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Srinivasan S. Radiation-Tolerant Fibrivirga spp. from Rhizosphere Soil: Genome Insights and Potential in Agriculture. Genes (Basel) 2024; 15:1048. [PMID: 39202408 PMCID: PMC11354047 DOI: 10.3390/genes15081048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 09/03/2024] Open
Abstract
The rhizosphere of plants contains a wide range of microorganisms that can be cultivated and used for the benefit of agricultural practices. From garden soil near the rhizosphere region, Strain ES10-3-2-2 was isolated, and the cells were Gram-negative, aerobic, non-spore-forming rods that were 0.3-0.8 µm in diameter and 1.5-2.5 µm in length. The neighbor-joining method on 16S rDNA similarity revealed that the strain exhibited the highest sequence similarities with "Fibrivirga algicola JA-25" (99.2%) and Fibrella forsythia HMF5405T (97.3%). To further explore its biotechnological potentialities, we sequenced the complete genome of this strain employing the PacBio RSII sequencing platform. The genome of Strain ES10-3-2-2 comprises a 6,408,035 bp circular chromosome with a 52.8% GC content, including 5038 protein-coding genes and 52 RNA genes. The sequencing also identified three plasmids measuring 212,574 bp, 175,683 bp, and 81,564 bp. Intriguingly, annotations derived from the NCBI-PGAP, eggnog, and KEGG databases indicated the presence of genes affiliated with radiation-resistance pathway genes and plant-growth promotor key/biofertilization-related genes regarding Fe acquisition, K and P assimilation, CO2 fixation, and Fe solubilization, with essential roles in agroecosystems, as well as genes related to siderophore regulation. Additionally, T1SS, T6SS, and T9SS secretion systems are present in this species, like plant-associated bacteria. The inoculation of Strain ES10-3-2-2 to Arabidopsis significantly increases the fresh shoot and root biomass, thereby maintaining the plant quality compared to uninoculated controls. This work represents a link between radiation tolerance and the plant-growth mechanism of Strain ES10-3-2-2 based on in vitro experiments and bioinformatic approaches. Overall, the radiation-tolerant bacteria might enable the development of microbiological preparations that are extremely effective at increasing plant biomass and soil fertility, both of which are crucial for sustainable agriculture.
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Affiliation(s)
- Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 01797, Republic of Korea
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Belykh E, Maystrenko T, Velegzhaninov I, Tavleeva M, Rasova E, Rybak A. Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review. Microorganisms 2024; 12:733. [PMID: 38674676 PMCID: PMC11051952 DOI: 10.3390/microorganisms12040733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.
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Affiliation(s)
- Elena Belykh
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Tatiana Maystrenko
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Ilya Velegzhaninov
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Marina Tavleeva
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
- Department of Biology, Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prospekt, Syktyvkar 167001, Russia
| | - Elena Rasova
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Anna Rybak
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
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Ovuru KF, Izah SC, Ogidi OI, Imarhiagbe O, Ogwu MC. Slaughterhouse facilities in developing nations: sanitation and hygiene practices, microbial contaminants and sustainable management system. Food Sci Biotechnol 2024; 33:519-537. [PMID: 38274182 PMCID: PMC10805746 DOI: 10.1007/s10068-023-01406-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/19/2023] [Accepted: 07/26/2023] [Indexed: 01/27/2024] Open
Abstract
Poor personal and environmental hygiene and sanitary conditions of abattoirs in developing countries in sub-Saharan Africa have been implicated in the occurrence and spread of foodborne diseases. This focused review aims to evaluate the sanitation and hygiene practices of slaughterhouses in selected sub-Saharan African countries as well as the microbial (bacterial) contaminants associated with these slaughterhouses. Pathogenic microorganisms of public health importance have been associated with these slaughterhouses due to poor hygiene conditions, non-formal occupational health and safety training, and poor knowledge of workers as well as substandard infrastructures and crude tools in these facilities. Put together, these conditions enable the growth, survival, transmission, and proliferation of foodborne pathogens such as bacteria, parasites, and viruses. To address this issue, there is a need to assess the poor environmental and personal hygiene of butchers and other abattoir workers, the inaccessibility of potable water, waste management practices, and the lack of appropriate infrastructure and technology, which have been identified as some of the enabling factors for bacteria, fungi, and viruses. Sustainable strategies should include instituting regulations that are backed by law.
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Affiliation(s)
- Kurotimipa Frank Ovuru
- Neglected Tropical Diseases Programme, Directorate of Public Health, Ministry of Health, Yenagoa, Bayelsa State Nigeria
| | - Sylvester Chibueze Izah
- Department of Microbiology, Faculty of Science, Bayelsa Medical University, Yenagoa, Bayelsa State Nigeria
| | - Odangowei Inetiminebi Ogidi
- Department of Biochemistry, School of Applied Sciences, Federal Polytechnic Ekowe, Ekowe, Bayelsa State Nigeria
| | - Odoligie Imarhiagbe
- London School of Science and Technology, 50 Rocky Lane, Aston, Birmingham, B6 5RQ UK
| | - Matthew Chidozie Ogwu
- Goodnight Family Department of Sustainable Development, Appalachian State University, 212 Living Learning Center, 305 Bodenheimer Drive, Boone, NC 28608 USA
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Ellington AJ, Walters K, Christner BC, Fox S, Bonfantine K, Walker C, Lampman P, Vuono DC, Strickland M, Lambert K, Kobziar LN. Dispersal of microbes from grassland fire smoke to soils. THE ISME JOURNAL 2024; 18:wrae203. [PMID: 39404077 PMCID: PMC11525542 DOI: 10.1093/ismejo/wrae203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 09/23/2024] [Accepted: 10/14/2024] [Indexed: 11/02/2024]
Abstract
Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments. Soils either containing the native microbial community or presterilized by γ-irradiation were inundated with various doses of smoke from native tallgrass prairie grasses. Smoke-inundated, γ-irradiated soils exhibited significantly higher respiration rates than both smoke-inundated, native soils and γ-irradiated soils exposed to ambient air only. Microbial communities in γ-irradiated soils were significantly different between smoke-treated and control soils, which supports the hypothesis that wildland fire smoke can act as a dispersal agent. Community compositions differed based on smoke dose, incubation time, and soil type. Concentrations of phosphate and microbial biomass carbon and nitrogen together with pH were significant predictors of community composition. Source tracking analysis attributed smoke as contributing nearly 30% of the taxa found in smoke-inundated, γ-irradiated soils, suggesting smoke may play a role in the recovery of microbial communities in similar damaged soils. Our findings demonstrate that short-distance microbial dispersal by biomass burning smoke can influence the assembly processes of microbial communities in soils and has implications for a broad range of subjects including agriculture, restoration, plant disease, and biodiversity.
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Affiliation(s)
- Adam J Ellington
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, P.O. Box 110700 Gainesville, FL 32611, United States
| | - Kendra Walters
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, 1031 N. Academic Way, Coeur d’Alene, ID 83814, United States
| | - Brent C Christner
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, P.O. Box 110700 Gainesville, FL 32611, United States
| | - Sam Fox
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, 1031 N. Academic Way, Coeur d’Alene, ID 83814, United States
| | - Krista Bonfantine
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, 1031 N. Academic Way, Coeur d’Alene, ID 83814, United States
| | - Cassie Walker
- Department of Biology, Brigham Young University – Idaho, 525 S Center St., Rexburg, ID 83460, United States
| | - Phinehas Lampman
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, 1031 N. Academic Way, Coeur d’Alene, ID 83814, United States
| | - David C Vuono
- Department of Civil and Environmental Engineering, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401, United States
| | - Michael Strickland
- Department of Soil and Water Systems, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844, United States
| | - Katie Lambert
- Department of Soil and Water Systems, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844, United States
| | - Leda N Kobziar
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, 1031 N. Academic Way, Coeur d’Alene, ID 83814, United States
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Zhang G, Shen Z, Fu G. Geo-Distribution Patterns of Soil Fungal Community of Pennisetum flaccidum in Tibet. J Fungi (Basel) 2022; 8:1230. [PMID: 36422051 PMCID: PMC9699603 DOI: 10.3390/jof8111230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 08/27/2023] Open
Abstract
Pennisetum flaccidum can be used as a pioneer species for the restoration of degraded grasslands and as a high-quality forage for local yak and sheep in alpine regions. The geographical distribution pattern of soil fungal community can modify that of P. flaccidum. A field survey along 32 sampling sites was conducted to explore the geo-distribution patterns of soil fungal community of P. flaccidum in Tibet. Soil fungal species, phylogenetic and function diversity generally had a closer correlation with longitude/elevation than latitude. The geo-distribution patterns of soil fungal species, phylogenetic and function diversity varied with soil depth. Soil fungal species, phylogenetic and function diversity had dissimilar geo-distribution patterns. Precipitation had stronger impacts on total abundance, species α-diversity, phylogenetic α-diversity, and function β-diversity than temperature for both topsoil (0-10 cm depth) and subtopsoil (10-20 cm depth). Furthermore, precipitation had stronger impacts on function α-diversity for topsoil, species β-diversity for topsoil, and phylogenetic β-diversity for subtopsoil than temperature. The combination of species, phylogenetic and function diversity can better reflect geo-distribution patterns of soil fungal community. Compared to global warming, the impact of precipitation change on the variation in soil fungal community of P. flaccidum should be given more attention.
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Affiliation(s)
| | | | - Gang Fu
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
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Clasen LA, Detheridge AP, Scullion J, Griffith GW. Soil stabilisation for DNA metabarcoding of plants and fungi. Implications for sampling at remote locations or via third-parties. METABARCODING AND METAGENOMICS 2020. [DOI: 10.3897/mbmg.4.58365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Storage of soil samples prior to metagenomic analysis presents a problem. If field sites are remote or if samples are collected by third parties, transport to analytical laboratories may take several days or even weeks. The bulk of such samples and requirement for later homogenisation precludes the convenient use of a stabilisation buffer, so samples are usually cooled or frozen during transit. There has been limited testing of the most appropriate storage methods for later study of soil organisms by eDNA approaches. Here we tested a range of storage methods on two contrasting soils, comparing these methods to the control of freezing at -80 °C, followed by freeze-drying. To our knowledge, this is the first study to examine the effect of storage conditions on eukaryote DNA in soil, including both viable organisms (fungi) and DNA contained within dying/dead tissues (plants). For fungi, the best storage regimes (closest to the control) were storage at 4 °C (for up to 14 d) or active air-drying at room temperature. The worst treatments involved initial freezing, followed by thawing which led to significant later spoilage. The key spoilage organisms were identified as Metarhizium carneum and Mortierella spp., with a general increase in saprotrophic fungi and reduced abundances of mycorrhizal/biotrophic fungi. Plant data showed a similar pattern, but with greater variability in community structure, especially in the freeze-thaw treatments, probably due to stochastic variation in substrates for fungal decomposition, algal proliferation and some seed germination. In the absence of freeze drying facilities, samples should be shipped refrigerated, but not frozen if there is any risk of thawing.
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