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Crowther TW, Rappuoli R, Corinaldesi C, Danovaro R, Donohue TJ, Huisman J, Stein LY, Timmis JK, Timmis K, Anderson MZ, Bakken LR, Baylis M, Behrenfeld MJ, Boyd PW, Brettell I, Cavicchioli R, Delavaux CS, Foreman CM, Jansson JK, Koskella B, Milligan-McClellan K, North JA, Peterson D, Pizza M, Ramos JL, Reay D, Remais JV, Rich VI, Ripple WJ, Singh BK, Smith GR, Stewart FJ, Sullivan MB, van den Hoogen J, van Oppen MJH, Webster NS, Zohner CM, van Galen LG. Scientists' call to action: Microbes, planetary health, and the Sustainable Development Goals. Cell 2024; 187:5195-5216. [PMID: 39303686 DOI: 10.1016/j.cell.2024.07.051] [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: 10/18/2023] [Revised: 07/05/2024] [Accepted: 07/27/2024] [Indexed: 09/22/2024]
Abstract
Microorganisms, including bacteria, archaea, viruses, fungi, and protists, are essential to life on Earth and the functioning of the biosphere. Here, we discuss the key roles of microorganisms in achieving the United Nations Sustainable Development Goals (SDGs), highlighting recent and emerging advances in microbial research and technology that can facilitate our transition toward a sustainable future. Given the central role of microorganisms in the biochemical processing of elements, synthesizing new materials, supporting human health, and facilitating life in managed and natural landscapes, microbial research and technologies are directly or indirectly relevant for achieving each of the SDGs. More importantly, the ubiquitous and global role of microbes means that they present new opportunities for synergistically accelerating progress toward multiple sustainability goals. By effectively managing microbial health, we can achieve solutions that address multiple sustainability targets ranging from climate and human health to food and energy production. Emerging international policy frameworks should reflect the vital importance of microorganisms in achieving a sustainable future.
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Affiliation(s)
- Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland; Restor Eco AG, Zürich 8001, Switzerland.
| | - Rino Rappuoli
- Fondazione Biotecnopolo di Siena, Siena 53100, Italy.
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona 60131, Italy; National Biodiversity Future Center, Palermo 90133, Italy
| | - Roberto Danovaro
- National Biodiversity Future Center, Palermo 90133, Italy; Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona 60131, Italy
| | - Timothy J Donohue
- Wisconsin Energy Institute, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam 94240, the Netherlands
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - James Kenneth Timmis
- Institute of Political Science, University of Freiburg, Freiburg 79085, Germany; Athena Institute for Research on Innovation and Communication in Health and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081, the Netherlands
| | - Kenneth Timmis
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig 38106, Germany
| | - Matthew Z Anderson
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas 1433, Norway
| | - Matthew Baylis
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Cheshire, Neston CH64 7TE, UK
| | - Michael J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7004, Australia
| | - Ian Brettell
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Camille S Delavaux
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Christine M Foreman
- Department of Chemical and Biological Engineering and Center for Biofilm Engineering, Montana State University, Bozeman, MT 59718, USA
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kat Milligan-McClellan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA
| | - Justin A North
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Devin Peterson
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA
| | - Mariagrazia Pizza
- Department of Life Sciences, CBRB Center, Imperial College, London SW7 2AZ, UK
| | - Juan L Ramos
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada 18008, Spain
| | - David Reay
- School of GeoSciences, The University of Edinburgh, Edinburgh EH8 9XP, UK
| | - Justin V Remais
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Virginia I Rich
- Center of Microbiome Science, Byrd Polar and Climate Research, and Microbiology Department, The Ohio State University, Columbus, OH 43214, USA
| | - William J Ripple
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331-5704, USA
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Gabriel Reuben Smith
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Frank J Stewart
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Center of Microbiome Science, and EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
| | - Johan van den Hoogen
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia; School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nicole S Webster
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7004, Australia; Australian Institute of Marine Science, Townsville, QLD 4810, Australia; Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD 4072, Australia
| | - Constantin M Zohner
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Laura G van Galen
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland; Society for the Protection of Underground Networks (SPUN), Dover, DE 19901, USA.
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Khan A, Khan MS, Hadi F, Khan Q, Ali K, Saddiq G. Risk assessment and soil heavy metal contamination near marble processing plants (MPPs) in district Malakand, Pakistan. Sci Rep 2024; 14:21533. [PMID: 39278940 PMCID: PMC11403003 DOI: 10.1038/s41598-024-72346-7] [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: 07/23/2024] [Accepted: 09/05/2024] [Indexed: 09/18/2024] Open
Abstract
Soil heavy metals (HMs) pollution is a growing global concern, mainly in regions with rapid industrial growth. This study assessed the concentrations, potential sources, and health risks of HMs in agricultural soils near marble processing plants in Malakand, Pakistan. A total of 21 soil samples were analyzed for essential and toxic HMs via inductively coupled plasma‒optical emission spectrometry (ICP‒OES), and probabilistic health risks were evaluated via Monte Carlo simulation. The concentrations (mg/kg) of Ca (29,250), P (805.5) and Cd (4.5) exceeded the average shale limits of 22,100, 700, and 3.0 mg/kg, respectively, and indices such as Nemerow's synthetic contamination index (NSCI) and the geoaccumulation index (Igeo) categorized the soil sites as moderately polluted. The potential ecological risk index (PERI) indicated considerable to high ecological risk for As and Cd. The deterministic analysis indicated non-carcinogenic risks for children (HI > 1), whereas the probabilistic analysis suggested no significant risk (HI < 1) for both adults and children. Both methods indicated that the total cancer risk for Cr, Ni, Cd, and As exceeded the USEPA safety limits of 1.0E-06 and 1.0E-04. Sensitivity analysis identified heavy metal concentration, exposure duration, and frequency as key risk factors. The study suggested that HM contamination is mainly anthropogenic, poses a threat to soil and human health, and highlights the need for management strategies and surveillance programs to mitigate these risks.
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Affiliation(s)
- Asghar Khan
- Department of Botany, Islamia College, Peshawar, Pakistan.
- Department of Botany, Government Degree College, Totakan, District Malakand, Pakistan.
| | | | - Fazal Hadi
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Qaisar Khan
- Material Chemistry Laboratory, University of Malakand, Chakdara, Pakistan
| | - Kishwar Ali
- College of General Education, University of Doha for Science and Technology, Arab League Street, P.O. Box 24449, Doha, Qatar
| | - Ghulam Saddiq
- Department of Physics, Islamia College, Peshawar, Pakistan
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Samin OB, Algeelani NAA, Bathich A, Omar M, Mansoor M, Khan A. Optimizing agricultural data security: harnessing IoT and AI with Latency Aware Accuracy Index (LAAI). PeerJ Comput Sci 2024; 10:e2276. [PMID: 39314708 PMCID: PMC11419661 DOI: 10.7717/peerj-cs.2276] [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: 04/09/2024] [Accepted: 07/30/2024] [Indexed: 09/25/2024]
Abstract
The integration of Internet of Things (IoT) and artificial intelligence (AI) technologies into modern agriculture has profound implications on data collection, management, and decision-making processes. However, ensuring the security of agricultural data has consistently posed a significant challenge. This study presents a novel evaluation metric titled Latency Aware Accuracy Index (LAAI) for the purpose of optimizing data security in the agricultural sector. The LAAI uses the combined capacities of the IoT and AI in addition to the latency aspect. The use of IoT tools for data collection and AI algorithms for analysis makes farming operation more productive. The LAAI metric is a more holistic way to determine data accuracy while considering latency limitations. This ensures that farmers and other end-users are fed trustworthy information in a timely manner. This unified measure not only makes the data more secure but gives farmers the information that helps them to make smart decisions and, thus, drives healthier farming and food security.
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Affiliation(s)
- Omar Bin Samin
- Center of Excellence in IT, Institute of Management Sciences (IMSciences), Peshawar, Peshawar, Pakistan
- Faculty of Computer & Information Technology, Al-Madinah International University, Kuala Lumpur, Malaysia
| | - Nasir Ahmed Abdulkhader Algeelani
- Faculty of Computer & Information Technology, Al-Madinah International University, Kuala Lumpur, Malaysia
- Institute of Engineering, Electrical and Electronic Engineering, Hanze University of Applied Science, Groningen, Netherlands
| | - Ammar Bathich
- Faculty of Computer & Information Technology, Al-Madinah International University, Kuala Lumpur, Malaysia
| | - Maryam Omar
- Veritas Analytica, Leverify, Seattle, United States of America
| | - Musadaq Mansoor
- Faculty of Computer Science and Engineering, Ghulam Ishaq Khan Institute of Engineering Sciences and Technology, Topi, Pakistan
| | - Amir Khan
- Center of Excellence in IT, Institute of Management Sciences (IMSciences), Peshawar, Peshawar, Pakistan
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Gao H, Guo Z, He X, Yang J, Jiang L, Yang A, Xiao X, Xu R. Stress mitigation mechanism of rice leaf microbiota amid atmospheric deposition of heavy metals. CHEMOSPHERE 2024; 362:142680. [PMID: 38908447 DOI: 10.1016/j.chemosphere.2024.142680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/01/2024] [Accepted: 06/20/2024] [Indexed: 06/24/2024]
Abstract
Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition and promoting plant growth remain poorly understood. This study demonstrates that elevated atmospheric HM deposition on rice leaves significantly shapes distinct epiphytic and endophytic microbiota across all growth stages. HM stress consistently leads to the dominance of epiphytic Pantoea and endophytic Microbacterium in rice leaves, particularly during the booting and filling stages. Leaf-bound HMs stimulate the differentiation of specialized microbial communities in both endophytic and epiphytic compartments, thereby regulating leaf microbial interactions. Metagenomic binning retrieved high-quality genomes of keystone leaf microorganisms, indicating their potential for essential metabolic functions. Notably, Pantoea and Microbacterium show significant HM resistance, plant growth-promoting capabilities, and diverse element cycling functions. They possess genes associated with metal(loid) resistance, such as ars and czc, suggesting their ability to detoxify arsenic(As) and cadmium(Cd). They also support carbon, nitrogen, and sulfur cycling, with genes linked to carbon fixation, nitrogen fixation, and sulfur reduction. Additionally, these bacteria may enhance plant stress resistance and growth by producing antioxidants, phytohormones, and other beneficial compounds, potentially improving HM stress tolerance and nutrient availability in rice plants. This study shows that atmospheric HMs affect rice leaf microbial communities, prompting plants to seek microbial help to combat stress. The unique composition and metabolic potential of rice leaf microbiota offer a novel perspective for mitigating adverse stress induced by atmospheric HM deposition. This contributes to the utilization of leaf microbiota to alleviate the negative impact of heavy metal deposition on rice development and food security.
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Affiliation(s)
- Hanbing Gao
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Zhaohui Guo
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Xiao He
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Jinbo Yang
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Li Jiang
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Aiping Yang
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Xiyuan Xiao
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Rui Xu
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China.
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Jia X, Lin S, Zhang Q, Wang Y, Hong L, Li M, Zhang S, Wang T, Jia M, Luo Y, Ye J, Wang H. The Ability of Different Tea Tree Germplasm Resources in South China to Aggregate Rhizosphere Soil Characteristic Fungi Affects Tea Quality. PLANTS (BASEL, SWITZERLAND) 2024; 13:2029. [PMID: 39124147 PMCID: PMC11314174 DOI: 10.3390/plants13152029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/11/2024] [Accepted: 07/21/2024] [Indexed: 08/12/2024]
Abstract
It is generally recognized that the quality differences in plant germplasm resources are genetically determined, and that only a good "pedigree" can have good quality. Ecological memory of plants and rhizosphere soil fungi provides a new perspective to understand this phenomenon. Here, we selected 45 tea tree germplasm resources and analyzed the rhizosphere soil fungi, nutrient content and tea quality. We found that the ecological memory of tea trees for soil fungi led to the recruitment and aggregation of dominant fungal populations that were similar across tea tree varieties, differing only in the number of fungi. We performed continuous simulation and validation to identify four characteristic fungal genera that determined the quality differences. Further analysis showed that the greater the recruitment and aggregation of Saitozyma and Archaeorhizomyces by tea trees, the greater the rejection of Chaetomium and Trechispora, the higher the available nutrient content in the soil and the better the tea quality. In summary, our study presents a new perspective, showing that ecological memory between tea trees and rhizosphere soil fungi leads to differences in plants' ability to recruit and aggregate characteristic fungi, which is one of the most important determinants of tea quality. The artificial inoculation of rhizosphere fungi may reconstruct the ecological memory of tea trees and substantially improve their quality.
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Affiliation(s)
- Xiaoli Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
| | - Shaoxiong Lin
- College of Life Science, Longyan University, Longyan 364012, China
| | - Qi Zhang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
| | - Yuhua Wang
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lei Hong
- College of Life Science, Longyan University, Longyan 364012, China
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingzhe Li
- College of Life Science, Longyan University, Longyan 364012, China
| | - Shuqi Zhang
- College of Life Science, Longyan University, Longyan 364012, China
| | - Tingting Wang
- College of Life Science, Longyan University, Longyan 364012, China
| | - Miao Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
| | - Yangxin Luo
- College of Life Science, Longyan University, Longyan 364012, China
| | - Jianghua Ye
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
| | - Haibin Wang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
- College of Life Science, Longyan University, Longyan 364012, China
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Minoretti P, Emanuele E. From Agriculture to Clinics: Unlocking the Potential of Magnetized Water for Planetary and Human Health. Cureus 2024; 16:e64104. [PMID: 39114250 PMCID: PMC11305696 DOI: 10.7759/cureus.64104] [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] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Magnetized water (MW) is a form of liquid water that has been exposed to a magnetic field to alter its hydrogen bonding structure, resulting in the formation of water molecule clusters of various sizes and configurations connected by hydrogen bonds. This magnetization process induces several changes in the physicochemical properties of water, such as increased pH, electrical conductivity, and dissolved oxygen content, as well as decreased surface tension, density, and evaporation temperature compared to untreated water. In this narrative review, we explore the effective utilization of MW in agriculture, where it has a well-established history of applications, and its potential for direct applications in the medical field, which are currently at the forefront of research. MW is one of the most promising innovations for facilitating the transition from unsustainable to sustainable agriculture, which is expected to yield positive human health outcomes by promoting the consumption of less processed foods and reducing resource consumption. In addition to these indirect effects on human health, preclinical research utilizing animal models has demonstrated that water magnetization exerts beneficial effects on diabetes, renal function, bone health, and fertility. These health benefits appear to stem from the ability of MW to increase the activity of antioxidant enzymes while decreasing lipid peroxidation and inflammatory markers. In terms of direct human applications, MW has been primarily studied in the fields of dentistry and dermatology. MW mouthrinse has consistently shown efficacy against Streptococcus mutans, with studies reporting comparable effects to chlorhexidine. In dermatology, the topical application of MW has demonstrated improvements in skin biophysical parameters, increased hair count and hair mass index, and promoted the healing of challenging wounds. Intriguingly, these effects on human skin seem to be mediated by local activation of autophagy, potentially through mild alkaline stress. In conclusion, this review underscores the promising role of MW in promoting a holistic approach to planetary and human health. Future studies should focus on standardizing the magnetization process, exploring the molecular mechanisms underlying MW-induced autophagy, and investigating the potential of MW as a complementary strategy for treating human diseases characterized by impaired autophagy.
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Mesa-Ramos L, Palacios OA, Adame-Gallegos JR, Chávez-Flores D, Nevárez-Moorillón GV. Assessing antibiotic residues in sediments from mangrove ecosystems: A review. MARINE POLLUTION BULLETIN 2024; 204:116512. [PMID: 38810504 DOI: 10.1016/j.marpolbul.2024.116512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024]
Abstract
Antibiotics' widespread and abusive use in aquaculture and livestock leads to extensive environmental dissemination and dispersion, consequently increasing antibiotic-resistant bacteria in marine ecosystems. Hence, there is an increased need for efficient methods for identifying and quantifying antibiotic residues in soils and sediments. From a review of the last 20 years, we propose and compare different chromatographic techniques for detecting and quantifying antibiotics in sediment samples from marine ecosystems, particularly in mangrove forest sediments. The methods typically include three stages: extraction of antibiotics from the solid matrix, cleaning, and concentration of samples before quantification. We address the leading causes of the occurrence of antibiotics in marine ecosystem sediments and analyze the most appropriate methods for each analytical stage. Ultimately, selecting a method for identifying antibiotic residues depends on multiple factors, ranging from the nature and physicochemical properties of the analytes to the availability of the necessary equipment and the available resources.
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Affiliation(s)
- Liber Mesa-Ramos
- Facultad de Ciencias Químicas Universidad Autónoma de Chihuahua. Chihuahua, Chihuahua CP 31125, Mexico
| | - Oskar A Palacios
- Facultad de Ciencias Químicas Universidad Autónoma de Chihuahua. Chihuahua, Chihuahua CP 31125, Mexico
| | - Jaime Raúl Adame-Gallegos
- Facultad de Ciencias Químicas Universidad Autónoma de Chihuahua. Chihuahua, Chihuahua CP 31125, Mexico
| | - David Chávez-Flores
- Facultad de Ciencias Químicas Universidad Autónoma de Chihuahua. Chihuahua, Chihuahua CP 31125, Mexico
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Jia X, Lin S, Wang Y, Zhang Q, Jia M, Li M, Chen Y, Cheng P, Hong L, Zhang Y, Ye J, Wang H. Recruitment and Aggregation Capacity of Tea Trees to Rhizosphere Soil Characteristic Bacteria Affects the Quality of Tea Leaves. PLANTS (BASEL, SWITZERLAND) 2024; 13:1686. [PMID: 38931118 PMCID: PMC11207862 DOI: 10.3390/plants13121686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
There are obvious differences in quality between different varieties of the same plant, and it is not clear whether they can be effectively distinguished from each other from a bacterial point of view. In this study, 44 tea tree varieties (Camellia sinensis) were used to analyze the rhizosphere soil bacterial community using high-throughput sequencing technology, and five types of machine deep learning were used for modeling to obtain characteristic microorganisms that can effectively differentiate different varieties, and validation was performed. The relationship between characteristic microorganisms, soil nutrient transformation, and tea quality formation was further analyzed. It was found that 44 tea tree varieties were classified into two groups (group A and group B) and the characteristic bacteria that distinguished them came from 23 genera. Secondly, the content of rhizosphere soil available nutrients (available nitrogen, available phosphorus, and available potassium) and tea quality indexes (tea polyphenols, theanine, and caffeine) was significantly higher in group A than in group B. The classification result based on both was consistent with the above bacteria. This study provides a new insight and research methodology into the main reasons for the formation of quality differences among different varieties of the same plant.
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Affiliation(s)
- Xiaoli Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Shaoxiong Lin
- College of Life Science, Longyan University, Longyan 364012, China
| | - Yuhua Wang
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qi Zhang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Miao Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Mingzhe Li
- College of Life Science, Longyan University, Longyan 364012, China
| | - Yiling Chen
- College of Life Science, Longyan University, Longyan 364012, China
| | - Pengyuan Cheng
- College of Life Science, Longyan University, Longyan 364012, China
| | - Lei Hong
- College of Life Science, Longyan University, Longyan 364012, China
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ying Zhang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Jianghua Ye
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Haibin Wang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
- College of Life Science, Longyan University, Longyan 364012, China
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Pedrinho A, Karas PA, Kanellopoulos A, Feray E, Korman I, Wittenberg G, Ramot O, Karpouzas DG. The effect of natural products used as pesticides on the soil microbiota: OECD 216 nitrogen transformation test fails to identify effects that were detected via q-PCR microbial abundance measurement. PEST MANAGEMENT SCIENCE 2024; 80:2563-2576. [PMID: 38243771 DOI: 10.1002/ps.7961] [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: 09/22/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND Natural products present an environmentally attractive alternative to synthetic pesticides which have been implicated in the off-target effect. Currently, the assessment of pesticide toxicity on soil microorganisms relies on the OECD 216 N transformation assay (OECD stands for the Organisation Economic Co-operation and Development, which is a key international standard-setting organisation). We tested the hypotheses that (i) the OECD 216 assay fails to identify unacceptable effects of pesticides on soil microbiota compared to more advanced molecular and standardized tests, and (ii) the natural products tested (dihydrochalcone, isoflavone, aliphatic phenol, and spinosad) are less toxic to soil microbiota compared to a synthetic pesticide compound (3,5-dichloraniline). We determined the following in three different soils: (i) ammonium (NH4 +) and nitrate (NO3 -) soil concentrations, as dictated by the OECD 216 test, and (ii) the abundance of phylogenetically (bacteria and fungi) and functionally distinct microbial groups [ammonia-oxidizing archaea (AOA) and bacteria (AOB)] using quantitative polymerase chain reaction (q-PCR). RESULTS All pesticides tested exhibited limited persistence, with spinosad demonstrating the highest persistence. None of the pesticides tested showed clear dose-dependent effects on NH4 + and NO3 - levels and the observed effects were <25% of the control, suggesting no unacceptable impacts on soil microorganisms. In contrast, q-PCR measurements revealed (i) distinct negative effects on the abundance of total bacteria and fungi, which were though limited to one of the studied soils, and (ii) a significant reduction in the abundance of both AOA and AOB across soils. This reduction was attributed to both natural products and 3,5-dichloraniline. CONCLUSION Our findings strongly advocate for a revision of the current regulatory framework regarding the toxicity of pesticides to soil microbiota, which should integrate advanced and well-standardized tools. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Alexandre Pedrinho
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
- Metabolic Insights Ltd, Ness Ziona, Israel
| | - Panagiotis A Karas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Alexandros Kanellopoulos
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Emma Feray
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
- National Museum of Natural History, Paris, France
| | - Ido Korman
- Metabolic Insights Ltd, Ness Ziona, Israel
| | | | - Ofir Ramot
- Metabolic Insights Ltd, Ness Ziona, Israel
| | - Dimitrios G Karpouzas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
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10
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Timmis K, Hallsworth JE. This is the Age of Microbial Technology: Crucial roles of learned societies and academies. Microb Biotechnol 2024; 17:e14450. [PMID: 38683674 PMCID: PMC11057497 DOI: 10.1111/1751-7915.14450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 03/07/2024] [Indexed: 05/02/2024] Open
Abstract
Microbial technologies constitute a huge and unique potential for confronting major humanitarian and biosphere challenges, especially in the realms of sustainability and providing basic goods and services where they are needed and particularly in low-resource settings. These technologies are evolving rapidly. Powerful approaches are being developed to create novel products, processes, and circular economies, including new prophylactics and therapies in healthcare, bioelectric systems, and whole-cell understanding of metabolism that provides novel insights into mechanisms and how they can be utilised for applications. The modulation of microbiomes promises to create important applications and mitigate problems in a number of spheres. Collectively, microbial technologies save millions of lives each year and have the potential, through increased deployment, to save many more. They help restore environmental health, improve soil fertility, enable regenerative agriculture, reduce biodiversity losses, reduce pollution, and mitigate polluted environments. Many microbial technologies may be considered to be 'healing' technologies - healing of humans, of other members of the biosphere, and of the environment. This is the Age of Microbial Technology. However, the current exploitation of microbial technologies in the service of humanity and planetary health is woefully inadequate and this failing unnecessarily costs many lives and biosphere deterioration. Microbiologists - the practitioners of these healing technologies - have a special, preordained responsibility to promote and increase their deployment for the good of humanity and the planet. To do this effectively - to actually make a difference - microbiologists will need to partner with key enablers and gatekeepers, players such as other scientists with essential complementary skills like bioengineering and bioinformatics, politicians, financiers, and captains of industry, international organisations, and the general public. Orchestration and coordination of the establishment and functioning of effective partnerships will best be accomplished by learned societies, their academies, and the international umbrella organisations of learned societies. Effective dedication of players to the tasks at hand will require unstinting support from employers, particularly the heads of institutes of higher education and of research establishments. Humanity and the biosphere are currently facing challenges to their survival not experienced for millennia. Effectively confronting these challenges is existential, and microbiologists and their learned societies have pivotal roles to play: they must step up and act now.
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Affiliation(s)
- Kenneth Timmis
- Institute for MicrobiologyTechnical University of BraunschweigBraunschweigGermany
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
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11
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Bernal P. How are microbes helping end hunger? Microb Biotechnol 2024; 17:e14432. [PMID: 38465536 PMCID: PMC10926054 DOI: 10.1111/1751-7915.14432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/12/2024] Open
Abstract
This article explores the potential of microbiology to positively impact all aspects of the food supply chain, improving the quantity, quality, safety, and nutritional value of food products by providing innovative ways of growing, processing, and preserving food and thus contributing to Zero Hunger, one of the Sustainable Development Goals (SDGs) of the United Nations.
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Affiliation(s)
- Patricia Bernal
- Departamento de Microbiología, Facultad de BiologíaUniversidad de SevillaSevilleSpain
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12
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He M, Han Y, Gao Y, Han M, Duan L. Decoding the metabolomic responses of Caragana tibetica to livestock grazing in fragile ecosystems. FRONTIERS IN PLANT SCIENCE 2024; 15:1339424. [PMID: 38525150 PMCID: PMC10959174 DOI: 10.3389/fpls.2024.1339424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/07/2024] [Indexed: 03/26/2024]
Abstract
The population of Caragana tibetica, situated on the edge of the typical grassland-to-desert transition in the Mu Us Sandy Land, plays a vital ecological role in maintaining stability within the regional fragile ecosystem. Despite the consistent growth of C. tibetica following animal grazing, the biological mechanisms underlying its compensatory growth in response to livestock consumption remain unclear. Analyzing 48 metabolomic profiles from C. tibetica, our study reveals that the grazing process induces significant changes in the metabolic pathways of C. tibetica branches. Differential metabolites show correlations with soluble protein content, catalase, peroxidase, superoxide dismutase, malondialdehyde, and proline levels. Moreover, machine learning models built on these differential metabolites accurately predict the intensity of C. tibetica grazing (with an accuracy of 83.3%). The content of various metabolites, indicative of plant stress responses, including Enterolactone, Narceine, and Folcepri, exhibits significant variations in response to varying grazing intensities (P<0.05). Our investigation reveals that elevated grazing intensity intensifies the stress response in C. tibetica, triggering heightened antioxidative defenses and stress-induced biochemical activities. Distinctive metabolites play a pivotal role in responding to stress, facilitating the plant's adaptation to environmental challenges and fostering regeneration.
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Affiliation(s)
- Minghui He
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanlong Han
- College of Desert Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Hangjin Desert Ecological Position Research Station, Ordos, Inner Mongolia, China
| | - Yong Gao
- College of Desert Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Min Han
- College of Desert Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Liqing Duan
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
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13
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Behr JH, Kuhl-Nagel T, Sommermann L, Moradtalab N, Chowdhury SP, Schloter M, Windisch S, Schellenberg I, Maccario L, Sørensen SJ, Rothballer M, Geistlinger J, Smalla K, Ludewig U, Neumann G, Grosch R, Babin D. Long-term conservation tillage with reduced nitrogen fertilization intensity can improve winter wheat health via positive plant-microorganism feedback in the rhizosphere. FEMS Microbiol Ecol 2024; 100:fiae003. [PMID: 38224956 PMCID: PMC10847717 DOI: 10.1093/femsec/fiae003] [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: 11/09/2023] [Revised: 12/21/2023] [Accepted: 01/12/2024] [Indexed: 01/17/2024] Open
Abstract
Microbiome-based solutions are regarded key for sustainable agroecosystems. However, it is unclear how agricultural practices affect the rhizosphere microbiome, plant-microorganism interactions and crop performance under field conditions. Therefore, we installed root observation windows in a winter wheat field cultivated either under long-term mouldboard plough (MP) or cultivator tillage (CT). Each tillage practice was also compared at two nitrogen (N) fertilization intensities, intensive (recommended N-supply with pesticides/growth regulators) or extensive (reduced N-supply, no fungicides/growth regulators). Shoot biomass, root exudates and rhizosphere metabolites, physiological stress indicators, and gene expression were analyzed together with the rhizosphere microbiome (bacterial/archaeal 16S rRNA gene, fungal ITS amplicon, and shotgun metagenome sequencing) shortly before flowering. Compared to MP, the rhizosphere of CT winter wheat contained more primary and secondary metabolites, especially benzoxazinoid derivatives. Potential copiotrophic and plant-beneficial taxa (e.g. Bacillus, Devosia, and Trichoderma) as well as functional genes (e.g. siderophore production, trehalose synthase, and ACC deaminase) were enriched in the CT rhizosphere, suggesting that tillage affected belowground plant-microorganism interactions. In addition, physiological stress markers were suppressed in CT winter wheat compared to MP. In summary, tillage practice was a major driver of crop performance, root deposits, and rhizosphere microbiome interactions, while the N-fertilization intensity was also relevant, but less important.
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Affiliation(s)
- Jan Helge Behr
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Theresa Kuhl-Nagel
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Loreen Sommermann
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Narges Moradtalab
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Soumitra Paul Chowdhury
- Institute of Network Biology
, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis
(COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Saskia Windisch
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Ingo Schellenberg
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Lorrie Maccario
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Michael Rothballer
- Institute of Network Biology
, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Joerg Geistlinger
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Uwe Ludewig
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Günter Neumann
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Doreen Babin
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
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Jiménez‐Guerrero I, López‐Baena FJ, Borrero‐de Acuña JM, Pérez‐Montaño F. Membrane vesicle engineering with "à la carte" bacterial-immunogenic molecules for organism-free plant vaccination. Microb Biotechnol 2023; 16:2223-2235. [PMID: 37530752 PMCID: PMC10686165 DOI: 10.1111/1751-7915.14323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 08/03/2023] Open
Abstract
The United Nations heralds a world population exponential increase exceeding 9.7 billion by 2050. This poses the challenge of covering the nutritional needs of an overpopulated world by the hand of preserving the environment. Extensive agriculture practices harnessed the employment of fertilizers and pesticides to boost crop productivity and prevent economic and harvest yield losses attributed to plagues and diseases. Unfortunately, the concomitant hazardous effects stemmed from such agriculture techniques are cumbersome, that is, biodiversity loss, soils and waters contaminations, and human and animal poisoning. Hence, the so-called 'green agriculture' research revolves around designing novel biopesticides and plant growth-promoting bio-agents to the end of curbing the detrimental effects. In this field, microbe-plant interactions studies offer multiple possibilities for reshaping the plant holobiont physiology to its benefit. Along these lines, bacterial extracellular membrane vesicles emerge as an appealing molecular tool to capitalize on. These nanoparticles convey a manifold of molecules that mediate intricate bacteria-plant interactions including plant immunomodulation. Herein, we bring into the spotlight bacterial extracellular membrane vesicle engineering to encase immunomodulatory effectors into their cargo for their application as biocontrol agents. The overarching goal is achieving plant priming by deploying its innate immune responses thereby preventing upcoming infections.
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15
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Zhang M, Kong Z, Fu H, Shu X, Xue Q, Lai H, Guo Q. Rhizosphere microbial ecological characteristics of strawberry root rot. Front Microbiol 2023; 14:1286740. [PMID: 38033596 PMCID: PMC10687216 DOI: 10.3389/fmicb.2023.1286740] [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: 08/31/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Strawberry (Fragaria × ananassa Duch.) holds a preeminent position among small fruits globally due to its delectable fruits and significant economic value. However, strawberry cultivation is hampered by various plant diseases, hindering the sustainable development of the strawberry industry. The occurrence of plant diseases is closely linked to imbalance in rhizosphere microbial community structure. Methods In the present study, a systematic analysis of the differences and correlations among non-culturable microorganisms, cultivable microbial communities, and soil nutrients in rhizosphere soil, root surface soil, and non-rhizosphere soil of healthy and diseased strawberry plants affected by root rot was conducted. The goal was to explore the relationship between strawberry root rot occurrence and rhizosphere microbial community structure. Results According to the results, strawberry root rot altered microbial community diversity, influenced fungal community composition in strawberry roots, reduced microbial interaction network stability, and enriched more endophytic-phytopathogenic bacteria and saprophytic bacteria. In addition, the number of bacteria isolated from the root surface soil of diseased plants was significantly higher than that of healthy plants. Discussion In summary, the diseased strawberry plants changed microbial community diversity, fungal species composition, and enriched functional microorganisms significantly, in addition to reshaping the microbial co-occurrence network. The results provide a theoretical basis for revealing the microecological mechanism of strawberry root rot and the ecological prevention and control of strawberry root rot from a microbial ecology perspective.
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Affiliation(s)
| | | | | | | | | | | | - Qiao Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
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16
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La Cono V, Messina E, Reva O, Smedile F, La Spada G, Crisafi F, Marturano L, Miguez N, Ferrer M, Selivanova EA, Golyshina OV, Golyshin PN, Rohde M, Krupovic M, Merkel AY, Sorokin DY, Hallsworth JE, Yakimov MM. Nanohaloarchaea as beneficiaries of xylan degradation by haloarchaea. Microb Biotechnol 2023; 16:1803-1822. [PMID: 37317055 PMCID: PMC10443357 DOI: 10.1111/1751-7915.14272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/18/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Climate change, desertification, salinisation of soils and the changing hydrology of the Earth are creating or modifying microbial habitats at all scales including the oceans, saline groundwaters and brine lakes. In environments that are saline or hypersaline, the biodegradation of recalcitrant plant and animal polysaccharides can be inhibited by salt-induced microbial stress and/or by limitation of the metabolic capabilities of halophilic microbes. We recently demonstrated that the chitinolytic haloarchaeon Halomicrobium can serve as the host for an ectosymbiont, nanohaloarchaeon 'Candidatus Nanohalobium constans'. Here, we consider whether nanohaloarchaea can benefit from the haloarchaea-mediated degradation of xylan, a major hemicellulose component of wood. Using samples of natural evaporitic brines and anthropogenic solar salterns, we describe genome-inferred trophic relations in two extremely halophilic xylan-degrading three-member consortia. We succeeded in genome assembly and closure for all members of both xylan-degrading cultures and elucidated the respective food chains within these consortia. We provide evidence that ectosymbiontic nanohaloarchaea is an active ecophysiological component of extremely halophilic xylan-degrading communities (although by proxy) in hypersaline environments. In each consortium, nanohaloarchaea occur as ectosymbionts of Haloferax, which in turn act as scavenger of oligosaccharides produced by xylan-hydrolysing Halorhabdus. We further obtained and characterised the nanohaloarchaea-host associations using microscopy, multi-omics and cultivation approaches. The current study also doubled culturable nanohaloarchaeal symbionts and demonstrated that these enigmatic nano-sized archaea can be readily isolated in binary co-cultures using an appropriate enrichment strategy. We discuss the implications of xylan degradation by halophiles in biotechnology and for the United Nation's Sustainable Development Goals.
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Affiliation(s)
| | | | - Oleg Reva
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Centre for Bioinformatics and Computational BiologyUniversity of PretoriaPretoriaSouth Africa
| | | | | | | | | | - Noa Miguez
- Instituto de Catalisis y Petroleoquimica (ICP), CSICMadridSpain
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSICMadridSpain
| | - Elena A. Selivanova
- Institute for Cellular and Intracellular SymbiosisUral Branch, Russian Academy of SciencesOrenburgRussia
| | | | | | - Manfred Rohde
- Central Facility for MicrobiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Mart Krupovic
- Institut PasteurUniversité Paris Cité, Archaeal Virology UnitParisFrance
| | - Alexander Y. Merkel
- Winogradsky Institute of MicrobiologyResearch Centre of Biotechnology, Russian Academy of SciencesMoscowRussia
| | - Dimitry Y. Sorokin
- Winogradsky Institute of MicrobiologyResearch Centre of Biotechnology, Russian Academy of SciencesMoscowRussia
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastNorthern IrelandUK
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17
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Zeng G, Liu Z, Guo Z, He J, Ye Y, Xu H, Hu T. Compost with spent mushroom substrate and chicken manure enhances rice seedling quality and reduces soil-borne pathogens. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27681-z. [PMID: 37258808 DOI: 10.1007/s11356-023-27681-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/12/2023] [Indexed: 06/02/2023]
Abstract
Using cultivated soils for rice seedlings can reduce the sustainability of arable land and thus giving negative impacts to food production. As a substitute, spent mushroom compost (SMC), which has high water-holding capacity and nutrient content, shows great potentials. To determine the impacts of the proportion of SMC and paddy soil on seedling quality, rhizosphere microbial characteristics, and fungal pathogens in rice seedling substrates, we conducted a 21-day pot experiment for rice seedling under five treatments: CK, 100% paddy soil; R1, 20% SMC and 80% paddy soil; R2, 50% SMC and 50% paddy soil; R3, 80% SMC and 20% paddy soil; and R4, 100% SMC. The results showed that incorporating SMC into the substrate, especially at 50% volume (R2), increased seedling growth and vitality at the seedling growth stage without external fertilization. Moreover, the SMC amendment increased microbial activity and promoted rice seedling recruitment of plant growth-promoting rhizobacteria (PGPR) and fungi (PGPF). In addition, using SMC significantly reduced the abundance of pathogenic fungi, especially Magnaporthe grisea. Overall, the multi-faceted benefits exhibit the strong possibilities of using SMC in sustainable rice productions.
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Affiliation(s)
- Guiyang Zeng
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, People's Republic of China
| | - Zhihui Liu
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China
| | - Zhangliang Guo
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, People's Republic of China
| | - Jinfeng He
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China
| | - Yingying Ye
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China
| | - Huaqin Xu
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China.
| | - Teng Hu
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China
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18
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Hallsworth JE, Udaondo Z, Pedrós‐Alió C, Höfer J, Benison KC, Lloyd KG, Cordero RJB, de Campos CBL, Yakimov MM, Amils R. Scientific novelty beyond the experiment. Microb Biotechnol 2023; 16:1131-1173. [PMID: 36786388 PMCID: PMC10221578 DOI: 10.1111/1751-7915.14222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 02/15/2023] Open
Abstract
Practical experiments drive important scientific discoveries in biology, but theory-based research studies also contribute novel-sometimes paradigm-changing-findings. Here, we appraise the roles of theory-based approaches focusing on the experiment-dominated wet-biology research areas of microbial growth and survival, cell physiology, host-pathogen interactions, and competitive or symbiotic interactions. Additional examples relate to analyses of genome-sequence data, climate change and planetary health, habitability, and astrobiology. We assess the importance of thought at each step of the research process; the roles of natural philosophy, and inconsistencies in logic and language, as drivers of scientific progress; the value of thought experiments; the use and limitations of artificial intelligence technologies, including their potential for interdisciplinary and transdisciplinary research; and other instances when theory is the most-direct and most-scientifically robust route to scientific novelty including the development of techniques for practical experimentation or fieldwork. We highlight the intrinsic need for human engagement in scientific innovation, an issue pertinent to the ongoing controversy over papers authored using/authored by artificial intelligence (such as the large language model/chatbot ChatGPT). Other issues discussed are the way in which aspects of language can bias thinking towards the spatial rather than the temporal (and how this biased thinking can lead to skewed scientific terminology); receptivity to research that is non-mainstream; and the importance of theory-based science in education and epistemology. Whereas we briefly highlight classic works (those by Oakes Ames, Francis H.C. Crick and James D. Watson, Charles R. Darwin, Albert Einstein, James E. Lovelock, Lynn Margulis, Gilbert Ryle, Erwin R.J.A. Schrödinger, Alan M. Turing, and others), the focus is on microbiology studies that are more-recent, discussing these in the context of the scientific process and the types of scientific novelty that they represent. These include several studies carried out during the 2020 to 2022 lockdowns of the COVID-19 pandemic when access to research laboratories was disallowed (or limited). We interviewed the authors of some of the featured microbiology-related papers and-although we ourselves are involved in laboratory experiments and practical fieldwork-also drew from our own research experiences showing that such studies can not only produce new scientific findings but can also transcend barriers between disciplines, act counter to scientific reductionism, integrate biological data across different timescales and levels of complexity, and circumvent constraints imposed by practical techniques. In relation to urgent research needs, we believe that climate change and other global challenges may require approaches beyond the experiment.
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Affiliation(s)
- John E. Hallsworth
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - Zulema Udaondo
- Department of Biomedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Carlos Pedrós‐Alió
- Department of Systems BiologyCentro Nacional de Biotecnología (CSIC)MadridSpain
| | - Juan Höfer
- Escuela de Ciencias del MarPontificia Universidad Católica de ValparaísoValparaísoChile
| | - Kathleen C. Benison
- Department of Geology and GeographyWest Virginia UniversityMorgantownWest VirginiaUSA
| | - Karen G. Lloyd
- Microbiology DepartmentUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Radamés J. B. Cordero
- Department of Molecular Microbiology and ImmunologyJohns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
| | - Claudia B. L. de Campos
- Institute of Science and TechnologyUniversidade Federal de Sao Paulo (UNIFESP)São José dos CamposSPBrazil
| | | | - Ricardo Amils
- Department of Molecular Biology, Centro de Biología Molecular Severo Ochoa (CSIC‐UAM)Nicolás Cabrera n° 1, Universidad Autónoma de MadridMadridSpain
- Department of Planetology and HabitabilityCentro de Astrobiología (INTA‐CSIC)Torrejón de ArdozSpain
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19
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Anand S, Hallsworth JE, Timmis J, Verstraete W, Casadevall A, Ramos JL, Sood U, Kumar R, Hira P, Dogra Rawat C, Kumar A, Lal S, Lal R, Timmis K. Weaponising microbes for peace. Microb Biotechnol 2023; 16:1091-1111. [PMID: 36880421 PMCID: PMC10221547 DOI: 10.1111/1751-7915.14224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 03/08/2023] Open
Abstract
There is much human disadvantage and unmet need in the world, including deficits in basic resources and services considered to be human rights, such as drinking water, sanitation and hygiene, healthy nutrition, access to basic healthcare, and a clean environment. Furthermore, there are substantive asymmetries in the distribution of key resources among peoples. These deficits and asymmetries can lead to local and regional crises among peoples competing for limited resources, which, in turn, can become sources of discontent and conflict. Such conflicts have the potential to escalate into regional wars and even lead to global instability. Ergo: in addition to moral and ethical imperatives to level up, to ensure that all peoples have basic resources and services essential for healthy living and to reduce inequalities, all nations have a self-interest to pursue with determination all available avenues to promote peace through reducing sources of conflicts in the world. Microorganisms and pertinent microbial technologies have unique and exceptional abilities to provide, or contribute to the provision of, basic resources and services that are lacking in many parts of the world, and thereby address key deficits that might constitute sources of conflict. However, the deployment of such technologies to this end is seriously underexploited. Here, we highlight some of the key available and emerging technologies that demand greater consideration and exploitation in endeavours to eliminate unnecessary deprivations, enable healthy lives of all and remove preventable grounds for competition over limited resources that can escalate into conflicts in the world. We exhort central actors: microbiologists, funding agencies and philanthropic organisations, politicians worldwide and international governmental and non-governmental organisations, to engage - in full partnership - with all relevant stakeholders, to 'weaponise' microbes and microbial technologies to fight resource deficits and asymmetries, in particular among the most vulnerable populations, and thereby create humanitarian conditions more conducive to harmony and peace.
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Affiliation(s)
- Shailly Anand
- Department of ZoologyDeen Dayal Upadhyaya College, University of DelhiDelhiIndia
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - James Timmis
- Athena Institute for Research on Innovation and Communication in Health and Life SciencesVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityGhentBelgium
| | - Arturo Casadevall
- Department of MedicineJohns Hopkins School of Public Health and School of MedicineBaltimoreMarylandUSA
| | | | - Utkarsh Sood
- Department of ZoologyKirori Mal College, University of DelhiDelhiIndia
| | - Roshan Kumar
- Post‐Graduate Department of ZoologyMagadh UniversityBodh GayaBiharIndia
| | - Princy Hira
- Department of ZoologyMaitreyi College, University of DelhiNew DelhiIndia
| | | | - Abhilash Kumar
- Department of ZoologyRamjas College, University of DelhiDelhiIndia
| | - Sukanya Lal
- PhiXgen Pvt. LtdGurugram, GurgaonHaryanaIndia
| | - Rup Lal
- Acharya Narendra Dev College, University of DelhiGovindpuri, Kalkaji, New DelhiIndia
| | - Kenneth Timmis
- Institute of Microbiology, Technical University BraunschweigBraunschweigGermany
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20
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Peng Y, Guan CY, Samuel AZ. Editorial: Exploring complex biosphere molecular signaling networks: plant-microbes symbiosis at microscopic to macroscopic levels. FRONTIERS IN PLANT SCIENCE 2023; 14:1199162. [PMID: 37304722 PMCID: PMC10254790 DOI: 10.3389/fpls.2023.1199162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/03/2023] [Indexed: 06/13/2023]
Affiliation(s)
- Yutao Peng
- School of Agriculture, Sun Yat-Sen University, Shenzhen, China
| | - Chung-Yu Guan
- Department of Environmental Engineering, College of Engineering, National Ilan University, Yilan, Taiwan
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21
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Noel D, Hallsworth JE, Gelhaye E, Darnet S, Sormani R, Morel-Rouhier M. Modes-of-action of antifungal compounds: Stressors and (target-site-specific) toxins, toxicants, or Toxin-stressors. Microb Biotechnol 2023. [PMID: 37191200 DOI: 10.1111/1751-7915.14242] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/11/2023] [Accepted: 02/16/2023] [Indexed: 05/17/2023] Open
Abstract
Fungi and antifungal compounds are relevant to the United Nation's Sustainable Development Goals. However, the modes-of-action of antifungals-whether they are naturally occurring substances or anthropogenic fungicides-are often unknown or are misallocated in terms of their mechanistic category. Here, we consider the most effective approaches to identifying whether antifungal substances are cellular stressors, toxins/toxicants (that are target-site-specific), or have a hybrid mode-of-action as Toxin-stressors (that induce cellular stress yet are target-site-specific). This newly described 'toxin-stressor' category includes some photosensitisers that target the cell membrane and, once activated by light or ultraviolet radiation, cause oxidative damage. We provide a glossary of terms and a diagrammatic representation of diverse types of stressors, toxic substances, and Toxin-stressors, a classification that is pertinent to inhibitory substances not only for fungi but for all types of cellular life. A decision-tree approach can also be used to help differentiate toxic substances from cellular stressors (Curr Opin Biotechnol 2015 33: 228-259). For compounds that target specific sites in the cell, we evaluate the relative merits of using metabolite analyses, chemical genetics, chemoproteomics, transcriptomics, and the target-based drug-discovery approach (based on that used in pharmaceutical research), focusing on both ascomycete models and the less-studied basidiomycete fungi. Chemical genetic methods to elucidate modes-of-action currently have limited application for fungi where molecular tools are not yet available; we discuss ways to circumvent this bottleneck. We also discuss ecologically commonplace scenarios in which multiple substances act to limit the functionality of the fungal cell and a number of as-yet-unresolved questions about the modes-of-action of antifungal compounds pertaining to the Sustainable Development Goals.
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Affiliation(s)
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Eric Gelhaye
- Université de Lorraine, INRAE, IAM, Nancy, France
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22
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Timmis K. A Road to Microbiology Literacy (and More): an Opportunity for a Paradigm Change in Teaching. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2023; 24:e00019-23. [PMID: 37089226 PMCID: PMC10117087 DOI: 10.1128/jmbe.00019-23] [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: 02/08/2023] [Accepted: 03/07/2023] [Indexed: 05/03/2023]
Abstract
Microbial activities pervasively impact the wellbeing of all organisms, including humans, and the functioning of the planet itself. In order for society to form informed opinions and take effective actions related to its welfare, it must be able to understand the causes of issues of importance and to appreciate the range of possible responses and their likely effectiveness. Society must become microbiology literate. The International Microbiology Literacy Initiative is creating a comprehensive range of teaching resources that will constitute a child-centric school curriculum of societally relevant microbiology. The core of the teaching resources, the lessons, are somewhat unusual in that each one is designed to be essentially stand-alone, so courses can be individually structured by teachers according to their perception of what is interesting and important for their charges. Moreover, the lessons deal not only with societally pertinent microbial activities, but also discuss and propose discussion of their relevance to sustainable development, of their impact on policies and decisions (personal, community, and national), and of issues of stewardship and stakeholder responsibilities. The class lessons are complemented by other child-centric teaching resources whose functions are to add value, to stimulate pupil imagination and excitement in discovery, to engage pupil interest and enthusiasm for topics like sustainability, climate change, international cooperation, citizen science, etc., and to empower pupils as stakeholders in their microbiology education and as educators and multiplicators.
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Affiliation(s)
- Kenneth Timmis
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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23
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Sagova-Mareckova M, Omelka M, Kopecky J. The Golden Goal of Soil Management: Disease-Suppressive Soils. PHYTOPATHOLOGY 2023; 113:741-752. [PMID: 36510361 DOI: 10.1094/phyto-09-22-0324-kd] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Disease-suppressive soils encompass specific plant-pathogen-microbial interactions and represent a rare example of an agroecosystem where soil conditions and microbiome together prevent the pathogen from causing disease. Such soils have the potential to serve as a model for characterizing soil pathogen-related aspects of soil health, but the mechanisms driving the establishment of suppressive soils vary and are often poorly characterized. Yet, they can serve as a resource for identifying markers for beneficial activities of soil microorganisms concerning pathogen prevention. Many recent studies have focused on the nature of disease-suppressive soils, but it has remained difficult to predict where and when they will occur. This review outlines current knowledge on the distribution of these soils, soil manipulations leading to pathogen suppression, and markers including bacterial and fungal diversity, enzymes, and secondary metabolites. The importance to consider soil legacy in research on the principles that define suppressive soils is also highlighted. The goal is to extend the context in which we understand, study, and use disease-suppressive soils by evaluating the relationships in which they occur and function. Finally, we suggest that disease-suppressive soils are critical not only for the development of indicators of soil health, but also for the exploration of general ecological principles about the surrounding landscape, effects of deeper layers of the soil profile, little studied soil organisms, and their interactions for future use in modern agriculture.
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Affiliation(s)
- Marketa Sagova-Mareckova
- Group Epidemiology and Ecology of Microorganisms, Crop Research Institute, Drnovska 507, Prague 6-Ruzyne, 161 06, Czechia
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamycka 129, 165 00, Prague-Suchdol, Czechia
| | - Marek Omelka
- Faculty of Mathematics and Physics, Department of Probability and Mathematical Statistics, Charles University, Sokolovska 83, Prague 8, 186 75, Czechia
| | - Jan Kopecky
- Group Epidemiology and Ecology of Microorganisms, Crop Research Institute, Drnovska 507, Prague 6-Ruzyne, 161 06, Czechia
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24
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Sadeq BM, Tan Kee Zuan A, Kasim S, Mui Yun W, Othman NMI, Alkooranee JT, Chompa SS, Akter A, Rahman ME. Humic Acid-Amended Formulation Improves Shelf-Life of Plant Growth-Promoting Rhizobacteria (PGPR) Under Laboratory Conditions. PERTANIKA JOURNAL OF SCIENCE AND TECHNOLOGY 2023. [DOI: 10.47836/pjst.31.3.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) is a soil bacterium that positively impacts soil and crops. These microbes invade plant roots, promote plant growth, and improve crop yield production. Bacillus subtilis is a type of PGPR with a short shelf-life due to its structural and cellular components, with a non-producing resistance structure (spores). Therefore, optimum formulations must be developed to prolong the bacterial shelf-life by adding humic acid (HA) as an amendment that could benefit the microbes by providing shelter and carbon sources for bacteria. Thus, a study was undertaken to develop a biofertilizer formulation from locally isolated PGPR, using HA as an amendment. Four doses of HA (0, 0.01, 0.05, and 0.1%) were added to tryptic soy broth (TSB) media and inoculated with B. subtilis (UPMB10), Bacillus tequilensis (UPMRB9) and the combination of both strains. The shelf-life was recorded, and viable cells count and optical density were used to determine the bacterial population and growth trend at monthly intervals and endospores detection using the malachite green staining method. After 12 months of incubation, TSB amended with 0.1% HA recorded the highest bacterial population significantly with inoculation of UPMRB9, followed by mixed strains and UPMB10 at 1.8x107 CFUmL-1, 2.8x107 CFUmL-1and 8.9x106 CFUmL-1, respectively. Results showed that a higher concentration of HA has successfully prolonged the bacterial shelf-life with minimal cell loss. Thus, this study has shown that the optimum concentration of humic acid can extend the bacterial shelf-life and improve the quality of a biofertilizer.
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Timmis K. Microbiology education: a significant path to sustainably improve the human and biosphere condition. MICROLIFE 2023; 4:uqad013. [PMID: 37223743 PMCID: PMC10117706 DOI: 10.1093/femsml/uqad013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 02/06/2023] [Accepted: 03/08/2023] [Indexed: 05/25/2023]
Abstract
In this short piece, I connect the dots between the pervasive influence of microbial activities on our health and that of the planet, including their positive and negative roles in current polycrises, our ability to influence microbes to promote their positive influences and mitigate their negative impacts, the roles of everyone as stewards and stakeholders in personal, family, community, national, and global wellbeing, the need for stewards and stakeholders to possess relevant information in order to fulfil their roles and obligations, and the compelling case for microbiology literacy and introduction of a societally relevant microbiology curriculum in school.
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Affiliation(s)
- Kenneth Timmis
- Institute of Microbiology, Technical University of Braunschweig, D-38106 Braunschweig, Germany
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26
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Marasco R, Ramond JB, Van Goethem MW, Rossi F, Daffonchio D. Diamonds in the rough: Dryland microorganisms are ecological engineers to restore degraded land and mitigate desertification. Microb Biotechnol 2023. [PMID: 36641786 PMCID: PMC10364308 DOI: 10.1111/1751-7915.14216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/16/2023] Open
Abstract
Our planet teeters on the brink of massive ecosystem collapses, and arid regions experience manifold environmental and climatic challenges that increase the magnitude of selective pressures on already stressed ecosystems. Ultimately, this leads to their aridification and desertification, that is, to simplified and barren ecosystems (with proportionally less microbial load and diversity) with altered functions and food webs and modification of microbial community network. Thus, preserving and restoring soil health in such a fragile biome could help buffer climate change's effects. We argue that microorganisms and the protection of their functional properties and networks are key to fight desertification. Specifically, we claim that it is rational, possible and certainly practical to rely on native dryland edaphic microorganisms and microbial communities as well as dryland plants and their associated microbiota to conserve and restore soil health and mitigate soil depletion in newly aridified lands. Furthermore, this will meet the objective of protecting/stabilizing (and even enhancing) soil biodiversity globally. Without urgent conservation and restoration actions that take into account microbial diversity, we will ultimately, and simply, not have anything to protect anymore.
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Affiliation(s)
- Ramona Marasco
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Jean-Baptiste Ramond
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marc W Van Goethem
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Federico Rossi
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, Pisa, Italy
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
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27
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Bonfante P. How to reconnect mycorrhizal research with natural environments. Environ Microbiol 2023; 25:59-63. [PMID: 36655714 DOI: 10.1111/1462-2920.16199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023]
Affiliation(s)
- Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
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28
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Timmis K. Environmental Microbiology is 25! Environ Microbiol 2023; 25:1-4. [PMID: 36043245 DOI: 10.1111/1462-2920.16163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Kenneth Timmis
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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29
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Timmis K. Microbiology education and human stewardship of Planet Earth: The generational contract. Environ Microbiol 2023; 25:49-53. [PMID: 36314688 DOI: 10.1111/1462-2920.16272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Kenneth Timmis
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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30
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Ganesh J, Singh V, Hewitt K, Kaundal A. Exploration of the rhizosphere microbiome of native plant Ceanothus velutinus - an excellent resource of plant growth-promoting bacteria. FRONTIERS IN PLANT SCIENCE 2022; 13:979069. [PMID: 36589081 PMCID: PMC9798410 DOI: 10.3389/fpls.2022.979069] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Continuous demand for an increase in food production due to climate change and a steady rise in world population requires stress-resilient, sustainable agriculture. Overuse of chemical fertilizers and monoculture farming to achieve this goal deteriorated soil health and negatively affected its microbiome. The rhizosphere microbiome of a plant plays a significant role in its growth and development and promotes the plant's overall health through nutrient uptake/availability, stress tolerance, and biocontrol activity. The Intermountain West (IW) region of the US is rich in native plants recommended for low water use landscaping because of their drought tolerance. The rhizosphere microbiome of these native plants is an excellent resource for plant growth-promoting rhizobacteria (PGPR) to use these microbes as biofertilizers and biostimulants to enhance food production, mitigate environmental stresses and an alternative for chemical fertilizer, and improve soil health. Here, we isolated, purified, identified, and characterized 64 bacterial isolates from a native plant, Ceanothus velutinus, commonly known as snowbrush ceanothus, from the natural habitat and the greenhouse-grown native soil-treated snowbrush ceanothus plants. We also conducted a microbial diversity analysis of the rhizosphere of greenhouse-grown native soil-treated and untreated plants (control). Twenty-seven of the 64 isolates were from the rhizosphere of the native region, and 36 were from the greenhouse-grown native soil-treated plants. These isolates were also tested for plant growth-promoting (PGP) traits such as their ability to produce catalase, siderophore, and indole acetic acid, fix atmospheric nitrogen and solubilize phosphate. Thirteen bacterial isolates tested positive for all five plant growth-promoting abilities and belonged to the genera Pantoea, Pseudomonas, Bacillus, and Ancylobacter. Besides, there are isolates belonging to the genus Streptomyces, Bacillus, Peribacillus, Variovorax, Xenophilus, Brevundimonas, and Priestia, which exhibit at least one of the plant growth-promoting activities. This initial screen provided a list of potential PGPR to test for plant health improvement on model and crop plants. Most of the bacterial isolates in this study have a great potential to become biofertilizers and bio-stimulants.
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Affiliation(s)
| | | | | | - Amita Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
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31
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Rodrigues-dos Santos AS, Rebelo-Romão I, Zhang H, Vílchez JI. Discerning Transcriptomic and Biochemical Responses of Arabidopsis thaliana Treated with the Biofertilizer Strain Priestia megaterium YC4-R4: Boosting Plant Central and Secondary Metabolism. PLANTS (BASEL, SWITZERLAND) 2022; 11:3039. [PMID: 36432768 PMCID: PMC9697256 DOI: 10.3390/plants11223039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
As a response to the current challenges in agriculture, the application of alternatives to a more sustainable management is required. Thus, biofertilizers begin to emerge as a reliable alternative to improve crop development and resistance to stresses. Among other effects on the plant, the use of beneficial strains may cause changes in their metabolic regulation, as in cell wall biogenesis and in nutrient/ion transportation, improving their growth process. Previous works showed that inoculation with the strain Priestia megaterium YC4-R4 effectively promoted vegetative growth of Arabidopsis thaliana Col-0 plants. Hence, the present work recorded a strain-mediated induction of several pathways of the central and secondary metabolism of the plant, as the induction of lipid, cellulose, phenol, and flavonoid biosynthesis, by using transcriptomic and biochemical analyses.
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Affiliation(s)
| | - Inês Rebelo-Romão
- Instituto de Tecnologia Química e Biológica (ITQB)-NOVA Lisboa, 2780-157 Oeiras, Portugal
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Juan Ignacio Vílchez
- Instituto de Tecnologia Química e Biológica (ITQB)-NOVA Lisboa, 2780-157 Oeiras, Portugal
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai 200032, China
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Liu Y, Štefanič P, Miao Y, Xue Y, Xun W, Zhang N, Shen Q, Zhang R, Xu Z, Mandic-Mulec I. Housekeeping gene gyrA, a potential molecular marker for Bacillus ecology study. AMB Express 2022; 12:133. [DOI: 10.1186/s13568-022-01477-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/15/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractBacillus is a genus of microorganisms (bacteria) and contains many important commercial species used in industry, agriculture and healthcare. Many different Bacilli are relatively well understood at the single-cell level; however, molecular tools that determine the diversity and ecology of Bacillus community are limited, which limits our understanding of how the Bacillus community works. In the present study, we investigated the potential of the housekeeping gene gyrA as a molecular marker for determining the diversity of Bacillus species. The amplification efficiency for Bacillus species diversity could be greatly improved by primer design. Therefore, we designed a novel primer pair gyrA3 that can detect at least 92 Bacillus species and related species. For B. amyloliquefaciens, B. pumilus, and B. megaterium, we observed that the high variability of the gyrA gene allows for more detailed clustering at the subspecies level that cannot be achieved by the 16S rRNA gene. Since gyrA provides better phylogenetic resolution than 16S rRNA and informs on the diversity of the Bacillus community, we propose that the gyrA gene may have broad application prospects in the study of Bacillus ecology.
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Ruan Z, Xu M, Xing Y, Jiang Q, Yang B, Jiang J, Xu X. Interspecies Metabolic Interactions in a Synergistic Consortium Drive Efficient Degradation of the Herbicide Bromoxynil Octanoate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11613-11622. [PMID: 36089742 DOI: 10.1021/acs.jafc.2c03057] [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: 06/15/2023]
Abstract
Microbial communities play vital roles in biogeochemical cycles, allowing biodegradation of a wide range of pollutants. Although many studies have shown the importance of interspecies interactions on activities of communities, fully elucidating the complex interactions in microbial communities is still challenging. Here, we isolated a consortium containing two bacterial strains (Acinetobacter sp. AG3 and Bacillus sp. R45), which could mineralize bromoxynil octanoate (BO) with higher efficiency than either strain individually. The BO degradation pathway by the synergistic consortium was elucidated, and interspecies interactions in the consortium were explored using genome-scale metabolic models (GSMMs). Modeling showed that growth and degradation enhancements were driven by metabolic interactions, such as syntrophic exchanges of small metabolites in the consortium. Besides, nutritional enhancers were predicted to improve BO degradation, which were tested experimentally. Overall, our results will enhance our understanding of microbial mineralization of BO by consortia and promote the application of microbial communities for bioremediation.
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Affiliation(s)
- Zhepu Ruan
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Mengjun Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Youwen Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Qi Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Bingang Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
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de Lorenzo V. Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210395. [PMID: 35757882 PMCID: PMC9234819 DOI: 10.1098/rstb.2021.0395] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Contemporary synthetic biology-based biotechnologies are generating tools and strategies for reprogramming genomes for specific purposes, including improvement and/or creation of microbial processes for tackling climate change. While such activities typically work well at a laboratory or bioreactor scale, the challenge of their extensive delivery to multiple spatio-temporal dimensions has hardly been tackled thus far. This state of affairs creates a research niche for what could be called Environmental Galenics (EG), i.e. the science and technology of releasing designed biological agents into deteriorated ecosystems for the sake of their safe and effective recovery. Such endeavour asks not just for an optimal performance of the biological activity at stake, but also the material form and formulation of the agents, their propagation and their interplay with the physico-chemical scenario where they are expected to perform. EG also encompasses adopting available physical carriers of microorganisms and channels of horizontal gene transfer as potential paths for spreading beneficial activities through environmental microbiomes. While some of these propositions may sound unsettling to anti-genetically modified organisms sensitivities, they may also fall under the tag of TINA (there is no alternative) technologies in the cases where a mere reduction of emissions will not help the revitalization of irreversibly lost ecosystems. This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid 28049, Spain
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35
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D'Agui HM, van der Heyde ME, Nevill PG, Mousavi‐Derazmahalleh M, Dixon KW, Moreira‐Grez B, Valliere JM. Evaluating biological properties of topsoil for post‐mining ecological restoration: different assessment methods give different results. Restor Ecol 2022. [DOI: 10.1111/rec.13738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haylee M. D'Agui
- ARC Centre for Mine Site Restoration School of Molecular and life Sciences, Curtin University, Kent Street Bentley Western Australia Australia 6102
| | - Mieke E. van der Heyde
- ARC Centre for Mine Site Restoration School of Molecular and life Sciences, Curtin University, Kent Street Bentley Western Australia Australia 6102
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences, Curtin University, Kent Street Bentley Western Australia 6102
| | - Paul G. Nevill
- ARC Centre for Mine Site Restoration School of Molecular and life Sciences, Curtin University, Kent Street Bentley Western Australia Australia 6102
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences, Curtin University, Kent Street Bentley Western Australia 6102
| | - Mahsa Mousavi‐Derazmahalleh
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences, Curtin University, Kent Street Bentley Western Australia 6102
| | - Kingsley W. Dixon
- ARC Centre for Mine Site Restoration School of Molecular and life Sciences, Curtin University, Kent Street Bentley Western Australia Australia 6102
| | - Benjamin Moreira‐Grez
- UWA School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway Crawley Western Australia Australia 6009
| | - Justin M. Valliere
- ARC Centre for Mine Site Restoration School of Molecular and life Sciences, Curtin University, Kent Street Bentley Western Australia Australia 6102
- UWA School of Biological Sciences, University of Western Australia, 35 Stirling Highway Crawley Western Australia Australia 6009
- California State University, Dominguez Hills, 1000 E Victoria Street Carson California USA 90747
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Meng M, Li Y, Yao H. Plasmid-Mediated Transfer of Antibiotic Resistance Genes in Soil. Antibiotics (Basel) 2022; 11:antibiotics11040525. [PMID: 35453275 PMCID: PMC9024699 DOI: 10.3390/antibiotics11040525] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/09/2022] [Accepted: 04/13/2022] [Indexed: 12/18/2022] Open
Abstract
Due to selective pressure from the widespread use of antibiotics, antibiotic resistance genes (ARGs) are found in human hosts, plants, and animals and virtually all natural environments. Their migration and transmission in different environmental media are often more harmful than antibiotics themselves. ARGs mainly move between different microorganisms through a variety of mobile genetic elements (MGEs), such as plasmids and phages. The soil environment is regarded as the most microbially active biosphere on the Earth’s surface and is closely related to human activities. With the increase in human activity, soils are becoming increasingly contaminated with antibiotics and ARGs. Soil plasmids play an important role in this process. This paper reviews the current scenario of plasmid-mediated migration and transmission of ARGs in natural environments and under different antibiotic selection pressures, summarizes the current methods of plasmid extraction and analysis, and briefly introduces the mechanism of plasmid splice transfer using the F factor as an example. However, as the global spread of drug-resistant bacteria has increased and the knowledge of MGEs improves, the contribution of soil plasmids to resistance gene transmission needs to be further investigated. The prevalence of multidrug-resistant bacteria has also made the effective prevention of the transmission of resistance genes through the plasmid-bacteria pathway a major research priority.
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Affiliation(s)
- Miaoling Meng
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, China;
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China;
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, China;
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China;
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- Correspondence: ; Tel.: +86-0574-8678-4812
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Timmis K, Ramos JL, Verstraete W. Microbial biotechnology to assure national security of supplies of essential resources: energy, food and water, medical reagents, waste disposal and a circular economy. Microb Biotechnol 2022; 15:1021-1025. [PMID: 35322937 PMCID: PMC8966030 DOI: 10.1111/1751-7915.14049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 11/17/2022] Open
Abstract
The core responsibility of governments is the security of their citizens, and this means inter alia protecting their safety, nutrition and health. Microbiology and microbial biotechnology have key roles to play in improving supply security of essential resources. In this paper, we discuss the urgent need to fully and immediately exploit existing microbial biotechnologies to maximize supply security of energy, food and medical supplies, and of waste management, and to invest in new research specifically targetting supply security of essential resources.
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Affiliation(s)
- Kenneth Timmis
- Institute of MicrobiologyTechnical UniversityBraunschweigGermany
| | | | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityGhentBelgium
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Shi W, Xing Y, Zhu Y, Gao N, Ying Y. Diverse responses of pqqC- and phoD-harbouring bacterial communities to variation in soil properties of Moso bamboo forests. Microb Biotechnol 2022; 15:2097-2111. [PMID: 35298867 PMCID: PMC9249317 DOI: 10.1111/1751-7915.14029] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/30/2022] Open
Abstract
Phosphate‐mobilizing bacteria (PMB) play a critical role in the regulation of phosphorus availability in the soil. The microbial genes pqqC and phoD encode pyrroloquinoline quinone synthase and bacterial alkaline phosphatase, respectively, which regulate inorganic and organic phosphorus mobilization, and are therefore used as PMB markers. We examined the effects of soil properties in three Moso bamboo forest sites on the PMB communities that were profiled using high‐throughput sequencing. We observed differentiated responses of pqqC‐ and phoD‐harbouring PMB communities to various soil conditions. There was significant variation among the sites in the diversity and structure of the phoD‐harbouring community, which correlated with variation in phosphorus levels and non‐capillary porosity; soil organic carbon and soil water content also affected the structure of the phoD‐harbouring community. However, no significant difference in the diversity of pqqC‐harbouring community was observed among different sites, while the structure of the pqqC‐harbouring bacteria community was affected by soil organic carbon and soil total nitrogen, but not soil phosphorus levels. Overall, changes in soil conditions affected the phoD‐harbouring community more than the pqqC‐harbouring community. These findings provide a new insight to explore the effects of soil conditions on microbial communities that solubilize inorganic phosphate and mineralize organic phosphate.
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Affiliation(s)
- Wenhui Shi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yijing Xing
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Ying Zhu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Ning Gao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yeqing Ying
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
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39
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Timmis K, Hallsworth JE. The darkest microbiome-a post-human biosphere. Microb Biotechnol 2022; 15:176-185. [PMID: 34843168 PMCID: PMC8719803 DOI: 10.1111/1751-7915.13976] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 01/05/2023] Open
Abstract
Microbial technology is exceptional among human activities and endeavours in its range of applications that benefit humanity, even exceeding those of chemistry. What is more, microbial technologists are among the most creative scientists, and the scope of the field continuously expands as new ideas and applications emerge. Notwithstanding this diversity of applications, given the dire predictions for the fate of the surface biosphere as a result of current trajectories of global warming, the future of microbial biotechnology research must have a single purpose, namely to help secure the future of life on Earth. Everything else will, by comparison, be irrelevant. Crucially, microbes themselves play pivotal roles in climate (Cavicchioli et al., Nature Revs Microbiol 17: 569-586, 2019). To enable realization of their full potential in humanity's effort to survive, development of new and transformative global warming-relevant technologies must become the lynchpin of microbial biotechnology research and development. As a consequence, microbial biotechnologists must consider constraining their usual degree of freedom, and re-orienting their focus towards planetary-biosphere exigences. And they must actively seek alliances and synergies with others to get the job done as fast as humanly possible; they need to enthusiastically embrace and join the global effort, subordinating where necessary individual aspirations to the common good (the amazing speed with which new COVID-19 diagnostics and vaccines were developed and implemented demonstrates what is possible given creativity, singleness of purpose and funding). In terms of priorities, some will be obvious, others less so, with some only becoming revealed after dedicated effort yields new insights/opens new vistas. We therefore refrain from developing a priority list here. Rather, we consider what is likely to happen to the Earth's biosphere if we (and the rest of humanity) fail to rescue it. We do so with the aim of galvanizing the formulation and implementation of strategic and financial science policy decisions that will maximally stimulate the development of relevant new microbial technologies, and maximally exploit available technologies, to repair existing environmental damage and mitigate against future deterioration.
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Affiliation(s)
- Kenneth Timmis
- Institute of MicrobiologyTechnical University of BraunschweigBraunschweigGermany
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García-Franco A, Godoy P, de la Torre J, Duque E, Ramos JL. United Nations sustainability development goals approached from the side of the biological production of fuels. Microb Biotechnol 2021; 14:1871-1877. [PMID: 34427993 PMCID: PMC8449664 DOI: 10.1111/1751-7915.13912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 08/09/2021] [Indexed: 01/07/2023] Open
Affiliation(s)
- Ana García-Franco
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain.,Programa de Bioquímica y Biología Molecular, University of Granada, Granada, Spain
| | - Patricia Godoy
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain
| | | | - Estrella Duque
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain
| | - Juan L Ramos
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain
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Mills S, Ross RP. Colliding and interacting microbiomes and microbial communities - consequences for human health. Environ Microbiol 2021; 23:7341-7354. [PMID: 34390616 DOI: 10.1111/1462-2920.15722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/26/2022]
Abstract
Living 'things' coexist with microorganisms, known as the microbiota/microbiome that provides essential physiological functions to its host. Despite this reliance, the microbiome is malleable and can be altered by several factors including birth-mode, age, antibiotics, nutrition, and disease. In this minireview, we consider how other microbiomes and microbial communities impact the host microbiome and the host through the concept of microbiome collisions (initial exposures) and interactions. Interactions include changes in host microbiome composition and functionality and/or host responses. Understanding the impact of other microbiomes and microbial communities on the microbiome and host are important considering the decline in human microbiota diversity in the developed world - paralleled by the surge of non-communicable, inflammatory-based diseases. Thus, surrounding ourselves with rich and diverse beneficial microbiomes and microbial communities to collide and interact with should help to diminish the loss in microbial diversity and protect from certain diseases. In the same vein, our microbiomes not only influence our health but potentially the health of those close to us. We also consider strategies for enhanced host microbiome collisions and interactions through the surrounding environment that ensure increased microbiome diversity and functionality contributing to enhanced symbiotic return to the host in terms of health benefit.
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Affiliation(s)
- Susan Mills
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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