1
|
Qiao L, Wu Y, Ren C, Li T, Guo Y, Zhao A. Benthic foraminiferal community structure and its response to heavy metals revealed using environmental DNA/RNA metabarcoding in Yueqing Bay, East China Sea. MARINE POLLUTION BULLETIN 2025; 217:118126. [PMID: 40347747 DOI: 10.1016/j.marpolbul.2025.118126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Revised: 04/18/2025] [Accepted: 05/06/2025] [Indexed: 05/14/2025]
Abstract
Foraminifera are among the most important components of benthic communities widely used as indicators of marine environmental changes. Determining the effect of heavy metal pollution on benthic foraminifera is a key requirement for evaluating the health of coastal ecosystems. In this study, environmental DNA (eDNA) and RNA (eRNA) metabarcoding was used to evaluate the benthic foraminiferal community structure and diversity in Yueqing Bay, East China Sea. A total of 45 genera were identified, of which Operculina was predominant. eDNA metabarcoding revealed higher species richness and molecular diversity than did eRNA, with higher values being recorded in the Oujiang Estuary and outer bay than in the inner and central bays. Exploring the relationship between the benthic foraminiferal community and heavy metals showed that Cu was a key factor affecting structure and diversity at the eRNA level. Findings suggest that Nummulites, Ammonia, and Haynesina may be sensitive to Cu pollution, while Parasorites may be tolerant to Zn and Pb.
Collapse
Affiliation(s)
- Ling Qiao
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Yuqi Wu
- School of Fishery, Zhejiang Ocean University, Zhoushan 316004, China
| | - Chengzhe Ren
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316004, China
| | - Tiejun Li
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China.
| | - Yuanming Guo
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Anran Zhao
- School of Fishery, Zhejiang Ocean University, Zhoushan 316004, China
| |
Collapse
|
2
|
Gómez-Martínez D, Selvin MA, Nilsson AK, Carmona E, Ngou JS, Kristiansson E, Nilsson RH, Corcoll N. Environmental concentrations of the fungicide tebuconazole alter microbial biodiversity and trigger biofilm-released transformation products. CHEMOSPHERE 2024; 369:143854. [PMID: 39615850 DOI: 10.1016/j.chemosphere.2024.143854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 10/13/2024] [Accepted: 11/27/2024] [Indexed: 12/07/2024]
Abstract
Freshwater microbial communities are integral components of riverine biodiversity. The ecological effects of toxic chemical pollutants, such as fungicides (e.g., tebuconazole), on microbial abundance and diversity are needed for risk assessment and regulation. The emergence of RNA metabarcoding approaches allow us to describe at unprecedented resolution the microbial diversity of the active part of a microbial community. Our study assesses the ecotoxicological impact of chronic and acute tebuconazole exposures on fungal, bacterial, and algal biomass and biodiversity of aquatic fungi and bacteria in stream biofilms using an RNA metabarcoding approach. In addition, the study uses HPLC-MS to evaluate the capability of biofilms to metabolize tebuconazole. Natural biofilm communities from a Swedish stream were exposed chronically (24 days) and acutely (96 h) to environmental concentrations of tebuconazole (10 and 100 μg/L) in microcosms conditions. The diversity and community structure of fungi and bacteria was assessed by ITS2 and 16S cDNA amplicon-sequencing, respectively. Biofilms chronically exposed to tebuconazole produced and released unidentified transformation products into the water column, suggesting a biotransformation capability following 24 days of uninterrupted exposure. The fungal biomass markedly decreased by a biomass loss of 40% when chronically exposed to 10 μg/L, and 60% when chronically exposed to 100 μg/L. Bacterial and algal biomass remained comparable with the controls in all tebuconazole treatments. Fungal and bacterial alpha diversity metrics were not significantly impacted, although a decreasing trend in fungal richness was observed with the treatments. However, beta diversity was significantly impacted in both fungal and bacterial compartments. Chronic exposures resulted in a shift in community composition, where taxa potentially more tolerant to tebuconazole (i.e. Lecanoromycetes) replaced more sensitive taxa (i.e. Malasseziomycetes). This study indicates that tebuconazole at environmental concentrations might pose a risk to freshwater systems, mainly due to its high toxicity to fungi.
Collapse
Affiliation(s)
- Daniela Gómez-Martínez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Department of Biological and Environmental Sciences, Centre for Future Chemical Risk Assessment and Management Strategies (FRAM) and Gothenburg Global Biodiversity Center (GGBC), University of Gothenburg, Gothenburg, Sweden.
| | - Mary A Selvin
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Anders K Nilsson
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Eric Carmona
- Atmospheric Chemistry Department, Leibniz Institute for Tropospheric Research, Leipzig, Germany.
| | - Judith Sorel Ngou
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden; Department of Biological and Environmental Sciences, Centre for Future Chemical Risk Assessment and Management Strategies (FRAM) and Gothenburg Global Biodiversity Center (GGBC), University of Gothenburg, Gothenburg, Sweden.
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Center, University of Gothenburg, Gothenburg, Sweden.
| | - Natàlia Corcoll
- Department of Biological and Environmental Sciences, Centre for Future Chemical Risk Assessment and Management Strategies (FRAM) and Gothenburg Global Biodiversity Center (GGBC), University of Gothenburg, Gothenburg, Sweden.
| |
Collapse
|
3
|
Hatano Y, Matsuoka S, Doi H, Tateno R, Hasegawa M, Osono T. Evaluation of the persistence of Epichloë endophyte and its possible effect on fungal assemblages in dead leaf sheaths. Fungal Biol 2024; 128:2325-2332. [PMID: 39643400 DOI: 10.1016/j.funbio.2024.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 10/31/2024] [Accepted: 11/13/2024] [Indexed: 12/09/2024]
Abstract
The systemic fungal endophytes of the genus Epichloë inhabit the aerial part of host grasses. Recent studies have reported that Epichloë affects the non-systemic endophytic assemblages in live leaves, but few studies that have demonstrated the occurrence of Epichloë and its effect on fungal assemblages in dead leaves. We proposed a hypothesis that Epichloë decreases from live to dead leaves but affects the non-systemic endophytic assemblages also in dead leaves. To test this hypothesis, we sampled leaf sheaths from four leaf types (live, senescent, attached dead and fallen dead) of two native grass species Elymus racemifer and Elymus tsukushiensis var. transiens in Japan and assessed for fungi by DNA metabarcoding. The occurrence of Epichloë OTU was significantly greater in E. tsukushiensis var. transiens than in E. racemifer and varied significantly between the four-leaf types, with decreased and no detections in attached dead and fallen dead leaves, respectively. The composition of non-systemic endophytic assemblages was also significantly affected by the presence/absence of Epichloë OTU, leaf type, host grass species and their interactions. These results supported our hypothesis and suggested that Epichloë can indirectly lead to the changes in belowground processes such as litter decomposition by affecting saprotrophic fungi in dead leaves.
Collapse
Affiliation(s)
- Yuki Hatano
- Graduate School of Science and Engineering, Doshisha University, Kyoto, 610-0394, Japan.
| | - Shunsuke Matsuoka
- Field Science Education and Research Center, Kyoto University, Kyoto, 606-8502, Japan
| | - Hideyuki Doi
- Graduate School of Informatics, Kyoto University, Kyoto, 606-8501, Japan
| | - Ryunosuke Tateno
- Field Science Education and Research Center, Kyoto University, Kyoto, 606-8502, Japan
| | - Motohiro Hasegawa
- Faculty of Science and Engineering, Doshisha University, Kyoto, 610-0394, Japan
| | - Takashi Osono
- Faculty of Science and Engineering, Doshisha University, Kyoto, 610-0394, Japan
| |
Collapse
|
4
|
Jackson VLN, Grevesse T, Kilias ES, Onda DFL, Young KF, Allen MJ, Walsh DA, Lovejoy C, Monier A. Vulnerability of Arctic Ocean microbial eukaryotes to sea ice loss. Sci Rep 2024; 14:28896. [PMID: 39572565 PMCID: PMC11582671 DOI: 10.1038/s41598-024-77821-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 10/25/2024] [Indexed: 11/24/2024] Open
Abstract
The Arctic Ocean (AO) is changing at an unprecedented rate, with ongoing sea ice loss, warming and freshening impacting the extent and duration of primary productivity over summer months. Surface microbial eukaryotes are vulnerable to such changes, but basic knowledge of the spatial variability of surface communities is limited. Here, we sampled microbial eukaryotes in surface waters of the Beaufort Sea from four contrasting environments: the Canada Basin (open ocean), the Mackenzie Trough (river-influenced), the Nuvuk region (coastal) and the under-ice system of the Canada Basin. Microbial community structure and composition varied significantly among the systems, with the most phylogenetically diverse communities being found in the more coastal systems. Further analysis of environmental factors showed potential vulnerability to change in the most specialised community, which was found in the samples taken in water immediately beneath the sea ice, and where the community was distinguished by rare species. In the context of ongoing sea ice loss, specialised ice-associated microbial assemblages may transition towards more generalist assemblages, with implications for the eventual loss of biodiversity and associated ecosystem function in the Arctic Ocean.
Collapse
Affiliation(s)
- Victoria L N Jackson
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK
- Biosciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Thomas Grevesse
- Biology Department, Concordia University, Montréal, QC, H4B 1R6, Canada
| | - Estelle S Kilias
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK
- Biosciences, University of Exeter, Exeter, EX4 4QD, UK
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Deo F L Onda
- The Marine Science Institute, University of the Philippines, Manila, Philippines
| | | | | | - David A Walsh
- Biology Department, Concordia University, Montréal, QC, H4B 1R6, Canada
| | - Connie Lovejoy
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Adam Monier
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.
- Biosciences, University of Exeter, Exeter, EX4 4QD, UK.
| |
Collapse
|
5
|
Muvunyi CM, Ngabonziza JCS, Florence M, Mukagatare I, Twagirumukiza M, Ahmed A, Siddig EE. Diversity and Distribution of Fungal Infections in Rwanda: High Risk and Gaps in Knowledge, Policy, and Interventions. J Fungi (Basel) 2024; 10:658. [PMID: 39330417 PMCID: PMC11433616 DOI: 10.3390/jof10090658] [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: 07/08/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 09/28/2024] Open
Abstract
Fungal infections (FIs) are spreading globally, raising a significant public health concern. However, its documentation remains sparse in Africa, particularly in Rwanda. This report provides a comprehensive review of FIs in Rwanda based on a systematic review of reports published between 1972 and 2022. The findings reveal a rich diversity of fungal pathogens, including Blastomyces, Candida, Cryptococcus, Histoplasma, Microsporum, Pneumocystis, Rhinosporidium, and Trichophyton caused human infections. Candida infections predominantly affect the vagina mucosa, while Histoplasma duboisi was linked to disseminated infections. Other pathogens, such as Blastomyces dermatitidis and Rhinosporidium seeberi, were associated with cerebellar and nasal mucosa infections, respectively. The widespread observation of soilborne fungi affecting bean crops highlights the pathogens' threat to agricultural productivity, food security, and socioeconomic stability, as well as potential health impacts on humans, animals, and the environment. Of particular importance is that there is no information about FIs among animals in the country. Moreover, the analysis underscores significant limitations in the detection, reporting, and healthcare services related to FIs in the country, indicating gaps in diagnostic capacity and surveillance systems. This is underscored by the predominant use of traditional diagnostic techniques, including culture, cytology, and histopathology in the absence of integrating more sensitive and specific molecular tools in investigating FIs. Developing the diagnostic capacities and national surveillance systems are urgently needed to improve the health of crops, animals, and humans, as well as food security and socioeconomic stability in Rwanda. Also, it is important to indicate severe gaps in the evidence to inform policymaking, guide strategic planning, and improve healthcare and public health services, underscoring the urgent need to build national capacity in fungal diagnosis, surveillance, and research. Raising awareness among the public, scientific community, healthcare providers, and policymakers remains crucial. Furthermore, this report reveals the threats of FIs on public health and food insecurity in Rwanda. A multisectoral one health strategy is essential in research and intervention to determine and reduce the health and safety impacts of fungal pathogens on humans, animals, and the environment.
Collapse
Affiliation(s)
| | - Jean Claude Semuto Ngabonziza
- Department of Clinical Biology, University of Rwanda, Kigali P.O. Box 3900, Rwanda
- Research, Innovation and Data Science Division, Rwanda Biomedical Centre, Kigali P.O. Box 7162, Rwanda
| | - Masaisa Florence
- Department of Internal Medicine and Hematology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 7162, Rwanda
- Clinical Education and Research Division, Kigali University Teaching Hospital, Kigali P.O. Box 655, Rwanda
| | - Isabelle Mukagatare
- Biomedical Services Department, Rwanda Biomedical Centre, Kigali P.O. Box 7162, Rwanda
| | - Marc Twagirumukiza
- Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Ayman Ahmed
- Rwanda Biomedical Centre, Kigali P.O. Box 7162, Rwanda;
- Institute of Endemic Diseases, University of Khartoum, Khartoum 11111, Sudan
| | - Emmanuel Edwar Siddig
- Unit of Applied Medical Sciences, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum 11111, Sudan;
| |
Collapse
|
6
|
Zhang Y, Qiu Y, Liu K, Zhong W, Yang J, Altermatt F, Zhang X. Evaluating eDNA and eRNA metabarcoding for aquatic biodiversity assessment: From bacteria to vertebrates. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 21:100441. [PMID: 39027464 PMCID: PMC11254946 DOI: 10.1016/j.ese.2024.100441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024]
Abstract
The monitoring and management of aquatic ecosystems depend on precise estimates of biodiversity. Metabarcoding analyses of environmental nucleic acids (eNAs), including environmental DNA (eDNA) and environmental RNA (eRNA), have garnered attention for their cost-effective and non-invasive biomonitoring capabilities. However, the accuracy of biodiversity estimates obtained through eNAs can vary among different organismal groups. Here we evaluate the performance of eDNA and eRNA metabarcoding across nine organismal groups, ranging from bacteria to terrestrial vertebrates, in three cross-sections of the Yangtze River, China. We observe robust complementarity between eDNA and eRNA data. The relative detectability of eNAs was notably influenced by major taxonomic groups and organismal sizes, with eDNA providing more robust signals for larger organisms. Both eDNA and eRNA exhibited similar cross-sectional and longitudinal patterns. However, the detectability of larger organisms declined in eRNA metabarcoding, possibly due to differential RNA release and decay among different organismal groups or sizes. While underscoring the potential of eDNA and eRNA in large river biomonitoring, we emphasize the need for differential interpretation of eDNA versus eRNA data. This highlights the importance of careful method selection and interpretation in biomonitoring studies.
Collapse
Affiliation(s)
- Yan Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Yu Qiu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Kai Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wenjun Zhong
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| |
Collapse
|
7
|
Mamadashvili G, Brin A, Chumak M, Diedus V, Drössler L, Förster B, Georgiev KB, Ghrejyan T, Hleb R, Kalashian M, Kamburov I, Karagyan G, Kevlishvili J, Khutsishvili Z, Larrieu L, Mazmanyan M, Petrov PI, Tabunidze L, Bässler C, Müller J. Drivers of wood-inhabiting fungal diversity in European and Oriental beech forests. Ecol Evol 2024; 14:e11660. [PMID: 38962025 PMCID: PMC11220834 DOI: 10.1002/ece3.11660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/26/2024] [Accepted: 06/13/2024] [Indexed: 07/05/2024] Open
Abstract
The hyperdiverse wood-inhabiting fungi play a crucial role in the global carbon cycle, but often are threatened by deadwood removal, particularly in temperate forests dominated by European beech (Fagus sylvatica) and Oriental beech (Fagus orientalis). To study the impact of abiotic drivers, deadwood factors, forest management and biogeographical patterns in forests of both beech species on fungal composition and diversity, we collected 215 deadwood-drilling samples in 18 forests from France to Armenia and identified fungi by meta-barcoding. In our analyses, we distinguished the patterns driven by rare, common, and dominant species using Hill numbers. Despite a broad overlap in species, the fungal composition with focus on rare species was determined by Fagus species, deadwood type, deadwood diameter, precipitation, temperature, and management status in decreasing order. Shifting the focus on common and dominant species, only Fagus species, both climate variables and deadwood type remained. The richness of species within the deadwood objects increased significantly only with decay stage. Gamma diversity in European beech forests was higher than in Oriental beech forests. We revealed the highest gamma diversity for old-growth forests of European beech when focusing on dominant species. Our results implicate that deadwood retention efforts, focusing on dominant fungi species, critical for the decay process, should be distributed across precipitation and temperature gradients and both Fagus species. Strategies focusing on rare species should additionally focus on different diameters and on the conservation of old-growth forests.
Collapse
Affiliation(s)
- Giorgi Mamadashvili
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical BiologyBiocenter, University of WürzburgRauhenebrachGermany
| | - Antoine Brin
- Sciences and digital departmentUniversity of Toulouse, Ecole d'Ingénieurs de PURPAN, UMR INRAE‐INPT DYNAFORToulouseFrance
| | - Maksym Chumak
- Department of Entomology and Biodiversity PreservationUzhhorod National UniversityUzhhorodUkraine
| | - Valeriia Diedus
- State Museum of Natural History, National Academy of Sciences of UkraineLvivUkraine
| | - Lars Drössler
- Forestry Research and Competence Center ThüringenForst AöRGothaGermany
| | - Bernhard Förster
- Chair for Strategic Landscape Planning and ManagementTechnical University of MunichFreisingGermany
| | - Kostadin B. Georgiev
- Hessian State Agency for Nature Conservation, Environment and GeologyHesseGermany
| | - Tigran Ghrejyan
- Laboratory of Entomology and Soil ZoologyScientific Center of Zoology and Hydroecology NAS RAYerevanArmenia
| | - Ruslan Hleb
- Forestry laboratoryCarpathian Biosphere ReserveRakhivUkraine
| | - Mark Kalashian
- Laboratory of Entomology and Soil ZoologyScientific Center of Zoology and Hydroecology NAS RAYerevanArmenia
| | - Ivan Kamburov
- Strandzha Nature Park DirectorateMalko TarnovoBulgaria
| | - Gayane Karagyan
- Laboratory of Entomology and Soil ZoologyScientific Center of Zoology and Hydroecology NAS RAYerevanArmenia
| | | | | | - Laurent Larrieu
- Université de Toulouse, INRAE, UMR DYNAFORCastanet‐TolosanFrance
- CNPF‐CRPF OccitanieFrance
| | - Meri Mazmanyan
- Laboratory of Entomology and Soil ZoologyScientific Center of Zoology and Hydroecology NAS RAYerevanArmenia
| | - Peter I. Petrov
- University of Forestry Sofia, Field Base PetrohanBarziaBulgaria
| | | | - Claus Bässler
- Ecology of Fungi, Bayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
- Conservation and Research DepartmentBavarian Forest National ParkGrafenauGermany
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical BiologyBiocenter, University of WürzburgRauhenebrachGermany
- Conservation and Research DepartmentBavarian Forest National ParkGrafenauGermany
| |
Collapse
|
8
|
Rishan ST, Kline RJ, Rahman MS. New prospects of environmental RNA metabarcoding research in biological diversity, ecotoxicological monitoring, and detection of COVID-19: a critical review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:11406-11427. [PMID: 38183542 DOI: 10.1007/s11356-023-31776-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/26/2023] [Indexed: 01/08/2024]
Abstract
Ecosystems are multifaceted and complex systems and understanding their composition is crucial for the implementation of efficient conservation and management. Conventional approaches to biodiversity surveys can have limitations in detecting the complete range of species present. In contrast, the study of environmental RNA (eRNA) offers a non-invasive and comprehensive method for monitoring and evaluating biodiversity across different ecosystems. Similar to eDNA, the examination of genetic material found in environmental samples can identify and measure many species, including ones that pose challenges to traditional methods. However, eRNA is degraded quickly and therefore shows promise in detection of living organisms closer to their actual location than eDNA methods. This method provides a comprehensive perspective on the well-being of ecosystems, facilitating the development of focused conservation approaches to save at-risk species and uphold ecological equilibrium. Furthermore, eRNA has been recognized as a valuable method for the identification of COVID-19 in the environment, besides its established uses in biodiversity protection. The SARS-CoV-2 virus, which is accountable for the worldwide epidemic, releases RNA particles into the surrounding environment via human waste, providing insights into the feasibility of detecting it in wastewater and other samples taken from the environment. In this article, we critically reviewed the recent research activities that use the eRNA method, including its utilization in biodiversity conservation, ecological surveillance, and ecotoxicological monitoring as well as its innovative potential in identifying COVID-19. Through this review, the reader can understand the recent developments, prospects, and challenges of eRNA research in ecosystem management and biodiversity conservation.
Collapse
Affiliation(s)
- Sakib Tahmid Rishan
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Richard J Kline
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Md Saydur Rahman
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA.
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA.
| |
Collapse
|
9
|
Grishkan I, Kidron GJ, Rodriguez-Berbel N, Miralles I, Ortega R. Altitudinal Gradient and Soil Depth as Sources of Variations in Fungal Communities Revealed by Culture-Dependent and Culture-Independent Methods in the Negev Desert, Israel. Microorganisms 2023; 11:1761. [PMID: 37512933 PMCID: PMC10383159 DOI: 10.3390/microorganisms11071761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
We examined fungal communities in soil profiles of 0-10 cm depth along the altitudinal gradient of 250-530-990 m.a.s.l. at the Central Negev Desert, Israel, which benefit from similar annual precipitation (95 mm). In the soil samples collected in the summer of 2020, a mycobiota accounting for 169 species was revealed by both culture-dependent and culture-independent (DNA-based) methodologies. The impact of soil depth on the variations in fungal communities was stronger than the impact of altitude. Both methodologies displayed a similar tendency in the composition of fungal communities: the prevalence of melanin-containing species with many-celled large spores (mainly Alternaria spp.) in the uppermost layers and the depth-wise increase in the proportion of light-colored species producing a high amount of small one-celled spores. The culturable and the DNA-based fungal communities had only 13 species in common. The differences were attributed to the pros and cons of each method. Nevertheless, despite the drawbacks, the employment of both methodologies has an advantage in providing a more comprehensive picture of fungal diversity in soils.
Collapse
Affiliation(s)
- Isabella Grishkan
- Institute of Evolution, University of Haifa, 199 Aba Khoushy Ave, Mount Carmel, Haifa 3498838, Israel
| | - Giora J Kidron
- Institute of Earth Sciences, The Hebrew University of Jerusalem, Givat Ram Campus, Jerusalem 91904, Israel
| | - Natalia Rodriguez-Berbel
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agrifood, University of Almeria, E-04120 Almería, Spain
| | - Isabel Miralles
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agrifood, University of Almeria, E-04120 Almería, Spain
| | - Raúl Ortega
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agrifood, University of Almeria, E-04120 Almería, Spain
| |
Collapse
|
10
|
Environmental DNA (eDNA): Powerful Technique for Biodiversity Conservation. J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
11
|
Neidel V, Sint D, Wallinger C, Traugott M. RNA allows identifying the consumption of carrion prey. Mol Ecol Resour 2022; 22:2662-2671. [PMID: 35668675 PMCID: PMC9541938 DOI: 10.1111/1755-0998.13659] [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: 11/15/2021] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
Abstract
Facultative scavenging by predatory carnivores is a prevalent but frequently underestimated feeding strategy. DNA‐based methods for diet analysis, however, do not allow to distinguish between scavenging and predation, thus, the significance of scavenging on population dynamics and resource partitioning is widely unknown. Here, we present a methodological innovation to differentiate between scavenging and fresh prey consumption using prey RNA as a target molecule. We hypothesized that the rapid post‐mortem breakdown of RNA in prey tissue should lead to a significantly lower detection probability of prey RNA than DNA when carrion rather than fresh prey is consumed. To test this hypothesis, ground beetles (Pseudoophonus rufipes [De Geer]) were offered either fresh or 1‐day‐old dead Drosophila melanogaster fruit flies (carrion). The detectability of prey RNA and DNA in the beetles' regurgitates was assessed with diagnostic Drosophila‐specific RT‐PCR and PCR assays at 0, 6, 12, 24 and 48 h post‐feeding. After fresh fly consumption, prey RNA and DNA were detectable equally well at all times. When carrion prey was consumed, the detection strength of prey RNA immediately after feeding was significantly lower than that of prey DNA and reached zero in most samples within 6 h of digestion. Our findings provide evidence that prey RNA allows distinguishing between the consumption of fresh and scavenged prey, thereby overcoming a long‐known weakness of molecular diet analysis. The assessment of prey RNA offers a generally applicable approach for examining the importance of scavenging in food webs to unravel its functional consequences for populations, communities, and ecosystems.
Collapse
Affiliation(s)
- Veronika Neidel
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Daniela Sint
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Corinna Wallinger
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Michael Traugott
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
| |
Collapse
|
12
|
Baeshen M, Alkaladi A, Alhejen A, Bataweel N, Abdelkader H, Suliman abuzahrah S. Exploring the Taxonomic and Functional Diversity of Marine Benthic Micro-Eukaryotes Along the Red Sea Coast of Jeddah City. Saudi J Biol Sci 2022; 29:103342. [PMID: 35846388 PMCID: PMC9278075 DOI: 10.1016/j.sjbs.2022.103342] [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: 12/15/2021] [Revised: 05/07/2022] [Accepted: 06/10/2022] [Indexed: 11/16/2022] Open
Abstract
Backgrounds Diverse marine habitats along Jeddah's Red Sea coast support rich biodiversity. Few studies have been done on its diverse communities, especially its microbial counterparts. Metagenomic analysis of marine benthic micro-eukaryotic communities was performed for the first time on the Red Sea coast of Jeddah. This research looks into their community structure and metabolic potential. Methods Next-generation sequencing was used to examine the micro-eukaryotic communities of seven sedimentary soil samples from four Jeddah coast locations. After isolating DNA from seven benthic sedimentary soil samples, the 18S rDNA V4 regions were amplified and sequenced on the Illumina MiSeq. It was also verified using an Agilent Technologies 2100 Bioanalyzer with a DNA 1000 chip (Agilent Technologies, Fisher Scientific). A standard curve of fluorescence readings generated by qPCR quantification using the Illumina library was achieved using the GS FLX library. Metagenomic data analysis was used to evaluate the microbial communities' biochemical and enzymatic allocations in studied samples. Results Blast analysis showed that the top ten phyla were Annelida, Eukaryota, Diatomea, Porifera, Phragmoplastophyta, Arthropoda, Dinoflagellata, Xenacoelomorpha Nematoda, and uncultured. Annelida was also found in the highest percentage (93%), in the sample M followed by Porifera (64%), the most abundant in the control sample then Eukaryotes (61%), Phragmatoplastophyta (55%), Arthropoda, and Diatomea (the least common) (32%). community diversity analysis: using Shannon and inverse Simpson indices showed sediment composition to be effective. Also, PICRUST2 indicated that the most abundant pathways were pyruvate fermentation to isobutanol, pyrimidine deoxyribonucleotide phosphorylation, adenosine ribonucleotide de novo biosynthesis, guanosine ribonucleotide de novo biosynthesis, NAD salvage pathway I, the super pathway of glyoxylate bypass and aerobic respiration I (cytochrome c). Conclusion Results showed that high throughput metagenomics could reveal species diversity and estimate gene profiles. Environmental factors appear to be more important than geographic variation in determining the structure of these microbial communities. This study provides the first report of marine benthic micro-eukaryotic communities found on the Red Sea coast of Jeddah and will serve as a good platform for future research.
Collapse
|
13
|
Adamo M, Comtet-Marre S, Büttner E, Kellner H, Luis P, Vallon L, Prego R, Hofrichter M, Girlanda M, Peyret P, Marmeisse R. Fungal dye-decolorizing peroxidase diversity: roles in either intra- or extracellular processes. Appl Microbiol Biotechnol 2022; 106:2993-3007. [PMID: 35435459 PMCID: PMC9064869 DOI: 10.1007/s00253-022-11923-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 01/13/2023]
Abstract
Fungal dye-decolorizing peroxidases (DyPs) have found applications in the treatment of dye-contaminated industrial wastes or to improve biomass digestibility. Their roles in fungal biology are uncertain, although it has been repeatedly suggested that they could participate in lignin degradation and/or modification. Using a comprehensive set of 162 fully sequenced fungal species, we defined seven distinct fungal DyP clades on basis of a sequence similarity network. Sequences from one of these clades clearly diverged from all others, having on average the lower isoelectric points and hydropathy indices, the highest number of N-glycosylation sites, and N-terminal sequence peptides for secretion. Putative proteins from this clade are absent from brown-rot and ectomycorrhizal species that have lost the capability of degrading lignin enzymatically. They are almost exclusively present in white-rot and other saprotrophic Basidiomycota that digest lignin enzymatically, thus lending support for a specific role of DyPs from this clade in biochemical lignin modification. Additional nearly full-length fungal DyP genes were isolated from the environment by sequence capture by hybridization; they all belonged to the clade of the presumably secreted DyPs and to another related clade. We suggest focusing our attention on the presumably intracellular DyPs from the other clades, which have not been characterized thus far and could represent enzyme proteins with novel catalytic properties. KEY POINTS: • A fungal DyP phylogeny delineates seven main sequence clades. • Putative extracellular DyPs form a single clade of Basidiomycota sequences. • Extracellular DyPs are associated to white-rot fungi.
Collapse
Affiliation(s)
- Martino Adamo
- Department of Life Sciences and Systems Biology (DBIOS), Università Degli Studi Di Torino, 25 Viale P.A. Mattioli, 10125, Torino, Italy.
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, UMR Ecologie Microbienne, VetAgro Sup43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France.
| | | | - Enrico Büttner
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Zittau, Germany
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Zittau, Germany
| | - Patricia Luis
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, UMR Ecologie Microbienne, VetAgro Sup43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
| | - Laurent Vallon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, UMR Ecologie Microbienne, VetAgro Sup43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
| | - Rocio Prego
- Université Clermont Auvergne, INRAE, MEDiS, 63000, Clermont-Ferrand, France
| | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Zittau, Germany
| | - Mariangela Girlanda
- Department of Life Sciences and Systems Biology (DBIOS), Università Degli Studi Di Torino, 25 Viale P.A. Mattioli, 10125, Torino, Italy
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDiS, 63000, Clermont-Ferrand, France
| | - Roland Marmeisse
- Department of Life Sciences and Systems Biology (DBIOS), Università Degli Studi Di Torino, 25 Viale P.A. Mattioli, 10125, Torino, Italy
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, UMR Ecologie Microbienne, VetAgro Sup43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université Des Antilles, CP39, 57 rue Cuvier, 75005, Paris, France
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), 25 Viale P.A. Mattioli, 10125, Torino, Italy
| |
Collapse
|
14
|
Forecasting the number of species of asexually reproducing fungi (Ascomycota and Basidiomycota). FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00500-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
15
|
Caboň M, Galvánek D, Detheridge AP, Griffith GW, Maráková S, Adamčík S. Mulching has negative impact on fungal and plant diversity in Slovak oligotrophic grasslands. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2021.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|