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Kurata S, Mano S, Nakahama N, Hirota SK, Suyama Y, Ito M. Development of mitochondrial DNA cytochrome c oxidase subunit I primer sets to construct DNA barcoding library using next-generation sequencing. Biodivers Data J 2024; 12:e117014. [PMID: 38933488 PMCID: PMC11199957 DOI: 10.3897/bdj.12.e117014] [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: 12/07/2023] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Insects are one of the most diverse eukaryotic groups on the planet, with one million or more species present, including those yet undescribed. The DNA barcoding system has been developed, which has aided in the identification of cryptic species and undescribed species. The mitochondrial cytochrome c oxidase I region (mtDNA COI) has been utilised for the barcoding analysis of insect taxa. Thereafter, next-generation sequencing (NGS) technology has been developed, allowing for rapid acquisition of massive amounts of sequence data for genetic analyses. Although NGS-based PCR primers designed to amplify the mtDNA COI region have been developed, their target regions were only a part of COI region and/or there were taxonomic bias for PCR amplification. As the mtDNA COI region is a traditional DNA marker for the DNA barcoding system, modified primers for this region would greatly contribute to taxonomic studies. In this study, we redesigned previously developed PCR primer sets that targetted the mtDNA COI barcoding region to improve amplification efficiency and to enable us to conduct sequencing analysis on NGS. As a result, the redesigned primer sets achieved a high success rate (> 85%) for species examined in this study, covering four insect orders (Coleoptera, Lepidoptera, Orthoptera and Odonata). Thus, by combining the primers with developed primer sets for 12S or 16S rRNA regions, we can conduct more detailed taxonomic, phylogeographic and conservation genetic studies using NGS.
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Affiliation(s)
- Seikan Kurata
- Tomakomai Experimental Forest, Hokkaido University, Tomakomai, JapanTomakomai Experimental Forest, Hokkaido UniversityTomakomaiJapan
| | - Shota Mano
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, JapanFaculty of Bioresource Sciences, Akita Prefectural UniversityAkitaJapan
| | - Naoyuki Nakahama
- Institute of Natural and Environmental Sciences, University of Hyogo, hyogo, JapanInstitute of Natural and Environmental Sciences, University of HyogohyogoJapan
| | - Shun K Hirota
- Botanical Gardens, Osaka Metropolitan University, Osaka, JapanBotanical Gardens, Osaka Metropolitan UniversityOsakaJapan
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Miyagi, JapanGraduate School of Agricultural Science, Tohoku UniversityMiyagiJapan
| | - Motomi Ito
- Komaba museum, University of Tokyo, Tokyo, JapanKomaba museum, University of TokyoTokyoJapan
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Gong F, He C, Li X, Wang K, Li M, Zhou X, Xu M, He X. Impacts of fertilization methods on Salvia miltiorrhiza quality and characteristics of the epiphytic microbial community. FRONTIERS IN PLANT SCIENCE 2024; 15:1395628. [PMID: 38817929 PMCID: PMC11138495 DOI: 10.3389/fpls.2024.1395628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
Plant epiphytic microorganisms have established a unique symbiotic relationship with plants, which has a significant impact on their growth, immune defense, and environmental adaptation. However, the impact of fertilization methods on the epiphytic microbial community and their correlation with the yield and quality of medicinal plant was still unclear. In current study, we conducted a field fertilization experiment and analyzed the composition of epiphytic bacterial and fungal communities employing high throughput sequencing data in different organs (roots, stems, and leaves) of Salvia miltiorrhiza, as well as their correlation with plant growth. The results showed that fertilization significantly affected the active ingredients and hormone content, soil physicochemical properties, and the composition of epiphytic microbial communities. After fertilization, the plant surface was enriched with a core microbial community mainly composed of bacteria from Firmicutes, Proteobacteria, and Actinobacteria, as well as fungi from Zygomycota and Ascomycota. Additionally, plant growth hormones were the principal factors leading to alterations in the epiphytic microbial community of S. miltiorrhiza. Thus, the most effective method of fertilization involved the application of base fertilizer in combination with foliar fertilizer. This study provides a new perspective for studying the correlation between microbial community function and the quality of S. miltiorrhiza, and also provides a theoretical basis for the cultivation and sustainable development of high-quality medicinal plants.
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Affiliation(s)
- Feng Gong
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Chao He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xianen Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kehan Wang
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Min Li
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Xiangyun Zhou
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Minghui Xu
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Xueli He
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
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3
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Aguadé-Gorgorió G, Anderson AR, Solé R. Modeling tumors as species-rich ecological communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590504. [PMID: 38712062 PMCID: PMC11071393 DOI: 10.1101/2024.04.22.590504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Many advanced cancers resist therapeutic intervention. This process is fundamentally related to intra-tumor heterogeneity: multiple cell populations, each with different mutational and phenotypic signatures, coexist within a tumor and its metastatic nodes. Like species in an ecosystem, many cancer cell populations are intertwined in a complex network of ecological interactions. Most mathematical models of tumor ecology, however, cannot account for such phenotypic diversity nor are able to predict its consequences. Here we propose that the Generalized Lotka-Volterra model (GLV), a standard tool to describe complex, species-rich ecological communities, provides a suitable framework to describe the ecology of heterogeneous tumors. We develop a GLV model of tumor growth and discuss how its emerging properties, such as outgrowth and multistability, provide a new understanding of the disease. Additionally, we discuss potential extensions of the model and their application to three active areas of cancer research, namely phenotypic plasticity, the cancer-immune interplay and the resistance of metastatic tumors to treatment. Our work outlines a set of questions and a tentative road map for further research in cancer ecology.
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Affiliation(s)
| | - Alexander R.A. Anderson
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, USA
| | - Ricard Solé
- ICREA-Complex Systems Lab, UPF-PRBB, Dr. Aiguader 80, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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Zhang J, Xia X, Huang W, Li Y, Lin X, Li Y, Yang Z. Photoaging of biodegradable nanoplastics regulates their toxicity to aquatic insects (Chironomus kiinensis) by impairing gut and disrupting intestinal microbiota. ENVIRONMENT INTERNATIONAL 2024; 185:108483. [PMID: 38382402 DOI: 10.1016/j.envint.2024.108483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/23/2024]
Abstract
Biodegradable plastic, a widely used ecofriendly alternative to conventional plastic, easily form nanoplastics (NPs) upon environmental weathering. However, the effects and underlying mechanisms governing the toxicity of photoaged biodegradable NPs to aquatic insects are not understood. In this study, we investigated the photoaging of polylactic acid nanoplastics (PLA-NPs, a typical biodegradable plastic) that were placed under xenon arc lamp for 50 days and 100 days and compared the toxicity of virgin and photoaged PLA-NPs to Chironomus kiinensis (a dominant aquatic insect). The results showed that photoaged PLA-NPs significantly decreased the body weight, body length and emergence rate of C. kiinensis. Additionally, photoaged PLA-NPs induced more severe gut oxidative stress, histological damage, and inflammatory responses than virgin PLA-NPs. Furthermore, the alpha diversity of gut microbiota was lower in photoaged PLA-NPs group than virgin PLA-NPs. The relative abundance of key gut bacteria related to intestinal barrier defense, immunity, and nutrient absorption was reduced more significantly in photoaged PLA-NPs group than virgin PLA, indirectly leading to stronger gut damage and growth reduction. A stronger impact of photoaged PLA-NPs on the gut and its microbiota occurred because photoaging reduced the size of NPs from 255.5 nm (virgin PLA) to 217.1 nm (PLA-50) and 182.5 nm (PLA-100), induced surface oxidation and enhancement of oxidative potential, and improved the stability of NPs, thereby exacerbating toxicity on the gut and its microbiota. This study provides insights into the effects of biodegradable NPs on aquatic insects and highlights the importance of considering biodegradable nanoplastic aging in risk assessments.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xinghui Xia
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Wei Huang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yang Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xiaohan Lin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yao Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Zhifeng Yang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China; Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China.
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Zhang J, Xia X, Ma C, Zhang S, Li K, Yang Y, Yang Z. Nanoplastics Affect the Bioaccumulation and Gut Toxicity of Emerging Perfluoroalkyl Acid Alternatives to Aquatic Insects ( Chironomus kiinensis): Importance of Plastic Surface Charge. ACS NANO 2024. [PMID: 38323841 DOI: 10.1021/acsnano.3c12009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Persistent organic pollutants (POPs) have been widely suggested as contributors to the aquatic insect biomass decline, and their bioavailability is affected by engineered particles. However, the toxicity effects of emerging ionizable POPs mediated by differentially charged engineered nanoparticles on aquatic insects are unknown. In this study, 6:2 chlorinated polyfluoroalkyl ether sulfonate (F-53B, an emerging perfluoroalkyl acid alternative) was selected as a model emerging ionizable POP; the effect of differentially charged nanoplastics (NPs, 50 nm, 0.5 g/kg) on F-53B bioaccumulation and gut toxicity to Chironomus kiinensis were investigated through histopathology, biochemical index, and gut microbiota analysis. The results showed that when the dissolved concentration of F-53B remained constant, the presence of NPs enhanced the adverse effects on larval growth, emergence, gut oxidative stress and inflammation induced by F-53B, and the enhancement caused by positively charged NP-associated F-53B was stronger than that caused by the negatively charged one. This was mainly because positively charged NPs, due to their greater adsorption capacity and higher bioavailable fraction of associated F-53B, increased the bioaccumulation of F-53B in larvae more significantly than negatively charged NPs. In addition, positively charged NPs interact more easily with gut biomembranes and microbes with a negative charge, further increasing the probability of F-53B interacting with gut biomembranes and microbiota and thereby aggravating gut damage and key microbial dysbacteriosis related to gut health. These findings demonstrate that the surface charge of NPs can regulate the bioaccumulation and toxicity of ionizable POPs to aquatic insects.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xinghui Xia
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Chuanxin Ma
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Shangwei Zhang
- Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhuhai 519087, China
| | - Kaixuan Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yingying Yang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Zhifeng Yang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
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Askelson KK, Spellman GM, Irwin D. Genomic divergence and introgression between cryptic species of a widespread North American songbird. Mol Ecol 2023; 32:6839-6853. [PMID: 37916530 DOI: 10.1111/mec.17169] [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: 11/23/2022] [Accepted: 09/20/2023] [Indexed: 11/03/2023]
Abstract
Analysis of genomic variation among related populations can sometimes reveal distinct species that were previously undescribed due to similar morphological appearances, and close examination of such cases can provide much insight regarding speciation. Genomic data can also reveal the role of reticulate evolution in differentiation and speciation. White-breasted nuthatches (Sitta carolinensis) are widely distributed North American songbirds that are currently classified as a single species but have been suspected to represent a case of cryptic speciation. Previous genetic analyses suggested four divergent groups, but it was unclear whether these represented multiple reproductively isolated species. Using extensive genomic sampling of over 350 white-breasted nuthatches from across North America and a new chromosome-level reference genome, we asked if white-breasted nuthatches are comprised of multiple species and whether introgression has occurred between divergent populations. Genomic variation of over 300,000 loci revealed four highly differentiated populations (Pacific, n = 45; Eastern, n = 23; Rocky Mountains North, n = 138; and Rocky Mountains South, n = 150) with geographic ranges that are adjacent. We observed a moderate degree of admixture between Rocky Mountain populations but only a small number of hybrids between the Rockies and the Eastern population. The rarity of hybrids together with high levels of differentiation between populations is supportive of populations having some level of reproductive isolation. Between populations, we show evidence for introgression from a divergent ghost lineage of white-breasted nuthatches into the Rocky Mountains South population, which is otherwise closely related to Rocky Mountains North. We conclude that white-breasted nuthatches are best considered at least three species and that ghost lineage introgression has contributed to differentiation between the two Rocky Mountain populations. White-breasted nuthatches provide a dramatic case of morphological similarity despite high genomic differentiation, and the varying levels of reproductive isolation among the four groups provide an example of the speciation continuum.
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Affiliation(s)
- Kenneth K Askelson
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature & Science, Denver, Colorado, USA
| | - Darren Irwin
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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Boero F, Mergeay J. Darwin's feathers: Eco-evolutionary biology, predictions and policy. ADVANCES IN MARINE BIOLOGY 2023; 95:91-111. [PMID: 37923540 DOI: 10.1016/bs.amb.2023.08.004] [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: 11/07/2023]
Abstract
The scientific community is often asked to predict the future state of the environment and, to do so, the structure (biodiversity) and the functions (ecosystem functioning) of the investigated systems must be described and understood. In his "handful of feathers" metaphor, Charles Darwin explained the difference between simple and predictable systems, obeying definite laws, and complex (and unpredictable) systems, featured by innumerable components and interactions among them. In order not to waste efforts in impossible enterprises, it is crucial to ascertain if accurate predictions are possible in a given domain, and to what extent they might be reliable. Since ecology and evolution (together forming "natural history") deal with complex historical systems that are extremely sensitive to initial conditions and to contingencies or 'black swans', it is inherently impossible to accurately predict their future states. Notwithstanding this impossibility, policy makers are asking the community of ecological and evolutionary biologists to predict the future. The struggle for funding induces many supposed naturalists to do so, also because other types of scientists (from engineers to modellers) are keen to sell predictions (usually in form of solutions) to policy makers that are willing to pay for them. This paper is a plea for bio-ecological realism. The "mission" of ecologists and evolutionary biologists (natural historians) is not to predict the future state of inherently unpredictable systems, but to convince policy makers that we must live with uncertainties. Natural history, however, can provide knowledge-based wisdom to face the uncertainties about the future. Natural historians produce scenarios that are of great help in figuring out how to manage our relationship with the rest of nature.
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Affiliation(s)
- Ferdinando Boero
- Fondazione Dohrn, Museo Darwin Dohrn, Villa Comunale, Napoli, Italy; CNR-IAS, Genova, Italy.
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Gaverstraat, Geraardsbergen, Belgium; Laboratory of Aquatic Ecology and Evolutionary Biology, KULeuven, Deberiotstraat, Leuven, Belgium
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Boyd JN, Baskauf C, Lindsay A, Anderson JT, Brzyski J, Cruse‐Sanders J. Phenotypic plasticity and genetic diversity shed light on endemism of rare Boechera perstellata and its potential vulnerability to climate warming. Ecol Evol 2023; 13:e10540. [PMID: 37720057 PMCID: PMC10502469 DOI: 10.1002/ece3.10540] [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: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/19/2023] Open
Abstract
The rapid pace of contemporary environmental change puts many species at risk, especially rare species constrained by limited capacity to adapt or migrate due to low genetic diversity and/or fitness. But the ability to acclimate can provide another way to persist through change. We compared the capacity of rare Boechera perstellata (Braun's rockcress) and widespread B. laevigata to acclimate to change. We investigated the phenotypic plasticity of growth, biomass allocation, and leaf morphology of individuals of B. perstellata and B. laevigata propagated from seed collected from several populations throughout their ranges in a growth chamber experiment to assess their capacity to acclimate. Concurrently, we assessed the genetic diversity of sampled populations using 17 microsatellite loci to assess evolutionary potential. Plasticity was limited in both rare B. perstellata and widespread B. laevigata, but differences in the plasticity of root traits between species suggest that B. perstellata may have less capacity to acclimate to change. In contrast to its widespread congener, B. perstellata exhibited no plasticity in response to temperature and weaker plastic responses to water availability. As expected, B. perstellata also had lower levels of observed heterozygosity than B. laevigata at the species level, but population-level trends in diversity measures were inconsistent due to high heterogeneity among B. laevigata populations. Overall, the ability of phenotypic plasticity to broadly explain the rarity of B. perstellata versus commonness of B. laevigata is limited. However, some contextual aspects of our plasticity findings compared with its relatively low genetic variability may shed light on the narrow range and habitat associations of B. perstellata and suggest its vulnerability to climate warming due to acclimatory and evolutionary constraints.
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Affiliation(s)
- Jennifer Nagel Boyd
- Department of Biology, Geology, and Environmental ScienceUniversity of Tennessee at ChattanoogaChattanoogaTennesseeUSA
| | - Carol Baskauf
- Department of BiologyAustin Peay State UniversityClarksvilleTennesseeUSA
| | - Annie Lindsay
- Department of BiologyAustin Peay State UniversityClarksvilleTennesseeUSA
| | - Jill T. Anderson
- Department of Genetics, Odum School of Ecology, Davison Life SciencesUniversity of GeorgiaAthensGeorgiaUSA
| | - Jessica Brzyski
- Department of BiologySeton Hill UniversityGreensburgPennsylvaniaUSA
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Zhou X, Lennon JT, Lu X, Ruan A. Anthropogenic activities mediate stratification and stability of microbial communities in freshwater sediments. MICROBIOME 2023; 11:191. [PMID: 37626433 PMCID: PMC10464086 DOI: 10.1186/s40168-023-01612-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/04/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND Freshwater sediment microbes are crucial decomposers that play a key role in regulating biogeochemical cycles and greenhouse gas emissions. They often exhibit a highly ordered structure along depth profiles. This stratification not only reflects redox effects but also provides valuable insights into historical transitions, as sediments serve as important archives for tracing environmental history. The Anthropocene, a candidate geological epoch, has recently garnered significant attention. However, the human impact on sediment zonation under the cover of natural redox niches remains poorly understood. Dam construction stands as one of the most far-reaching anthropogenic modifications of aquatic ecosystems. Here we attempted to identify the ecological imprint of damming on freshwater sediment microbiome. RESULTS We conducted a year-round survey on the sediment profiles of Lake Chaohu, a large shallow lake in China. Through depth-discrete shotgun metagenomics, metataxonomics, and geophysiochemical analyses, we unveiled a unique prokaryotic hierarchy shaped by the interplay of redox regime and historical damming (labeled by the 137Cs peak in AD 1963). Dam-induced initial differentiation was further amplified by nitrogen and methane metabolism, forming an abrupt transition governing nitrate-methane metabolic interaction and gaseous methane sequestration depth. Using a random forest algorithm, we identified damming-sensitive taxa that possess distinctive metabolic strategies, including energy-saving mechanisms, unique motility behavior, and deep-environment preferences. Moreover, null model analysis showed that damming altered microbial community assembly, from a selection-oriented deterministic process above to a more stochastic, dispersal-limited one below. Temporal investigation unveiled the rapid transition zone as an ecotone, characterized by high species richness, low community stability, and emergent stochasticity. Path analysis revealed the observed emergent stochasticity primarily came from the high metabolic flexibility, which potentially contributed to both ecological and statistical neutralities. CONCLUSIONS We delineate a picture in which dam-induced modifications in nutrient availability and sedimentation rates impact microbial metabolic activities and generate great changes in the community structure, assembly, and stability of the freshwater sediment microbiome. These findings reflect profound ecological and biogeochemical ramifications of human-Earth system interactions and help re-examine the mainstream views on the formation of sediment microbial stratification. Video Abstract.
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Affiliation(s)
- Xiaotian Zhou
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210024, China
- College of Hydrology and Water Resources, Hohai University, Nanjing, 210024, China
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Xiang Lu
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210024, China
- College of Hydrology and Water Resources, Hohai University, Nanjing, 210024, China
| | - Aidong Ruan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210024, China.
- College of Hydrology and Water Resources, Hohai University, Nanjing, 210024, China.
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Fishman FJ, Lennon JT. Macroevolutionary constraints on global microbial diversity. Ecol Evol 2023; 13:e10403. [PMID: 37560179 PMCID: PMC10408003 DOI: 10.1002/ece3.10403] [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: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Biologists have long sought to quantify the number of species on Earth. Often missing from these efforts is the contribution of microorganisms, the smallest but most abundant form of life on the planet. Despite recent large‐scale sampling efforts, estimates of global microbial diversity span many orders of magnitude. It is important to consider how speciation and extinction over the last 4 billion years constrain inventories of biodiversity. We parameterized macroevolutionary models based on birth–death processes that assume constant and universal speciation and extinction rates. The models reveal that richness beyond 1012 species is feasible and in agreement with empirical predictions. Additional simulations suggest that mass extinction events do not place hard limits on modern‐day microbial diversity. Together, our study provides independent support for a massive global‐scale microbiome while shedding light on the upper limits of life on Earth.
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Affiliation(s)
- Ford J. Fishman
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
| | - Jay T. Lennon
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
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Gu YF, Shu JP, Lu YJ, Shen H, Shao W, Zhou Y, Sun QM, Chen JB, Liu BD, Yan YH. Insights into cryptic speciation of quillworts in China. PLANT DIVERSITY 2023; 45:284-301. [PMID: 37397601 PMCID: PMC10311115 DOI: 10.1016/j.pld.2022.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/24/2022] [Accepted: 11/08/2022] [Indexed: 07/04/2023]
Abstract
Cryptic species are commonly misidentified because of high morphological similarities to other species. One group of plants that may harbor large numbers of cryptic species is the quillworts (Isoëtes spp.), an ancient aquatic plant lineage. Although over 350 species of Isoëtes have been reported globally, only ten species have been recorded in China. The aim of this study is to better understand Isoëtes species diversity in China. For this purpose, we systematically explored the phylogeny and evolution of Isoëtes using complete chloroplast genome (plastome) data, spore morphology, chromosome number, genetic structure, and haplotypes of almost all Chinese Isoëtes populations. We identified three ploidy levels of Isoëtes in China-diploid (2n = 22), tetraploid (2n = 44), and hexaploid (2n = 66). We also found four megaspore and microspore ornamentation types in diploids, six in tetraploids, and three in hexaploids. Phylogenetic analyses confirmed that I. hypsophila as the ancestral group of the genus and revealed that Isoëtes diploids, tetraploids, and hexaploids do not form monophyletic clades. Most individual species possess a single genetic structure; however, several samples have conflicting positions on the phylogenetic tree based on SNPs and the tree based on plastome data. All 36 samples shared 22 haplotypes. Divergence time analysis showed that I. hypsophila diverged in the early Eocene (∼48.05 Ma), and most other Isoëtes species diverged 3-20 Ma. Additionally, different species of Isoëtes were found to inhabit different water systems and environments along the Yangtze River. These findings provide new insights into the relationships among Isoëtes species in China, where highly similar morphologic populations may harbor many cryptic species.
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Affiliation(s)
- Yu-Feng Gu
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, 150025, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Jiang-Ping Shu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Yi-Jun Lu
- Zhejiang University City College, Hangzhou, 310015, China
| | - Hui Shen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Wen Shao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yan Zhou
- Jiande Xin'anjiang Forest Farm, Jiande, 311600, China
| | - Qi-Meng Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Jian-Bing Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Bao-Dong Liu
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, 150025, China
| | - Yue-Hong Yan
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
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12
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Biological Characteristics and Energy Metabolism of Migrating Insects. Metabolites 2023; 13:metabo13030439. [PMID: 36984878 PMCID: PMC10055822 DOI: 10.3390/metabo13030439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Through long-distance migration, insects not only find suitable breeding locations and increase the survival space and opportunities for the population but also facilitate large-scale material, energy, and information flow between regions, which is important in maintaining the stability of agricultural ecosystems and wider natural ecosystems. In this study, we summarize the changes in biological characteristics such as morphology, ovarian development, reproduction, and flight capability during the seasonal migration of the insect. In consideration of global research work, the interaction between flight and reproduction, the influence and regulation of the insulin-like and juvenile hormone on the flight and reproductive activities of migrating insects, and the types of energy substances, metabolic processes, and hormone regulation processes during insect flight are elaborated. This systematic review of the latest advances in the studies on insect migration biology and energy metabolism will help readers to better understand the biological behavior and regulation mechanism of the energy metabolism of insect migration.
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13
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Beaugrand G. Towards an Understanding of Large-Scale Biodiversity Patterns on Land and in the Sea. BIOLOGY 2023; 12:biology12030339. [PMID: 36979031 PMCID: PMC10044889 DOI: 10.3390/biology12030339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/25/2023]
Abstract
This review presents a recent theory named ‘macroecological theory on the arrangement of life’ (METAL). This theory is based on the concept of the ecological niche and shows that the niche-environment (including climate) interaction is fundamental to explain many phenomena observed in nature from the individual to the community level (e.g., phenology, biogeographical shifts, and community arrangement and reorganisation, gradual or abrupt). The application of the theory in climate change biology as well as individual and species ecology has been presented elsewhere. In this review, I show how METAL explains why there are more species at low than high latitudes, why the peak of biodiversity is located at mid-latitudes in the oceanic domain and at the equator in the terrestrial domain, and finally why there are more terrestrial than marine species, despite the fact that biodiversity has emerged in the oceans. I postulate that the arrangement of planetary biodiversity is mathematically constrained, a constraint we previously called ‘the great chessboard of life’, which determines the maximum number of species that may colonise a given region or domain. This theory also makes it possible to reconstruct past biodiversity and understand how biodiversity could be reorganised in the context of anthropogenic climate change.
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Affiliation(s)
- Grégory Beaugrand
- CNRS, Univ. Littoral Côte d'Opale, Univ. Lille, UMR 8187 LOG, F-62930 Wimereux, France
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14
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Liu Y, Xu C, Dong W, Chen X, Zhang W, Sun Y, Wang G, Wang Y, Zhou S. What determines plant species diversity along the Modern Silk Road in the east? IMETA 2023; 2:e74. [PMID: 38868351 PMCID: PMC10989921 DOI: 10.1002/imt2.74] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 06/14/2024]
Abstract
As primary producers, plants provide food, oxygen, and other resources for global ecosystems, and should therefore be given priority in biodiversity protection. Most biodiversity research focuses on biodiversity hotspots, while biodiversity coldspots, such as deserts, are largely ignored. We propose that the factors shaping plant species diversity differ between biodiversity hot spots and cold spots, especially for desert ecosystems. To test this hypothesis, we investigated plant species diversity along the Modern Silk Road in the Northwest China desert, an area characterized by low precipitation, scarce vegetation, a limited number of species, and variable human activities. Surface soil was sampled from 144 plots, environmental DNA (eDNA) was extracted from soil samples, and seed plant species were identified using DNA metabarcoding technology. A total of 671 seed plant species were detected, which was more diverse than indicated by plot survey data. Plant species diversity gradually decreased from east to west along the Silk Road. In this area, temperature determines plant species diversity more than precipitation. Additionally, human activity has altered plant species diversity by introducing crops and invasive plants and eliminating environmentally adapted indigenous plants. Our results demonstrate the potential of eDNA metabarcoding technology for plant species diversity surveying. Desert plants have adapted to dry environments by relying on underground water or utilizing occasional rainfall as ephemerals, which are often not visible during surface surveys because of their short aboveground life cycle but can be detected with eDNA metabarcoding technology. Groundwater maintenance and human activity control are recommended for plant species diversity conservation and desertification control.
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Affiliation(s)
- Yanlei Liu
- School of Landscape and Ecological EngineeringHebei University of EngineeringHandanChina
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Xun Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
- Hulunbuir UniversityHulunbuirChina
| | - Wen Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Yuzhe Sun
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Guohong Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Yufei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
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15
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Odonata (Insecta) Communities in a Lowland Mixed Mosaic Forest in Central Kalimantan, Indonesia. ECOLOGIES 2023. [DOI: 10.3390/ecologies4010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Assessing a taxon’s response to change in environmental variables is fundamental knowledge to understanding trends in species diversity, abundance, and distribution patterns. This is particularly needed on Borneo, where knowledge on Odonata populations in different habitats is poor. To address this gap, we present the first study investigating the relationship between morphology and species distribution of Odonata communities in a heath (kerangas)-dominated mixed-mosaic-lowland forest in southern Borneo. We sampled 250-m line transects in three habitat types: mixed peatcswamp, kerangas, and low-pole peatcswamp, with weekly surveys from December 2019 to February 2020. A total of 309 individuals were detected from 25 species. Anisoptera and Zygoptera diversity was the highest in mixed peatcswamp and lowest in low pole, while abundance was the highest in low pole and lowest in kerangas; with kerangas notably harboring a very small sample size. Odonata community assemblages differed most between mixed peat swamp and low pole. Morphological data were compared between suborders and habitats. Anisoptera showed significantly larger thoraces, hindwings, and hindwing-to-body ratio than Zygoptera. Anisoptera in low pole were significantly smaller in body, thorax, and hindwing compared to both kerangas and mixed peat swamp. Anisoptera showed a strong association with pools and Zygoptera with flowing water. Heterogeneity, habitat characteristics, presence of specialists, body size, and the interaction between species’ morphological traits and habitat characteristics likely explained the trends observed.
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16
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Kumar R, Gaur S, Agarwal M, Menon B, Goel N, Mrigpuri P, Spalgais S, Priya A, Kumar K, Meena R, Sankararaman N, Verma A, Gupta V, Sonal, Prakash A, Safwan MA, Behera D, Singh A, Arora N, Prasad R, Padukudru M, Kant S, Janmeja A, Mohan A, Jain V, Nagendra Prasad K, Nagaraju K, Goyal M. Indian Guidelines for diagnosis of respiratory allergy. INDIAN JOURNAL OF ALLERGY, ASTHMA AND IMMUNOLOGY 2023. [DOI: 10.4103/0972-6691.367373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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Rogers AD, Appeltans W, Assis J, Ballance LT, Cury P, Duarte C, Favoretto F, Hynes LA, Kumagai JA, Lovelock CE, Miloslavich P, Niamir A, Obura D, O'Leary BC, Ramirez-Llodra E, Reygondeau G, Roberts C, Sadovy Y, Steeds O, Sutton T, Tittensor DP, Velarde E, Woodall L, Aburto-Oropeza O. Discovering marine biodiversity in the 21st century. ADVANCES IN MARINE BIOLOGY 2022; 93:23-115. [PMID: 36435592 DOI: 10.1016/bs.amb.2022.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We review the current knowledge of the biodiversity of the ocean as well as the levels of decline and threat for species and habitats. The lack of understanding of the distribution of life in the ocean is identified as a significant barrier to restoring its biodiversity and health. We explore why the science of taxonomy has failed to deliver knowledge of what species are present in the ocean, how they are distributed and how they are responding to global and regional to local anthropogenic pressures. This failure prevents nations from meeting their international commitments to conserve marine biodiversity with the results that investment in taxonomy has declined in many countries. We explore a range of new technologies and approaches for discovery of marine species and their detection and monitoring. These include: imaging methods, molecular approaches, active and passive acoustics, the use of interconnected databases and citizen science. Whilst no one method is suitable for discovering or detecting all groups of organisms many are complementary and have been combined to give a more complete picture of biodiversity in marine ecosystems. We conclude that integrated approaches represent the best way forwards for accelerating species discovery, description and biodiversity assessment. Examples of integrated taxonomic approaches are identified from terrestrial ecosystems. Such integrated taxonomic approaches require the adoption of cybertaxonomy approaches and will be boosted by new autonomous sampling platforms and development of machine-speed exchange of digital information between databases.
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Affiliation(s)
- Alex D Rogers
- REV Ocean, Lysaker, Norway; Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom.
| | - Ward Appeltans
- Intergovernmental Oceanographic Commission of UNESCO, Oostende, Belgium
| | - Jorge Assis
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Lisa T Ballance
- Marine Mammal Institute, Oregon State University, Newport, OR, United States
| | | | - Carlos Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | - Fabio Favoretto
- Autonomous University of Baja California Sur, La Paz, Baja California Sur, Mexico
| | - Lisa A Hynes
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Joy A Kumagai
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt am Main, Germany
| | - Catherine E Lovelock
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Patricia Miloslavich
- Scientific Committee on Oceanic Research (SCOR), College of Earth, Ocean and Environment, University of Delaware, Newark, DE, United States; Departamento de Estudios Ambientales, Universidad Simón Bolívar, Venezuela & Scientific Committee for Oceanic Research (SCOR), Newark, DE, United States
| | - Aidin Niamir
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt am Main, Germany
| | | | - Bethan C O'Leary
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom; Department of Environment and Geography, University of York, York, United Kingdom
| | - Eva Ramirez-Llodra
- REV Ocean, Lysaker, Norway; Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Gabriel Reygondeau
- Yale Center for Biodiversity Movement and Global Change, Yale University, New Haven, CT, United States; Nippon Foundation-Nereus Program, Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
| | - Callum Roberts
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Yvonne Sadovy
- School of Biological Sciences, Swire Institute of Marine Science, The University of Hong Kong, Hong Kong
| | - Oliver Steeds
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Tracey Sutton
- Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, Dania Beach, FL, United States
| | | | - Enriqueta Velarde
- Instituto de Ciencias Marinas y Pesquerías, Universidad Veracruzana, Veracruz, Mexico
| | - Lucy Woodall
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom; Department of Zoology, University of Oxford, Oxford, United Kingdom
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18
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Large-scale genetic investigation of nematode diversity and their phylogenetic patterns in New Zealand's marine animals. Parasitology 2022; 149:1794-1809. [PMID: 36200520 PMCID: PMC10090774 DOI: 10.1017/s003118202200138x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nematodes constitute one of the most speciose metazoan groups on earth, and a significant proportion of them have parasitic life styles. Zooparasitic nematodes have zoonotic, commercial and ecological significance within natural systems. Due to their generally small size and hidden nature within their hosts, and the fact that species discrimination using traditional morphological characteristics is often challenging, their biodiversity is not well known, especially within marine ecosystems. For instance, the majority of New Zealand's marine animals have never been the subject of nematode studies, and many currently known nematodes in New Zealand await confirmation of their species identity with modern taxonomic techniques. In this study, we present the results of an extensive biodiversity survey and phylogenetic analyses of parasitic nematodes infecting New Zealand's marine animals. We used genetic data to differentiate nematodes to the lowest taxonomic level possible and present phylogenies of the dominant clades to illustrate their genetic diversity in New Zealand. Our findings reveal a high diversity of parasitic nematodes (23 taxa) infecting New Zealand's marine animals (62 of 94 free-living animal species investigated). The novel data collected here provide a solid baseline for future assessments of change in diversity and distribution of parasitic nematodes.
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19
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Hu J, Amor DR, Barbier M, Bunin G, Gore J. Emergent phases of ecological diversity and dynamics mapped in microcosms. Science 2022; 378:85-89. [PMID: 36201585 DOI: 10.1126/science.abm7841] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
From tropical forests to gut microbiomes, ecological communities host notably high numbers of coexisting species. Beyond high biodiversity, communities exhibit a range of complex dynamics that are difficult to explain under a unified framework. Using bacterial microcosms, we performed a direct test of theory predicting that simple community-level features dictate emergent behaviors of communities. As either the number of species or the strength of interactions increases, we show that microbial ecosystems transition between three distinct dynamical phases, from a stable equilibrium in which all species coexist to partial coexistence to emergence of persistent fluctuations in species abundances, in the order predicted by theory. Under fixed conditions, high biodiversity and fluctuations reinforce each other. Our results demonstrate predictable emergent patterns of diversity and dynamics in ecological communities.
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Affiliation(s)
- Jiliang Hu
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel R Amor
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthieu Barbier
- CIRAD, UMR PHIM, 34090 Montpellier, France.,PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Guy Bunin
- Department of Physics, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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20
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Leclerc MA, Guivarc'h L, Lazzari CR, Pincebourde S. Thermal tolerance of two Diptera that pollinate thermogenic plants. J Therm Biol 2022; 109:103339. [DOI: 10.1016/j.jtherbio.2022.103339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/06/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022]
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21
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Verpoorte R, Kim HK, Choi YH. Trivialities in metabolomics: Artifacts in extraction and analysis. Front Mol Biosci 2022; 9:972190. [PMID: 36158577 PMCID: PMC9493124 DOI: 10.3389/fmolb.2022.972190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
The aim of this review is to show the risks of artifact formation in metabolomics analyses. Metabolomics has developed in a major tool in system biology approaches to unravel the metabolic networks that are the basis of life. Presently TLC, LC-MS, GC-MS, MS-MS and nuclear magnetic resonance are applied to analyze the metabolome of all kind of biomaterials. These analytical methods require robust preanalytical protocols to extract the small molecules from the biomatrix. The quality of the metabolomics analyses depends on protocols for collecting and processing of the biomaterial, including the methods for drying, grinding and extraction. Also the final preparation of the samples for instrumental analysis is crucial for highly reproducible analyses. The risks of artifact formation in these steps are reviewed from the point of view of the commonly used solvents. Examples of various artifacts formed through chemical reactions between solvents or contaminations with functional groups in the analytes are discussed. These reactions involve, for example, the formation of esters, trans-esterifications, hemiacetal and acetal formation, N-oxidations, and the formation of carbinolamines. It concerns chemical reactions with hydroxyl-, aldehyde-, keto-, carboxyl-, ester-, and amine functional groups. In the analytical steps, artifacts in LC may come from the stationary phase or reactions of the eluent with analytes. Differences between the solvent of the injected sample and the LC-mobile phase may cause distortions of the retention of analytes. In all analytical methods, poorly soluble compounds will be in all samples at saturation level, thus hiding a potential marker function. Finally a full identification of compounds remains a major hurdle in metabolomics, it requires a full set of spectral data, including methods for confirming the absolute stereochemistry. The putative identifications found in supplemental data of many studies, unfortunately, often become “truly” identified compounds in papers citing these results. Proper validation of the protocols for preanalytical and analytical procedures is essential for reproducible analyses in metabolomics.
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Affiliation(s)
- R. Verpoorte
- Natural Products Laboratory, Institute of Biology Leiden, Leiden University, Leiden, The, Netherlands
- *Correspondence: R. Verpoorte,
| | - H. K. Kim
- Natural Products Laboratory, Institute of Biology Leiden, Leiden University, Leiden, The, Netherlands
| | - Y. H. Choi
- Natural Products Laboratory, Institute of Biology Leiden, Leiden University, Leiden, The, Netherlands
- College of Pharmacy, Kyung Hee Univeristy, Seoul, South Korea
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22
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Wu MH, Xue K, Wei PJ, Jia YL, Zhang Y, Chen SY. Soil microbial distribution and assembly are related to vegetation biomass in the alpine permafrost regions of the Qinghai-Tibet Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155259. [PMID: 35452733 DOI: 10.1016/j.scitotenv.2022.155259] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/09/2022] [Accepted: 04/09/2022] [Indexed: 06/14/2023]
Abstract
It is generally believed that there is a vegetation succession sequence from alpine marsh meadow to desert in the alpine ecosystem of the Qinghai-Tibet Plateau. However, we still have a limited understanding about distribution patterns and community assemblies of microorganisms' response to such vegetation changes. Hence, across a gradient represented by three types of alpine vegetation from swamp meadow to meadow to steppe, the soil bacterial, fungal and archaeal diversity was evaluated and then associated with their assembly processes, and glacier foreland vegetation was also surveyed as a case out of this gradient. Vegetation biomass was found to decrease significantly along the vegetation gradient. In contrast to irregular shifts in alpha diversity, bacterial and fungal beta diversities that were dominated by species replacement components (71.07-79.08%) significantly increased with the decreasing gradient in vegetation biomass (P < 0.05). These trends of increase were also found in the extent of stochastic bacterial and fungal assembly. Moreover, an increase in microbial beta diversity but a decrease in beta nearest taxon index were observed along with increased discrepancy in vegetation biomass (P < 0.001). Stepwise regression analyses and structural equation models suggested that vegetation biomass was the major variable that was related to microbial distribution and community assembly, and there might be associations between the dominance of species replacements and stochastic assembly. These findings enhanced our recognition of the relationship between vegetation and soil microorganisms and would facilitate the development of vegetation-microbe feedback models in alpine ecosystems.
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Affiliation(s)
- Ming-Hui Wu
- Cryosphere and Eco-Environment Research Station of Shule River Headwaters, National Field Science Observation and Research Station of Yulong Snow Mountain Cryosphere and Sustainable Development, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Xue
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pei-Jie Wei
- Cryosphere and Eco-Environment Research Station of Shule River Headwaters, National Field Science Observation and Research Station of Yulong Snow Mountain Cryosphere and Sustainable Development, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying-Lan Jia
- Cryosphere and Eco-Environment Research Station of Shule River Headwaters, National Field Science Observation and Research Station of Yulong Snow Mountain Cryosphere and Sustainable Development, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- Long-term National Scientific Research Base of the Qilian Mountain National Park, Xining, Qinghai 810000, China
| | - Sheng-Yun Chen
- Cryosphere and Eco-Environment Research Station of Shule River Headwaters, National Field Science Observation and Research Station of Yulong Snow Mountain Cryosphere and Sustainable Development, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China; Long-term National Scientific Research Base of the Qilian Mountain National Park, Xining, Qinghai 810000, China.
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23
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Walton K, Scarsbrook L, Mitchell KJ, Verry AJF, Marshall BA, Rawlence NJ, Spencer HG. Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone. Mol Ecol Resour 2022; 23:118-130. [PMID: 35951485 PMCID: PMC10087340 DOI: 10.1111/1755-0998.13696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/15/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Abstract
Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near-complete mitogenomes from 22 specimens including 12 dry-preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra-short fragments and hybridization-capture of single-stranded DNA libraries. Phylogenetic analyses revealed three major, well-supported clades comprising samples from: 1) the Three Kings Islands; 2) the Auckland, Chatham and Antipodes Islands; and 3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our non-reliance on freshly collected or ethanol-preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult-to-sample populations. Broader application of these comparatively cost-effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research.
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Affiliation(s)
- Kerry Walton
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand
| | - Lachie Scarsbrook
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand.,Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, 1 South Parks Road, OX1 3TG, University of Oxford, Oxford, United Kingdom
| | - Kieren J Mitchell
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand
| | - Alexander J F Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand.,Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Bruce A Marshall
- Museum of New Zealand Te Papa Tongarewa, 169 Tory St, Te Aro, 6011, Wellington, New Zealand
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand
| | - Hamish G Spencer
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Box 56, Dunedin 9054, PO, New Zealand
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24
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Novel Sources of Bioactive Molecules: Gut Microbiome of Species Routinely Exposed to Microorganisms. Vet Sci 2022; 9:vetsci9080380. [PMID: 35893773 PMCID: PMC9331562 DOI: 10.3390/vetsci9080380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The majority of antibiotics available in the market are produced by bacteria isolated from soil. However, the low-hanging fruit has been picked; hence, there is a need to mine bacteria from unusual sources. With this in mind, it is important to note that animals and pests, such as cockroaches, snake, crocodiles, water monitor lizards, etc., come across pathogenic bacteria regularly, yet flourish in contaminated environments. These species must have developed methods to defend themselves against pathogens. Besides the immunity they may confer, bacteria associated with animals/pests may offer a potential source of novel antibacterial agents. This paper discusses the current knowledge of bacteria isolated from land and marine animals with antibacterial properties and proposes untapped sources for the isolation of bacteria to mine potentially novel antibiotic molecules. Abstract The development of novel bioactive molecules is urgently needed, especially with increasing fatalities occurring due to infections by bacteria and escalating numbers of multiple-drug-resistant bacteria. Several lines of evidence show that the gut microbiome of cockroaches, snakes, crocodiles, water monitor lizards, and other species may possess molecules that are bioactive. As these animals are routinely exposed to a variety of microorganisms in their natural environments, it is likely that they have developed methods to counter these microbes, which may be a contributing factor in their persistence on the planet for millions of years. In addition to the immune system, the gut microbiota of a host may thwart colonization of the gastro-intestine by pathogenic and/or foreign microorganisms through two mechanisms: (i) production of molecules with antibacterial potential targeting foreign microorganisms, or (ii) production of molecules that trigger host immunity targeting foreign microorganisms that penetrate the host. Herein, we discuss and deliberate on the current literature examining antibacterial activities that stem from the gut bacteria of animals such as crocodiles, cockroaches, and water monitor lizards, amongst other interesting species, which likely encounter a plethora of microorganisms in their natural environments. The overall aim is to unveil a potential library of novel bioactive molecules for the benefit of human health and for utilization against infectious diseases.
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Doherty JF, Matthews BJ. Host Manipulation, Gene Editing, and Non-Traditional Model Organisms: A New Frontier for Behavioral Research? FRONTIERS IN INSECT SCIENCE 2022; 2:938644. [PMID: 38468779 PMCID: PMC10926399 DOI: 10.3389/finsc.2022.938644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/13/2022] [Indexed: 03/13/2024]
Abstract
Insects and parasites dominate the biosphere, in terms of known biodiversity and mode of life, respectively. Consequently, insects play a part in many host-parasite systems, either as parasite, host, or both. Moreover, a lot of these systems involve adaptive parasite-induced changes of host phenotype (typically behavior or morphology), which is commonly known as host manipulation. While many host manipulation systems have been described within the last few decades, the proximate mechanisms that underpin host phenotypic change are still largely unknown. Given the intimate co-evolutionary history of host-parasite systems, teasing apart the intricate network of biochemical reactions involved in host manipulation requires the integration of various complementary technologies. In this perspective, we stress the importance of multidisciplinary research on host manipulation, such as high-throughput sequencing methods (genomics and transcriptomics) to search for candidate mechanisms that are activated during a manipulation event. Then, we argue that gene editing technologies, specifically the CRISPR-Cas9 system, are a powerful way to test for the functional roles of candidate mechanisms, in both the parasite and the host. Finally, given the sheer diversity of unique host-parasite systems discovered to date, there is indeed a tremendous potential to create novel non-traditional model systems that could greatly expand our capacity to test the fundamental aspects of behavior and behavioral regulation.
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Abstract
Biological taxonomy rests on a long tail of publications spanning nearly three centuries. Not only is this literature vital to resolving disputes about taxonomy and nomenclature, for many species it represents a key source-indeed sometimes the only source-of information about that species. Unlike other disciplines such as biomedicine, the taxonomic community lacks a centralised, curated literature database (the "bibliography of life"). This article argues that Wikidata can be that database as it has flexible and sophisticated models of bibliographic information, and an active community of people and programs ("bots") adding, editing, and curating that information.
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Affiliation(s)
- Roderic D. M. Page
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
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27
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28
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Novaes RLM, Wilson DE, Moratelli R. Catalogue of primary types of Neotropical Myotis (Chiroptera, Vespertilionidae). Zookeys 2022; 1105:127-164. [PMID: 36760324 PMCID: PMC9848626 DOI: 10.3897/zookeys.1105.85055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/06/2022] [Indexed: 11/12/2022] Open
Abstract
Myotis comprises a diverse group of vespertilionid bats with worldwide distribution. Neotropical Myotis have an accentuated phenotypic conservatism, which makes species delimitation and identification difficult, hindering our understanding of the diversity, distribution, and phylogenetic relationships of taxa. To encourage new systematic reviews of the genus, a catalogue of the primary types and names is presented, current and in synonymy, for Neotropical Myotis. Currently 33 valid species (and three subspecies) are recognized, and their primary types are deposited in 12 scientific collections in the USA (30 types), Brazil (two types), England (two types), and France (one type). The names of 29 Neotropical Myotis species currently in synonymy were found. However, it is possible that some synonyms represent independent evolutionary lineages, considering recent results provided by taxonomic revisions.
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Affiliation(s)
- Roberto Leonan M. Novaes
- Fundação Oswaldo Cruz, Fiocruz Mata Atlântica, R. Sampaio Correa s/n, Taquara, 22713-560, Rio de Janeiro, BrazilFundação Oswaldo Cruz, Fiocruz Mata AtlânticaRio de JaneiroBrazil
| | - Don E. Wilson
- Smithsonian Institution, National Museum of Natural History, Division of Mammals. 10th St. & Constitution Ave. NW, 20013-7012, Washington, DC, USANational Museum of Natural HistoryWashington, DCUnited States of America
| | - Ricardo Moratelli
- Fundação Oswaldo Cruz, Fiocruz Mata Atlântica, R. Sampaio Correa s/n, Taquara, 22713-560, Rio de Janeiro, BrazilFundação Oswaldo Cruz, Fiocruz Mata AtlânticaRio de JaneiroBrazil
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Sun L, Deng R, Liu J, Lai M, Wu J, Liu X, Shahid MQ. An overview of sucrose transporter (SUT) genes family in rice. Mol Biol Rep 2022; 49:5685-5695. [PMID: 35699859 DOI: 10.1007/s11033-022-07611-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/17/2022] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Photosynthesis provides the energy basis for the life activities of plants by producing organic compounds, mainly sugar. As the main energy form of photosynthesis, sugar affects the growth and development of plants. During long-distance transportation, sucrose is the main form of transportation. The rate of sugar transport and the allocation of carbohydrates affect the biomass of crops and are closely related to the reproductive growth of crops. MAIN TEXT The transportation of sugar is divided into active transportation and passive transportation. So how does the sucrose transporters (SUT) genes, which are the main carriers of sucrose in active transportation, affect the performance of rice agronomic traits is still to be explored. In this article, we describe the structure of inflorescence and review the transport forms and metabolic processes of sucrose in rice, such as how CO2 is fixed, carbohydrate assimilation, and transport of organic matter. Sucrose transporters exhibited remarkable effects on the development of reproductive organs in rice. CONCLUSIONS Here, the effects of different factors, such as the effects of anthers morphology on starch enrichment of pollen, effects of biotic and abiotic factors on sucrose transporters, effects of changes in trace elements on sucrose transporters, were discussed. Moreover, the regulation of transcription or translation level provides ideas for future research on sucrose transporters.
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Affiliation(s)
- Lixia Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Ruilian Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jingwen Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Mingyu Lai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China. .,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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Hugot JP, Feliu C, Ribas A. Human parasites as tracers of the evolution of their hosts. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 100:105262. [PMID: 35245684 DOI: 10.1016/j.meegid.2022.105262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Because parasite data reveal essential information about the behavior and history of their hosts, it is possible to use them as tracers of host evolution. A table built from the analysis of the data contained in the book by Ashford and Crewe "The Parasites of Homo sapiens" allows counting and cross comparing the parasites according to the main descriptors used by the authors: Taxonomic groups, for each group number of parasites species identified in humans; Status, numbers of reported human cases and their dispersion; Geographic distribution, parasite specific richness recorded in biogeographic regions; Habitat, parasite location in or on the human body; Transmission, contamination pathways to man; Hosts, non-human hosts, which have a role in the maintenance of a parasite; Host-specificity status, relative role of man or other hosts in the maintenance of parasite populations. A strong positive correlation is observed between the number of parasites species recorded in humans and the global parasite species richness for each taxonomic group. About 74% of the parasites recorded in humans are rare, sporadic or nowhere common; 10% only are common or abundant worldwide. The Palearctic exhibits the highest parasite species diversity; the Oriental, Nearctic, Neotropical and Aethiopian regions have roughly similar richness values; the Australian Region is the poorest. Earliest domesticated animals, such as dog, cat, cattle or pig, share more parasite species with Humans than tardily domesticated as horse, rabbit or camel. More than one third of our parasites have elected our alimentary canal as a home and about two third are using the digestive tract path for contamination. Time of occupancy of new territories, diversity in feeding habits and commensalism with other animals, widely explain Human particular parasite richness. As suggested by the authors: "There must be few parasitic species which have never had the opportunity to infect a human".
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Affiliation(s)
- Jean-Pierre Hugot
- Muséum National d'Histoire Naturelle, ISYEB, MNHN, CNRS (UMR 7205), UPMC, EPHE, UA, 55, rue Buffon, F-75231 Paris, France.
| | - Carlos Feliu
- IRBio (Institut de Recerca de la Biodiversitat, Universitat de Barcelona), Avda. Diagonal, s/n, 08028 Barcelona, Spain.
| | - Alexis Ribas
- Parasitology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Science, IRBio (Research Institute of Biodiversity), University of Barcelona, Barcelona, Spain.
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31
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Bank S, Bradler S. A second view on the evolution of flight in stick and leaf insects (Phasmatodea). BMC Ecol Evol 2022; 22:62. [PMID: 35549660 PMCID: PMC9097326 DOI: 10.1186/s12862-022-02018-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 04/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The re-evolution of complex characters is generally considered impossible, yet, studies of recent years have provided several examples of phenotypic reversals shown to violate Dollo's law. Along these lines, the regain of wings in stick and leaf insects (Phasmatodea) was hypothesised to have occurred several times independently after an ancestral loss, a scenario controversially discussed among evolutionary biologists due to overestimation of the potential for trait reacquisition as well as to the lack of taxonomic data. RESULTS We revisited the recovery of wings by reconstructing a phylogeny based on a comprehensive taxon sample of over 500 representative phasmatodean species to infer the evolutionary history of wings. We additionally explored the presence of ocelli, the photoreceptive organs used for flight stabilisation in winged insects, which might provide further information for interpreting flight evolution. Our findings support an ancestral loss of wings and that the ancestors of most major lineages were wingless. While the evolution of ocelli was estimated to be dependent on the presence of (fully-developed) wings, ocelli are nevertheless absent in the majority of all examined winged species and only appear in the members of few subordinate clades, albeit winged and volant taxa are found in every euphasmatodean lineage. CONCLUSION In this study, we explored the evolutionary history of wings in Phasmatodea and demonstrate that the disjunct distribution of ocelli substantiates the hypothesis on their regain and thus on trait reacquisition in general. Evidence from the fossil record as well as future studies focussing on the underlying genetic mechanisms are needed to validate our findings and to further assess the evolutionary process of phenotypic reversals.
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Affiliation(s)
- Sarah Bank
- Department of Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany.
| | - Sven Bradler
- Department of Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
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32
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Boyd JN, Odell J, Cruse‐Sanders J, Rogers W, Anderson JT, Baskauf C, Brzyski J. Phenotypic plasticity and genetic diversity elucidate rarity and vulnerability of an endangered riparian plant. Ecosphere 2022. [DOI: 10.1002/ecs2.3996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jennifer Nagel Boyd
- Department of Biology, Geology, and Environmental Science University of Tennessee at Chattanooga Chattanooga Tennessee USA
| | - Jared Odell
- Department of Biology, Geology, and Environmental Science University of Tennessee at Chattanooga Chattanooga Tennessee USA
| | - Jennifer Cruse‐Sanders
- Department of Genetics Odum School of Ecology, Davison Life Sciences, University of Georgia Athens Georgia USA
| | - Will Rogers
- Department of Biology, Geology, and Environmental Science University of Tennessee at Chattanooga Chattanooga Tennessee USA
- State Botanical Garden of Georgia University of Georgia Athens Georgia USA
| | - Jill T. Anderson
- Department of Biology, Geology, and Environmental Science University of Tennessee at Chattanooga Chattanooga Tennessee USA
- Department of Genetics Odum School of Ecology, Davison Life Sciences, University of Georgia Athens Georgia USA
- State Botanical Garden of Georgia University of Georgia Athens Georgia USA
| | - Carol Baskauf
- Department of Biology Austin Peay State University Clarksville Tennessee USA
| | - Jessica Brzyski
- Department of Biology Seton Hill University Greensburg Pennsylvania USA
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33
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Wei DP, Gentekaki E, Hyde KD, Xiao YP, Luangharn T, Tian Q, Wang YB, Lumyong S. https://invertebratefungi.org/: an expert-curated web-based platform for the identification and classification of invertebrate-associated fungi and fungus-like organisms. Database (Oxford) 2022; 2022:6562128. [PMID: 35363307 PMCID: PMC9216569 DOI: 10.1093/database/baac021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/17/2022] [Accepted: 03/21/2022] [Indexed: 11/14/2022]
Abstract
Fungi are the major decomposers in terrestrial and aquatic ecosystems, playing essential roles in biogeochemical cycles and food webs. The Fungi kingdom encompasses a diverse array of taxa that often form intimate relationships with other organisms, including plants, insects, algae, cyanobacteria and even other fungi. Fungal parasites of insects are known as entomopathogenic fungi and are the causative agents of serious disease and/or mortality of their hosts. Entomopathogens produce distinct metabolic compounds with roles in pathogenicity, virulence and host–parasite interactions. Thus, the potential of discovering new bioactive compounds useful in biocontrol and pharmaceutical industries is high. Given the significance of entomopathogenic fungi, the rapid research advances and the increased interest, it has become necessary to organize all available and incoming data. The website https://invertebratefungi.org/ has been developed to serve this purpose by gathering and updating entomopathogenic genera/species information. Notes of entomopathogenic genera will be provided with emphasis on their taxonomic status. Information on other invertebrates, such as rotifers, will also be included. Descriptions, photographic plates, information on distribution and host (where applicable) along with molecular data and other interesting details will also be provided. The website is easily and freely accessible to users. Instructions concerning the platform architecture and functionality of the website are introduced herein. The platform is currently being expanded and will be continuously updated as part of the effort to enrich knowledge on this group of fungi. Database URL: https://invertebratefungi.org/
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Affiliation(s)
- De-Ping Wei
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Panlong District, Kunming, Yunnan, P.R. 650201, China.,Center of Excellence in Fungal Research (CEFR), Mae Fah Luang University, Muang District, Chiang Rai 57100, Thailand.,Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Mueang Chiang Mai, Chiang Mai 50200, Thailand
| | - Eleni Gentekaki
- Center of Excellence in Fungal Research (CEFR), Mae Fah Luang University, Muang District, Chiang Rai 57100, Thailand.,School of Science, Mae Fah Luang University, Muang District, Chiang Rai 57100, Thailand
| | - Kevin D Hyde
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Panlong District, Kunming, Yunnan, P.R. 650201, China.,Center of Excellence in Fungal Research (CEFR), Mae Fah Luang University, Muang District, Chiang Rai 57100, Thailand.,Innovative Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Haizhu District, Guangzhou 510225, P.R. China.,Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Mueang Chiang Mai, Chiang Mai 50200, Thailand
| | - Yuan-Pin Xiao
- Center of Excellence in Fungal Research (CEFR), Mae Fah Luang University, Muang District, Chiang Rai 57100, Thailand.,School of Science, Mae Fah Luang University, Muang District, Chiang Rai 57100, Thailand
| | - Thatsanee Luangharn
- Center of Excellence in Fungal Research (CEFR), Mae Fah Luang University, Muang District, Chiang Rai 57100, Thailand
| | - Qing Tian
- Center of Excellence in Fungal Research (CEFR), Mae Fah Luang University, Muang District, Chiang Rai 57100, Thailand.,School of Science, Mae Fah Luang University, Muang District, Chiang Rai 57100, Thailand
| | - Yuan-Bing Wang
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Wuhua District, Yunnan, P.R. 650091, China
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Mueang Chiang Mai, Chiang Mai 50200, Thailand.,Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Mueang Chiang Mai, Chiang Mai 50200, Thailand.,Academy of Science, The Royal Society of Thailand, Dusit District, Bangkok 10300, Thailand
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34
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Ritchie AM, Hua X, Bromham L. Diversification Rate is Associated with Rate of Molecular Evolution in Ray-Finned Fish (Actinopterygii). J Mol Evol 2022; 90:200-214. [PMID: 35262772 PMCID: PMC8975766 DOI: 10.1007/s00239-022-10052-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 02/24/2022] [Indexed: 10/27/2022]
Abstract
Understanding the factors that drive diversification of taxa across the tree of life is a key focus of macroevolutionary research. While the effects of life history, ecology, climate and geography on diversity have been studied for many taxa, the relationship between molecular evolution and diversification has received less attention. However, correlations between rates of molecular evolution and diversification rate have been detected in a range of taxa, including reptiles, plants and birds. A correlation between rates of molecular evolution and diversification rate is a prediction of several evolutionary theories, including the evolutionary speed hypothesis which links variation in mutation rates to differences in speciation rates. If it is widespread, such correlations could also have significant practical impacts, if they are not adequately accounted for in phylogenetic inference of evolutionary rates and timescales. Ray-finned fish (Actinopterygii) offer a prime target to test for this relationship due to their extreme variation in clade size suggesting a wide range of diversification rates. We employ both a sister-pairs approach and a whole-tree approach to test for correlations between substitution rate and net diversification. We also collect life history and ecological trait data and account for potential confounding factors including body size, latitude, max depth and reef association. We find evidence to support a relationship between diversification and synonymous rates of nuclear evolution across two published backbone phylogenies, as well as weak evidence for a relationship between mitochondrial nonsynonymous rates and diversification at the genus level.
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Affiliation(s)
- Andrew M Ritchie
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia. .,Research School of Biological Sciences, Australian National University, Robertson Building, 134 Linnaeus Way, Canberra, ACT 2600, Australia.
| | - Xia Hua
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia.,Mathematical Sciences Institute, Australian National University, Canberra, ACT 2600, Australia
| | - Lindell Bromham
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia
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35
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Kwak HJ, Lee SG, Park SC, Kim JH, Weisblat DA, Park C, Cho SJ. Head transcriptome profiling of glossiphoniid leech ( Helobdella austinensis) reveals clues about proboscis development. Open Biol 2022; 12:210298. [PMID: 35232253 PMCID: PMC8889196 DOI: 10.1098/rsob.210298] [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] [Indexed: 01/09/2023] Open
Abstract
Cephalization refers to the evolutionary trend towards the concentration of neural tissues, sensory organs, mouth and associated structures at the front end of bilaterian animals. Comprehensive studies on gene expression related to the anterior formation in invertebrate models are currently lacking. In this study, we performed de novo transcriptional profiling on a proboscis-bearing leech (Helobdella austinensis) to identify differentially expressed genes (DEGs) in the anterior versus other parts of the body, in particular to find clues as to the development of the proboscis. Between the head and the body, 132 head-specific DEGs were identified, of which we chose 11 to investigate their developmental function during embryogenesis. Analysis of the spatial expression of these genes using in situ hybridization showed that they were characteristically expressed in the anterior region of the developing embryo, including the proboscis. Our results provide information on the genes related to head formation and insights into the function of proboscis-related genes during organogenesis with the potential roles of genes not yet characterized.
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Affiliation(s)
- Hee-Jin Kwak
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea,Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Sung-Gwon Lee
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Soon Cheol Park
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jung-Hyeuk Kim
- Wildlife Disease Response Team, National Institute of Wildlife Disease Control and Prevention, Incheon 22689, Republic of Korea
| | - David A. Weisblat
- Department of Molecular and Cell Biology, University of California, 385 Weill Hall, Berkeley, CA 94720-3200, USA
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
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36
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Lanz-Mendoza H, Contreras-Garduño J. Innate immune memory in invertebrates: Concept and potential mechanisms. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 127:104285. [PMID: 34626688 DOI: 10.1016/j.dci.2021.104285] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/19/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
Invertebrates are the protagonists of a recent paradigm shift because they now show that vertebrates are not the only group with immune memory. This review discusses the concept of immune priming, its characteristics, and differences with trained immunity and immune enhancement. We include an update of the current status of immune priming within generations in different groups of invertebrates which now include work in 5 Phyla: Ctenophora, Cnidaria, Mollusca, Nematoda, and Arthropoda. Clearly, few Phyla have been studied. We also resume and discuss the effector mechanism related to immune memory, including integrating viral elements into the genome, endoreplication, and epigenetics. The roles of other elements are incorporated, such as hemocytes, immune pathways, and metabolisms. We conclude that taking care of the experimental procedure will discern if results provide or do not support the invertebrates' immune memory and that regarding mechanisms, indeed, there are no studies on the immune memory mechanisms, this is how specificity is reached, and how and where the immune memory is stored and how is recall upon subsequent encounters. Finally, we discuss the possibility of having more than one mechanism working in different groups of invertebrates depending on the environmental conditions.
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Affiliation(s)
- Humberto Lanz-Mendoza
- Centro de Investigaciones sobre Enfermedades Infecciosas, INSP, Cuernavaca, Morelos, Mexico.
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37
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Vorburger C. Defensive Symbionts and the Evolution of Parasitoid Host Specialization. ANNUAL REVIEW OF ENTOMOLOGY 2022; 67:329-346. [PMID: 34614366 DOI: 10.1146/annurev-ento-072621-062042] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Insect host-parasitoid interactions abound in nature and are characterized by a high degree of host specialization. In addition to their behavioral and immune defenses, many host species rely on heritable bacterial endosymbionts for defense against parasitoids. Studies on aphids and flies show that resistance conferred by symbionts can be very strong and highly specific, possibly as a result of variation in symbiont-produced toxins. I argue that defensive symbionts are therefore an important source of diversifying selection, promoting the evolution of host specialization by parasitoids. This is likely to affect the structure of host-parasitoid food webs. I consider potential changes in terms of food web complexity, although the nature of these effects will also be influenced by whether maternally transmitted symbionts have some capacity for lateral transfer. This is discussed in the light of available evidence for horizontal transmission routes. Finally, I propose that defensive mutualisms other than microbial endosymbionts may also exert diversifying selection on insect parasitoids.
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Affiliation(s)
- Christoph Vorburger
- Department of Aquatic Ecology, Eawag, 8600 Dübendorf, Switzerland;
- Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
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38
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Håkansson J, Jiang W, Xue Q, Zheng X, Ding M, Agarwal AA, Elemans CPH. Aerodynamics and motor control of ultrasonic vocalizations for social communication in mice and rats. BMC Biol 2022; 20:3. [PMID: 34996429 PMCID: PMC8742360 DOI: 10.1186/s12915-021-01185-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 11/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rodent ultrasonic vocalizations (USVs) are crucial to their social communication and a widely used translational tool for linking gene mutations to behavior. To maximize the causal interpretation of experimental treatments, we need to understand how neural control affects USV production. However, both the aerodynamics of USV production and its neural control remain poorly understood. RESULTS Here, we test three intralaryngeal whistle mechanisms-the wall and alar edge impingement, and shallow cavity tone-by combining in vitro larynx physiology and individual-based 3D airway reconstructions with fluid dynamics simulations. Our results show that in the mouse and rat larynx, USVs are produced by a glottal jet impinging on the thyroid inner wall. Furthermore, we implemented an empirically based motor control model that predicts motor gesture trajectories of USV call types. CONCLUSIONS Our results identify wall impingement as the aerodynamic mechanism of USV production in rats and mice. Furthermore, our empirically based motor control model shows that both neural and anatomical components contribute to USV production, which suggests that changes in strain specific USVs or USV changes in disease models can result from both altered motor programs and laryngeal geometry. Our work provides a quantitative neuromechanical framework to evaluate the contributions of brain and body in shaping USVs and a first step in linking descending motor control to USV production.
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Affiliation(s)
- Jonas Håkansson
- Department of Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Weili Jiang
- Department of Mechanical Engineering, University of Maine, Orono, ME, 04469, USA
| | - Qian Xue
- Department of Mechanical Engineering, University of Maine, Orono, ME, 04469, USA
| | - Xudong Zheng
- Department of Mechanical Engineering, University of Maine, Orono, ME, 04469, USA
| | - Ming Ding
- Department of Orthopaedic Surgery and Traumatology, Odense University Hospital, 5000, Odense C, Denmark
- Department of Clinical Research, University of Southern Denmark, 5000, Odense C, Denmark
| | - Anurag A Agarwal
- Department of Engineering, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Coen P H Elemans
- Department of Biology, University of Southern Denmark, 5230, Odense M, Denmark.
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Marschalek DA, Deutschman DH. Differing insect communities and reduced decomposition rates suggest compromised ecosystem functioning in urban preserves of southern California. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2021.e01996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Experimental evidence for neonicotinoid driven decline in aquatic emerging insects. Proc Natl Acad Sci U S A 2021; 118:2105692118. [PMID: 34697235 PMCID: PMC8612350 DOI: 10.1073/pnas.2105692118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 11/18/2022] Open
Abstract
Survey data show a large-scale decline in insects. This global decline is often linked to human actions in intensive agricultural areas. To investigate whether this decline has a causal relationship with neonicotinoid insecticides, we performed an outdoor experiment with representative surface water concentrations of the neonicotinoid thiacloprid. We exposed naturally formed aquatic communities to increasing neonicotinoid concentrations and monitored insect emergence during a 3-mo period. We show that increasing neonicotinoid concentrations strongly decreased the abundance and biomass of five major insect orders that together comprised >99% of the 55,574 collected insects as well as the diversity of the most species-rich freshwater family, thus showing a causal relation between insect decline and neonicotinoids. There is an ongoing unprecedented loss in insects, both in terms of richness and biomass. The usage of pesticides, especially neonicotinoid insecticides, has been widely suggested to be a contributor to this decline. However, the risks of neonicotinoids to natural insect populations have remained largely unknown due to a lack of field-realistic experiments. Here, we used an outdoor experiment to determine effects of field-realistic concentrations of the commonly applied neonicotinoid thiacloprid on the emergence of naturally assembled aquatic insect populations. Following application, all major orders of emerging aquatic insects (Coleoptera, Diptera, Ephemeroptera, Odonata, and Trichoptera) declined strongly in both abundance and biomass. At the highest concentration (10 µg/L), emergence of most orders was nearly absent. Diversity of the most species-rich family, Chironomidae, decreased by 50% at more commonly observed concentrations (1 µg/L) and was generally reduced to a single species at the highest concentration. Our experimental findings thereby showcase a causal link of neonicotinoids and the ongoing insect decline. Given the urgency of the insect decline, our results highlight the need to reconsider the mass usage of neonicotinoids to preserve freshwater insects as well as the life and services depending on them.
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Bilinski T, Bylak A, Kukuła K, Zadrag-Tecza R. Senescence as a trade-off between successful land colonisation and longevity: critical review and analysis of a hypothesis. PeerJ 2021; 9:e12286. [PMID: 34760360 PMCID: PMC8570163 DOI: 10.7717/peerj.12286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/20/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Most common terrestrial animal clades exhibit senescence, suggesting strong adaptive value of this trait. However, there is little support for senescence correlated with specific adaptations. Nevertheless, insects, mammals, and birds, which are the most common terrestrial animal clades that show symptoms of senescence, evolved from clades that predominantly did not show symptoms of senescence. Thus, we aimed to examine senescence in the context of the ecology and life histories of the main clades of animals, including humans, and to formulate hypotheses to explain the causes and origin of senescence in the major clades of terrestrial animals. METHODOLOGY We reviewed literature from 1950 to 2020 concerning life expectancy, the existence of senescence, and the adaptive characteristics of the major groups of animals. We then proposed a relationship between senescence and environmental factors, considering the biology of these groups of animals. We constructed a model showing the phylogenetic relationships between animal clades in the context of the major stages of evolution, distinguishing between senescent and biologically 'immortal' clades of animals. Finally, we synthesised current data on senescence with the most important concepts and theories explaining the origin and mechanisms of senescence. Although this categorisation into different senescent phenotypes may be simplistic, we used this to propose a framework for understanding senescence. RESULTS We found that terrestrial mammals, insects, and birds show senescence, even though they likely evolved from non-senescent ancestors. Moreover, secondarily aquatic animals show lower rate of senescence than their terrestrial counterparts. Based on the possible life histories of these groups and the analysis of the most important factors affecting the transition from a non-senescent to senescent phenotype, we conclude that aging has evolved, not as a direct effect, but as a correlated response of selection on developmental strategies, and that this occurred separately within each clade. Adoption of specific life history strategies could thus have far-reaching effects in terms of senescence and lifespan. CONCLUSIONS Our analysis strongly suggests that senescence may have emerged as a side effect of the evolution of adaptive features that allowed the colonisation of land. Senescence in mammals may be a compromise between land colonisation and longevity. This hypothesis, is supported by palaeobiological and ecological evidence. We hope that the development of new research methodologies and the availability of more data could be used to test this hypothesis and shed greater light on the evolution of senescence.
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Affiliation(s)
- Tomasz Bilinski
- Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszów, Rzeszów, Poland
| | - Aneta Bylak
- Department of Ecology and Environmental Protection; Institute of Agricultural Sciences, Land Management and Environmental Protection, University of Rzeszów, Rzeszów, Poland
| | - Krzysztof Kukuła
- Department of Ecology and Environmental Protection; Institute of Agricultural Sciences, Land Management and Environmental Protection, University of Rzeszów, Rzeszów, Poland
| | - Renata Zadrag-Tecza
- Department of Biochemistry and Cell Biology, Institute of Biology and Biotechnology, University of Rzeszów, Rzeszów, Poland
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Boero F. The future ocean we want. ADVANCES IN MARINE BIOLOGY 2021; 90:51-63. [PMID: 34728054 DOI: 10.1016/bs.amb.2021.07.001] [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: 06/13/2023]
Abstract
Backcasting involves the design of a desirable future that is not simply predicted with forecasts being, instead, proactively aimed at with effective action. So far, all initiatives towards sustainability failed, probably due to lack of investments in the acquisition of knowledge on the structure and the function of natural systems (i.e. biodiversity and ecosystem functioning), and to the reliance on models and estimates based on incomplete data.
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Affiliation(s)
- Ferdinando Boero
- Dipartimento di Biologia, Università di Napoli Federico II, Naples, Italy; Stazione Zoologica Anton Dohrn, Naples, Italy; CNR-IAS, Genoa, Italy.
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Wilkinson BH, Ivany LC, Drummond CN. Estimating vertebrate biodiversity using the tempo of taxonomy – a view from Hubbert’s peak. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Reservoirs of natural resources are finite and, with increasing exploitation, production typically increases, reaches a maximum (Hubbert’s peak) and then declines. Similarly, species are the currency of biodiversity, and recognized numbers are dependent upon successful discovery. Since 1758, taxonomists have exploited a shrinking reservoir of as-yet-unnamed vertebrate taxa such that rates of species description at first rose, reached a peak and then declined. Since about 1950, increases in research funding and technological advances have fostered a renewed increase in rates of discovery that continues today. Many attempts to estimate global biodiversity are forecasts from data on past rates of description. Here we show that rates of discovery of new vertebrate taxa have been dependent upon the size (richness) of the taxonomic pool under consideration and the intensity of ‘sampling’ effected by taxonomists in their efforts to discover new forms. Because neither the current number of as-yet-to-be-described taxa nor future amounts of taxonomic efforts can be known a priori, attempts to produce an accurate estimate of total global biodiversity based on past rates of discovery are largely unconstrained.
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Affiliation(s)
- Bruce H Wilkinson
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
- Department of Earth and Environmental Sciences, Syracuse University, Syracuse, NY, USA
| | - Linda C Ivany
- Department of Earth and Environmental Sciences, Syracuse University, Syracuse, NY, USA
| | - Carl N Drummond
- Department of Physics, Purdue University Fort Wayne, Fort Wayne, IN, USA
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Viacava P, Baker AM, Blomberg SP, Phillips MJ, Weisbecker V. Using 3D geometric morphometrics to aid taxonomic and ecological understanding of a recent speciation event within a small Australian marsupial (Antechinus: Dasyuridae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Abstract
Taxonomic distinction of species forms the foundation of biodiversity assessments and conservation priorities. However, traditional morphological and/or genetics-based taxonomic assessments frequently miss the opportunity of elaborating on the ecological and functional context of species diversification. Here, we used 3D geometric morphometrics of the cranium to improve taxonomic differentiation and add ecomorphological characterization of a young cryptic divergence within the carnivorous marsupial genus Antechinus. Specifically, we used 168 museum specimens to characterize the recently proposed clades A. stuartii ‘south’, A. stuartii ‘north’ and A. subtropicus. Beyond slight differences attributable to overall size (and, therefore, not necessarily diagnostic), we also found clear allometry-independent shape variation. This allowed us to define new, easily measured diagnostic traits in the palate, which differentiate the three clades. Contrary to previous suggestions, we found no support for a latitudinal gradient as causing the differentiation between the clades. However, skull shape co-varied with temperature and precipitation seasonality, suggesting that the clades may be adapted to environmental variables that are likely to be impacted by climate change. Our study demonstrates the use of 3D geometric morphometrics to improve taxonomic diagnosis of cryptic mammalian species, while providing perspectives on the adaptive origins and potential future threats of mammalian diversity.
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Affiliation(s)
- Pietro Viacava
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Andrew M Baker
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
- Natural Environments Program, Queensland Museum, South Brisbane, Queensland, Australia
| | - Simone P Blomberg
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Matthew J Phillips
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Vera Weisbecker
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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Caetano R, Ispolatov Y, Doebeli M. Evolution of diversity in metabolic strategies. eLife 2021; 10:67764. [PMID: 34350825 PMCID: PMC8428844 DOI: 10.7554/elife.67764] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the origin and maintenance of biodiversity is a fundamental problem. Many theoretical approaches have been investigating ecological interactions, such as competition, as potential drivers of diversification. Classical consumer-resource models predict that the number of coexisting species should not exceed the number of distinct resources, a phenomenon known as the competitive exclusion principle. It has recently been argued that including physiological tradeoffs in consumer-resource models can lead to violations of this principle and to ecological coexistence of very high numbers of species. Here, we show that these results crucially depend on the functional form of the tradeoff. We investigate the evolutionary dynamics of resource use constrained by tradeoffs and show that if the tradeoffs are non-linear, the system either does not diversify or diversifies into a number of coexisting species that do not exceed the number of resources. In particular, very high diversity can only be observed for linear tradeoffs.
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Affiliation(s)
- Rodrigo Caetano
- Departamento de Física, Universidade Federal do Paraná, Curitiba, Brazil
| | - Yaroslav Ispolatov
- Departamento de Fisica, Universidad de Santiago de Chile, Santiago, Chile
| | - Michael Doebeli
- Department of Zoology, University of British Columbia, Vancouver, Canada
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Dole SA, Hulcr J, Cognato AI. Species-rich bark and ambrosia beetle fauna (Coleoptera, Curculionidae, Scolytinae) of the Ecuadorian Amazonian Forest Canopy. Zookeys 2021; 1044:797-813. [PMID: 34183892 PMCID: PMC8222217 DOI: 10.3897/zookeys.1044.57849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/03/2020] [Indexed: 11/22/2022] Open
Abstract
Canopy fogging was used to sample the diversity of bark and ambrosia beetles (Coleoptera, Curculionidae, Scolytinae) at two western Amazonian rainforest sites in Ecuador. Sampling was conducted by Dr Terry Erwin and assistants from 1994–2006 and yielded 1158 samples containing 2500 scolytine specimens representing more than 400 morphospecies. Here, we analyze a subset of these data representing two ecological groups: true bark beetles (52 morphospecies) and ambrosia beetles (69 morphospecies). A high percentage of these taxa occurred as singletons and doubletons and their species accumulation curves did not reach an asymptote. Diversity estimates placed the total scolytine species richness for this taxon subset present at the two sites between 260 and 323 species. The α-diversity was remarkably high at each site, while the apparently high β-diversity was an artifact of undersampling, as shown by a Monte Carlo resampling analysis. This study demonstrates the utility of canopy fogging for the discovery of new scolytine taxa and for approximate diversity assessment, but a substantially greater sampling effort would be needed for conclusive alpha as well as beta diversity estimates.
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Affiliation(s)
- Stephanie A Dole
- Department of Entomology, California Academy of Sciences 55 Music Concourse Drive, San Francisco, CA 94118, USA Department of Entomology, California Academy of Sciences San Francisco United States of America
| | - Jiri Hulcr
- School of Forest Research and Conservation, University of Florida 136 Newins-Ziegler Hall, Gainesville, FL 32611, USA University of Florida Gainesville United States of America
| | - Anthony I Cognato
- Department of Entomology, Michigan State University 288 Farm Ln. East Lansing, MI 48824, USA Michigan State University East Lansing United States of America
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Zhao N, Saavedra S, Liu YY. Impact of colonization history on the composition of ecological systems. Phys Rev E 2021; 103:052403. [PMID: 34134331 PMCID: PMC8217719 DOI: 10.1103/physreve.103.052403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/21/2021] [Indexed: 11/07/2022]
Abstract
Observational studies of ecological systems have shown that different species compositions can arise from distinct species arrival orders during community assembly-also known as colonization history. The presence of multiple interior equilibria in the positive orthant of the state space of the population dynamics will naturally lead to history dependency of the final state. However, it is still unclear whether and under which conditions colonization history will dominate community composition in the absence of multiple interior equilibria. Here, by considering that only one species can invade at a time and there are no recurrent invasions, we show clear evidence that the colonization history can have a big impact on the composition of ecological systems even in the absence of multiple interior equilibria. In particular, we first derive two simple rules to determine whether the composition of a community will depend on its colonization history in the absence of multiple interior equilibria and recurrent invasions. Then we apply them to communities governed by generalized Lotka-Volterra (gLV) dynamics and propose a numerical scheme to measure the probability of colonization history dependence. Finally, we show, via numerical simulations, that for gLV dynamics with a single interior equilibrium, the probability that community composition is dominated by colonization history increases monotonically with community size, network connectivity, and the variation of intrinsic growth rates across species. These results reveal that in the absence of multiple interior equilibria and recurrent invasions, community composition is a probabilistic process mediated by ecological dynamics via the interspecific variation and the size of regional pools.
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Affiliation(s)
- Nannan Zhao
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Applied Mathematics, Northwestern Polytechnical University, Xi’an, 710129, China
| | - Serguei Saavedra
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Center for Cancer Systems Biology, Dana Farber Cancer Institute, Boston, MA, 02115, USA
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Prokaryotic diversity of tropical coastal sand dunes ecosystem using metagenomics. 3 Biotech 2021; 11:252. [PMID: 33968595 DOI: 10.1007/s13205-021-02809-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/23/2021] [Indexed: 10/21/2022] Open
Abstract
Coastal sand dunes (CSDs), unique, stressed and hostile habitats act as a barrier between marine and terrestrial ecosystems. CSDs are stressed in terms of nutrition and fluctuating physio-chemical conditions. CSD is classified into several types, each of which presents different challenges for life forms. This study focuses on exploring bacterial and archaeal diversity and community structure in four CSD namely, Embryo, Fore, Gray, and Mature dunes of Keri beach, Goa along the west coast of India. The study was carried out using Next Generation Sequencing of hypervariable V3-V4 regions of the 16S rRNA gene using Illumina HiSeq platform. The present study hypothesizes that the prokaryotic communities at each dune may be different and could have different role in the ecosystem. The NGS for Embryo, Fore, Gray, and Mature dunes gave 1,045,447, 1,451,753, 1,321,867, and 1,537,758 paired-end reads, respectively, out of which 54,500, 50,032, 37,819, and 111,186 were retained through various quality filtrations. A total of 74, 63, 65, and 65% of OTUs, respectively, remained unknown at the species level. The highest bacterial and archaeal abundance was reported from Mature and Embryo dunes, respectively. Phylum Actinobacteria dominated the Embryo, Fore, and Mature dunes, whereas phylum Proteobacteria was the dominant in the Gray dune. Streptomyces was predominant in overall CSD followed by Bacillus, Acidobacterium, and Kouleothrix. The commonly and exclusively found members in each dune are cataloged. The highest species dominance, diversity, species richness, and abundance were observed in Embryo, Fore, Gray, and Mature dunes, respectively. The present study clearly elucidates that each dune has a distinct microbial community structure. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02809-5.
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Pincebourde S, Dillon ME, Woods HA. Body size determines the thermal coupling between insects and plant surfaces. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13801] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Sylvain Pincebourde
- Institut de Recherche sur la Biologie de l'Insecte UMR 7261 CNRS ‐ Université de Tours Tours France
| | - Michael E. Dillon
- Department of Zoology & Physiology and Program in Ecology University of Wyoming Laramie WY USA
| | - H. Arthur Woods
- Division of Biological Sciences University of Montana Missoula MT USA
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