geomorphology, biochemistry, and biological assemblages. However, there is a lack of research regarding the effects of beaver activities on freshwater meiofauna. In this study, we investigated the taxonomic and functional composition of the benthic copepod assemblage of a segment of the Tiber River (Italy) where a beaver dam, created about 7 weeks before our survey, had formed a semi-lentic habitat upstream and a lotic habitat downstream of the dam. We also analyzed the copepod assemblage before and after a flood event that destroyed the beaver dam, providing a unique opportunity to observe changes in a naturally reversing scenario. Our analyses revealed that, while the taxonomic composition and functional traits of the copepod assemblage remained largely unchanged across the recently formed semi-lentic and lotic habitats, substantial differences were evident between the dammed and undammed states. The dammed state showed lower copepod abundances, biomass, and functionality than the undammed one. These results highlight the role of beaver dams in changing the composition and functionality of meiofaunal assemblages offering insights into the dynamic interactions within aquatic ecosystems.
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Grants
- Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022 adopted by the Italian Ministry of University and Research, CUP B83C22002930006, Project title "National Biodiversity Future Center-NBFC National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4-Call for tender No. 3138 of 16 December 2021, rectified by Decree n.3175 of 18 December 2021 of the Italian Ministry of University and Research funded by the European Union-NextGenerationEU
- Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022 adopted by the Italian Ministry of University and Research, CUP B83C22002930006, Project title "National Biodiversity Future Center-NBFC National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4-Call for tender No. 3138 of 16 December 2021, rectified by Decree n.3175 of 18 December 2021 of the Italian Ministry of University and Research funded by the European Union-NextGenerationEU
- Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022 adopted by the Italian Ministry of University and Research, CUP B83C22002930006, Project title "National Biodiversity Future Center-NBFC National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4-Call for tender No. 3138 of 16 December 2021, rectified by Decree n.3175 of 18 December 2021 of the Italian Ministry of University and Research funded by the European Union-NextGenerationEU
- National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4-Call for tender No. 3138 of 16 December 2021, rectified by Decree n.3175 of 18 December 2021 of the Italian Ministry of University and Research funded by the European Union–NextGenerationEU
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Affiliation(s)
- T Di Lorenzo
- National Research Council of Italy, Research Institute on Terrestrial Ecosystems (CN-IRET), Florence, Italy.
- NBFC (National Biodiversity Future Center), 90133, Palermo, Italy.
| | - A Tabilio Di Camillo
- National Research Council of Italy, Research Institute on Terrestrial Ecosystems (CN-IRET), Florence, Italy
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - E Mori
- National Research Council of Italy, Research Institute on Terrestrial Ecosystems (CN-IRET), Florence, Italy
- NBFC (National Biodiversity Future Center), 90133, Palermo, Italy
| | - A Viviano
- National Research Council of Italy, Research Institute on Terrestrial Ecosystems (CN-IRET), Florence, Italy
| | - G Mazza
- National Research Council of Italy, Research Institute on Terrestrial Ecosystems (CN-IRET), Florence, Italy
- NBFC (National Biodiversity Future Center), 90133, Palermo, Italy
- CREA Research Centre for Plant Protection and Certification (CREA‑DC), Florence, Italy
| | - A Pontalti
- National Research Council of Italy, Research Institute on Terrestrial Ecosystems (CN-IRET), Florence, Italy
| | - M Rogora
- National Research Council of Italy, Water Research Institute (CNR-IRSA), Verbania Pallanza, Italy
| | - B Fiasca
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - M Di Cicco
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - D M P Galassi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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11
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Müller R. Bioinspiration from bats and new paradigms for autonomy in natural environments. BIOINSPIRATION & BIOMIMETICS 2024; 19:033001. [PMID: 38452384 DOI: 10.1088/1748-3190/ad311e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 03/07/2024] [Indexed: 03/09/2024]
Abstract
Achieving autonomous operation in complex natural environment remains an unsolved challenge. Conventional engineering approaches to this problem have focused on collecting large amounts of sensory data that are used to create detailed digital models of the environment. However, this only postpones solving the challenge of identifying the relevant sensory information and linking it to action control to the domain of the digital world model. Furthermore, it imposes high demands in terms of computing power and introduces large processing latencies that hamper autonomous real-time performance. Certain species of bats that are able to navigate and hunt their prey in dense vegetation could be a biological model system for an alternative approach to addressing the fundamental issues associated with autonomy in complex natural environments. Bats navigating in dense vegetation rely on clutter echoes, i.e. signals that consist of unresolved contributions from many scatters. Yet, the animals are able to extract the relevant information from these input signals with brains that are often less than 1 g in mass. Pilot results indicate that information relevant to location identification and passageway finding can be directly obtained from clutter echoes, opening up the possibility that the bats' skill can be replicated in man-made autonomous systems.
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Affiliation(s)
- Rolf Müller
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA 24061, United States of America
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12
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Ji Y, Liu X, Lv H, Guo Y, Nie W. Effects of Lonicerae flos and Turmeric extracts on growth performance and intestinal health of yellow-feathered broilers. Poult Sci 2024; 103:103488. [PMID: 38335669 PMCID: PMC10869291 DOI: 10.1016/j.psj.2024.103488] [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: 12/01/2023] [Revised: 01/11/2024] [Accepted: 01/18/2024] [Indexed: 02/12/2024] Open
Abstract
This experiment aimed to investigate the effect of Lonicerae flos and Turmeric extracts (LTE) added to diets on growth performance and intestinal health of broilers. A total of 720 healthy 21-day-old yellow-feathered broilers were randomly divided into 3 treatment groups, with 6 replicates and 40 broilers per replicate. These 3 dietary treatments included a basal diet + 0 g/t LTE (CON), a basal diet + 300 g/t LTE (LTE300), and a basal diet + 500 g/t LTE (LTE500). The results showed that dietary supplementation of LTE linearly increased (P < 0.05) average daily gain (d 21-38) and average daily feed intake (d 21-60). At d 60, LTE300 had the highest serum total antioxidant capacity and total superoxide dismutase (P < 0.05), and LTE500 had the lowest malondialdehyde level (P < 0.05) among the three groups. Moreover, compared to CON, LTE300 significantly (P < 0.05) reduced endotoxin (d 38 and d 60) and diamine oxidase activity (d 38); LTE500 significantly (P < 0.05) reduced endotoxin (d 38 and d 60) and diamine oxidase levels (d 60) in the serum. LTE groups significantly (P < 0.05) increased ileal the ratio of villus height to crypt depth and serum immunoglobulin G. Furthermore, dietary supplementation of LTE also improved the intestinal epithelial barrier by the up-regulated mRNA expression of Claudin-1, Occludin and zonula occludens-1, and decreased the mRNA expression of interleukin-2, interleukin-8, tumor necrosis factor-α, nuclear factor κB, myeloid differentiation factor 88 and toll-like receptor 4. Compared to CON, 16S rRNA sequencing analysis showed that LTE300 had a better effect on the microbial diversity and composition in the ileum, and Bacillus and Lactobacillus_agilis were significantly enriched in LTE300. PICRUSt results showed that LTE300 was significantly (P < 0.05) enriched in four pathway pathways at KEGG level 2. In conclusion, dietary supplementation with LTE improved growth performance and intestinal health by enhancing antioxidant capacity, intestinal barrier and immune function, and regulating intestinal flora of yellow-feathered broilers.
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Affiliation(s)
- Yunru Ji
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xingbo Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huiyuan Lv
- Beijing Centre Biology Co., Ltd., Beijing 102600, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wei Nie
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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13
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Wu Y, Yang Z, Chen S, Sui M, Zhang G, Liu Q, Chen D, Ding F, Zang L. How do species richness and its component dependence vary along the natural restoration in extremely heterogeneous forest ecosystems? JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120265. [PMID: 38382441 DOI: 10.1016/j.jenvman.2024.120265] [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: 07/30/2023] [Revised: 10/17/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
Giant habitat heterogeneity is an important factor contributing to the high species richness (SR) in karst forests. Yet, the driving factor behind the alterations in SR patterns during natural restoration remains unclear. In this study, we established the forest dynamics plots along the natural restoration sequence (including shrub-tree mixed forest stage (SC), secondary forest stage (SG) and old-growth forest sage (OG)) in degraded karst forests to compare the SR and the dependence on its components (including total community abundance, species abundance distribution (SAD), and conspecific spatial aggregation (CSA)) among stages of natural restoration. By evaluating the degree of contribution of the components to local SR and rarefied SR, we found that the SG exhibited the highest local SR, while the rarefied SR remained increasing along the restoration sequence after controlling the sample size. At SC-SG stage, SAD and CSA contributed negatively to the differences in SR, while abundance made a positive contribution to SR differences. At SG-OG, abundance contributed positively to the difference in SR at all scales, while SAD contributed negatively at small scales. No significant contribution of CSA was found at observed scales. In addition, local SR varied more significantly with PIE than with abundance. Our research emphasizes the importance of eliminating the influence of abundance on species richness in forest ecology and management, as well as the significance of separately evaluating the components that shape the diversity patterns.
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Affiliation(s)
- Yuhang Wu
- Research Center of Forest Ecology, Collage of Forestry, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Zeyu Yang
- Research Center of Forest Ecology, Collage of Forestry, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Shiren Chen
- Research Center of Forest Ecology, Collage of Forestry, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Mingzhen Sui
- Research Center of Forest Ecology, Collage of Forestry, Guizhou University, Guiyang, Guizhou, 550025, China; Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, National Forestry and Grassland Administration, Libo, Guizhou, 558400, China
| | - Guangqi Zhang
- Research Center of Forest Ecology, Collage of Forestry, Guizhou University, Guiyang, Guizhou, 550025, China; Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, National Forestry and Grassland Administration, Libo, Guizhou, 558400, China
| | - Qingfu Liu
- Research Center of Forest Ecology, Collage of Forestry, Guizhou University, Guiyang, Guizhou, 550025, China; Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, National Forestry and Grassland Administration, Libo, Guizhou, 558400, China
| | - Danmei Chen
- Research Center of Forest Ecology, Collage of Forestry, Guizhou University, Guiyang, Guizhou, 550025, China; Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, National Forestry and Grassland Administration, Libo, Guizhou, 558400, China
| | - Fangjun Ding
- Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, National Forestry and Grassland Administration, Libo, Guizhou, 558400, China
| | - Lipeng Zang
- Research Center of Forest Ecology, Collage of Forestry, Guizhou University, Guiyang, Guizhou, 550025, China; Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, National Forestry and Grassland Administration, Libo, Guizhou, 558400, China.
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14
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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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15
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Lu N, Yang H, Zhou X, Tan Y, Cai W, Jiang Q, Lu Y, Chen Y, He H, Wang S. The loss of plant functional groups increased arthropod diversity in an alpine meadow on the Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2024; 15:1305768. [PMID: 38434435 PMCID: PMC10904612 DOI: 10.3389/fpls.2024.1305768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
Plant species loss, driven by global changes and human activities, can have cascading effects on other trophic levels, such as arthropods, and alter the multitrophic structure of ecosystems. While the relationship between plant diversity and arthropod communities has been well-documented, few studies have explored the effects of species composition variation or plant functional groups. In this study, we conducted a long-term plant removal experiment to investigate the impact of plant functional group loss (specifically targeting tall grasses and sedges, as well as tall or short forbs) on arthropod diversity and their functional groups. Our findings revealed that the removal of plant functional groups resulted in increased arthropod richness, abundance and the exponential of Shannon entropy, contrary to the commonly observed positive correlation between plant diversity and consumer diversity. Furthermore, the removal of different plant groups had varying impacts on arthropod trophic levels. The removal of forbs had a more pronounced impact on herbivores compared to graminoids, but this impact did not consistently cascade to higher-trophic arthropods. Notably, the removal of short forbs had a more significant impact on predators, as evidenced by the increased richness, abundance, the exponential of Shannon entropy, inverse Simpson index and inverse Berger-Parker index of carnivores and abundance of omnivores, likely attributable to distinct underlying mechanisms. Our results highlight the importance of plant species identity in shaping arthropod communities in alpine grasslands. This study emphasizes the crucial role of high plant species diversity in controlling arthropods in natural grasslands, particularly in the context of plant diversity loss caused by global changes and human activities.
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Affiliation(s)
- Ningna Lu
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Hainian Yang
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Xianhui Zhou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yun Tan
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Wei Cai
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Qin Jiang
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Ying Lu
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Yangyang Chen
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Haocheng He
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Sheng Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
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16
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Lawson L, Edge CB, Fortin M, Jackson DA. Temporal change in urban fish biodiversity-Gains, losses, and drivers of change. Ecol Evol 2024; 14:e10845. [PMID: 38327686 PMCID: PMC10847622 DOI: 10.1002/ece3.10845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/13/2023] [Accepted: 12/26/2023] [Indexed: 02/09/2024] Open
Abstract
Our aim was to examine temporal change in alpha and beta diversity of freshwater fish communities in rivers that have urbanized over the same period to understand the influence of changes in land use and river connectivity on community change. We used biological (2001-2018), land use (2000-2015), and connectivity data (1987-2017) from Toronto, Ontario, Canada. We used linear mixed effects models to determine the strength of upstream land use, connectivity, and their changes over time to explain temporal change in alpha and beta diversity indices. We examined beta diversity using the temporal beta diversity index (TBI) to assess site-specific community change. The TBI was partitioned into gains and losses, and species-specific changes in abundance were assessed using paired t-tests. There were more gains than losses across the study sites as measured by TBI. We found little to no significant differences in species-specific abundances at aggregated spatial scales (study region, watershed, stream order). We found different relationships between landscape and connectivity variables with the biodiversity indices tested; however, almost all estimated confidence intervals overlapped with zero and had low goodness-of-fit. More fish biodiversity gains than losses were found across the study region, as measured by TBI. We found TBI to be a useful indicator of change as it identifies key sites to further investigate. We found two high value TBI sites gained non-native species, and one site shifted from a cool-water to warm-water species dominated community, both of which have management implications. Upstream catchment land use and connectivity had poor explanatory power for change in the measured biodiversity indices. Ultimately, such spatial-temporal datasets are invaluable and can reveal trends in biodiversity useful for environmental management when considering competing interests involved with urban sprawl in the ongoing "Decade on Restoration."
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Affiliation(s)
- Lauren Lawson
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Christopher B. Edge
- Natural Resources CanadaCanadian Forest Service Atlantic Forestry CenterFrederictonNew BrunswickCanada
| | - Marie‐Josée Fortin
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Donald A. Jackson
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
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17
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Yang JH, Park JW, Kim HS, Lee S, Yerke AM, Jaiswal YS, Williams LL, Hwang S, Moon KH. Effects of Antibiotic Residues on Fish Gut Microbiome Dysbiosis and Mucosal Barrier-Related Pathogen Susceptibility in Zebrafish Experimental Model. Antibiotics (Basel) 2024; 13:82. [PMID: 38247641 PMCID: PMC10812462 DOI: 10.3390/antibiotics13010082] [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: 12/13/2023] [Revised: 01/05/2024] [Accepted: 01/13/2024] [Indexed: 01/23/2024] Open
Abstract
The symbiotic community of microorganisms in the gut plays an important role in the health of the host. While many previous studies have been performed on the interactions between the gut microbiome and the host in mammals, studies in fish are still lacking. In this study, we investigated changes in the intestinal microbiome and pathogen susceptibility of zebrafish (Danio rerio) following chronic antibiotics exposure. The chronic antibiotics exposure assay was performed on zebrafish for 30 days using oxytetracycline (Otc), sulfamethoxazole/trimethoprim (Smx/Tmp), or erythromycin (Ery), which are antibiotics widely used in the aquaculture industry. The microbiome analysis indicated that Fusobacteria, Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla in the gut microbiome of the zebrafish used in this study. However, in Smx/Tmp-treated zebrafish, the compositions of Fusobacteria and Proteobacteria were changed significantly, and in Ery-treated zebrafish, the compositions of Proteobacteria and Firmicutes were altered significantly. Although alpha diversity analysis showed that there was no significant difference in the richness, beta diversity analysis revealed a community imbalance in the gut microbiome of all chronically antibiotics-exposed zebrafish. Intriguingly, in zebrafish with dysbiosis in the gut microbiome, the pathogen susceptibility to Edwardsiella piscicida, a representative Gram-negative fish pathogen, was reduced. Gut microbiome imbalance resulted in a higher count of goblet cells in intestinal tissue and an upregulation of genes related to the intestinal mucosal barrier. In addition, as innate immunity was enhanced by the increased mucosal barrier, immune and stress-related gene expression in the intestinal tissue was downregulated. In this study, we provide new insight into the effect of gut microbiome dysbiosis on pathogen susceptibility.
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Affiliation(s)
- Jun Hyeok Yang
- Laboratory of Marine Microbiology, Division of Convergence of Marine Science, Korea Maritime & Ocean University, Busan 49112, Republic of Korea; (J.H.Y.); (J.W.P.); (H.S.K.)
- Department of Marine Bioscience and Environment, Korea Maritime & Ocean University, Busan 49112, Republic of Korea
| | - Jeong Woo Park
- Laboratory of Marine Microbiology, Division of Convergence of Marine Science, Korea Maritime & Ocean University, Busan 49112, Republic of Korea; (J.H.Y.); (J.W.P.); (H.S.K.)
- Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, Korea Maritime & Ocean University, Busan 49112, Republic of Korea
| | - Ho Sung Kim
- Laboratory of Marine Microbiology, Division of Convergence of Marine Science, Korea Maritime & Ocean University, Busan 49112, Republic of Korea; (J.H.Y.); (J.W.P.); (H.S.K.)
- Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, Korea Maritime & Ocean University, Busan 49112, Republic of Korea
| | - Seungki Lee
- National Institute of Biological Resources, Environmental Research Complex, Incheon 22689, Republic of Korea;
| | - Aaron M. Yerke
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA;
| | - Yogini S. Jaiswal
- Center for Excellence in Post Harvest Technologies, North Carolina Agricultural and Technical State University, The North Carolina Research Campus, 500 Laureate Way, Kannapolis, NC 28081, USA; (Y.S.J.); (L.L.W.)
| | - Leonard L. Williams
- Center for Excellence in Post Harvest Technologies, North Carolina Agricultural and Technical State University, The North Carolina Research Campus, 500 Laureate Way, Kannapolis, NC 28081, USA; (Y.S.J.); (L.L.W.)
| | - Sungmin Hwang
- Division of Practical Research, Honam National Institute Biological Resources, Mokpo-si 58762, Republic of Korea
| | - Ki Hwan Moon
- Laboratory of Marine Microbiology, Division of Convergence of Marine Science, Korea Maritime & Ocean University, Busan 49112, Republic of Korea; (J.H.Y.); (J.W.P.); (H.S.K.)
- Department of Marine Bioscience and Environment, Korea Maritime & Ocean University, Busan 49112, Republic of Korea
- Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, Korea Maritime & Ocean University, Busan 49112, Republic of Korea
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18
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Iqbal A, Maqsood Ur Rehman M, Sajjad W, Degen AA, Rafiq M, Jiahuan N, Khan S, Shang Z. Patterns of bacterial communities in the rhizosphere and rhizoplane of alpine wet meadows. ENVIRONMENTAL RESEARCH 2024; 241:117672. [PMID: 37980986 DOI: 10.1016/j.envres.2023.117672] [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: 10/18/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023]
Abstract
Wet meadows, a type of wetland, are vulnerable to climate change and human activity, impacting soil properties and microorganisms that are crucial to the ecosystem processes of wet meadows. To decipher the ecological mechanisms and processes involved in wet meadows, it is necessary to examine the bacterial communities associated with plant roots. To gain valuable insight into the microbial dynamics of alpine wet meadows, we used Illumina MiSeq sequencing to investigate how environmental factors shape the bacterial communities thriving in the rhizosphere and rhizoplane of three plant species: Cremanthodium ellisii, Caltha scaposa, and Cremanthodium lineare. The most abundant bacterial phyla in rhizosphere and rhizoplane were Proteobacteria > Firmicutes > Actinobacteria, while Macrococcus, Lactococcus, and Exiguobacterium were the most abundant bacterial genera between rhizosphere and rhizoplane. The mantel test, network, and structure equation models revealed that bacterial communities of rhizosphere were shaped by total nitrogen (TN), soil water content (SWC), soil organic carbon (SOC), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), pH, however, rhizoplane bacterial communities exhibited varying results. The bacterial communities exhibited significant heterogeneity, with stochastic process predominating in both the rhizosphere and rhizoplane. PICRUSt2 and FAPROTAX analysis revealed substantial differences in key biogeochemical cycles and metabolic functional predictions. It was concluded that root compartments significantly influenced the bacterial communities, although plant species and elevation asserted varying effects. This study portrays how physicochemical properties, plant species, and elevations can shift the overall structure and functional repertoire of bacterial communities in alpine wet meadows.
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Affiliation(s)
- Awais Iqbal
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Muhammad Maqsood Ur Rehman
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Abraham Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva, 8410500, Israel
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Baluchistan University of IT, Engineering and Management Sciences, Quetta, Pakistan
| | - Niu Jiahuan
- Department of Health and Environmental Sciences, Xian Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Salman Khan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhanhuan Shang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
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19
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Vernier CL, Nguyen LA, Gernat T, Ahmed AC, Chen Z, Robinson GE. Gut microbiota contribute to variations in honey bee foraging intensity. THE ISME JOURNAL 2024; 18:wrae030. [PMID: 38412118 PMCID: PMC11008687 DOI: 10.1093/ismejo/wrae030] [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: 11/08/2023] [Revised: 01/17/2024] [Accepted: 02/23/2024] [Indexed: 02/29/2024]
Abstract
Gut microbiomes are increasingly recognized for mediating diverse biological aspects of their hosts, including complex behavioral phenotypes. Although many studies have reported that experimental disruptions to the gut microbial community result in atypical host behavior, studies that address how gut microbes contribute to adaptive behavioral trait variation are rare. Eusocial insects represent a powerful model to test this, because of their simple gut microbiota and complex division of labor characterized by colony-level variation in behavioral phenotypes. Although previous studies report correlational differences in gut microbial community associated with division of labor, here, we provide evidence that gut microbes play a causal role in defining differences in foraging behavior between European honey bees (Apis mellifera). We found that gut microbial community structure differed between hive-based nurse bees and bees that leave the hive to forage for floral resources. These differences were associated with variation in the abundance of individual microbes, including Bifidobacterium asteroides, Bombilactobacillus mellis, and Lactobacillus melliventris. Manipulations of colony demography and individual foraging experience suggested that differences in gut microbial community composition were associated with task experience. Moreover, single-microbe inoculations with B. asteroides, B. mellis, and L. melliventris caused effects on foraging intensity. These results demonstrate that gut microbes contribute to division of labor in a social insect, and support a role of gut microbes in modulating host behavioral trait variation.
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Affiliation(s)
- Cassondra L Vernier
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Lan Anh Nguyen
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Tim Gernat
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Amy Cash Ahmed
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Zhenqing Chen
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61810, United States
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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20
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Zhou Y, Meng F, Ochieng B, Xu J, Zhang L, Kimirei IA, Feng M, Zhu L, Wang J. Climate and Environmental Variables Drive Stream Biofilm Bacterial and Fungal Diversity on Tropical Mountainsides. MICROBIAL ECOLOGY 2024; 87:28. [PMID: 38182675 DOI: 10.1007/s00248-023-02335-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 12/22/2023] [Indexed: 01/07/2024]
Abstract
High mountain freshwater systems are particularly sensitive to the impacts of global warming and relevant environmental changes. Microorganisms contribute substantially to biogeochemical processes, yet their distribution patterns and driving mechanism in alpine streams remain understudied. Here, we examined the bacterial and fungal community compositions in stream biofilm along the elevational gradient of 745-1874 m on Mt. Kilimanjaro and explored their alpha and beta diversity patterns and the underlying environmental drivers. We found that the species richness and evenness monotonically increased towards higher elevations for bacteria, while were non-significant for fungi. However, both bacterial and fungal communities showed consistent elevational distance-decay relationships, i.e., the dissimilarity of assemblage composition increased with greater elevational differences. Bacterial alpha diversity patterns were mainly affected by chemical variables such as total nitrogen and phosphorus, while fungi were affected by physical variables such as riparian shading and stream width. Notably, climatic variables such as mean annual temperature strongly affected the elevational succession of bacterial and fungal community compositions. Our study is the first exploration of microbial biodiversity and their underlying driving mechanisms for stream ecosystems in tropical alpine regions. Our findings provide insights on the response patterns of tropical aquatic microbial community composition and diversity under climate change.
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Affiliation(s)
- Yanan Zhou
- College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Fanfan Meng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Beryl Ochieng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianing Xu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Lu Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | | | - Muhua Feng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
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21
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Ozeri E, Zehavi M, Ziv-Ukelson M. New algorithms for structure informed genome rearrangement. Algorithms Mol Biol 2023; 18:17. [PMID: 38037088 PMCID: PMC10691145 DOI: 10.1186/s13015-023-00239-x] [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: 03/30/2023] [Accepted: 08/17/2023] [Indexed: 12/02/2023] Open
Abstract
We define two new computational problems in the domain of perfect genome rearrangements, and propose three algorithms to solve them. The rearrangement scenarios modeled by the problems consider Reversal and Block Interchange operations, and a PQ-tree is utilized to guide the allowed operations and to compute their weights. In the first problem, [Formula: see text] ([Formula: see text]), we define the basic structure-informed rearrangement measure. Here, we assume that the gene order members of the gene cluster from which the PQ-tree is constructed are permutations. The PQ-tree representing the gene cluster is ordered such that the series of gene IDs spelled by its leaves is equivalent to that of the reference gene order. Then, a structure-informed genome rearrangement distance is computed between the ordered PQ-tree and the target gene order. The second problem, [Formula: see text] ([Formula: see text]), generalizes [Formula: see text], where the gene order members are not necessarily permutations and the structure informed rearrangement measure is extended to also consider up to [Formula: see text] and [Formula: see text] gene insertion and deletion operations, respectively, when modelling the PQ-tree informed divergence process from the reference gene order to the target gene order. The first algorithm solves [Formula: see text] in [Formula: see text] time and [Formula: see text] space, where [Formula: see text] is the maximum number of children of a node, n is the length of the string and the number of leaves in the tree, and [Formula: see text] and [Formula: see text] are the number of P-nodes and Q-nodes in the tree, respectively. If one of the penalties of [Formula: see text] is 0, then the algorithm runs in [Formula: see text] time and [Formula: see text] space. The second algorithm solves [Formula: see text] in [Formula: see text] time and [Formula: see text] space, where [Formula: see text] is the maximum number of children of a node, n is the length of the string, m is the number of leaves in the tree, [Formula: see text] and [Formula: see text] are the number of P-nodes and Q-nodes in the tree, respectively, and allowing up to [Formula: see text] deletions from the tree and up to [Formula: see text] deletions from the string. The third algorithm is intended to reduce the space complexity of the second algorithm. It solves a variant of the problem (where one of the penalties of [Formula: see text] is 0) in [Formula: see text] time and [Formula: see text] space. The algorithm is implemented as a software tool, denoted MEM-Rearrange, and applied to the comparative and evolutionary analysis of 59 chromosomal gene clusters extracted from a dataset of 1487 prokaryotic genomes.
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Affiliation(s)
- Eden Ozeri
- Department of Computer Science, Ben Gurion University of the Negev, Be'er Sheva, Israel.
| | - Meirav Zehavi
- Department of Computer Science, Ben Gurion University of the Negev, Be'er Sheva, Israel
| | - Michal Ziv-Ukelson
- Department of Computer Science, Ben Gurion University of the Negev, Be'er Sheva, Israel
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22
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Zhu P, Pan B, Li Z, He H, Hou Y, Zhao G. Responses of biodiversity to microhabitat heterogeneity in debris flow gullies: Assessing the impact of hydrological disturbance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166509. [PMID: 37619718 DOI: 10.1016/j.scitotenv.2023.166509] [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: 04/26/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
Rivers play a vital role in the maintenance of the biosphere and human society, since they participate in the global water cycle and provide varied habitats to support biodiversity. Microhabitat heterogeneity is regarded as a key factor driving biodiversity and it plays an active ecological role in different types of mountain rivers. Whether river microhabitat heterogeneity exhibits the same ecological patterns across hydrological periods remains unclear. Here, we analyzed the changes in macroinvertebrate community composition, functional traits, and multi-faceted α-diversity in five debris flow gullies in the Xiaojiang River Basin (southwestern China) between two different hydrological periods. We explored the responses of biodiversity to river microhabitat heterogeneity and its driving factors before and after hydrological disturbance. The results indicated that river microhabitat heterogeneity and three facets of macroinvertebrate α-diversity decreased after hydrological disturbance, with macroinvertebrate state traits becoming more unbalanced. Macroinvertebrate taxonomic diversity increased with increasing river microhabitat heterogeneity across hydrological periods, and this pattern was more prominent before hydrological disturbance. A high correlation emerged between macroinvertebrate phylogenetic diversity and river microhabitat heterogeneity only before hydrological disturbance. Hydrogeomorphic parameters prominently affected macroinvertebrate communities before hydrological disturbance. Water environmental parameters worked together with hydrogeomorphic parameters to shape macroinvertebrate communities in hydrologically disturbed debris flow gullies, indicating a reduced ecological role of river microhabitat heterogeneity. The ecological health of debris flow gullies can be improved by increasing vegetation coverage on river bank slopes to increase slope stability and mitigate hydrological disturbances, as well as placing large rocks into river channels to enhance riverbed stability and create habitats for more biological groups.
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Affiliation(s)
- Penghui Zhu
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi, China
| | - Baozhu Pan
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi, China.
| | - Zhiwei Li
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, Hubei, China
| | - Haoran He
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi, China
| | - Yiming Hou
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi, China
| | - Gengnan Zhao
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi, China
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23
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Câmara PEAS, de Menezes GCA, Lopes FAC, da Silva Paiva T, Carvalho-Silva M, Convey P, Amorim ET, Rosa LH. Investigating non-fungal eukaryotic diversity in snow in the Antarctic Peninsula region using DNA metabarcoding. Extremophiles 2023; 28:3. [PMID: 37962679 DOI: 10.1007/s00792-023-01322-2] [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: 08/14/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023]
Abstract
Snow is a unique microhabitat, despite being a harsh environment, multiple life forms have adapted to survive in it. While algae, bacteria and fungi are dominant microorganisms in Antarctic snow, little is known about other organisms that may be present in this habitat. We used metabarcoding to investigate DNA sequence diversity of non-fungal eukaryotes present in snow obtained from six different sites across the Maritime Antarctica. A total of 20 taxa were assigned to obtained sequences, representing five Kingdoms (Chromista, Protozoa, Viridiplantae and Metazoa) and four phyla (Ciliophora, Cercozoa, Chlorophyta and Cnidaria). The highest diversity indices were detected in Trinity Peninsula followed by Robert Island, Arctowski Peninsula, Deception Island, King George Island and Snow Island. The most abundant assignments were to Trebouxiophyceae, followed by Chlamydomonas nivalis and Chlamidomonadales. No taxa were detected at all sites. Three potentially new records for Antarctica were detected: two Ciliophora (Aspidisca magna and Stokesia sp.) and the green algae Trebouxia potteri. Our data suggested that similarities found between the sites may be more related with snow physicochemical properties rather than geographic proximity or latitude. This study provides new insights into the diversity and distribution of eukaryotic organisms in Antarctic snow.
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Affiliation(s)
- Paulo E A S Câmara
- Departamento de Botânica, Universidade de Brasília, Brasília, 70910-900, Brasil.
- Algas E Plantas, Pós Graduação Em Fungos, Universidade Federal de Santa Catarina, Florianoplis, Santa Catarina, Brazil.
| | - Graciéle C A de Menezes
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brasil
| | - Fabyano A C Lopes
- Laboratório de Microbiologia, Universidade Federal Do Tocantins, Porto Nacional, Brazil
| | - Thiago da Silva Paiva
- Laboratório de Protistologia, Instituto de Biologia, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park, 2006, South Africa
- Biodiversity of Antarctic and Sub-Antarctic Ecosystems (BASE), Santiago, Chile
| | - Eduardo T Amorim
- Centro Nacional de Conservação da Flora/Instituto de Pesquisas Jardim Botânico Do Rio de Janeiro (CNCFlora/JBRJ), Rio de Janeiro, Brazil
| | - Luiz H Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brasil
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24
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Karolaakso T, Autio R, Suontausta P, Leppänen H, Suokas K, Rissanen P, Tuomisto MT, Pirkola S. Patterns of mental health services and mood disorder disability pensions: a standard comparison of Finland's three largest hospital districts. BMC Psychiatry 2023; 23:828. [PMID: 37957646 PMCID: PMC10644417 DOI: 10.1186/s12888-023-05342-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
INTRODUCTION Mental disorders are one of the most common and disabling health conditions worldwide. There is however no consensus on the best practice of system level mental health services (MHS) provision, in order to prevent e.g. mood disorder disability pensions (DPs). We analyzed the MHS provision between Finland's three largest hospital districts Helsinki and Uusimaa (HUS), Southwest Finland and Pirkanmaa, with known differences in mood disorder DP risk but presumably equal rates of mood disorder prevalence. METHODS We used public MHS data analyzed with the standardized DEscription and Evaluation of Services and DirectoriEs for Long Term Care (DESDE-LTC) mapping tool, focusing on all MHS, outpatient care provision, local services without and with gatekeeping, and centralized services. We also collected demographic data based on the European Socio-Demographic Schedule (ESDS). As a novel approach, the Gini-Simpson Diversity Index (GSDI) was calculated for the districts. RESULTS Evident differences were observed regarding the districts' MHS factors. As the hospital district with lower DP risk, HUS was characterized by the highest level of regional socioeconomic prosperity as well as high service richness and diversity. With a nationally average DP risk, Southwest Finland had the highest number of MHS personnel in full-time equivalents (FTE) per 100 000 inhabitants. Pirkanmaa, with a higher DP risk, had overall the lowest service richness and the lowest FTE of the three districts in all MHS, outpatient care and local services with gatekeeping. CONCLUSIONS Our findings indicate that greater richness and diversity of MHS, especially in outpatient and community-based settings, may serve as indicators of a balanced, high-quality service system that is more effective in preventing mood disorder DP and meeting the different needs of the population. In addition, the need for sufficient resourcing in all MHS and outpatient services is indicated. We suggest using diversity indices to complement the measuring and reporting of regional service variation.
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Affiliation(s)
- Tino Karolaakso
- Faculty of Social Sciences (Psychology), Tampere University, Arvo Ylpön katu 34, Tampere, FI- 33520, Finland.
- Psychiatry, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
| | - Reija Autio
- Faculty of Social Sciences (Unit of Health Sciences), Tampere University, Tampere, Finland
| | - Petra Suontausta
- Faculty of Social Sciences (Unit of Health Sciences), Tampere University, Tampere, Finland
| | - Helena Leppänen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kimmo Suokas
- Faculty of Social Sciences (Unit of Health Sciences), Tampere University, Tampere, Finland
| | - Päivi Rissanen
- Faculty of Social Sciences (Unit of Health Sciences), Tampere University, Tampere, Finland
| | - Martti T Tuomisto
- Faculty of Social Sciences (Psychology), Tampere University, Arvo Ylpön katu 34, Tampere, FI- 33520, Finland
| | - Sami Pirkola
- Faculty of Social Sciences (Unit of Health Sciences), Tampere University, Tampere, Finland
- Department of Adult Psychiatry, Tampere University Hospital, Tampere, Finland
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25
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Centeno Mejia AA, Bravo Gaete MF. Exploring the Entropy Complex Networks with Latent Interaction. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1535. [PMID: 37998227 PMCID: PMC10670619 DOI: 10.3390/e25111535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/16/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Abstract
In the present work, we study the introduction of a latent interaction index, examining its impact on the formation and development of complex networks. This index takes into account both observed and unobserved heterogeneity per node in order to overcome the limitations of traditional compositional similarity indices, particularly when dealing with large networks comprising numerous nodes. In this way, it effectively captures specific information about participating nodes while mitigating estimation problems based on network structures. Furthermore, we develop a Shannon-type entropy function to characterize the density of networks and establish optimal bounds for this estimation by leveraging the network topology. Additionally, we demonstrate some asymptotic properties of pointwise estimation using this function. Through this approach, we analyze the compositional structural dynamics, providing valuable insights into the complex interactions within the network. Our proposed method offers a promising tool for studying and understanding the intricate relationships within complex networks and their implications under parameter specification. We perform simulations and comparisons with the formation of Erdös-Rényi and Barabási-Alber-type networks and Erdös-Rényi and Shannon-type entropy. Finally, we apply our models to the detection of microbial communities.
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Affiliation(s)
- Alex Arturo Centeno Mejia
- Doctorado en Modelamiento Matemático Aplicado, Universidad Católica del Maule, Avenida San Miguel, Talca 3605, Chile
| | - Moisés Felipe Bravo Gaete
- Departamento de Matemáticas, Física y Estadística, Facultad de Ciencias Básicas, Universidad Católica del Maule, Avenida San Miguel, Talca 3605, Chile;
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26
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Zhang G, Liu T, Zhao D, Sun X, Xing W, Zhang S, Yan L. External magnetic field have significant effects on diversity of magnetotactic bacteria in sediments from Yangtze River, Chagan Lake and Zhalong Wetland in China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 266:115604. [PMID: 37871562 DOI: 10.1016/j.ecoenv.2023.115604] [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: 05/09/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 10/25/2023]
Abstract
Magnetotactic bacteria (MTB) can rapidly relocate to optimal habitats by magnetotaxis, and play an important role in iron biogeochemical cycling. This study aimed to evaluate the contribution of the external magnetostatic field to the diversity of MTB in freshwater sediments from Yangtze River (Changjiang River, CJ), Chagan Lake (CGH) and Zhalong Wetland (ZL). The magnetic field intensity was tightly associated with the community richness of MTB in CJ, whereas it was closely related to the diversity of MTB in CGH and ZL (p < 0.05), elucidating a significant variation in the community composition of MTB. Magnetic exposure time appeared more significant correlation with community richness than diversity for MTB in CJ and CGH (p < 0.05), while an opposite relationship existed in ZL (p < 0.01). Herbaspirillum (93.81-96.48 %) dominated in the sediments of these surfacewatesr regardless of waterbody types, while it shifted to Magnetospirillum in ZL under 100 Gs magnetic field. The network connectivity and stability of MTB deteriorate with the increase of magnetic field intensity. Functional analysis showed that the Two-component system and ABC transporter system of MTB obviously responded to magnetic field intensity and exposure time. Our findings will pave the way to understanding the response mechanism of MTB community in freshwater sediments to the external magnetostatic field.
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Affiliation(s)
- Guojing Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang, China
| | - Tao Liu
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang, China; Key Laboratory of Low‑Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang, China
| | - Dan Zhao
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang, China
| | - Xindi Sun
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang, China
| | - Weijia Xing
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang, China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang, China
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang, China; Key Laboratory of Low‑Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang, China.
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27
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Sankone C, Bedwell C, McCreadie J. Regional β-Diversity of Stream Insects in Coastal Alabama Is Correlated with Stream Conditions, Not Distance among Sites. INSECTS 2023; 14:847. [PMID: 37999046 PMCID: PMC10671468 DOI: 10.3390/insects14110847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023]
Abstract
β-diversity is often measured over both spatial and temporal gradients of elevation, latitude, and environmental conditions. It is of particular interest to ecologists, as it provides opportunities to test and infer potential causal mechanisms determining local species assemblages. However, studies of invertebrate β-diversity, especially aquatic insects, have lagged far behind other biota. Using partial Mantel tests, we explored the associations between β-diversity of insects found in the coastal streams of Alabama, USA, and stream conditions and distances among sites. β-diversity was expressed using the Sørensen index, βSor, stream conditions were expressed as principal components (PCs), and distances as Euclidean distances (km) among sites. We also investigated the impact of seasonality (fall, summer) and taxonomic resolution (genus, species) on βSor. Regardless of season, βSor was significantly correlated (p < 0.01; r > 0.44) with stream conditions (stream size and water chemistry), while taxonomic resolution had minimal effect on associations between βSor and stream conditions. Distance was never correlated with changes in βSor (p > 0.05). We extended the use of the Sørensen pair-wise index to a multiple-site dissimilarity, βMult, which was partitioned into patterns of spatial turnover (βTurn) and nestedness (βNest). Changes in βMult were driven mostly by turnover rather than nestedness.
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Affiliation(s)
- Carlos Sankone
- Biology Department, University of South Alabama, Mobile, AL 36688, USA;
| | - Chris Bedwell
- Bedwell Biological LLC., 2617 Grey Stone Rd, Henderson, NV 89074, USA;
| | - John McCreadie
- Biology Department, University of South Alabama, Mobile, AL 36688, USA;
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28
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O'Shaughnessy KA, Knights AM, Hawkins SJ, Hanley ME, Lunt P, Thompson RC, Firth LB. Metrics matter: Multiple diversity metrics at different spatial scales are needed to understand species diversity in urban environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:164958. [PMID: 37331387 DOI: 10.1016/j.scitotenv.2023.164958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
Worldwide, natural habitats are being replaced by artificial structures due to urbanisation. Planning of such modifications should strive for environmental net gain that benefits biodiversity and ecosystems. Alpha (α) and gamma (γ) diversity are often used to assess 'impact' but are insensitive metrics. We test several diversity measures across two spatial scales to compare species diversity in natural and artificial habitats. We show γ-diversity indicates equivalency in biodiversity between natural and artificial habitats, but natural habitats support greater taxon (α) and functional richness. Within-site β-diversity was also greater in natural habitats, but among-site β-diversity was greater in artificial habitats, contradicting the commonly held view that urban ecosystems are more biologically homogenous than natural ecosystems. This study suggests artificial habitats may in fact provide novel habitat for biodiversity, challenges the applicability of the urban homogenisation concept and highlights a significant limitation of using just α-diversity (i.e., multiple metrics are needed and recommended) for assessing environmental net gain and attaining biodiversity conservation goals.
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Affiliation(s)
- Kathryn A O'Shaughnessy
- School of Geography, Earth and Environmental Science, University of Plymouth, Plymouth, United Kingdom; APEM Ltd, Heaton Mersey, Stockport, United Kingdom.
| | - Antony M Knights
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom.
| | - Stephen J Hawkins
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom; School of Ocean and Earth Science, University of Southampton, National Oceanography Centre Southampton, Southampton, United Kingdom; The Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, United Kingdom.
| | - Mick E Hanley
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom.
| | - Paul Lunt
- School of Geography, Earth and Environmental Science, University of Plymouth, Plymouth, United Kingdom.
| | - Richard C Thompson
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom.
| | - Louise B Firth
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom.
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29
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Huang Z, Su Y, Lin S, Wu G, Cheng H, Huang G. Elevational patterns of microbial species richness and evenness across climatic zones and taxonomic scales. Ecol Evol 2023; 13:e10594. [PMID: 37818244 PMCID: PMC10560872 DOI: 10.1002/ece3.10594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/01/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Understanding the elevational patterns of soil microbial diversity is crucial for microbial biogeography, yet the elevational patterns of diversity across different climatic zones, trophic levels, and taxonomic levels remain unclear. In this study, we investigated the elevational patterns of species richness, species evenness and the relationship between species richness and evenness (RRE) in the forest soil bacterial and fungal communities and individual phyla across three climatic zones (tropical, subtropical, and cold temperate). Our results revealed that soil bacterial richness (alpha diversity) decreased with elevation, while fungal richness exhibited a hump-shaped pattern in the tropical and cold-temperate forests. Elevational patterns of evenness in bacterial and fungal communities showed the hump-shaped pattern across climatic zones, except for bacterial evenness in the tropical forest. Both bacterial and fungal richness and evenness were positively correlated in the subtropical and cold-temperate forests, while negatively correlated for bacteria in the tropical forest. The richness and evenness of soil microorganisms across different regions were controlled by climatic and edaphic factors. Soil pH was the most important factor associated with the variations in bacterial richness and evenness, while mean annual temperature explained the major variations in fungal richness. Our results addressed that the varieties of elevational patterns of microbial diversity in climatic zones and taxonomic levels, further indicating that richness and evenness may respond differently to environmental gradients.
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Affiliation(s)
- Zhengyi Huang
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Yangui Su
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Sinuo Lin
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Guopeng Wu
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Hao Cheng
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Gang Huang
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
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Bezerra WCA, Figueiredo GM, Kozlowsky-Suzuki B. Can we meaningfully estimate the impacts of climate on zooplankton biodiversity? A review on uses and limitations of marine time series. MARINE POLLUTION BULLETIN 2023; 195:115515. [PMID: 37716130 DOI: 10.1016/j.marpolbul.2023.115515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/18/2023]
Abstract
Climate events compromise ecosystems functioning and services. Marine zooplankton play a key role linking primary producers and higher consumers, in the carbon export to deeper regions, and respond quickly to environmental change. We conducted a systematic review to assess the effects of climate on marine zooplankton diversity. We describe the major findings, uses and limitations raised in the literature from worldwide time series ≥5 years. Thirty-five studies were included and only 6 presented extractable data (i.e., those that could be extracted from images) for the most studied group (i.e., copepods). Responses to climate were conflicting, and studies were mostly restricted to the global north, applied richness, alpha- and beta-diversity equally, and had a large number of unresolved taxonomic identification. Standardized open long-term data would meaningfully help unveiling assemblage reorganization and allow meta-analyses to improve our understanding of the effects of climate change and variability on zooplankton biodiversity.
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Affiliation(s)
- Wellen Cristina Alves Bezerra
- Instituto de Biociências, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Av. Pasteur 458, CEP: 22290-240, Urca, Rio de Janeiro, RJ, Brazil
| | - Gisela Mandali Figueiredo
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Professor Rodolfo Rocco 211, CCS, Cidade Universitária, CEP: 21941-902, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
| | - Betina Kozlowsky-Suzuki
- Departmento de Ecologia e Recursos Marinhos, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Av. Pasteur 458, CEP: 22290-240, Urca, Rio de Janeiro, RJ, Brazil.
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Vandoren R, Gielis S, Laukens K, Meysman P. Identification of TCR repertoire patterns linked with anti-cancer immunotherapy. Methods Cell Biol 2023; 183:115-142. [PMID: 38548409 DOI: 10.1016/bs.mcb.2023.05.001] [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] [Indexed: 04/02/2024]
Abstract
The highly diverse T cell receptor (TCR) repertoire is a crucial component of the adaptive immune system that aids in the protection against a wide variety of pathogens. This TCR repertoire, comprising the collection of all TCRs in an individual, is a valuable source of information on both recent and ongoing T cell activation. Cancer cells, like pathogens, have the ability to trigger an adaptive immune response. However, because cancer cells use a variety of strategies to escape immune responses, this is often insufficient to completely eradicate them. As a result, immunotherapy is a promising treatment option for cancer patients. This treatment is expected to increase T cell activation and subsequently alter the TCR repertoire composition in these patients. Monitoring TCR repertoires before and after immunotherapy can therefore provide additional insight into T cell responses and might identify cancer-associated TCR sequences. Here we present a computational strategy to identify those changes in the TCR repertoire that occur after treatment with immunotherapy. Since this method allows the identification of TCR patterns that might be treatment-associated, it can help future research by revealing those patterns that are related with response. This TCR analysis workflow is illustrated using public data from three different cancer patients who received anti-PD-1 treatment.
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Affiliation(s)
- Romi Vandoren
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | - Sofie Gielis
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium.
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Salas-Espejo E, Terrón-Camero LC, Ruiz JL, Molina NM, Andrés-León E. Exploring the Microbiome in Human Reproductive Tract: High-Throughput Methods for the Taxonomic Characterization of Microorganisms. Semin Reprod Med 2023; 41:125-143. [PMID: 38320576 DOI: 10.1055/s-0044-1779025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Microorganisms are important due to their widespread presence and multifaceted roles across various domains of life, ecology, and industries. In humans, they underlie the proper functioning of multiple systems crucial to well-being, including immunological and metabolic functions. Emerging research addressing the presence and roles of microorganisms within human reproduction is increasingly relevant. Studies implementing new methodologies (e.g., to investigate vaginal, uterine, and semen microenvironments) can now provide relevant insights into fertility, reproductive health, or pregnancy outcomes. In that sense, cutting-edge sequencing techniques, as well as others such as meta-metabolomics, culturomics, and meta-proteomics, are becoming more popular and accessible worldwide, allowing the characterization of microbiomes at unprecedented resolution. However, they frequently involve rather complex laboratory protocols and bioinformatics analyses, for which researchers may lack the required expertise. A suitable pipeline would successfully enable both taxonomic classification and functional profiling of the microbiome, providing easy-to-understand biological interpretations. However, the selection of an appropriate methodology would be crucial, as it directly impacts the reproducibility, accuracy, and quality of the results and observations. This review focuses on the different current microbiome-related techniques in the context of human reproduction, encompassing niches like vagina, endometrium, and seminal fluid. The most standard and reliable methods are 16S rRNA gene sequencing, metagenomics, and meta-transcriptomics, together with complementary approaches including meta-proteomics, meta-metabolomics, and culturomics. Finally, we also offer case examples and general recommendations about the most appropriate methods and workflows and discuss strengths and shortcomings for each technique.
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Affiliation(s)
- Eduardo Salas-Espejo
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Laura C Terrón-Camero
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
| | - José L Ruiz
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
| | - Nerea M Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Eduardo Andrés-León
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
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Silva AMM, Feiler HP, Lacerda-Júnior GV, Fernandes-Júnior PI, de Tarso Aidar S, de Araújo VAVP, Matteoli FP, de Araújo Pereira AP, de Melo IS, Cardoso EJBN. Arbuscular mycorrhizal fungi associated with the rhizosphere of an endemic terrestrial bromeliad and a grass in the Brazilian neotropical dry forest. Braz J Microbiol 2023; 54:1955-1967. [PMID: 37410249 PMCID: PMC10485230 DOI: 10.1007/s42770-023-01058-3] [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: 12/12/2022] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Arbuscular mycorrhizal fungi form symbiotic associations with 80-90% of all known plants, allowing the fungi to acquire plant-synthesized carbon, and confer an increased capacity for nutrient uptake by plants, improving tolerance to abiotic and biotic stresses. We aimed at characterizing the mycorrhizal community in the rhizosphere of Neoglaziovia variegata (so-called `caroa`) and Tripogonella spicata (so-called resurrection plant), using high-throughput sequencing of the partial 18S rRNA gene. Both plants are currently undergoing a bioprospecting program to find microbes with the potential of helping plants tolerate water stress. Sampling was carried out in the Caatinga biome, a neotropical dry forest, located in northeastern Brazil. Illumina MiSeq sequencing of 37 rhizosphere samples (19 for N. variegata and 18 for T. spicata) revealed a distinct mycorrhizal community between the studied plants. According to alpha diversity analyses, T. spicata showed the highest richness and diversity based on the Observed ASVs and the Shannon index, respectively. On the other hand, N. variegata showed higher modularity of the mycorrhizal network compared to T. spicata. The four most abundant genera found (higher than 10%) were Glomus, Gigaspora, Acaulospora, and Scutellospora, with Glomus being the most abundant in both plants. Nonetheless, Gigaspora, Diversispora, and Ambispora were found only in the rhizosphere of N. variegata, whilst Scutellospora, Paraglomus, and Archaeospora were exclusive to the rhizosphere of T. spicata. Therefore, the community of arbuscular mycorrhizal fungi of the rhizosphere of each plant encompasses a unique composition, structure and modularity, which can differentially assist them in the hostile environment.
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Affiliation(s)
- Antonio Marcos Miranda Silva
- “Luiz de Queiroz” College of Agriculture, Soil Science Department, University of São Paulo, Piracicaba, São Paulo 13418-900 Brazil
| | | | | | | | - Saulo de Tarso Aidar
- Brazilian Agricultural Research Corporation, Embrapa Semiárido, Petrolina, , Pernambuco 56302-970 Brazil
| | | | - Filipe Pereira Matteoli
- Faculty of Sciences, Department of Biological Sciences, Laboratory of Microbial Bioinformatics, São Paulo State University, Bauru, 17033-360 Brazil
| | | | - Itamar Soares de Melo
- Brazilian Agricultural Research Corporation, Embrapa Meio Ambiente, Jaguariúna, São Paulo 13918-110 Brazil
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Zhang K, He C, Qiu Y, Li X, Hu J, Fu B. ASSOCIATION OF ORAL MICROBIOTA AND PERIODONTAL DISEASE WITH LUNG CANCER: A SYSTEMATIC REVIEW AND META-ANALYSIS. J Evid Based Dent Pract 2023; 23:101897. [PMID: 37689446 DOI: 10.1016/j.jebdp.2023.101897] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 04/22/2023] [Accepted: 05/17/2023] [Indexed: 09/11/2023]
Abstract
OBJECTIVES Evidence of oral microbiota perturbations has been accumulated for lung cancers. This review focused on the oral microbiota alterations in population suffering from lung cancer. In addition, we also discussed conflicting data about the association between oral microbiota dysbiosis and risk of lung cancer. METHODS A systematic search was conducted in Medline, Embase, PubMed, and Cochrane Library databases. The studies evaluated diversity and abundance of oral microbes in healthy and lung cancer individuals as well as association of periodontal disease and pathogens with lung cancer. Of 3559 studies, 28 included studies were performed in qualitative analysis, and 25 studies were used in meta-analyses for quantitative assessment. Heterogeneity was analyzed by using I² and chi-squared Q test statistics. Statistical analyses were performed by using the RevMan 5.4 software. RESULTS Compared with the control, lung cancer patients had lower alpha diversity (Shannon: SMD = -0.54; 95% CI, -0.90 to -0.19; P < .01, I2 = 71%). In nested case-control studies, individuals with decreased alpha diversity tended to have an increased risk of lung cancer (observed species: HR = 0.90; 95% CI, 0.85-0.96; P < .01, I2 = 0%; Shannon: HR = 0.89; 95% CI, 0.83-0.95; P < .01, I2 = 0%). Overall, no strong evidence of association of relative abundance with specific oral microbes with lung cancers was found because of inconsistent data. No associations were found between periodontal pathogens and lung cancer risk (red complex: HR = 1.12, 95% CI: 0.42-3.02, P = .82, I2 = 62%; orange complex: HR =1.77, 95% CI: 0.78-3.98, P = .17, I2 = 36%), expect for Fusobacterium nucleatum (HR = 2.27, 95% CI: 1.13-4.58, P = .02, I2 = 0%). The positive association of periodontal disease with lung cancer risk was found (HR = 1.58, 95% CI: 1.25-2.00, P < .001, I2= 0%) with increase of periodontal diseases severity (HR = 2.39, 95% CI: 1.57-3.66, P < .001, I2 = 0%). However, such association was not found in never-smoker participants (HR = 1.00, 95% CI: 0.76-1.31, P = .37, I2= 7%). CONCLUSIONS Lower alpha diversity of oral microbiome may be associated with a greater risk of lung cancer and might serve as a predictive signal of lung cancer risk. There was no strong evidence of relative abundance of oral microbial taxa and periodontal pathogens in lung cancer patients. Fusobacterium nucleatum might be a potential microbial candidate of biomarkers in lung cancer. Periodontal disease may be positively associated with lung cancer risk by confounding of smoking, but not an independent risk factor.
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Affiliation(s)
- Kai Zhang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Cheng He
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yuan Qiu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Xiuyang Li
- Department of Epidemiology & Biostatistics, and Center for Clinical Big Data and Statistics, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jian Hu
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Baiping Fu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, Zhejiang, China.
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Colonetti T, Saggioratto MC, Grande AJ, Colonetti L, Junior JCD, Ceretta LB, Roever L, Silva FR, da Rosa MI. Gut and Vaginal Microbiota in the Endometriosis: Systematic Review and Meta-Analysis. BIOMED RESEARCH INTERNATIONAL 2023; 2023:2675966. [PMID: 38601772 PMCID: PMC11006450 DOI: 10.1155/2023/2675966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 03/21/2023] [Accepted: 05/05/2023] [Indexed: 04/12/2024]
Abstract
Background Endometriosis is a clinical condition associated with genetic, endocrine, and immunological factors, present in 6 to 10% of women of reproductive age. Currently, the human microbiota has been studied and associated with the evolution of diseases due to its influence on pathogenesis, indicating that changes in the colonization of microorganisms in the genitourinary and gastrointestinal systems can promote physiological changes that can trigger inflammatory and immunological processes and hormonal dysregulation, which can be linked to endometriosis. Thus, this systematic review and meta-analysis evaluated microbiota changes in women with endometriosis. Methods The following electronic databases were searched up to April 2022: Medline, Embase, Web of Science, Cochrane Library, and gray literature (Google Scholar), using the keywords "dysbiosis", "microbiome" and "endometriosis", combined with their synonyms. The observational studies conducted with women diagnosed with endometriosis and women without endometriosis as controls were included. For the analyses, a standard mean difference with a 95% confidence interval was used using RevMan software (version 5.4), and for methodological quality assessment, the Newcastle-Ottawa scale was used. Results A total of 16 studies were found in the literature assessing the composition of the microbiota in women with endometriosis, and no significant difference were found for changes in alpha diversity analysis in gut microbiota (SMD = -0.28; 95% CI = -0.70 to 0.14; P = 0.19; I2 = 52%; four studies, 357 participants) or vaginal microbiota (SMD = -0.68; 95% CI = -1.72 to 0.35; P = 0.19; I2 = 66%; two studies, 49 participants). Conclusion In intestinal and vaginal samples from women with endometriosis, alpha-diversity did not present a significant difference when compared to the control population. However, each study individually showed a possible relationship between the female microbiota and endometriosis. This trial is registered with CRD42021260972.
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Affiliation(s)
- Tamy Colonetti
- Laboratory of Biomedicine Translational, Universidade do Extremo Sul Catarinense, Av. Universitária, 1105-Bairro Universitário CEP, 88806-000 Criciúma, SC, Brazil
| | - Maria Carolina Saggioratto
- Laboratory of Biomedicine Translational, Universidade do Extremo Sul Catarinense, Av. Universitária, 1105-Bairro Universitário CEP, 88806-000 Criciúma, SC, Brazil
| | - Antonio José Grande
- Laboratory of Evidence-Based Practice, Universidade Estadual de Mato Grosso do Sul (UEMS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Laura Colonetti
- Laboratory of Biomedicine Translational, Universidade do Extremo Sul Catarinense, Av. Universitária, 1105-Bairro Universitário CEP, 88806-000 Criciúma, SC, Brazil
| | - João Carlos Denoni Junior
- Laboratory of Biomedicine Translational, Universidade do Extremo Sul Catarinense, Av. Universitária, 1105-Bairro Universitário CEP, 88806-000 Criciúma, SC, Brazil
| | - Luciane Bisognin Ceretta
- Postgraduate Program in Collective Health, Universidade do Extremo Sul Catarinense (UNESC), Criciúma, Santa Catarina, Brazil
| | - Leonardo Roever
- Department of Clinical Research, Federal University of Uberlândia, Uberlândia, Brazil
| | - Fábio Rosa Silva
- Laboratory of Biomedicine Translational, Universidade do Extremo Sul Catarinense, Av. Universitária, 1105-Bairro Universitário CEP, 88806-000 Criciúma, SC, Brazil
| | - Maria Inês da Rosa
- Laboratory of Biomedicine Translational, Universidade do Extremo Sul Catarinense, Av. Universitária, 1105-Bairro Universitário CEP, 88806-000 Criciúma, SC, Brazil
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Takano Y, Takekoshi S, Takano K, Matoba Y, Mukumoto M, Shirai O. Metagenomic analysis of ready biodegradability tests to ascertain the relationship between microbiota and the biodegradability of test chemicals. JOURNAL OF PESTICIDE SCIENCE 2023; 48:35-46. [PMID: 37361484 PMCID: PMC10288005 DOI: 10.1584/jpestics.d22-067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/10/2023] [Indexed: 06/28/2023]
Abstract
Ready biodegradability tests conducted in accordance with the Organisation for Economic Co-operation and Development guidelines (test 301C or test 301F) are performed using activated sludge (AS) prepared by the Chemicals Evaluation and Research Institute (AS-CERI) or that taken from a sewage treatment plant (AS-STP). It had been reported that AS-CERI had lower activity than AS-STP in biodegrading test chemicals, and that biodegradation was accelerated by increasing the volume of the test medium. However, these phenomena have not been clarified from the perspective of the microbiota. In this study, using metagenomic analysis, we first showed that the microbiota of AS-CERI was biased in its distribution of phyla, less diverse, and had greater lot-to-lot variability than that of AS-STP. Second, after cultivation for a long period of time, the microbiota of AS-STP and AS-CERI became more similar to each other in terms of community structure. Third, determining degraders of test substances when each substance was actively biodegraded was found to be an effective approach. Finally, we clarified experimentally that a large volume of test medium increased the number of species that could degrade test substances in the condition where the initial concentrations of each substance and AS-STP were kept constant.
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Affiliation(s)
- Yoshinari Takano
- Sumitomo Chemical Co., Ltd. Environmental Health Science Laboratory
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
| | - Saki Takekoshi
- Sumitomo Chemical Co., Ltd. Environmental Health Science Laboratory
| | - Kotaro Takano
- Sumitomo Chemical Co., Ltd. Environmental Health Science Laboratory
| | - Yoshihide Matoba
- Sumitomo Chemical Co., Ltd. Environmental Health Science Laboratory
| | - Makiko Mukumoto
- Sumitomo Chemical Co., Ltd. Environmental Health Science Laboratory
| | - Osamu Shirai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
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Ndatimana G, Nantege D, Arimoro FO. A review of the application of the macroinvertebrate-based multimetric indices (MMIs) for water quality monitoring in lakes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27559-0. [PMID: 37202638 DOI: 10.1007/s11356-023-27559-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/07/2023] [Indexed: 05/20/2023]
Abstract
The increasing stress on lake ecosystems is affecting their functioning such as providing goods and services to inhabiting organisms and riparian communities. Monitoring of water quality is important for sustainable management and restoration of lake ecosystems. However, the costs associated with traditional approaches have become prohibitive, while not giving reliable early warning signals on resource conditions. Thus, the current shift in the use of bioindicators and multimetric indices (MMIs) in the monitoring of water quality is currently gaining global recognition with more emphasis on its application in lotic ecosystems. Therefore, this paper provides an elaborated insight into the application of macroinvertebrate-based MMIs in lentic ecosystems and the successes achieved so far. The various metrics and indices, the development strategies, application challenges, the use of macroinvertebrates as bioindicators, and the future projection of enhancing MMI usage in lentic environment monitoring, particularly in developing countries, are extensively covered. The use of MMI as a rapid lake biomonitoring tool needs to be adopted for sustainable applications in lake ecosystem management and as an integrated approach to monitoring human-induced stress especially in developing countries where there is a paucity of information.
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Affiliation(s)
- Gilbert Ndatimana
- Applied Hydrobiology Unit, Department of Animal Biology, Federal University of Technology, PMB 65, Minna, Nigeria.
| | - Diana Nantege
- Applied Hydrobiology Unit, Department of Animal Biology, Federal University of Technology, PMB 65, Minna, Nigeria
| | - Francis O Arimoro
- Applied Hydrobiology Unit, Department of Animal Biology, Federal University of Technology, PMB 65, Minna, Nigeria
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Obame-Nkoghe J, Makanga BK, Zongo SB, Koumba AA, Komba P, Longo-Pendy NM, Mounioko F, Akone-Ella R, Nkoghe-Nkoghe LC, Ngangue-Salamba MF, Yangari P, Aboughe-Angone S, Fournet F, Kengne P, Paupy C. Urban Green Spaces and Vector-Borne Disease Risk in Africa: The Case of an Unclean Forested Park in Libreville (Gabon, Central Africa). INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20105774. [PMID: 37239503 DOI: 10.3390/ijerph20105774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/28/2023]
Abstract
In Africa, vector-borne diseases are a major public health issue, especially in cities. Urban greening is increasingly considered to promote inhabitants' well-being. However, the impact of urban green spaces on vector risk remains poorly investigated, particularly urban forests in poor hygienic conditions. Therefore, using larval sampling and human landing catches, this study investigated the mosquito diversity and the vector risk in a forest patch and its inhabited surroundings in Libreville, Gabon, central Africa. Among the 104 water containers explored, 94 (90.4%) were artificial (gutters, used tires, plastic bottles) and 10 (9.6%) were natural (puddles, streams, tree holes). In total, 770 mosquitoes belonging to 14 species were collected from such water containers (73.1% outside the forested area). The mosquito community was dominated by Aedes albopictus (33.5%), Culex quinquefasciatus (30.4%), and Lutzia tigripes (16.5%). Although mosquito diversity was almost double outside compared to inside the forest (Shannon diversity index: 1.3 vs. 0.7, respectively), the species relative abundance (Morisita-Horn index = 0.7) was similar. Ae. albopictus (86.1%) was the most aggressive species, putting people at risk of Aedes-borne viruses. This study highlights the importance of waste pollution in urban forested ecosystems as a potential driver of mosquito-borne diseases.
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Affiliation(s)
- Judicaël Obame-Nkoghe
- Laboratoire de Biologie Moléculaire et Cellulaire, Département de Biologie, Université des Sciences et Techniques de Masuku (USTM), Franceville BP 941, Gabon
- Unité de Recherche en Écologie de la Santé, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon
| | - Boris Kevin Makanga
- Institut de Recherche en Écologie Tropicale (IRET/CENAREST), Libreville BP 13354, Gabon
| | - Sylvie Brizard Zongo
- Laboratoire de Biologie Moléculaire et Cellulaire, Département de Biologie, Université des Sciences et Techniques de Masuku (USTM), Franceville BP 941, Gabon
- Département Faune et Aires Protégées, École Nationale des Eaux et Forêts (ENEF), Libreville BP 3960, Gabon
| | - Aubin Armel Koumba
- Institut de Recherche en Écologie Tropicale (IRET/CENAREST), Libreville BP 13354, Gabon
| | - Prune Komba
- Unité de Recherche GéoHydrosystèmes Continentaux (UR GéHCo), Département Géosciences et Environnement, Université de Tours, 37000 Tours, France
| | - Neil-Michel Longo-Pendy
- Unité de Recherche en Écologie de la Santé, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon
| | - Franck Mounioko
- Laboratoire de Biologie Moléculaire et Cellulaire, Département de Biologie, Université des Sciences et Techniques de Masuku (USTM), Franceville BP 941, Gabon
- Unité de Recherche en Écologie de la Santé, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon
| | - Rodolphe Akone-Ella
- Unité de Recherche en Écologie de la Santé, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon
| | - Lynda Chancelya Nkoghe-Nkoghe
- Unité de Recherche en Écologie de la Santé, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon
| | - Marc-Flaubert Ngangue-Salamba
- Unité de Recherche en Écologie de la Santé, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon
| | - Patrick Yangari
- Unité de Recherche en Écologie de la Santé, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon
| | - Sophie Aboughe-Angone
- Institut de Pharmacopée et de Médecine Traditionnelle (IPHAMETRA), Libreville BP 1156, Gabon
| | - Florence Fournet
- Unité Mixte de Recherche Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC), Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), 34193 Montpellier, France
| | - Pierre Kengne
- Unité de Recherche en Écologie de la Santé, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon
- Unité Mixte de Recherche Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC), Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), 34193 Montpellier, France
| | - Christophe Paupy
- Unité Mixte de Recherche Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC), Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), 34193 Montpellier, France
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Kusumawaty D, Augustine SMN, Aryani A, Effendi Y, Emran TB, Tallei TE. Configuration of gut bacterial community profile and their potential functionality in the digestive tract of the wild and cultivated Indonesian shortfin elver-phase eels ( Anguilla bicolor bicolor McClelland, 1844). 3 Biotech 2023; 13:153. [PMID: 37131968 PMCID: PMC10148933 DOI: 10.1007/s13205-023-03561-8] [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: 06/21/2022] [Accepted: 04/15/2023] [Indexed: 05/04/2023] Open
Abstract
This study aimed to explore the bacteria present in the digestive tracts of wild and cultivated Indonesian shortfin eel during the elver phase. The eel has high export potential due to its vitamin and micronutrient content, but slow growth and vulnerability to collapse in farm conditions hinder its cultivation. The microbiota in the eel's digestive tract is crucial for its health, particularly during the elver phase. This study used Next Generation Sequencing to analyze the community structure and diversity of bacteria in the eels' digestive tracts, focusing on the V3-V4 regions of the 16S rRNA gene. Mothur software was used for data analysis and PAST v.3.26 was used to calculate alpha diversity. The results showed that Proteobacteria (64.18%) and Firmicutes (33.55%) were the predominant phyla in the digestive tract of cultivated eels, while Bacteroidetes (54.16%), Firmicutes (14.71%), and Fusobacteria (10.56%) were predominant in wild eels. The most prevalent genera in cultivated and wild elver were Plesiomonas and Cetobacterium, respectively. The microbiota in the digestive tract of cultivated eels was diverse despite uneven distribution. The KEGG database analysis revealed that the primary function of the microbiome was to facilitate the eel's absorption of nutrients by contributing significantly to the metabolism of carbohydrates and amino acids. This study's findings can aid in assessing eel health and improving eel farming conditions.
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Affiliation(s)
- Diah Kusumawaty
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung, 40154 Indonesia
| | - Stella Melbournita Noor Augustine
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung, 40154 Indonesia
| | - Any Aryani
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung, 40154 Indonesia
| | - Yunus Effendi
- Department of Biology, Faculty of Science and Technology, Al-Azhar Indonesia University, Jakarta, 12110 Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381 Bangladesh
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, 95115 North Sulawesi Indonesia
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Pravdová M, Kolářová J, Grabicová K, Janáč M, Randák T, Ondračková M. Response of Parasite Community Composition to Aquatic Pollution in Common Carp ( Cyprinus carpio L.): A Semi-Experimental Study. Animals (Basel) 2023; 13:ani13091464. [PMID: 37174501 PMCID: PMC10177495 DOI: 10.3390/ani13091464] [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: 02/25/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
The response of parasite communities to aquatic contamination has been shown to vary with both type of pollutant and parasite lifestyle. In this semi-experimental study, we examined uptake of pharmaceutical compounds in common carp (Cyprinus carpio L.) restocked from a control pond to a treatment pond fed with organic pollution from a sewage treatment plant and assessed changes in parasite community composition and fish biometric parameters. The parasite community of restocked fish changed over the six-month exposure period, and the composition of pharmaceutical compounds in the liver and brain was almost the same as that in fish living in the treatment pond their whole life. While fish size and weight were significantly higher in both treatment groups compared to the control, condition indices, including condition factor, hepatosomatic index, and splenosomatic index, were significantly higher in control fish. Parasite diversity and species richness decreased at the polluted site, alongside a significant increase in the abundance of a single parasite species, Gyrodactylus sprostonae. Oviparous monogeneans of the Dactylogyridae and Diplozoidae families and parasitic crustaceans responded to pollution with a significant decrease in abundance, the reduction in numbers most likely related to the sensitivity of their free-living stages to pollution.
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Affiliation(s)
- Markéta Pravdová
- Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 00 Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jitka Kolářová
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25 Vodňany, Czech Republic
| | - Kateřina Grabicová
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25 Vodňany, Czech Republic
| | - Michal Janáč
- Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 00 Brno, Czech Republic
| | - Tomáš Randák
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25 Vodňany, Czech Republic
| | - Markéta Ondračková
- Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 00 Brno, Czech Republic
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Rodríguez-González S, Portela R, Córdoba-Aguilar A. Research trends in mosquito studies in urban areas. Acta Trop 2023; 241:106888. [PMID: 36889424 DOI: 10.1016/j.actatropica.2023.106888] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/27/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023]
Abstract
Urbanization is causing a significant impact on biodiversity and human health. The increase in vector-borne diseases in recent decades is linked to changes in the environment due to urbanization. We have reviewed published information on urban mosquitoes from around the globe to examine major study trends in terms of urbanization, and the type of arboviruses they vector. Our review showed a surge in research on urban mosquitoes in the past 15 years, with the majority of studies conducted in the Americas and focusing on Aedes aegypti and Ae. albopictus. However, the findings also highlight a lack of basic monitoring data on mosquito diversity and vector-borne diseases in many countries, which poses a challenge for disease control.
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Affiliation(s)
- Stephany Rodríguez-González
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México; Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, 04510 Coyoacán, Ciudad de México, Mexico
| | - Renato Portela
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, 04510 Coyoacán, Ciudad de México, Mexico
| | - Alex Córdoba-Aguilar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, 04510 Coyoacán, Ciudad de México, Mexico.
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Raffard A, Campana JLM, Legrand D, Schtickzelle N, Jacob S. Resident-Disperser Differences and Genetic Variability Affect Communities in Microcosms. Am Nat 2023; 201:363-375. [PMID: 36848519 DOI: 10.1086/722750] [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] [Indexed: 11/04/2022]
Abstract
AbstractDispersal is a key process mediating ecological and evolutionary dynamics. Its effects on the dynamics of spatially structured systems, population genetics, and species range distribution can depend on phenotypic differences between dispersing and nondispersing individuals. However, scaling up the importance of resident-disperser differences to communities and ecosystems has rarely been considered, in spite of intraspecific phenotypic variability being an important factor mediating community structure and productivity. Here, we used the ciliate Tetrahymena thermophila, in which phenotypic traits are known to differ between residents and dispersers, to test (i) whether these resident-disperser differences affect biomass and composition in competitive communities composed of four other Tetrahymena species and (ii) whether these effects are genotype dependent. We found that dispersers led to a lower community biomass compared with residents. This effect was highly consistent across the 20 T. thermophila genotypes used, despite intraspecific variability in resident-disperser phenotypic differences. We also found a significant genotypic effect on biomass production, showing that intraspecific variability has consequences for communities. Our study suggests that individual dispersal strategy can scale up to community productivity in a predictable way, opening new perspectives to the functioning of spatially structured ecosystems.
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Kulaš A, Žutinić P, Gulin Beljak V, Kepčija RM, Perić MS, Orlić S, Petrić IS, Marković T, Gligora Udovič M. Diversity of protist genera in periphyton of tufa-depositing karstic river. ANN MICROBIOL 2023. [DOI: 10.1186/s13213-023-01712-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023] Open
Abstract
Abstract
Purpose
In aquatic ecosystems, protists play a crucial role and cover numerous ecological functions. The karstic Krka River (Croatia) is a unique hotspot for high diversity of aquatic organisms, especially protists. The main objective of the present study was to obtain a detailed overview of the protist community structure in the periphyton of the Krka River and to determine the differences in protist diversity along the river.
Methods
Protist diversity was detected by amplicon sequencing of the hypervariable region V9 of the 18S rRNA gene, using the universal eukaryotic primer pair.
Results
The three main groups of protists were as follows: Ciliophora, Cercozoa, and Bacillariophyta. In terms of abundance of protist OTUs, the shade plot revealed an evident difference from the upstream to downstream river section, which increased between locations from Krka spring to Skradinski buk. Diversity was explored using measures of alpha and beta diversity. Alpha diversity showed an increasing trend in the downstream direction of the river. The location effect, or clustering/grouping of samples by location, was confirmed by the PERMANOVA permutation test of beta diversity.
Conclusion
The combination of alpha and beta diversity can help provide deeper insight into the study of diversity patterns, but also point out to decline in species diversity and allow for effective ways to protect aquatic karst habitats in future management.
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Liegeois M, Sartori M, Schwander T. What Ecological Factors Favor Parthenogenesis over Sexual Reproduction? A Study on the Facultatively Parthenogenetic Mayfly Alainites muticus in Natural Populations. Am Nat 2023; 201:229-240. [PMID: 36724461 DOI: 10.1086/722515] [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: 02/04/2023]
Abstract
AbstractDifferent reproductive modes are characterized by costs and benefits that depend on ecological contexts. For example, sex can provide benefits under complex biotic interactions, while its costs increase under mate limitation. Furthermore, ecological contexts often vary along abiotic gradients. Here, we study how these factors simultaneously influence the frequency of sex in the facultatively parthenogenetic mayfly Alainites muticus. We first verified that parthenogenesis translates into female-biased population sex ratios. We then measured the density of individuals (a proxy for mate limitation) and community diversity (biotic interaction complexity) for 159 A. muticus populations covering a broad altitudinal gradient and used structural equation modeling to investigate their direct and indirect influences on sex ratios. We found no effect of community diversity or altitude on sex ratios. Furthermore, even when females can reproduce parthenogenetically, they generally reproduce sexually, indicating that the benefits of sex exceed its costs in most situations. Sex ratios become female-biased only under low population densities, as expected if mate limitation was the main factor selecting for parthenogenesis. Mate limitation might be widespread in mayflies because of their short adult life span and limited dispersal, which can generate strong selection for reproductive assurance and may provide a stepping stone toward obligate parthenogenesis.
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Seo H, Yoon SY, ul-Haq A, Jo S, Kim S, Rahim MA, Park HA, Ghorbanian F, Kim MJ, Lee MY, Kim KH, Lee N, Won JH, Song HY. The Effects of Iron Deficiency on the Gut Microbiota in Women of Childbearing Age. Nutrients 2023; 15:nu15030691. [PMID: 36771397 PMCID: PMC9919165 DOI: 10.3390/nu15030691] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Iron deficiency anemia (IDA) is the most prevalent and common nutritional deficiency worldwide and is a global health problem with significant risk, particularly among women of reproductive age. Oral iron supplementation is the most widely used and cost-effective treatment for iron deficiency and IDA. However, there are limitations regarding side effects such as enteritis, treatment compliance, and bioavailability. Intestinal microbiome characteristic research has been recently conducted to overcome these issues, but more is needed. Against this background, a metagenomics study on the 16S gene in the feces of young women vulnerable to IDA was conducted. As a result of analyzing 16 normal subjects and 15 IDA patients, significant differences in bacterial community distribution were identified. In particular, a significant decrease in Faecalibacterium was characteristic in IDA patients compared with normal subjects. Furthermore, in the case of patients who recovered from IDA following iron supplementation treatment, it was confirmed that Faecalibacterium significantly recovered to normal levels. However, no significance in beta diversity was seen compared with before treatment. There were also no differences in the beta diversity results between the recovered and normal subjects. Therefore, intestinal dysbiosis during the disease state was considered to be restored as IDA improved. Although the results were derived from a limited number of subjects and additional research is needed, the results of this study are expected to be the basis for developing treatment and prevention strategies based on host-microbiome crosstalk in IDA.
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Affiliation(s)
- Hoonhee Seo
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan-si 31538, Republic of Korea
| | - Seug Yun Yoon
- Division of Hematology & Medical Oncology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
| | - Asad ul-Haq
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan-si 31538, Republic of Korea
| | - Sujin Jo
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si 31151, Republic of Korea
| | - Sukyung Kim
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan-si 31538, Republic of Korea
| | - Md Abdur Rahim
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si 31151, Republic of Korea
| | - Hyun-A Park
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si 31151, Republic of Korea
| | - Fatemeh Ghorbanian
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si 31151, Republic of Korea
| | - Min Jung Kim
- Division of Hematology & Medical Oncology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
| | - Min-Young Lee
- Division of Hematology & Medical Oncology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
| | - Kyoung Ha Kim
- Division of Hematology & Medical Oncology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
| | - Namsu Lee
- Division of Hematology & Medical Oncology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
| | - Jong-Ho Won
- Division of Hematology & Medical Oncology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
- Correspondence: (J.-H.W.); (H.-Y.S.)
| | - Ho-Yeon Song
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan-si 31538, Republic of Korea
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si 31151, Republic of Korea
- Correspondence: (J.-H.W.); (H.-Y.S.)
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46
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Benatti ALT, Polizeli MDLTDM. Lignocellulolytic Biocatalysts: The Main Players Involved in Multiple Biotechnological Processes for Biomass Valorization. Microorganisms 2023; 11:microorganisms11010162. [PMID: 36677454 PMCID: PMC9864444 DOI: 10.3390/microorganisms11010162] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/11/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023] Open
Abstract
Human population growth, industrialization, and globalization have caused several pressures on the planet's natural resources, culminating in the severe climate and environmental crisis which we are facing. Aiming to remedy and mitigate the impact of human activities on the environment, the use of lignocellulolytic enzymes for biofuel production, food, bioremediation, and other various industries, is presented as a more sustainable alternative. These enzymes are characterized as a group of enzymes capable of breaking down lignocellulosic biomass into its different monomer units, making it accessible for bioconversion into various products and applications in the most diverse industries. Among all the organisms that produce lignocellulolytic enzymes, microorganisms are seen as the primary sources for obtaining them. Therefore, this review proposes to discuss the fundamental aspects of the enzymes forming lignocellulolytic systems and the main microorganisms used to obtain them. In addition, different possible industrial applications for these enzymes will be discussed, as well as information about their production modes and considerations about recent advances and future perspectives in research in pursuit of expanding lignocellulolytic enzyme uses at an industrial scale.
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47
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Remmers JJ, Nielsen CK, Lesmeister DB. Anthropogenic and environmental influences on mammalian alpha and beta diversity in a hardwood forest landscape. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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48
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Gao J, Xu C, Zhang M, Liu J, Wu X, Cui C, Wei H, Peng J, Zheng R. Functional fiber enhances the effect of every-other-day fasting on insulin sensitivity by regulating the gut microecosystem. J Nutr Biochem 2022; 110:109122. [PMID: 35977666 DOI: 10.1016/j.jnutbio.2022.109122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 02/22/2022] [Accepted: 06/20/2022] [Indexed: 01/13/2023]
Abstract
Every-other-day fasting (EODF), which involves alternating days of fasting and feeding, has been reported to lower obesity, and dietary fibers can improve metabolism by altering gut microbiota. This study investigated whether the combination of functional fiber (FF) and EODF (FF-EODF) can further improve insulin sensitivity by regulating the composition of microbiota and curbing weight gain. Twenty-eight diet-induced obese (DIO) mice were randomly divided into four experimental groups (n=7): (1) ad-libitum (AL), (2) EODF, (3) 4% FF-EODF and (4) 6% FF-EODF. After exposure to a high-fat basal diet (HFD) for 12 weeks (1-12 weeks, period 1) and then to a normal chow diet (NCD) for 4 weeks (13-16 weeks, period 2). Compared with EODF alone, 6% FF-EODF treatment could significantly improve the insulin sensitivity of DIO mice without affecting their body weight during period 1(HFD), while significantly increasing satiety, energy consumption, weight, and adipose loss, and insulin sensitivity during period 2 (NCD). Meanwhile, FF-EODF showed a higher increase in short-chain fatty acids (SCFAs) and restored the proportion of induced intraepithelial lymphocytes in the intestinal epithelium compared to EODF alone. Although EODF could increase the relative abundances of Lactobacillus and Bifidobacteriumin, FF supplementation further increased the relative abundance of Lactobacillus, Bifidobacterium, and S24-7 in the intestine. This increase was positively correlated with the decrease in adiposity and insulin resistance, indicating that FF plays a key role in insulin improvement. Our study demonstrated the potential of FF-EODF in promoting insulin sensitivity and reducing body weight via beneficial regulation of gut microecosystem.
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Affiliation(s)
- Jianwei Gao
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chuanhui Xu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mengdi Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianhua Liu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaoyu Wu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chenbin Cui
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongkui Wei
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jian Peng
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
| | - Rong Zheng
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, China.
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Nagelkerken I, Connell SD. Ocean acidification drives global reshuffling of ecological communities. GLOBAL CHANGE BIOLOGY 2022; 28:7038-7048. [PMID: 36172974 PMCID: PMC9828364 DOI: 10.1111/gcb.16410] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 06/16/2023]
Abstract
The paradigm that climate change will alter global marine biodiversity is one of the most widely accepted. Yet, its predictions remain difficult to test because laboratory systems are inadequate at incorporating ecological complexity, and common biodiversity metrics have varying sensitivity to detect change. Here, we test for the prevalence of global responses in biodiversity and community-level change to future climate (acidification and warming) from studies at volcanic CO2 vents across four major global coastal ecosystems and studies in laboratory mesocosms. We detected globally replicable patterns of species replacements and community reshuffling under ocean acidification in major natural ecosystems, yet species diversity and other common biodiversity metrics were often insensitive to detect such community change, even under significant habitat loss. Where there was a lack of consistent patterns of biodiversity change, these were a function of similar numbers of studies observing negative versus positive species responses to climate stress. Laboratory studies showed weaker sensitivity to detect species replacements and community reshuffling in general. We conclude that common biodiversity metrics can be insensitive in revealing the anticipated effects of climate stress on biodiversity-even under significant biogenic habitat loss-and can mask widespread reshuffling of ecological communities in a future ocean. Although the influence of ocean acidification on community restructuring can be less evident than species loss, such changes can drive the dynamics of ecosystem stability or their functional change. Importantly, species identity matters, representing a substantial influence of future oceans.
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Affiliation(s)
- Ivan Nagelkerken
- Southern Seas Ecology Laboratories, School of Biological Sciences and The Environment InstituteThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Sean D. Connell
- Southern Seas Ecology Laboratories, School of Biological Sciences and The Environment InstituteThe University of AdelaideAdelaideSouth AustraliaAustralia
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50
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Sherwin WB. Bray-Curtis (AFD) differentiation in molecular ecology: Forecasting, an adjustment ( A A), and comparative performance in selection detection. Ecol Evol 2022; 12:e9176. [PMID: 36110882 PMCID: PMC9465203 DOI: 10.1002/ece3.9176] [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: 03/01/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 11/07/2022] Open
Abstract
Geographic genetic differentiation measures are used for purposes such as assessing genetic diversity and connectivity, and searching for signals of selection. Confirmation by unrelated measures can minimize false positives. A popular differentiation measure, Bray-Curtis, has been used increasingly in molecular ecology, renamed AFD (hereafter called BCAFD). Critically, BCAFD is expected to be partially independent of the commonly used Hill "Q-profile" measures. BCAFD needs scrutiny for potential biases, by examining limits on its value, and comparing simulations against expectations. BCAFD has two dependencies on within-population (alpha) variation, undesirable for a between-population (beta) measure. The first dependency is derived from similarity toG ST andF ST . The second dependency is that BCAFD cannot be larger than the highest allele proportion in either location (alpha variation), which can be overcome by data-filtering or by a modified statistic A A or "Adjusted AFD". The first dependency does not forestall applications such as assessing connectivity or selection, if we know the measure's null behavior under selective neutrality with specified conditions-which is shown in this article for A A, for equilibrium, and nonequilibrium, for the commonly used data type of single-nucleotide-polymorphisms (SNPs) in two locations. Thus, A A can be used in tandem with mathematically contrasting differentiation measures, with the aim of reducing false inferences. For detecting adaptive loci, the relative performance of A A and other measures was evaluated, showing that it is best to use two mathematically different measures simultaneously, and that A A is in one of the best such pairwise criteria. For any application, using A A, rather than BCAFD, avoids the counterintuitive limitation by maximum allele proportion within localities.
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Affiliation(s)
- William B. Sherwin
- Evolution and Ecology Research Centre, School of BEESUNSW‐SydneySydneyNew South WalesAustralia
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