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Jiang J, Hou R, Cui H, Tang Z, Yousif Abdellah YA, Chater CCC, Cheng K, Yu F, Liu D. Removal of artificial sweeteners in wastewater treatment plants and their degradation during sewage sludge composting with micro- and nano-sized kaolin. BIORESOURCE TECHNOLOGY 2024; 406:131060. [PMID: 38950831 DOI: 10.1016/j.biortech.2024.131060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/16/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
This study surveyed the fates of artificial sweeteners in influent, effluent, and sewage sludge (SS) in wastewater treatment plant, and investigated the effects of Micro-Kaolin (Micro-KL) and Nano-Kaolin (Nano-KL) on nitrogen transformation and sucralose (SUC) and acesulfame (ACE) degradation during SS composting. Results showed the cumulative rate of ACE and SUC in SS was ∼76 %. During SS composting, kaolin reduced NH3 emissions by 30.2-45.38 %, and N2O emissions by 38.4-38.9 %, while the Micro-KL and Nano-KL reduced nitrogen losses by 14.8 % and 12.5 %, respectively. Meanwhile, Micro-KL and Nano-KL increased ACE degradation by 76.8 % and 84.2 %, and SUC degradation by 75.3 % and 77.7 %, and significantly shifted microbial community structure. Furthermore, kaolin caused a positive association between Actinobacteria and sweetener degradation. Taken together, kaolin effectively inhibited nitrogen loss and promoted the degradation of ACE and SUC during the SS composting, which is of great significance for the removal of emerging organic pollutants in SS.
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Affiliation(s)
- Jishao Jiang
- School of Environment, Henan Normal University, Xinxiang, Henan 453007, China.
| | - Rui Hou
- School of Environment, Henan Normal University, Xinxiang, Henan 453007, China
| | - Huilin Cui
- School of Environment, Henan Normal University, Xinxiang, Henan 453007, China
| | - Zhuyu Tang
- School of Environment, Henan Normal University, Xinxiang, Henan 453007, China
| | - Yousif Abdelrahman Yousif Abdellah
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Caspar C C Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK; Plants, Photosynthesis, and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Ke Cheng
- School of Environment, Henan Normal University, Xinxiang, Henan 453007, China
| | - Fuqiang Yu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Dong Liu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.
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Orole OO, Adewumi T, Adefolalu A. Biological assessment and radiological impact in Keana, North Central Nigeria: environmental implication and metabolites production. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:756. [PMID: 39033483 DOI: 10.1007/s10661-024-12919-1] [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: 03/10/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
The objective of the research was to examine microbial characteristics, metabolites produced, and the potential radiological risks present in mining soils located in Keana, North Central Nigeria. Soil samples were collected from various locations within Keana, Nasarawa State. Bacterial isolation was carried out, and molecular techniques were employed to characterize the bacteria found in the collected soil samples. Additionally, the susceptibility of these isolates to antibiotics was determined, and the bacteria screened for their ability to produce metabolites. The isolated bacteria were classified into three groups: Actinobacteria, Firmicutes, and Proteobacteria. The analysis of the spectra revealed that 1595 compounds were produced, including carboxylic acids, nitro compounds, aldehydes, anhydrides, esters, ketones, amides, phenols, alcohols, alkanes, alkenes, alkynes, and arenes. Some of the metabolites produced were oleic acid, 1,3-dioxolane, linoelaidic acid and oleic acid, 1-nonadecene, butylated hydroxytoluene, diisooctyl phthalate, bis(2-ethylhexyl) phthalate among others, and 1,2-benzenedicarboxylic acid (85.32%) as the most produced metabolite. Among the antibiotics tested, levofloxacin and ciprofloxacin exhibited the strongest antibacterial properties against the isolates. Airborne gamma-ray spectrometry analysis identified elevated levels of potassium, thorium, and uranium in the soils, indicating potential environmental hazards. However, no significant correlation was found between the presence of bacteria and radioactive elements. These findings emphasize the importance of comprehensive environmental monitoring in Keana to address potential health risks associated with microbial contamination and radioactive materials. Additionally, the study highlighted the role of microbial diversity in Keana soils in promoting the production of secondary metabolites with potential applications in pharmaceutical and industrial sectors..
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Affiliation(s)
| | - Taiwo Adewumi
- Department of Physics, Federal University of Lafia, Lafia, Nasarawa State, Nigeria, 950101
| | - Adedotun Adefolalu
- Department of Biochemistry, Federal University of Lafia, Lafia, Nasarawa State, Nigeria, 950101
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Bartak D, Šachlová Š, Kašpar V, Říha J, Dobrev D, Večerník P, Hlaváčková V, Matulová M, Černá K. Dramatic loss of microbial viability in bentonite exposed to heat and gamma radiation: implications for deep geological repository. World J Microbiol Biotechnol 2024; 40:264. [PMID: 38990244 PMCID: PMC11239606 DOI: 10.1007/s11274-024-04069-w] [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: 04/11/2024] [Accepted: 06/30/2024] [Indexed: 07/12/2024]
Abstract
Bentonite is an integral part of the engineered barrier system (EBS) in deep geological repositories (DGR) for nuclear waste, but its indigenous microorganisms may jeopardize long-term EBS integrity. To predict microbial activity in DGRs, it is essential to understand microbial reactions to the early hot phase of DGR evolution. Two bentonites (BCV and MX-80) with varied bentonite/water ratios and saturation levels (compacted to 1600 kg.m- 3 dry density/powder/suspension), were subjected to heat (90-150 °C) and irradiation (0.4 Gy.h- 1) in the long-term experiments (up to 18 months). Molecular-genetic, microscopic, and cultivation-based techniques assessed microbial survivability. Exposure to 90 °C and 150 °C notably diminished microbial viability, irrespective of bentonite form, with negligible impacts from irradiation or sample type compared to temperature. Bentonite powder samples exhibited microbial recovery after 90 °C heating for up to 6 months but not 12 months in most cases; exposure to 150 °C had an even stronger effect. Further long-term experiments at additional temperatures combined with the mathematical prediction of temperature evolution in DGR are recommended to validate the possible evolution and spatial distribution of microbially depleted zones in bentonite buffer around the waste canisters and refine predictions of microbial effects over time in the DGR.
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Affiliation(s)
- Deepa Bartak
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec, 460 01, Czech Republic
| | - Šárka Šachlová
- Disposal Processes and Safety, ÚJV Řež, a. s., Hlavní 130, Husinec, 250 68, Czech Republic
| | - Vlastislav Kašpar
- Disposal Processes and Safety, ÚJV Řež, a. s., Hlavní 130, Husinec, 250 68, Czech Republic
| | - Jakub Říha
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec, 460 01, Czech Republic
| | - David Dobrev
- Disposal Processes and Safety, ÚJV Řež, a. s., Hlavní 130, Husinec, 250 68, Czech Republic
| | - Petr Večerník
- Disposal Processes and Safety, ÚJV Řež, a. s., Hlavní 130, Husinec, 250 68, Czech Republic
| | - Veronika Hlaváčková
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec, 460 01, Czech Republic
| | - Michaela Matulová
- Radioactive Waste Repository Authority, SÚRAO, Dlážděná 6, Prague, 11000, Czech Republic
| | - Kateřina Černá
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec, 460 01, Czech Republic.
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Oubohssaine M, Sbabou L, Aurag J. Potential of the plant growth-promoting rhizobacterium Rhodococcus qingshengii LMR356 in mitigating lead stress impact on Sulla spinosissima L. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:46002-46022. [PMID: 38980484 DOI: 10.1007/s11356-024-34150-8] [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: 02/15/2024] [Accepted: 06/24/2024] [Indexed: 07/10/2024]
Abstract
Mining-related lead (Pb) pollution of the soil poses serious hazards to ecosystems and living organisms, including humans. Improved heavy metal phytoremediation efficacy, achieved by using phytostabilizing plants assisted by plant-growth-promoting (PGP) microorganisms, has been presented as an effective strategy for remediating polluted soils. The objective of this research was to examine the response and potential of the plant-growth-promoting bacterium LMR356, a Rhodococcus qingshengii strain isolated from an abandoned mining soil, under lead stress conditions. Compared to non-contaminated culture media, the presence of lead induced a significant decrease in auxin production (from 21.17 to 2.65 μg mL-1) and phosphate solubilization (from 33.60 to 8.22 mg L-1), whereas other PGP traits increased drastically, such as 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity (from 38.17 to 71.37 nmol mg-1 h-1 α-ketobutyrate), siderophore production (from 69 to 83%), exopolysaccharide production (from 1952.28 to 3637.72 mg mL-1), biofilm formation, and motility. We, therefore, investigated the behavior of Sulla spinosissima L. in the presence or absence of this strain under a variety of experimental conditions. Under hydroponic conditions, Sulla plants showed endurance to varying lead concentrations (500-1000 μM). Inoculation of plants with Rhodococcus qingshengii strain LMR356 enhanced plant tolerance, as demonstrated by the increase in plant biomass (ranging from 14.41 to 79.12%) compared to non-inoculated Pb-stressed and non-stressed control plants. Antioxidant enzyme activities (increasing by -42.71 to 126.8%) and chlorophyll (383.33%) and carotenoid (613.04%) content were also augmented. In addition to its impact on plant lead tolerance, strain LMR356 showed a growth-promoting effect on Sulla plants when cultivated in sterilized non-contaminated sand. Parameters such as plant biomass (16.57%), chlorophyll (24.14%), and carotenoid (30%) contents, as well as ascorbate peroxidase (APX), peroxidase (POD), and catalase (CAT) activities, were all elevated compared to non-inoculated plants. Furthermore, when the same plant species was cultivated in highly polluted soil, inoculation increased plant biomass and improved its physiological properties. These findings demonstrate that LMR356 is a phytobeneficial bacterial strain capable of enhancing Sulla growth under normal conditions and improving its heavy metal tolerance in multi-polluted soils. Thus, it can be considered a promising biofertilizer candidate for growing Sulla spinosissima L. or other selected plants intended for application in restoration and stabilization initiatives aimed at reviving and safeguarding environmentally compromised and polluted soils after mining activities.
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Affiliation(s)
- Malika Oubohssaine
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, 10000, Rabat, Morocco.
| | - Laila Sbabou
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, 10000, Rabat, Morocco
| | - Jamal Aurag
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, 10000, Rabat, Morocco
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Mo J, Song Z, Che Y, Li J, Liu T, Feng J, Wang Z, Rong J, Gu S. Effects of aeolian deposition on soil properties and microbial carbon metabolism function in farmland of Songnen Plain, China. Sci Rep 2024; 14:14791. [PMID: 38926449 PMCID: PMC11208439 DOI: 10.1038/s41598-024-65578-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/21/2024] [Indexed: 06/28/2024] Open
Abstract
The effects of wind erosion, one of the crucial causes of soil desertification in the world, on the terrestrial ecosystem are well known. However, ecosystem responses regarding soil microbial carbon metabolism to sand deposition caused by wind erosion, a crucial driver of biogeochemical cycles, remain largely unclear. In this study, we collected soil samples from typical aeolian deposition farmland in the Songnen Plain of China to evaluate the effects of sand deposition on soil properties, microbial communities, and carbon metabolism function. We also determined the reads number of carbon metabolism-related genes by high-throughput sequencing technologies and evaluated the association between sand deposition and them. The results showed that long-term sand deposition resulted in soil infertile, roughness, and dryness. The impacts of sand deposition on topsoil were more severe than on deep soil. The diversity of soil microbial communities was significantly reduced due to sand deposition. The relative abundances of Nitrobacteraceae, Burkholderiaceae, and Rhodanobacteraceae belonging to α-Proteobacteria significantly decreased, while the relative abundances of Streptomycetaceae and Geodermatophilaceae belonging to Actinobacteria increased. The results of the metagenomic analysis showed that the gene abundances of carbohydrate metabolism and carbohydrate-activity enzyme (GH and CBM) significantly decreased with the increase of sand deposition amount. The changes in soil microbial community structure and carbon metabolism decreased soil carbon emissions and carbon cycling in aeolian deposition farmland, which may be the essential reasons for land degradation in aeolian deposition farmland.
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Affiliation(s)
- Jixian Mo
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
- College of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Ziwei Song
- College of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Yanjing Che
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Jie Li
- College of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Tianyi Liu
- College of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Jingyi Feng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Ziying Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Jiandong Rong
- Qiqihar Experimental Station, Heilongjiang Province Hydraulic Research Institute, Qiqihar, 161006, China
| | - Siyu Gu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
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Kalkreuter E, Kautsar SA, Yang D, Bader CD, Teijaro CN, Fluegel LL, Davis CM, Simpson JR, Lauterbach L, Steele AD, Gui C, Meng S, Li G, Viehrig K, Ye F, Su P, Kiefer AF, Nichols A, Cepeda AJ, Yan W, Fan B, Jiang Y, Adhikari A, Zheng CJ, Schuster L, Cowan TM, Smanski MJ, Chevrette MG, de Carvalho LPS, Shen B. The Natural Products Discovery Center: Release of the First 8490 Sequenced Strains for Exploring Actinobacteria Biosynthetic Diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.14.571759. [PMID: 38168313 PMCID: PMC10760148 DOI: 10.1101/2023.12.14.571759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Actinobacteria, the bacterial phylum most renowned for natural product discovery, has been established as a valuable source for drug discovery and biotechnology but is underrepresented within accessible genome and strain collections. Herein, we introduce the Natural Products Discovery Center (NPDC), featuring 122,449 strains assembled over eight decades, the genomes of the first 8490 NPDC strains (7142 Actinobacteria), and the online NPDC Portal making both strains and genomes publicly available. A comparative survey of RefSeq and NPDC Actinobacteria highlights the taxonomic and biosynthetic diversity within the NPDC collection, including three new genera, hundreds of new species, and ~7000 new gene cluster families. Selected examples demonstrate how the NPDC Portal's strain metadata, genomes, and biosynthetic gene clusters can be leveraged using genome mining approaches. Our findings underscore the ongoing significance of Actinobacteria in natural product discovery, and the NPDC serves as an unparalleled resource for both Actinobacteria strains and genomes.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Satria A. Kautsar
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Dong Yang
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Chantal D. Bader
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Christiana N. Teijaro
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Department of Discovery Chemistry, Bristol-Meyers Squibb, Princeton, NJ 08543
| | - Lucas L. Fluegel
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458
| | - Christina M. Davis
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458
| | - Johnathon R. Simpson
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Prepaire Labs, Pompano Beach, FL 33060
| | - Lukas Lauterbach
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Andrew D. Steele
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Chun Gui
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Song Meng
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: State Key Laboratory of Drug Research & Natural Products Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People’s Republic of China, Beijing, China 100049
| | - Gengnan Li
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Centivax Inc., South San Francisco, CA 94080
| | - Konrad Viehrig
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal 4450-208
| | - Fei Ye
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Department of Biological Chemistry & Molecular Pharmacology, Harvard University, Boston, MA 02115
| | - Ping Su
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: State Key Laboratory for Quality Assurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China 100700
| | - Alexander F. Kiefer
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Angela Nichols
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458
| | - Alexis J. Cepeda
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458
| | - Wei Yan
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: College of Plant Protection, Nanjing Agricultural University, Nanjing, China 210095
| | - Boyi Fan
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: School of Pharmacy, Nantong University, Nantong, China 226001
| | - Yanlong Jiang
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Department of Chemistry, Rice University, Houston, TX 77005
| | - Ajeeth Adhikari
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458
- Current address: Evercrisp Biosciences, San Francisco, CA 94109
| | - Cheng-Jian Zheng
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Current address: Faculty of Pharmacy, Naval Medical University, Shanghai, China 200433
| | - Layla Schuster
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603
| | - Tyler M. Cowan
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Michael J. Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN 55108
- Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108
| | - Marc G. Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603
- Genetics Institute, University of Florida, Gainesville, FL 32603
| | - Luiz P. S. de Carvalho
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
| | - Ben Shen
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458
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Turrini P, Chebbi A, Riggio FP, Visca P. The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives. Front Microbiol 2024; 15:1370520. [PMID: 38572233 PMCID: PMC10987966 DOI: 10.3389/fmicb.2024.1370520] [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: 01/14/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
Caves are ubiquitous subterranean voids, accounting for a still largely unexplored surface of the Earth underground. Due to the absence of sunlight and physical segregation, caves are naturally colonized by microorganisms that have developed distinctive capabilities to thrive under extreme conditions of darkness and oligotrophy. Here, the microbiomes colonizing three frequently studied cave types, i.e., limestone, sulfuric acid speleogenetic (SAS), and lava tubes among volcanic caves, have comparatively been reviewed. Geological configurations, nutrient availability, and energy flows in caves are key ecological drivers shaping cave microbiomes through photic, twilight, transient, and deep cave zones. Chemoheterotrophic microbial communities, whose sustenance depends on nutrients supplied from outside, are prevalent in limestone and volcanic caves, while elevated inorganic chemical energy is available in SAS caves, enabling primary production through chemolithoautotrophy. The 16S rRNA-based metataxonomic profiles of cave microbiomes were retrieved from previous studies employing the Illumina platform for sequencing the prokaryotic V3-V4 hypervariable region to compare the microbial community structures from different cave systems and environmental samples. Limestone caves and lava tubes are colonized by largely overlapping bacterial phyla, with the prevalence of Pseudomonadota and Actinomycetota, whereas the co-dominance of Pseudomonadota and Campylobacterota members characterizes SAS caves. Most of the metataxonomic profiling data have so far been collected from the twilight and transient zones, while deep cave zones remain elusive, deserving further exploration. Integrative approaches for future geomicrobiology studies are suggested to gain comprehensive insights into the different cave types and zones. This review also poses novel research questions for unveiling the metabolic and genomic capabilities of cave microorganisms, paving the way for their potential biotechnological applications.
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Affiliation(s)
- Paolo Turrini
- Department of Science, Roma Tre University, Rome, Italy
| | - Alif Chebbi
- Department of Science, Roma Tre University, Rome, Italy
| | | | - Paolo Visca
- Department of Science, Roma Tre University, Rome, Italy
- National Biodiversity Future Center, Palermo, Italy
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8
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Sevalho EDS, de Souza Rodrigues R, Queiroz Lima de Souza A, Duarte Leão de Souza A. Biotransformation of monoterpenes using Streptomyces strains from the rhizosphere of Inga edulis Martius from in an Amazonian urban forest fragment. Prep Biochem Biotechnol 2024:1-7. [PMID: 38469852 DOI: 10.1080/10826068.2024.2315476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
To investigate the biocatalytic potential of Amazonian actinomycetes for monoterpenes biotransformation. To carry out the present study, eleven actinomycetes of the genus Streptomyces isolated from inga-cipó (Inga edulis Mart.) rhizospheres were tested for their ability to bioconvert the substrates R-(+)-limonene, S-(-)-limonene, 1S-(-)-α-pinene, and (-)-β-pinene as sole carbon and energy source. According to gas chromatography-mass spectrometry analysis, three strains, LabMicra B270, LaBMicrA B310, and LaBMicrA B314, were able to biotransform 1S-(-)-α-pinene after 96 h of growth. However, Streptomyces LaBMicrA B270 was the most promising since it converted after only 72 h all the 1S-(-)-α-pinene mainly into cis-verbenol (74.9±1.24%) and verbenone (18.2±1.20%), compounds that have important biological activities and great industrial interest as additives in foods and cosmetics. These findings can stimulate the development of natural aromas using naturally abundant monoterpenes, ratify the potential of microorganisms from almost unexplored niches such as the Amazonian rhizosphere, and reinforce the importance of preserving those niches.
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Affiliation(s)
- Elison de Souza Sevalho
- Graduate Program in Biodiversity and Biotechnology of the BIONORTE Network (PPG-BIONORTE), Amazonas State University (UEA), Manaus, Amazonas, Brazil
- Analytical Center - Center of Multidisciplinary Support, Federal University of Amazonas (UFAM), Manaus, Amazonas, Brazil
| | - Rafael de Souza Rodrigues
- Graduate Program in Biodiversity and Biotechnology of the BIONORTE Network (PPG-BIONORTE), Amazonas State University (UEA), Manaus, Amazonas, Brazil
- Analytical Center - Center of Multidisciplinary Support, Federal University of Amazonas (UFAM), Manaus, Amazonas, Brazil
| | - Antonia Queiroz Lima de Souza
- Graduate Program in Biodiversity and Biotechnology of the BIONORTE Network (PPG-BIONORTE), Amazonas State University (UEA), Manaus, Amazonas, Brazil
- Analytical Center - Center of Multidisciplinary Support, Federal University of Amazonas (UFAM), Manaus, Amazonas, Brazil
- Faculty of Agricultural Sciences, Federal University of Amazonas (UFAM), Manaus, Amazonas, Brazil
| | - Afonso Duarte Leão de Souza
- Graduate Program in Biodiversity and Biotechnology of the BIONORTE Network (PPG-BIONORTE), Amazonas State University (UEA), Manaus, Amazonas, Brazil
- Analytical Center - Center of Multidisciplinary Support, Federal University of Amazonas (UFAM), Manaus, Amazonas, Brazil
- Department of Chemistry, Federal University of Amazonas (UFAM), Manaus, Amazonas, Brazil
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9
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Uesugi JHE, Dos Santos Caldas D, Coelho BBF, Prazes MCC, Omura LYE, Pismel JAR, Bezerra NV. Morphological diversity of actinobacteria isolated from oil palm compost (Elaeis guineensis). Braz J Microbiol 2024; 55:455-469. [PMID: 38010583 PMCID: PMC10920546 DOI: 10.1007/s42770-023-01178-w] [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: 05/28/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
Composting is a natural process of decomposition of organic matter that occurs by the action of microorganisms such as fungi, bacteria, and actinobacteria. The actinobacteria are present throughout the process due to their resistance to different environmental conditions. They are Gram-positive, filamentous bacteria with a high capacity for producing secondary metabolites of biotechnological importance. Thus, the objective of this work was to isolate and characterize actinobacteria from industrial composting soil of oil palm (Elaeis guineensis) in the municipality of Igarapé-Açu, Pará. Ten samples of the material were collected and seeded on soy tryptone agar, Reasoner's 2A agar, and Columbia agar, using the serial dilution technique. For morphological characterization of the strains, Gram staining and microculture were performed, and for biochemical characterization, the motility, triple sugar iron, Simmons citrate, maltose, phenylalanine, catalase, and DNAse tests were performed. It was observed that compost actinobacteria have a great diversity in morphological and metabolic production, which may be associated with the substrate and cultivation conditions. Therefore, palm oil compost material represents a rich source of bacterial biodiversity, bringing new perspectives for the bioprospecting of actinobacteria of biotechnological importance in little explored environments.
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Affiliation(s)
- Juliana Hiromi Emin Uesugi
- Laboratory of Applied Microbiology and Genetics of Microorganisms, Pará State University, Tv. Perebebuí, 2623, Marco, Belém, PA, Brazil
| | - Daniel Dos Santos Caldas
- Laboratory of Applied Microbiology and Genetics of Microorganisms, Pará State University, Tv. Perebebuí, 2623, Marco, Belém, PA, Brazil.
| | - Brunna Beatrys Farias Coelho
- Laboratory of Applied Microbiology and Genetics of Microorganisms, Pará State University, Tv. Perebebuí, 2623, Marco, Belém, PA, Brazil
| | - Maria Clara Coelho Prazes
- Laboratory of Applied Microbiology and Genetics of Microorganisms, Pará State University, Tv. Perebebuí, 2623, Marco, Belém, PA, Brazil
| | - Lucas Yukio Emin Omura
- Laboratory of Applied Microbiology and Genetics of Microorganisms, Pará State University, Tv. Perebebuí, 2623, Marco, Belém, PA, Brazil
| | - José Alyson Rocha Pismel
- Laboratory of Applied Microbiology and Genetics of Microorganisms, Pará State University, Tv. Perebebuí, 2623, Marco, Belém, PA, Brazil
| | - Nilson Veloso Bezerra
- Laboratory of Applied Microbiology and Genetics of Microorganisms, Pará State University, Tv. Perebebuí, 2623, Marco, Belém, PA, Brazil
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10
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Fenibo EO, Nkuna R, Matambo T. Impact of artisanal refining activities on bacterial diversity in a Niger Delta fallow land. Sci Rep 2024; 14:3866. [PMID: 38365802 PMCID: PMC10873323 DOI: 10.1038/s41598-024-53147-4] [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: 02/01/2023] [Accepted: 01/29/2024] [Indexed: 02/18/2024] Open
Abstract
Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence for Oilfield Chemical Research, University of Port Harcourt, Choba, Rivers State, Nigeria.
| | - Rosina Nkuna
- Department of Biotechnology, Faculty of Applied and Computer Sciences, Vaal University of Technology, Vanderbijlpark 1900, Gauteng, South Africa
- Centre for Competence in Environmental Biotechnology, College of Animal and Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
| | - Tonderayi Matambo
- Centre for Competence in Environmental Biotechnology, College of Animal and Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
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11
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Vishnupriya C, Mohamedrizwan K, Arya PR, Vijayakumar S, Kavitha R. Evaluation of heavy metal removal and antibiofilm efficiency of biologically synthesized chitosan- silver Nano-bio composite by a soil actinobacterium Glutamicibacter uratoxydans VRAK 24. Int J Biol Macromol 2024; 255:128032. [PMID: 37977462 DOI: 10.1016/j.ijbiomac.2023.128032] [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: 05/18/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
Biological synthesis of nanoparticles is cost-effective as well as safer than physical and chemical methods. This study focuses on the biological synthesis of silver nanoparticles using Glutamicibacter uratoxydans which remains still unexplored. The synthesized silver nanoparticles are encapsulated with chitosan to prepare nanobiocomposite. Actinobacteria were isolated from mesophilic soil and screened for heavy metal resistance. The potent heavy metal resistant isolate was identified by 16SrRNA sequencing and used for the biological synthesis of silver particles. The characterization of chitosan- silver nano-bio composite was carried out by UV-Vis spectroscopy, FTIR spectroscopy, and XRD. Morphology was analyzed by scanning electron microscopy. The particle size and stability were studied using Dynamic light scattering and Zeta potential analysis. The nano-bio composite was tested for lead removal efficiency and antibiofilm activity. The potent isolate was identified as Glutamicibacter uratoxydans and it was named as Glutamicibacter uratoxydans VRAK 24. The UV spectra showed maximum absorbance at 410 nm. The FTIR spectra and XRD confirmed chitosan encapsulation with silver nanoparticle. The size of nanobiocomposite was found to be 0.376. The stability of nanobiocomposite recorded a zeta potential value of -5.37 mV. The lead removal efficiency was found to be 87.69 %. In addition, the nanobiocomposite exhibited highest anti-biofilm activity against S.aureus when compared to E.coli. The research findings, concluded that the synthesized nanobiocomposite showed better anti-biofilm activity. Also, nanobiocomposite was found to be a good adsorbent for the removal of heavy metal lead.
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Affiliation(s)
- Chandrasekaran Vishnupriya
- Biomedical and Microbial Research Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Kadersulthan Mohamedrizwan
- Biomedical and Microbial Research Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - P R Arya
- Biomedical and Microbial Research Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | | | - Rangasamy Kavitha
- Biomedical and Microbial Research Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India.
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12
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Biagioli F, Coleine C, Delgado-Baquerizo M, Feng Y, Saiz-Jimenez C, Selbmann L. Outdoor climate drives diversity patterns of dominant microbial taxa in caves worldwide. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167674. [PMID: 37813267 DOI: 10.1016/j.scitotenv.2023.167674] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023]
Abstract
The cave microbiota is assumed to be shaped by indoor microclimate, biotic and abiotic factors, which are largely dependent from outside environmental conditions; however, this knowledge is available at local or regional scales only. To address this knowledge gap, we reanalyzed over 1050 bacterial and fungal communities of caves worldwide, and found that outdoor temperature and rainfall play a critical role in explaining differences in microbial diversity patterns of global caves, selecting specific dominant taxa across gradients of growing aridity conditions with arid climate leading to a reduction in total cave microbial diversity. Moreover, we found that fungal (from 186 to 1908 taxa) and bacterial (from 467 to 1619 taxa) diversity increased under temperate-tropical and temperate-continental climatic regions, respectively, highlighting an opposite preference for the two microbial compartments. We hypothesized that outdoor geographical, climatic variables and lithology are critical epistatic drivers in assembling microbial communities and their dominant taxa, whose ecological responses could be useful to predict the fate of these subterranean environments in the context of climate change. Our work elucidates the intimate connection between caves microbiota and surface ecosystems highlighting the sensitivity of cave microbial communities to climatic changes and environmental degradation. This work also provides a natural benchmark for the biogeographic information for caves globally and for protection strategies aiming at conservation of underground environments.
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Affiliation(s)
- Federico Biagioli
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012 Sevilla, Spain.
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210006 Nanjing, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, 210095 Nanjing, China
| | - Cesareo Saiz-Jimenez
- Microbiología Ambiental y Patrimonio Cultural, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012 Sevilla, Spain
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; Mycological Section, Italian Antarctic National Museum (MNA), Via al Porto Antico, 16128 Genoa, Italy
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13
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Martin-Pozas T, Cuezva S, Fernandez-Cortes A, Benavente D, Saiz-Jimenez C, Sanchez-Moral S. Prokaryotic communities inhabiting a high-radon subterranean ecosystem (Castañar Cave, Spain): Environmental and substrate-driven controls. Microbiol Res 2023; 277:127511. [PMID: 37852679 DOI: 10.1016/j.micres.2023.127511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Castañar Cave (Caceres, Spain) is a unique show cave known for its high natural radiation levels. This study presents a comprehensive analysis of its prokaryotic diversity, specifically focusing on investigating the influence of environmental conditions and substrate characteristics on the prokaryotic community structure in the cave sediments. Additionally, the research aims to evaluate the potential impact of human activities on the cave ecosystem. The identification of distinct bioclimatic zones within the cave was made possible through a combination of environmental and microbial monitoring (ATP assays). The results reveal sediment texture as a significant factor, notably affecting the structure, diversity, and phylogenetic variability of the microbial community, including both Bacteria and Archaea. The proportion of clay minerals in sediments plays a crucial role in regulating moisture levels and nutrient availability. These substrate properties collectively exert a significant selective pressure on the structure of prokaryotic communities within cave sediments. The molecular approach shows that heterotrophic bacteria, including those with chitinolytic enzymes, primarily inhabit the cave. Furthermore, chemoautotrophic nitrifiers such as the archaea Nitrososphaeria and the genus Nitrospira, as well as methanotrophic bacteria from the phyla Methylomirabilota, Pseudomonadota, and Verrucomicrobiota, are also present. Remarkably, despite being a show cave, the cave microbiota displays minimal impacts from human activities and the surface ecosystem. Prokaryotic populations exhibit stability in the innermost areas, while the tourist trail area experiences slightly higher biomass increases due to visitor traffic. This suggests that conservation efforts have successfully limited the entry of external nutrients into the innermost cave areas. Additionally, the results suggest that integrating biomarkers like ATP into environmental monitoring can significantly enhance the methods used to study the negative impacts of tourism on cave ecosystems.
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Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Soledad Cuezva
- Department of Geology, Geography and Environment, University of Alcala, 28805 Madrid, Spain.
| | | | - David Benavente
- Department of Environmental and Earth Sciences, University of Alicante, Campus San Vicente del Raspeig, 03690 Alicante, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil and Water Protection, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
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14
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Delbari Y, Mohassel Y, Kakaei E, Bahrami Y. Identification and anti-bacterial property of endophytic actinobacteria from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa. Sci Rep 2023; 13:13145. [PMID: 37573468 PMCID: PMC10423286 DOI: 10.1038/s41598-023-40478-x] [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: 03/29/2023] [Accepted: 08/10/2023] [Indexed: 08/14/2023] Open
Abstract
The arbitrary and overuses of antibiotics have resulted in the emergence of multidrug resistance bacteria which encounters human to a serious public health problem. Thus, there is an ever-increasing demand for discovery of novel effective antibiotics with new modes of function against resistant pathogens. Endophytic actinobacteria (EA) have currently been considered as one of the most prospective group of microorganisms for discovery of therapeutic agents. This study aimed to isolate EA from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa plants and to evaluate their antibacterial properties. The healthy samples were collected, dissected and surface-sterilized before cultured on four different selection media at 28 °C. Nine EA were isolated and identified based on morphological and molecular properties, and scanning electron micrograph analyses. Based on phylogenetic analysis, they were taxonomically grouped into four families Streptomycetaceae, Nocardiaceae, Micromonosporaceae, and Pseudonocardiaceae. Their branched aerial mycelia produced chains of cylindrical or cube or oval shaped spores with smooth or rough surfaces. Four strains; IKBG03, IKBG05, IKBG13, and IKBG17 had less than 98.65% sequence similarity to their closely related strains, which constitute them as novel species/strains. Besides, three strains; IKBG05, IKBG13, and IKBG18 were reported as endophytes for the first time. Preliminary antibacterial activity conducted on the all isolates revealed potent antibacterial effects against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. All isolates strongly inhibited the growth of at least one of the tested pathogens. Our results reveals that the test plants are novel sources for isolating a diverse group of rare and common actinobacteria that could produce a wide range of novel biologically active natural products with antibacterial activity which have a great potential in pharmaceutical and biotechnological applications.
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Affiliation(s)
- Yaser Delbari
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Yaser Mohassel
- Department of Clinical Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Elham Kakaei
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Yadollah Bahrami
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Department of Medical Biotechnology, School of Medicine, College of Medicine and Public Health, Flinders University, Adelaide, SA, 5042, Australia.
- Advanced Marine Biomanufacturing Laboratory, Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, SA, 5042, Australia.
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15
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Vagelas I, Reizopoulou A, Exadactylos A, Madesis P, Karapetsi L, Michail G. Stalactites Core Prospect as Environmental "Microbial Ark": The Actinomycetota Diversity Paradigm, First Reported from a Greek Cave. Pol J Microbiol 2023; 72:155-168. [PMID: 37314357 DOI: 10.33073/pjm-2023-016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/15/2023] [Indexed: 06/15/2023] Open
Abstract
Speleothems found in caves worldwide are considered the natural libraries of paleontology. Bacteria found in these ecosystems are generally limited to Proteobacteria and Actinomycetota, but rare microbiome and "Dark Matter" is generally under-investigated and often neglected. This research article discusses, for the first time to our knowledge, the diachronic diversity of Actinomycetota entrapped inside a cave stalactite. The planet's environmental microbial community profile of different eras can be stored in these refugia (speleothems). These speleothems could be an environmental "Microbial Ark" storing rare microbiome and "Dark Matter" bacterial communities evermore.
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Affiliation(s)
- Ioannis Vagelas
- 2Laboratory of Plant Pathology, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Angeliki Reizopoulou
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Athanasios Exadactylos
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Panagiotis Madesis
- 3Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Lefkothea Karapetsi
- 3Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
- 4Centre for Research and Technology (CERTH), Institute of Applied Biosciences (INAB), Thessaloniki, Greece
| | - George Michail
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
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16
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Brozel VS. Special Issue "Microbial Interactions in Soil": Editorial. Microorganisms 2023; 11:1260. [PMID: 37317234 DOI: 10.3390/microorganisms11051260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
Soils are home to a wide variety of microorganisms [...].
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Affiliation(s)
- Volker S Brozel
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa
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17
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Tistechok S, Roman I, Fedorenko V, Luzhetskyy A, Gromyko O. Diversity and bioactive potential of Actinomycetia from the rhizosphere soil of Juniperus excelsa. Folia Microbiol (Praha) 2023:10.1007/s12223-023-01047-x. [PMID: 36947395 PMCID: PMC10031196 DOI: 10.1007/s12223-023-01047-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/15/2023] [Indexed: 03/23/2023]
Abstract
Microbial natural products are among the main sources of compounds used in the medical biotechnology field for the purpose of drug development. However, as antibiotic resistance in pathogenic microorganisms is known to be increasing dramatically, there exists a need to develop new antibiotics. Actinomycetia have proven to be a good source of biologically active compounds, although the rediscovery of previously known compounds significantly slows down the introduction of new antibiotics. As a consequence, increasing attention is being paid to the isolation of actinomycete strains from previously unexplored sources, which can significantly increase the likelihood of discovering new biologically active compounds. This study investigated the diversity and bioactive potential of 372 actinomycete strains isolated from the rhizosphere soil of Juniperus excelsa M. Bieb. The examined actinomycete strains belonged to 11 genera, namely, Actinoplanes, Actinorectispora, Amycolatopsis, Kribbella, Micrococcus, Micromonospora, Nocardia, Promicromonospora, Rhodococcus, Saccharopolyspora and Streptomyces. The bioactive potential of each isolated actinomycete strain was determined on the basis of its ability to produce antimicrobial metabolites against Gram-positive and Gram-negative bacteria and yeast. Some 159 strains (42.74%) exhibited antimicrobial activity against at least one of the tested microbial strains. The dereplication analysis of the extract of the Streptomyces sp. Je 1-651 strain, which exhibited strong antimicrobial activity, led to the annotation of spiramycins and stambomycins. Moreover, the phylogenetic analysis based on the 16S rRNA gene sequence of the Je 1-651 strain revealed it to be close to the S. ambofaciens.
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Affiliation(s)
- Stepan Tistechok
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Ivan Roman
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbruecken, 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbruecken, 66123, Germany
| | - Oleksandr Gromyko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine.
- Microbial Culture Collection of Antibiotic Producers, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine.
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18
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Diversity of actinomycete and their metabolites isolated from Howz Soltan Lake, Iran. Arch Microbiol 2022; 205:24. [PMID: 36512155 DOI: 10.1007/s00203-022-03364-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
Saline environments are largely unexplored sources of actinomycetes with the potential to produce biologically active secondary metabolites. A total of 34 actinomycete isolates from water, sediments and mostly rhizosphere (82%) were collected from different sites at Howz Soltan Lake in Iran. Based on phylogenetic analysis, the isolates belonged to the genera Streptomyces, Nocardia and Saccharomonospora. Cytotoxic assay revealed extract from isolate act9 as the most potent (19.716±5.72 µg/ml) against the MDA-MB-231 human breast cancer cell. Also, 38% of the isolates showed antimicrobial activity against some of the test microorganisms. The ethyl-acetate extract of isolate act18 showed the strongest antibacterial effect against Staphylococcus aureus and MRSA, and was further analyzed by GC/MS. Ar-tumerone (26.41%) and butyl isodecyl phthalate (21.77 %) were the main constituents detected in the extract. This is the first time Ar-tumerone is being detected in a prokaryote. Isolate act18 showed a high 16S rRNA sequence similarity to that of Streptomyces youssoufiensis DSM 41920. In addition, a number of the isolates produced different enzymes including lipase, amylase, protease, gelatinase, urease and lecithinase. Some of the isolates belonging to the genera Streptomyces and Nocardia exhibited plant growth promoting activity such as increased seed germination, stem length and the number of Echium leaves during the 20 days. Findings from this study indicated the diversity and biosynthetic potential of actinomycetes from saline environment.
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Torres-Rodriguez JA, Reyes-Pérez JJ, Quiñones-Aguilar EE, Hernandez-Montiel LG. Actinomycete Potential as Biocontrol Agent of Phytopathogenic Fungi: Mechanisms, Source, and Applications. PLANTS (BASEL, SWITZERLAND) 2022; 11:3201. [PMID: 36501241 PMCID: PMC9736024 DOI: 10.3390/plants11233201] [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: 10/06/2022] [Revised: 11/09/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Synthetic fungicides have been the main control of phytopathogenic fungi. However, they cause harm to humans, animals, and the environment, as well as generating resistance in phytopathogenic fungi. In the last few decades, the use of microorganisms as biocontrol agents of phytopathogenic fungi has been an alternative to synthetic fungicide application. Actinomycetes isolated from terrestrial, marine, wetland, saline, and endophyte environments have been used for phytopathogenic fungus biocontrol. At present, there is a need for searching new secondary compounds and metabolites of different isolation sources of actinomycetes; however, little information is available on those isolated from other environments as biocontrol agents in agriculture. Therefore, the objective of this review is to compare the antifungal activity and the main mechanisms of action in actinomycetes isolated from different environments and to describe recent achievements of their application in agriculture. Although actinomycetes have potential as biocontrol agents of phytopathogenic fungi, few studies of actinomycetes are available of those from marine, saline, and wetland environments, which have equal or greater potential as biocontrol agents than isolates of actinomycetes from terrestrial environments.
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Affiliation(s)
- Juan A. Torres-Rodriguez
- Nanotechnology and Microbial Biocontrol Group, Centro de Investigaciones Biológicas del Noroeste, Av. Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, La Paz 23090, Mexico
| | - Juan J. Reyes-Pérez
- Facultad de Ciencias Pecuarias, Universidad Técnica Estatal de Quevedo, Av. Quito km 1.5 vía a Santo Domingo, Quevedo 120501, Ecuador
| | - Evangelina E. Quiñones-Aguilar
- Centro de Investigaciones y Asistencia en Tecnología y Diseño del Estado de Jalisco, Camino Arenero, El Bajío del Arenal, Guadalajara 45019, Mexico
| | - Luis G. Hernandez-Montiel
- Nanotechnology and Microbial Biocontrol Group, Centro de Investigaciones Biológicas del Noroeste, Av. Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, La Paz 23090, Mexico
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Nazari MT, Machado BS, Marchezi G, Crestani L, Ferrari V, Colla LM, Piccin JS. Use of soil actinomycetes for pharmaceutical, food, agricultural, and environmental purposes. 3 Biotech 2022; 12:232. [PMID: 35996673 PMCID: PMC9391553 DOI: 10.1007/s13205-022-03307-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/10/2022] [Indexed: 11/25/2022] Open
Abstract
In this article, we reviewed the international scientific production of the last years on actinomycetes isolated from soil aiming to report recent advances in using these microorganisms for different applications. The most promising genera, isolation conditions and procedures, pH, temperature, and NaCl tolerance of these bacteria were reported. Based on the content analysis of the articles, most studies have focused on the isolation and taxonomic description of new species of actinomycetes. Regarding the applications, the antimicrobial potential (antibacterial and antifungal) prevailed among the articles, followed by the production of enzymes (cellulases and chitinases, etc.), agricultural uses (plant growth promotion and phytopathogen control), bioremediation (organic and inorganic contaminants), among others. Furthermore, a wide range of growth capacity was verified, including temperatures from 4 to 60 °C (optimum: 28 °C), pH from 3 to 13 (optimum: 7), and NaCl tolerance up to 32% (optimum: 0-1%), which evidence a great tolerance for actinomycetes cultivation. Streptomyces was the genus with the highest incidence among the soil actinomycetes and the most exploited for different uses. Besides, the interest in isolating actinomycetes from soils in extreme environments (Antarctica and deserts, for example) is growing to explore the adaptive capacities of new strains and the secondary metabolites produced by these microorganisms for different industrial interests, especially for pharmaceutical, food, agricultural, and environmental purposes.
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Affiliation(s)
- Mateus Torres Nazari
- Graduate Program in Civil and Environmental Engineering, University of Passo Fundo, Campus I, L1 Building. BR 285, Bairro São José, Passo Fundo, RS CEP: 99052-900 - Zip Code 611 Brazil
| | - Bruna Strieder Machado
- Faculty of Engineering and Architecture, University of Passo Fundo, BR 285, Passo Fundo, RS Brazil
| | - Giovana Marchezi
- Faculty of Engineering and Architecture, University of Passo Fundo, BR 285, Passo Fundo, RS Brazil
| | - Larissa Crestani
- Graduate Program Chemical Engineering (PPGEQ), Federal University of Santa Maria (UFSM), Santa Maria, RS Brazil
| | - Valdecir Ferrari
- Graduate Program in Mining, Metallurgical and Materials Engineering (PPGE3M), Federal University of Rio Grande Do Sul (UFRGS), Porto Alegre, RS Brazil
| | - Luciane Maria Colla
- Graduate Program in Civil and Environmental Engineering, University of Passo Fundo, Campus I, L1 Building. BR 285, Bairro São José, Passo Fundo, RS CEP: 99052-900 - Zip Code 611 Brazil
| | - Jeferson Steffanello Piccin
- Graduate Program in Civil and Environmental Engineering, University of Passo Fundo, Campus I, L1 Building. BR 285, Bairro São José, Passo Fundo, RS CEP: 99052-900 - Zip Code 611 Brazil
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Jurado V, Del Rosal Y, Jimenez de Cisneros C, Liñan C, Martin-Pozas T, Gonzalez-Pimentel JL, Hermosin B, Saiz-Jimenez C. Microbial communities in carbonate precipitates from drip waters in Nerja Cave, Spain. PeerJ 2022; 10:e13399. [PMID: 35529484 PMCID: PMC9074860 DOI: 10.7717/peerj.13399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/17/2022] [Indexed: 01/14/2023] Open
Abstract
Research on cave microorganisms has mainly focused on the microbial communities thriving on speleothems, rocks and sediments; however, drip water bacteria and calcite precipitation has received less attention. In this study, microbial communities of carbonate precipitates from drip waters in Nerja, a show cave close to the sea in southeastern Spain, were investigated. We observed a pronounced difference in the bacterial composition of the precipitates, depending on the galleries and halls. The most abundant phylum in the precipitates of the halls close to the cave entrance was Proteobacteria, due to the low depth of this sector, the direct influence of a garden on the top soil and the infiltration of waters into the cave, as well as the abundance of members of the order Hyphomicrobiales, dispersing from plant roots, and other Betaproteobacteria and Gammaproteobacteria, common soil inhabitants. The influence of marine aerosols explained the presence of Marinobacter, Idiomarina, Thalassobaculum, Altererythrobacter and other bacteria due to the short distance from the cave to the sea. Nineteen out of forty six genera identified in the cave have been reported to precipitate carbonate and likely have a role in mineral deposition.
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Affiliation(s)
- Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia (IRNAS-CSIC), Sevilla, Spain
| | | | | | - Cristina Liñan
- Departamento de Ecologia y Geologia, Facultad de Ciencias, Universidad de Malaga, Malaga, Spain
| | | | | | - Bernardo Hermosin
- Instituto de Recursos Naturales y Agrobiologia (IRNAS-CSIC), Sevilla, Spain
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