1
|
Mumin R, Wang DD, Zhao W, Huang KC, Li JN, Sun YF, Cui BK. Spatial Distribution Patterns and Assembly Processes of Abundant and Rare Fungal Communities in Pinus sylvestris var. mongolica Forests. Microorganisms 2024; 12:977. [PMID: 38792806 PMCID: PMC11124154 DOI: 10.3390/microorganisms12050977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Revealing the biogeography and community assembly mechanisms of soil microorganisms is crucial in comprehending the diversity and maintenance of Pinus sylvestris var. mongolica forests. Here, we used high-throughput sequencing techniques and null model analysis to explore the distribution patterns and assembly processes of abundant, rare, and total fungal communities in P. sylvestris var. mongolica forests based on a large-scale soil survey across northern China. Compared to the abundant and total taxa, the diversity and composition of rare taxa were found to be more strongly influenced by regional changes and environmental factors. At the level of class, abundant and total taxa were dominated by Agaricomycetes and Leotiomycetes, while Agaricomycetes and Sordariomycetes were dominant in the rare taxa. In the functional guilds, symbiotrophic fungi were advantaged in the abundant and total taxa, and saprotrophic fungi were advantaged in the rare taxa. The null model revealed that the abundant, rare, and total taxa were mainly governed by stochastic processes. However, rare taxa were more influenced by deterministic processes. Precipitation and temperature were the key drivers in regulating the balance between stochastic and deterministic processes. This study provides new insights into both the biogeographical patterns and assembly processes of soil fungi in P. sylvestris var. mongolica forests.
Collapse
Affiliation(s)
| | | | | | | | | | - Yi-Fei Sun
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (R.M.); (D.-D.W.); (W.Z.); (K.-C.H.); (J.-N.L.)
| | - Bao-Kai Cui
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (R.M.); (D.-D.W.); (W.Z.); (K.-C.H.); (J.-N.L.)
| |
Collapse
|
2
|
Liao R, Liu Z, Dongchen W, Deng X, Ma E, Manzoor N, Lin C, Zhou S, Tong W, Zhou M, Li J, Mao Z. Integrated metabolomic and metagenomic strategies shed light on interactions among planting environments, rhizosphere microbiota, and metabolites of tobacco in Yunnan, China. Front Microbiol 2024; 15:1386150. [PMID: 38784812 PMCID: PMC11112021 DOI: 10.3389/fmicb.2024.1386150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Changes in climatic factors and rhizosphere microbiota led plants to adjust their metabolic strategies for survival under adverse environmental conditions. Changes in plant metabolites can mediate crop growth and development and interact with rhizosphere microbiota of the plant rhizosphere. To understand the interactions among environmental factors, rhizosphere microbiota, and metabolites of tobacco, a study was conducted by using integrated metagenomic and metabolomic strategies at four typical representative tobacco planting sites in Yunnan, China. The results showed that the agronomical and biochemical traits were significantly affected by temperature, precipitation (PREP), soil pH, and altitude. Correlation analyses revealed a significant positive correlation of temperature with length, width, and area of the leaf, while PREP correlated with plant height and effective leaf numbers. Furthermore, total sugar and reducing sugar contents of baked leaves were significantly higher, while the total nitrogen and total alkaloid levels were lower in tobacco leaves at site with low PREP. A total of 770 metabolites were detected with the highest number of different abundant metabolites (DMs) at Chuxiong (CX) with low PREP as compared to the other three sites, in which secondary metabolites were more abundant in both leaves and roots of tobacco. A total of 8,479 species, belonging to 2,094 genera with 420 individual bins (including 13 higher-quality bins) harboring 851,209 CDSs were detected. The phyla levels of microorganisms such as Euryarchaeota, Myxococcota, and Deinococcota were significantly enriched at the CX site, while Pseudomonadota was enriched at the high-temperature site with good PREP. The correlation analyses showed that the metabolic compounds in low-PREP site samples were positively correlated with Diaminobutyricimonas, Nissabacter, Alloactinosynnema, and Catellatospora and negatively correlated with Amniculibacterium, Nordella, Noviherbaspirillum, and Limnobacter, suggesting that the recruitment of Diaminobutyricimonas, Nissabacter, Alloactinosynnema, and Catellatospora in the rhizosphere induces the production and accumulation of secondary metabolites (SMs) (e.g., nitrogen compounds, terpenoids, and phenolics) for increasing drought tolerance with an unknown mechanism. The results of this study may promote the production and application of microbial fertilizers and agents such as Diaminobutyricimonas and Alloactinosynnema to assemble synthetic microbiota community or using their gene resources for better cultivation of tobacco as well as other crops in drought environments.
Collapse
Affiliation(s)
- Rentao Liao
- Yunnan Academy of Tobacco Agriculture Sciences, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, China
| | - Zhengjie Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, Kunming, China
| | - Wenhua Dongchen
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, Kunming, China
| | - Xiaopeng Deng
- Yunnan Academy of Tobacco Agriculture Sciences, Kunming, China
| | - Erdeng Ma
- Yunnan Academy of Tobacco Agriculture Sciences, Kunming, China
| | - Nazer Manzoor
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, China
| | - Chun Lin
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, Kunming, China
| | - Shaosong Zhou
- Agricultural Environmental Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Wenjie Tong
- Yunnan Academy of Tobacco Agriculture Sciences, Kunming, China
| | - Min Zhou
- Agricultural Environmental Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Junying Li
- Yunnan Academy of Tobacco Agriculture Sciences, Kunming, China
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, Kunming, China
- The Laboratory for Crop Production and Intelligent Agriculture, YNAU, Kunming, China
| |
Collapse
|
3
|
Cheng L, Mu H, Zhang X, Jiang P, Liu L, Li J. Deinococcus arenicola sp. nov., a novel radiation-resistant bacterium isolated from sandy soil in Antarctica. Int J Syst Evol Microbiol 2024; 74. [PMID: 38787370 DOI: 10.1099/ijsem.0.006397] [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] [Indexed: 05/25/2024] Open
Abstract
A Gram-stain-positive, aerobic, non-mobile and spherical strain, designated ZS9-10T, belonging to the genus Deinococcus was isolated from soil sampled at the Chinese Zhong Shan Station, Antarctica. Growth was observed in the presence of 0-4 % (w/v) NaCl, at pH 7.0-8.0 and at 4-25 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZS9-10T formed a lineage in the genus Deinococcus. It exhibited highest sequence similarity (97.4 %) to Deinococcus marmoris DSM 12784T. The major phospholipids of ZS9-10T were unidentified phosphoglycolipid, unidentified glycolipids and unidentified lipids. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C16 : 1 ω7c. MK-8 was the predominant respiratory quinone. The digital DNA-DNA hybridization and average nucleotide identity values between strain ZS9-10T and its close relative D. marmoris DSM 12784T were 27.4 and 83.9 %, respectively. Based on phenotypic, phylogenetic and genotypic data, a novel species, named Deinococcus arenicola sp. nov., is proposed. The type strain iis ZS9-10T (=CCTCC AB 2019392T=KCTC43192T).
Collapse
Affiliation(s)
- Li Cheng
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Hongmei Mu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Xinyu Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Peiqiang Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Lukuan Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Jing Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| |
Collapse
|
4
|
Belykh E, Maystrenko T, Velegzhaninov I, Tavleeva M, Rasova E, Rybak A. Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review. Microorganisms 2024; 12:733. [PMID: 38674676 PMCID: PMC11051952 DOI: 10.3390/microorganisms12040733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.
Collapse
Affiliation(s)
- Elena Belykh
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Tatiana Maystrenko
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Ilya Velegzhaninov
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Marina Tavleeva
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
- Department of Biology, Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prospekt, Syktyvkar 167001, Russia
| | - Elena Rasova
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Anna Rybak
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| |
Collapse
|
5
|
Ujaoney AK, Anaganti N, Padwal MK, Basu B. Tracing the serendipitous genesis of radiation resistance. Mol Microbiol 2024; 121:142-151. [PMID: 38082498 DOI: 10.1111/mmi.15208] [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: 06/05/2023] [Revised: 11/01/2023] [Accepted: 11/27/2023] [Indexed: 01/15/2024]
Abstract
Free-living organisms frequently encounter unfavorable abiotic environmental factors. Those who adapt and cope with sudden changes in the external environment survive. Desiccation is one of the most common and frequently encountered stresses in nature. On the contrary, ionizing radiations are limited to high local concentrations of naturally occurring radioactive materials and related anthropogenic activities. Yet, resistance to high doses of ionizing radiation is evident across the tree of life. The evolution of desiccation resistance has been linked to the evolution of ionizing radiation resistance, although, evidence to support the idea that the evolution of desiccation tolerance is a necessary precursor to ionizing radiation resistance is lacking. Moreover, the presence of radioresistance in hyperthermophiles suggests multiple paths lead to radiation resistance. In this minireview, we focus on the molecular aspects of damage dynamics and damage response pathways comprising protective and restorative functions with a definitive survival advantage, to explore the serendipitous genesis of ionizing radiation resistance.
Collapse
Affiliation(s)
- Aman Kumar Ujaoney
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Narasimha Anaganti
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Mahesh Kumar Padwal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| |
Collapse
|
6
|
Butterworth SJ, Barton F, Lloyd JR. Extremophilic microbial metabolism and radioactive waste disposal. Extremophiles 2023; 27:27. [PMID: 37839067 PMCID: PMC10577106 DOI: 10.1007/s00792-023-01312-4] [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: 03/02/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Decades of nuclear activities have left a legacy of hazardous radioactive waste, which must be isolated from the biosphere for over 100,000 years. The preferred option for safe waste disposal is a deep subsurface geological disposal facility (GDF). Due to the very long geological timescales required, and the complexity of materials to be disposed of (including a wide range of nutrients and electron donors/acceptors) microbial activity will likely play a pivotal role in the safe operation of these mega-facilities. A GDF environment provides many metabolic challenges to microbes that may inhabit the facility, including high temperature, pressure, radiation, alkalinity, and salinity, depending on the specific disposal concept employed. However, as our understanding of the boundaries of life is continuously challenged and expanded by the discovery of novel extremophiles in Earth's most inhospitable environments, it is becoming clear that microorganisms must be considered in GDF safety cases to ensure accurate predictions of long-term performance. This review explores extremophilic adaptations and how this knowledge can be applied to challenge our current assumptions on microbial activity in GDF environments. We conclude that regardless of concept, a GDF will consist of multiple extremes and it is of high importance to understand the limits of polyextremophiles under realistic environmental conditions.
Collapse
Affiliation(s)
- Sarah Jane Butterworth
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK
| | - Franky Barton
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
| | - Jonathan Richard Lloyd
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
| |
Collapse
|
7
|
Sadowska-Bartosz I, Bartosz G. Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance? Int J Radiat Biol 2023; 99:1803-1829. [PMID: 37498212 DOI: 10.1080/09553002.2023.2241895] [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: 01/09/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation. CONCLUSIONS The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.
Collapse
Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Grzegorz Bartosz
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| |
Collapse
|
8
|
Petit P, Hayoun K, Alpha-Bazin B, Armengaud J, Rivasseau C. First Isolation and Characterization of Bacteria from the Core's Cooling Pool of an Operating Nuclear Reactor. Microorganisms 2023; 11:1871. [PMID: 37630434 PMCID: PMC10456712 DOI: 10.3390/microorganisms11081871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 08/27/2023] Open
Abstract
Microbial life can thrive in the most inhospitable places, such as nuclear facilities with high levels of ionizing radiation. Using direct meta-analyses, we have previously highlighted the presence of bacteria belonging to twenty-five different genera in the highly radioactive water of the cooling pool of an operating nuclear reactor core. In the present study, we further characterize this specific environment by isolating and identifying some of these microorganisms and assessing their radiotolerance and their ability to decontaminate uranium. This metal is one of the major radioactive contaminants of anthropogenic origin in the environment due to the nuclear and mining industries and agricultural practices. The microorganisms isolated when sampling was performed during the reactor operation consisted mainly of Actinobacteria and Firmicutes, whereas Proteobacteria were dominant when sampling was performed during the reactor shutdown. We investigated their tolerance to gamma radiation under different conditions. Most of the bacterial strains studied were able to survive 200 Gy irradiation. Some were even able to withstand 1 kGy, with four of them showing more than 10% survival at this dose. We also assessed their uranium uptake capacity. Seven strains were able to remove almost all the uranium from a 5 µM solution. Four strains displayed high efficiency in decontaminating a 50 µM uranium solution, demonstrating promising potential for use in bioremediation processes in environments contaminated by radionuclides.
Collapse
Affiliation(s)
- Pauline Petit
- Université Grenoble Alpes, CEA, CNRS, IRIG, F-38000 Grenoble, France;
| | - Karim Hayoun
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-30200 Bagnols-sur-Cèze, France; (K.H.); (B.A.-B.); (J.A.)
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Université de Montpellier, F-30207 Bagnols-sur-Cèze, France
| | - Béatrice Alpha-Bazin
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-30200 Bagnols-sur-Cèze, France; (K.H.); (B.A.-B.); (J.A.)
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-30200 Bagnols-sur-Cèze, France; (K.H.); (B.A.-B.); (J.A.)
| | - Corinne Rivasseau
- Université Grenoble Alpes, CEA, CNRS, IRIG, F-38000 Grenoble, France;
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, F-91190 Gif-sur-Yvette, France
| |
Collapse
|
9
|
Sajjad W, Nadeem M, Alam T, Rehman AU, Abbasi SW, Ahmad S, Din G, Khan S, Badshah M, Gul S, Farman M, Shah AA. Biological Evaluation and Computational Studies of Methoxy-flavones from Newly Isolated Radioresistant Micromonospora aurantiaca Strain TMC-15. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04517-7. [PMID: 37115385 DOI: 10.1007/s12010-023-04517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 04/29/2023]
Abstract
This study aims to determine UV-B resistance and to investigate computational analysis and antioxidant potential of methoxy-flavones of Micromonospora aurantiaca TMC-15 isolated from Thal Desert, Pakistan. The cellular extract was purified through solid-phase extraction and UV-Vis spectrum analysis indicated absorption peaks at λmax 250 nm, 343 nm, and 380 nm that revealed the presence of methoxy-flavones named eupatilin and 5-hydroxyauranetin. The flavones were evaluated for their antioxidant as well as protein and lipid peroxidation inhibition potential using di(phenyl)-(2,4,6-trinitrophenyl) iminoazanium (DPPH), 2,4-dinitrophenyl hydrazine (DNPH), and thiobarbituric acid reactive substances (TBARS) assays, respectively. The methoxy-flavones were further studied for their docking affinity and interaction dynamics to determine their structural and energetic properties at the atomic level. The antioxidant potential, protein, and lipid oxidation inhibition and DNA damage preventive abilities were correlated as predicted by computational analysis. The eupatilin and 5-hydroxyauranetin binding potential to their targeted proteins 1N8Q and 1OG5 is - 4.1 and - 7.5 kcal/mol, respectively. Moreover, the eupatiline and 5-hydroxyauranetin complexes illustrate van der Waals contacts and strong hydrogen bonds to their respective enzymes target. Both in vitro studies and computational analysis results revealed that methoxy-flavones of Micromonospora aurantiaca TMC-15 can be used against radiation-mediated oxidative damages due to its kosmotrophic nature. The demonstration of good antioxidant activities not only protect DNA but also protein and lipid oxidation and therefore could be a good candidate in radioprotective drugs and as sunscreen due to its kosmotropic nature.
Collapse
Affiliation(s)
- Wasim Sajjad
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Mahnoor Nadeem
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Tayyaba Alam
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Asim Ur Rehman
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
| | - Ghufranud Din
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
- Department of Medical Laboratory Technology, University of Haripur, Haripur, 22620, Pakistan
| | - Samiullah Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Malik Badshah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Sarah Gul
- Department of Biological Sciences, Faculty of Basic and Applied Sciences, International Islamic University, Islamabad, Pakistan
| | - Muhammad Farman
- Department of Chemistry, Faculty of Natural Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Aamer Ali Shah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
| |
Collapse
|
10
|
aroF and cm2: potential molecular markers for the detection of stone-inhabiting Actinobacteria on cultural heritage sites. Arch Microbiol 2023; 205:32. [DOI: 10.1007/s00203-022-03368-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/08/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
|
11
|
Complementary Roles of Two DNA Protection Proteins from Deinococcus geothermalis. Int J Mol Sci 2022; 24:ijms24010469. [PMID: 36613913 PMCID: PMC9820295 DOI: 10.3390/ijms24010469] [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: 11/10/2022] [Revised: 12/17/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
The roles of two interrelated DNA protection protein in starved cells (Dps)-putative Dps Dgeo_0257 and Dgeo_0281-as orthologous proteins to DrDps1 for DNA binding, protection, and metal ion sensing were characterised in a Deinococcus geothermalis strain. Dgeo_0257 exhibited high DNA-binding affinity and formed a multimeric structure but lacked the conserved amino acid sequence for ferroxidase activity. In contrast, the Dgeo_0281 (DgDps1) protein was abundant in the early exponential phase, had a lower DNA-binding activity than Dgeo_0257, and was mainly observed in its monomeric or dimeric forms. Electrophoretic mobility shift assays demonstrated that both purified proteins bound nonspecifically to DNA, and their binding ability was affected by certain metal ions. For example, in the presence of ferrous and ferric ions, neither Dgeo_0257 nor Dgeo_0281 could readily bind to DNA. In contrast, both proteins exhibited more stable DNA binding in the presence of zinc and manganese ions. Mutants in which the dps gene was disrupted exhibited higher sensitivity to oxidative stress than the wild-type strain. Furthermore, the expression levels of each gene showed an opposite correlation under H2O2 treatment conditions. Collectively, these findings indicate that the putative Dps Dgeo_0257 and DgDps1 from D. geothermalis are involved in DNA binding and protection in complementary interplay ways compared to known Dps.
Collapse
|
12
|
Lee JH, Jung JH, Kim MK, Lim S. Deinococcus taeanensis sp. nov., a Radiation-Resistant Bacterium Isolated from a Coastal Dune. Curr Microbiol 2022; 79:334. [PMID: 36161362 PMCID: PMC9510100 DOI: 10.1007/s00284-022-03044-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/14/2022] [Indexed: 11/28/2022]
Abstract
A Gram-stain-negative, nonspore-forming, nonmotile, aerobic, rod-shaped, and very pale orange-colored bacterial strain, designated TS293T, was isolated from a sand sample obtained from a coastal dune after exposure to 3kGy of gamma (γ)-radiation. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the isolate was a member of the genus Deinococcus and clustered with D. deserti VCD115T. The genome of strain TS293T was 4.62 Mbp long (68.2% G + C content and 4124 predicted genes) divided into a 2.86Mb main chromosome and five plasmids. Many genes considered to be important to the γ-radiation and oxidative stress resistance of Deinococcus were conserved in TS293T, but genome features that could differentiate TS293T from D. deserti and D. radiodurans, the type species of the Deinococcus genus, were also detected. Strain TS293T showed resistance to γ-radiation with D10 values (i.e., the dose required to reduce the bacterial population by tenfold) of 3.1kGy. The predominant fatty acids of strain TS293T were summed feature 3 (C16:1ω6c and/or C16:1ω7c) and iso-C16:0. The major polar lipids were two unidentified phosphoglycolipids and one unidentified glycolipid. The main respiratory quinone was menaquinone-8. Based on the phylogenetic, genomic, physiological, and chemotaxonomic characteristics, strain TS293T represents a novel species, for which the name Deinococcus taeanensis sp. nov. is proposed. The type strain is TS293T (= KCTC 43191T = JCM 34027T).
Collapse
Affiliation(s)
- Ji Hee Lee
- Division of Pathogen Resource Management, Korea Disease Control and Prevention Agency, Cheongju, 28160, Republic of Korea
| | - Jong-Hyun Jung
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Min-Kyu Kim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sangyong Lim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
- Department of Radiation Science, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| |
Collapse
|
13
|
Bacterial Diversity Profiling of Desert Sand from Tierra Caliente, Mexico, Based on 16S rRNA Gene Amplicon Sequencing. Microbiol Resour Announc 2022; 11:e0078222. [PMID: 36000857 PMCID: PMC9476955 DOI: 10.1128/mra.00782-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Tierra Caliente is an arid region in Mexico, representing a reservoir of understudied xerophilic bacteria. Here, we report the bacterial amplicon sequencing characterization of desert sand collected from the Zicuirán-Infiernillo Biosphere Reserve within Tierra Caliente. Bacteria known to be resistant to desiccation and high radiation were detected.
Collapse
|
14
|
Shirsalimian MS, Mazidi SM, Amoozegar MA. The Lut Desert and Its Microbial Diversity: Recent Studies and Future Research. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722300014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
15
|
High Proportions of Radiation-Resistant Strains in Culturable Bacteria from the Taklimakan Desert. BIOLOGY 2022; 11:biology11040501. [PMID: 35453702 PMCID: PMC9030528 DOI: 10.3390/biology11040501] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 12/18/2022]
Abstract
Simple Summary Radiation-resistant extremophiles have frequently been found in the Taklimakan Desert, which is known for its harsh conditions. However, there is no systemic study investigating the diversity and proportion of radiation-resistant strains among culturable bacteria. The results of this study revealed the distribution of culturable bacteria in the Taklimakan Desert and indicated high proportions of radiation-resistant strains in the culturable bacteria. The study helps to better understand the ecological origin of radio-resistance and to quantitatively describe the desert as a common habitat for radiation-resistant extremophiles. Abstract The Taklimakan Desert located in China is the second-largest shifting sand desert in the world and is known for its harsh conditions. Types of γ-rays or UV radiation-resistant bacterial strains have been isolated from this desert. However, there is no information regarding the proportions of the radiation-resistant strains in the total culturable microbes. We isolated 352 bacterial strains from nine sites across the Taklimakan Desert from north to south. They belong to Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. The phylum Actinobacteria was the most predominant in abundance and Firmicutes had the highest species richness. Bacteroidetes had the lowest abundance and was found in four sites only, while the other three phyla were found in every site but with different distribution profiles. After irradiating with 1000 J/m2 and 6000 J/m2 UV-C, the strains with survival rates higher than 10% occupied 72.3% and 36.9% of all culturable bacteria, respectively. The members from Proteobacteria had the highest proportions, with survival rates higher than 10%. After radiation with 10 kGy γ-rays, Kocuria sp. TKL1057 and Planococcus sp. TKL1152 showed higher radiation-resistant capabilities than Deinococcus radiodurans R1. Besides obtaining several radiation-resistant extremophiles, this study measured the proportions of the radiation-resistant strains in the total culturable microbes for the first time. This study may help to better understand the origin of radioresistance, especially by quantitatively comparing proportions of radiation-resistant extremophiles from different environments in the future.
Collapse
|
16
|
Thiol Reductases in Deinococcus Bacteria and Roles in Stress Tolerance. Antioxidants (Basel) 2022; 11:antiox11030561. [PMID: 35326211 PMCID: PMC8945050 DOI: 10.3390/antiox11030561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 12/10/2022] Open
Abstract
Deinococcus species possess remarkable tolerance to extreme environmental conditions that generate oxidative damage to macromolecules. Among enzymes fulfilling key functions in metabolism regulation and stress responses, thiol reductases (TRs) harbour catalytic cysteines modulating the redox status of Cys and Met in partner proteins. We present here a detailed description of Deinococcus TRs regarding gene occurrence, sequence features, and physiological functions that remain poorly characterised in this genus. Two NADPH-dependent thiol-based systems are present in Deinococcus. One involves thioredoxins, disulfide reductases providing electrons to protein partners involved notably in peroxide scavenging or in preserving protein redox status. The other is based on bacillithiol, a low-molecular-weight redox molecule, and bacilliredoxin, which together protect Cys residues against overoxidation. Deinococcus species possess various types of thiol peroxidases whose electron supply depends either on NADPH via thioredoxins or on NADH via lipoylated proteins. Recent data gained on deletion mutants confirmed the importance of TRs in Deinococcus tolerance to oxidative treatments, but additional investigations are needed to delineate the redox network in which they operate, and their precise physiological roles. The large palette of Deinococcus TR representatives very likely constitutes an asset for the maintenance of redox homeostasis in harsh stress conditions.
Collapse
|
17
|
Park Y, Ten LN, Lee YK, Jung HY, Kim MK. Larkinella humicola sp. nov., a gamma radiation-resistant bacterium isolated from soil. Arch Microbiol 2022; 204:182. [PMID: 35179646 DOI: 10.1007/s00203-022-02790-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 01/16/2022] [Accepted: 02/01/2022] [Indexed: 11/02/2022]
Abstract
A Gram-negative, short rod-shaped, and pink-pigmented bacterial strain, designated MA1T, was isolated from a soil sample from Gijang-gun, Busan in Republic of Korea. The 16S rRNA gene sequence analysis showed that strain MA1T belonged to the genus Larkinella and was closely related to "Larkinella punicea" (97.5% similarity), Larkinella rosea 15J16-1T3AT (96.5%), and Larkinella knui 15J6-3T6T (96.2%). Polar lipid profile of strain MA1T contained phosphatidylethanolamine, two unidentified aminolipids, and three unidentified lipids. Menaquinone-7 was the only quinone and the main fatty acids were C16:1 ω5c (36.7%), iso-C15:0 (30.0%), iso-C17:0 3-OH (7.7%), and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c and/or iso-C15:0 2-OH) (7.3%). The genomic DNA G + C content was 52.3 mol% based on the whole-genome analysis. Strain MA1T exhibited a relatively low level of ANI and in silico DDH values with "Larkinella punicea" (91.9 and 47.1%, respectively), Larkinella rosea (79.7 and 23.3%), and Larkinella knui (81.9 and 25.7%). Based on its phenotypic properties and phylogenetic distinctiveness, strain MA1T should be classified in the genus Larkinella as a representative of a novel species, for which the name Larkinella humicola sp. nov. is proposed. The type strain is MA1T (= KCTC 72629T = NBRC 114191T).
Collapse
Affiliation(s)
- Yuna Park
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea
| | - Leonid N Ten
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Young Koung Lee
- Institute of Plasma Technology, Korea Institute of Fusion Energy, 37 Dongjangsan-ro, Gunsan, Jeollabuk, 54004, Republic of Korea
| | - Hee-Young Jung
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea. .,Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea.
| |
Collapse
|
18
|
Latorre-Pérez A, Gimeno-Valero H, Tanner K, Pascual J, Vilanova C, Porcar M. A Round Trip to the Desert: In situ Nanopore Sequencing Informs Targeted Bioprospecting. Front Microbiol 2021; 12:768240. [PMID: 34966365 PMCID: PMC8710813 DOI: 10.3389/fmicb.2021.768240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/15/2021] [Indexed: 12/26/2022] Open
Abstract
Bioprospecting expeditions are often performed in remote locations, in order to access previously unexplored samples. Nevertheless, the actual potential of those samples is only assessed once scientists are back in the laboratory, where a time-consuming screening must take place. This work evaluates the suitability of using Nanopore sequencing during a journey to the Tabernas Desert (Spain) for forecasting the potential of specific samples in terms of bacterial diversity and prevalence of radiation- and desiccation-resistant taxa, which were the target of the bioprospecting activities. Samples collected during the first day were analyzed through 16S rRNA gene sequencing using a mobile laboratory. Results enabled the identification of locations showing the greatest and the least potential, and a second, informed sampling was performed focusing on those sites. After finishing the expedition, a culture collection of 166 strains belonging to 50 different genera was established. Overall, Nanopore and culturing data correlated well, since samples holding a greater potential at the microbiome level also yielded a more interesting set of microbial isolates, whereas samples showing less biodiversity resulted in a reduced (and redundant) set of culturable bacteria. Thus, we anticipate that portable sequencers hold potential as key, easy-to-use tools for in situ-informed bioprospecting strategies.
Collapse
Affiliation(s)
| | | | | | | | | | - Manuel Porcar
- Darwin Bioprospecting Excellence S.L., Paterna, Spain
- Institute for Integrative Systems Biology I2SysBio (University of València-CSIC), Paterna, Spain
| |
Collapse
|
19
|
Vignale FA, Kurth D, Lencina AI, Poiré DG, Chihuailaf E, Muñoz-Herrera NC, Novoa F, Contreras M, Turjanski AG, Farías ME. Geobiology of Andean Microbial Ecosystems Discovered in Salar de Atacama, Chile. Front Microbiol 2021; 12:762076. [PMID: 34777316 PMCID: PMC8581658 DOI: 10.3389/fmicb.2021.762076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/28/2021] [Indexed: 11/23/2022] Open
Abstract
The Salar de Atacama in the Chilean Central Andes harbors unique microbial ecosystems due to extreme environmental conditions, such as high altitude, low oxygen pressure, high solar radiation, and high salinity. Combining X-ray diffraction analyses, scanning electron microscopy and molecular diversity studies, we have characterized twenty previously unexplored Andean microbial ecosystems in eight different lakes and wetlands from the middle-east and south-east regions of this salt flat. The mats and microbialites studied are mainly formed by calcium carbonate (aragonite and calcite) and halite, whereas the endoevaporites are composed predominantly of gypsum and halite. The carbonate-rich mats and microbialites are dominated by Bacteroidetes and Proteobacteria phyla. Within the phylum Proteobacteria, the most abundant classes are Alphaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. While in the phylum Bacteroidetes, the most abundant classes are Bacteroidia and Rhodothermia. Cyanobacteria, Chloroflexi, Planctomycetes, and Verrucomicrobia phyla are also well-represented in the majority of these systems. Gypsum endoevaporites, on the contrary, are dominated by Proteobacteria, Bacteroidetes, and Euryarchaeota phyla. The Cyanobacteria phylum is also abundant in these systems, but it is less represented in comparison to mats and microbialites. Regarding the eukaryotic taxa, diatoms are key structural components in most of the microbial ecosystems studied. The genera of diatoms identified were Achnanthes, Fallacia, Halamphora, Mastogloia, Navicula, Nitzschia, and Surirella. Normally, in the mats and microbialites, diatoms form nano-globular carbonate aggregates with filamentous cyanobacteria and other prokaryotic cells, suggesting their participation in the mineral precipitation process. This work expands our knowledge of the microbial ecosystems inhabiting the extreme environments from the Central Andes region, which is important to ensure their protection and conservation.
Collapse
Affiliation(s)
- Federico A. Vignale
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Argentina
- Laboratorio de Bioinformática Estructural, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniel Kurth
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Argentina
| | - Agustina I. Lencina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Argentina
| | - Daniel G. Poiré
- Centro de Investigaciones Geológicas (CIG), Universidad Nacional de La Plata (UNLP)-CONICET, La Plata, Argentina
| | | | | | | | | | - Adrián G. Turjanski
- Laboratorio de Bioinformática Estructural, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María E. Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Argentina
| |
Collapse
|
20
|
Kotsyurbenko OR, Cordova JA, Belov AA, Cheptsov VS, Kölbl D, Khrunyk YY, Kryuchkova MO, Milojevic T, Mogul R, Sasaki S, Słowik GP, Snytnikov V, Vorobyova EA. Exobiology of the Venusian Clouds: New Insights into Habitability through Terrestrial Models and Methods of Detection. ASTROBIOLOGY 2021; 21:1186-1205. [PMID: 34255549 PMCID: PMC9545807 DOI: 10.1089/ast.2020.2296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 04/16/2021] [Indexed: 06/13/2023]
Abstract
The search for life beyond Earth has focused on Mars and the icy moons Europa and Enceladus, all of which are considered a safe haven for life due to evidence of current or past water. The surface of Venus, on the other hand, has extreme conditions that make it a nonhabitable environment to life as we know it. This is in contrast, however, to its cloud layer, which, while still an extreme environment, may prove to be a safe haven for some extreme forms of life similar to extremophiles on Earth. We consider the venusian clouds a habitable environment based on the presence of (1) a solvent for biochemical reactions, (2) appropriate physicochemical conditions, (3) available energy, and (4) biologically relevant elements. The diversity of extreme microbial ecosystems on Earth has allowed us to identify terrestrial chemolithoautotrophic microorganisms that may be analogs to putative venusian organisms. Here, we hypothesize and describe biological processes that may be performed by such organisms in the venusian clouds. To detect putative venusian organisms, we describe potential biosignature detection methods, which include metal-microbial interactions and optical methods. Finally, we describe currently available technology that can potentially be used for modeling and simulation experiments.
Collapse
Affiliation(s)
- Oleg R. Kotsyurbenko
- Yugra State University, The Institute of Oil and Gas, School of Ecology, Khanty-Mansiysk, Russian Federation
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
| | - Jaime A. Cordova
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, USA
| | - Andrey A. Belov
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
- Moscow State University, Faculty of Soil Science, Moscow, Russian Federation
| | - Vladimir S. Cheptsov
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
- Moscow State University, Faculty of Soil Science, Moscow, Russian Federation
- Space Research Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | - Denise Kölbl
- Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Yuliya Y. Khrunyk
- Department of Heat Treatment and Physics of Metal, Ural Federal University, Ekaterinburg, Russian Federation
- M.N. Mikheev Institute of Metal Physics of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russian Federation
| | - Margarita O. Kryuchkova
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
- Moscow State University, Faculty of Soil Science, Moscow, Russian Federation
| | - Tetyana Milojevic
- Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, California, USA
| | - Satoshi Sasaki
- School of Biosciences and Biotechnology/School of Health Sciences, Tokyo University of Technology, Hachioji, Tokyo, Japan
| | - Grzegorz P. Słowik
- Institute of Materials and Biomedical Engineering, Faculty of Mechanical Engineering, University of Zielona Góra, Zielona Góra, Poland
| | - Valery Snytnikov
- Boreskov Institute of Catalysis, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
| | - Elena A. Vorobyova
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
- Moscow State University, Faculty of Soil Science, Moscow, Russian Federation
| |
Collapse
|
21
|
Lakra P, Verma H, Talwar C, Singh DN, Singhvi N, Lal R, Gupta V. Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans. Int J Syst Evol Microbiol 2021; 71. [PMID: 34236299 DOI: 10.1099/ijsem.0.004879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensis DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA-DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans.
Collapse
Affiliation(s)
- Priya Lakra
- Department of Zoology, University of Delhi, Delhi-110007, India
| | - Helianthous Verma
- Molecular Biology and Genomics Research Laboratory, Ramjas College, University of Delhi, Delhi-110007, India
| | - Chandni Talwar
- Department of Zoology, University of Delhi, Delhi-110007, India
| | | | - Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi-110007, India
| | - Rup Lal
- The Energy and Resources Institute, Lodhi Road, New Delhi-110003, India
- Present address: 6C, India Habitat Complex, Lodhi Road, New Delhi-110003, India & 101, GH-11, Sector 47, Gurugram, Haryana-122001, India
| | - Vipin Gupta
- PhiXGen Private Limited, Gurugram, Haryana-122001, India
| |
Collapse
|
22
|
Experimental evolution of extremophile resistance to ionizing radiation. Trends Genet 2021; 37:830-845. [PMID: 34088512 DOI: 10.1016/j.tig.2021.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 11/22/2022]
Abstract
A growing number of known species possess a remarkable characteristic - extreme resistance to the effects of ionizing radiation (IR). This review examines our current understanding of how organisms can adapt to and survive exposure to IR, one of the most toxic stressors known. The study of natural extremophiles such as Deinococcus radiodurans has revealed much. However, the evolution of Deinococcus was not driven by IR. Another approach, pioneered by Evelyn Witkin in 1946, is to utilize experimental evolution. Contributions to the IR-resistance phenotype affect multiple aspects of cell physiology, including DNA repair, removal of reactive oxygen species, the structure and packaging of DNA and the cell itself, and repair of iron-sulfur centers. Based on progress to date, we overview the diversity of mechanisms that can contribute to biological IR resistance arising as a result of either natural or experimental evolution.
Collapse
|
23
|
Castillo H, Li X, Smith GB. Deinococcus radiodurans UWO298 Dependence on Background Radiation for Optimal Growth. Front Genet 2021; 12:644292. [PMID: 34025716 PMCID: PMC8136434 DOI: 10.3389/fgene.2021.644292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 03/02/2021] [Indexed: 01/04/2023] Open
Abstract
Ionizing radiation is a major environmental variable for cells on Earth, and so organisms have adapted to either prevent or to repair damages caused by it, primarily from the appearance and accumulation of reactive oxygen species (ROS). In this study, we measured the differential gene expression in Deinococcus radiodurans UWO298 cultures deprived of background ionizing radiation (IR) while growing 605 m underground at the Waste Isolation Pilot Plant (WIPP), reducing the dose rate from 72.1 to 0.9 nGy h–1 from control to treatment, respectively. This reduction in IR dose rate delayed the entry into the exponential phase of the IR-shielded cultures, resulting in a lower biomass accumulation for the duration of the experiment. The RNASeq-based transcriptome analysis showed the differential expression of 0.2 and 2.7% of the D. radiodurans genome after 24 and 34 h of growth in liquid culture, respectively. Gene expression regulation after 34 h was characterized by the downregulation of genes involved in folding newly synthesized and denatured/misfolded proteins, in the assimilation of nitrogen for amino acid synthesis and in the control of copper transport and homeostasis to prevent oxidative stress. We also observed the upregulation of genes coding for proteins with transport and cell wall assembly roles. These results show that D. radiodurans is sensitive to the absence of background levels of ionizing radiation and suggest that its transcriptional response is insufficient to maintain optimal growth.
Collapse
Affiliation(s)
- Hugo Castillo
- Human Factors and Behavioral Neurobiology Department, Embry-Riddle Aeronautical University, Daytona Beach, FL, United States
| | - Xiaoping Li
- Virginia Tech Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Blacksburg, VA, United States
| | - Geoffrey B Smith
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
| |
Collapse
|
24
|
Balbín-Suárez A, Lucas M, Vetterlein D, Sørensen SJ, Winkelmann T, Smalla K, Jacquiod S. Exploring microbial determinants of apple replant disease (ARD): a microhabitat approach under split-root design. FEMS Microbiol Ecol 2021; 96:5921174. [PMID: 33045057 DOI: 10.1093/femsec/fiaa211] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
Apple replant disease (ARD) occurs worldwide in apple orchards and nurseries and leads to a severe growth and productivity decline. Despite research on the topic, its causality remains unclear. In a split-root experiment, we grew ARD-susceptible 'M26' apple rootstocks in different substrate combinations (+ARD: ARD soil; -ARD: gamma-irradiated ARD soil; and Control: soil with no apple history). We investigated the microbial community composition by 16S rRNA gene amplicon sequencing (bacteria and archaea) along the soil-root continuum (bulk soil, rhizosphere and rhizoplane). Significant differences in microbial community composition and structure were found between +ARD and -ARD or +ARD and Control along the soil-root continuum, even for plants exposed simultaneously to two different substrates (-ARD/+ARD and Control/+ARD). The substrates in the respective split-root compartment defined the assembly of root-associated microbial communities, being hardly influenced by the type of substrate in the respective neighbor compartment. Root-associated representatives from Actinobacteria were the most dynamic taxa in response to the treatments, suggesting a pivotal role in ARD. Altogether, we evidenced an altered state of the microbial community in the +ARD soil, displaying altered alpha- and beta-diversity, which in turn will also impact the normal development of apple rhizosphere and rhizoplane microbiota (dysbiosis), concurring with symptom appearance.
Collapse
Affiliation(s)
- Alicia Balbín-Suárez
- Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Maik Lucas
- Department of Soil System Science, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Str. 4, 06120 Halle/Saale, Germany.,Soil Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120 Halle/Saale, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Str. 4, 06120 Halle/Saale, Germany.,Soil Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120 Halle/Saale, Germany
| | - Søren J Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Copenhagen, Denmark
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Section Woody Plant and Propagation Physiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Samuel Jacquiod
- University of Copenhagen, Department of Biology, Section of Microbiology, Copenhagen, Denmark.,Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon, France
| |
Collapse
|
25
|
Obulisamy PK, Mehariya S. Polyhydroxyalkanoates from extremophiles: A review. BIORESOURCE TECHNOLOGY 2021; 325:124653. [PMID: 33465644 DOI: 10.1016/j.biortech.2020.124653] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Polyhydroxyalkanoates (PHAs) are group monomers/heteropolymers that are biodegradable and widely used in biomedical applications. They are considered as alternatives to fossil derived polymers and accumulated by microbes including extremophilic archaea as energy storage inclusions under nutrient limitations. The use of extremophilic archaea for PHA production is an economically viable option for conventional aerobic processes, but less is known about their pathways and PHA accumulation capacities. This review summarized: (a) specific adaptive mechanisms towards extreme environments by extremophiles and specific role of PHAs; (b) understanding of PHA synthesis/metabolism in archaea and specific functional genes; (c) genetic engineering and process engineering approaches required for high-rate PHA production using extremophilic archaea. To conclude, the future studies are suggested to understand the membrane lipids and PHAs accumulation to explain the adaptation mechanism of extremophiles and exploiting it for commercial production of PHAs.
Collapse
Affiliation(s)
| | - Sanjeet Mehariya
- Department of Engineering, University of Campania "Luigi Vanvitelli", Real Casa dell'Annunziata, Italy
| |
Collapse
|
26
|
Centurion VB, Lacerda-Júnior GV, Duarte AWF, Silva TR, Silva LJ, Rosa LH, Oliveira VM. Dynamics of microbial stress responses driven by abiotic changes along a temporal gradient in Deception Island, Maritime Antarctica. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143671. [PMID: 33248775 DOI: 10.1016/j.scitotenv.2020.143671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/21/2020] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Whalers Bay (WB), Deception Island, is an environment that can drastically change its temperature within a few meters. The main forms of life inhabiting this environment are microorganisms, which, due to the high diversity and their adaptive potential, can survive and thrive under harsh stress conditions. However, the genetic potential and mechanisms to cope with fluctuating adverse conditions as well as what extent environmental variations shape the microbial community over the years it is still unknown in Antarctic environments. In this work, sediments collected in a transect in Whalers Bay, Deception Island, during the Austral Summers of 2014, 2015 and 2017 were analyzed using shotgun metagenomics. Sequence data were further processed with the SqueezeMeta tool for assembly, gene prediction, mapping, taxonomic and functional annotations. Results showed that stress-related functions had the influence of temperatures and solar radiation observed in the years of 2015 and 2017. The most differentiated functions were the ones related to oxidative stress, comparing 2014 vs 2015 and 2014 vs 2017. The genes coding for HSP20 and oxidoreductases (nrdH, grxA, korC and korD), as well as the genes clpE, cspL, and operons mtrAB and vicKR, were differentially enriched between the years, most of them found in gram-positive bacteria. The selective pressures of temperature and radiation may have favored the growth of gram-positive bacteria in 2017, with emphasis on Arthrobacter genus. Data gathered in this work showed that temperature and solar radiation could potentially be the primary driving forces shaping the repertoire of stress-response genes for the maintenance of microbial diversity in WB Antarctic sediments.
Collapse
Affiliation(s)
- V B Centurion
- Microbial Resources Division, Research Center for Chemistry, Biology, and Agriculture (CPQBA), State University of Campinas - UNICAMP, Paulínia, SP CEP 13081-970, Brazil; Biology Institute, State University of Campinas - UNICAMP, Campinas, SP CEP: 13083-862, Brazil.
| | - G V Lacerda-Júnior
- Microbial Resources Division, Research Center for Chemistry, Biology, and Agriculture (CPQBA), State University of Campinas - UNICAMP, Paulínia, SP CEP 13081-970, Brazil; Brazilian Agricultural Research Corporation - EMBRAPA, Jaguariúna, SP CEP 13820-000, Brazil
| | - A W F Duarte
- Microbial Resources Division, Research Center for Chemistry, Biology, and Agriculture (CPQBA), State University of Campinas - UNICAMP, Paulínia, SP CEP 13081-970, Brazil; Federal University of Alagoas, Campus Arapiraca - UFAL, Arapiraca, AL CEP 57309-005, Brazil
| | - T R Silva
- Microbial Resources Division, Research Center for Chemistry, Biology, and Agriculture (CPQBA), State University of Campinas - UNICAMP, Paulínia, SP CEP 13081-970, Brazil
| | - L J Silva
- Brazilian Agricultural Research Corporation - EMBRAPA, Jaguariúna, SP CEP 13820-000, Brazil
| | - L H Rosa
- Institute of Biological Sciences, Federal University of Minas Gerais - UFMG, Belo Horizonte, MG CEP 31270-901, Brazil.
| | - V M Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology, and Agriculture (CPQBA), State University of Campinas - UNICAMP, Paulínia, SP CEP 13081-970, Brazil.
| |
Collapse
|
27
|
George SF, Fierer N, Levy JS, Adams B. Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity. Front Microbiol 2021; 12:616730. [PMID: 33584618 PMCID: PMC7873294 DOI: 10.3389/fmicb.2021.616730] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/04/2021] [Indexed: 11/19/2022] Open
Abstract
Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.
Collapse
Affiliation(s)
- Scott F George
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States
| | - Joseph S Levy
- Department of Geology, Colgate University, Hamilton, NY, United States
| | - Byron Adams
- Department of Biology, Brigham Young University, Provo, UT, United States.,Monte L. Bean Museum, Brigham Young University, Provo, UT, United States
| |
Collapse
|
28
|
Lee JH, Jung JH, Kim MK, Choe HN, Seong CN, Lim S. Spirosoma taeanense sp. nov., a radiation resistant bacterium isolated from a coastal sand dune. Antonie van Leeuwenhoek 2021; 114:151-159. [PMID: 33449223 DOI: 10.1007/s10482-020-01508-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/27/2020] [Indexed: 11/24/2022]
Abstract
An aerobic, Gram-negative, non-motile, non-spore-forming, rod-shaped, and pale yellow-colored bacterial strain, designated TS118T, was isolated from a sand sample obtained from a coastal sand dune after exposure to 3 kGy of gamma radiation. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the genus Spirosoma and most closely related to Spirosoma metallicum PR1014kT (95.1% similarity). The genome of strain TS118T is constituted by one chromosome (5,691,492 bp) and one plasmid (28,440 bp) and has a G + C content of 52.7%. The genome contains 4641 protein coding sequences (CDSs), 38 tRNAs, and 11 rRNAs. The predominant fatty acids of strain TS118T were C16:1 ω5c, iso-C15:0, C16:0, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), and iso-C17:0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified amino lipid and an unidentified aminophospholipid. The main respiratory quinone was menaquinone-7 (MK-7). The novel strain showed resistance to gamma radiation with a D10 value (i.e., the dose required to reduce the bacterial population by tenfold) of 4.3 kGy. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain TS118T represents a novel species, for which the name Spirosoma taeanense sp. nov. is proposed. The type strain is TS118T (=KCTC 72898T =JCM 34024T).
Collapse
Affiliation(s)
- Ji Hee Lee
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Jong-Hyun Jung
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Min-Kyu Kim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Han Na Choe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Sangyong Lim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea. .,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| |
Collapse
|
29
|
Guesmi S, Pujic P, Nouioui I, Dubost A, Najjari A, Ghedira K, Igual JM, Miotello G, Cherif A, Armengaud J, Klenk HP, Normand P, Sghaier H. Ionizing-radiation-resistant Kocuria rhizophila PT10 isolated from the Tunisian Sahara xerophyte Panicum turgidum: Polyphasic characterization and proteogenomic arsenal. Genomics 2020; 113:317-330. [PMID: 33279651 DOI: 10.1016/j.ygeno.2020.11.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/17/2020] [Accepted: 11/29/2020] [Indexed: 10/22/2022]
Abstract
A new strain belonging to the genus Kocuria, designed PT10, was isolated from irradiated roots of the xerophyte Panicum turgidum. Isolate PT10 is a Gram-positive, coccoid, aerobic and ionizing-radiation (IR)-resistant actinobacterium. PT10 has shown an ability to survive under extreme conditions, such as gamma irradiation, desiccation and high concentration of hydrogen peroxide. Phenotypic, chemotaxonomic and comparative genome analyses support the assignment of strain PT10 (LMG 31102 = DSM 108617) as Kocuria rhizophila. The complete genome sequence of PT10 consists of one chromosome (2,656,287 bps), with a 70.7% G + C content and comprises 2481 protein-coding sequences. A total of 1487 proteins were identified by LC-MS/MS profiling. In silico analyses revealed that the proteome of the oxidation-tolerant PT10 possesses several features explaining its IR-resistant phenotype and many adaptive pathways implicated in response to environmental pressures - desiccation, cold, reactive oxygen species and other stressors.
Collapse
Affiliation(s)
- Sihem Guesmi
- National Agronomy Institute of Tunisia, 43, Avenue Charles Nicolle, 1082 Tunis, Mahrajène, Tunisia; Laboratory ″Energy and Matter for Development of Nuclear Sciences″ (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Tunisia.
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, Lyon, France; CNRS, UMR 5557, Ecologie Microbienne, 69622 Villeurbanne, Cedex, INRA, UMR1418, Villeurbanne, France
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne NE1 7RU, UK; Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Afef Najjari
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR03ES03 Microorganismes et Biomolécules Actives, 2092 Tunis, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, 13, Place Pasteur, Tunis 1002, Tunisia
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Guylaine Miotello
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Jean Armengaud
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne NE1 7RU, UK
| | | | - Haïtham Sghaier
- Laboratory ″Energy and Matter for Development of Nuclear Sciences″ (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Tunisia; Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia.
| |
Collapse
|
30
|
Romsdahl J, Schultzhaus Z, Chen A, Liu J, Ewing A, Hervey J, Wang Z. Adaptive evolution of a melanized fungus reveals robust augmentation of radiation resistance by abrogating non-homologous end-joining. Environ Microbiol 2020; 23:3627-3645. [PMID: 33078510 DOI: 10.1111/1462-2920.15285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/22/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023]
Abstract
Fungi have been observed to exhibit resistance to high levels of ionizing radiation despite sharing most DNA repair mechanisms with other eukaryotes. Radioresistance, in fact, is such a common feature in fungi that it is difficult to identify species that exhibit widely different radiosensitivities, which in turn has hampered the identification of genetic elements responsible for this resistance phenotype. Due to the inherent mutagenic properties of radiation exposure, however, this can be addressed through adaptive laboratory evolution for increased ionizing radiation resistance. Here, using the black yeast Exophiala dermatitidis, we demonstrate that resistance to γ-radiation can be greatly increased through repeated rounds of irradiation and outgrowth. Moreover, we find that the small genome size of fungi situates them as a relatively simple functional genomics platform for identification of mutations associated with ionizing radiation resistance. This enabled the identification of genetic mutations in genes encoding proteins with a broad range of functions from 10 evolved strains. Specifically, we find that greatly increased resistance to γ-radiation is achieved in E. dermatitidis through disruption of the non-homologous end-joining pathway, with three individual evolutionary paths converging to abolish this DNA repair process. This result suggests that non-homologous end-joining, even in haploid cells where homologous chromosomes are not present during much of the cell cycle, is an impediment to repair of radiation-induced lesions in this organism, and that the relative levels of homologous and non-homologous repair in a given fungal species may play a major role in its radiation resistance.
Collapse
Affiliation(s)
- Jillian Romsdahl
- National Research Council Postdoctoral Research Associate, Naval Research Laboratory, Washington, DC, USA
| | - Zachary Schultzhaus
- Center for Biomolecular Sciences and Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Amy Chen
- Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | - Jing Liu
- Thomas Jefferson High School for Science and Technology, Alexandria, VA, USA
| | | | - Judson Hervey
- Center for Biomolecular Sciences and Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Zheng Wang
- Center for Biomolecular Sciences and Engineering, US Naval Research Laboratory, Washington, DC, USA
| |
Collapse
|
31
|
Monaco P, Divino F, Naclerio G, Bucci A. Microbial community analysis with a specific statistical approach after a record breaking snowfall in Southern Italy. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01604-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Abstract
Purpose
Snow and ice ecosystems present unexpectedly high microbial abundance and diversity. Although arctic and alpine snow environments have been intensively investigated from a microbiological point of view, few studies have been conducted in the Apennines. Accordingly, the main purpose of this research was to analyze the microbial communities of the snow collected in two different locations of Capracotta municipality (Southern Italy) after a snowfall record occurred on March 2015 (256 cm of snow in less than 24 h).
Methods
Bacterial communities were analyzed by the Next-Generation Sequencing techniques. Furthermore, a specific statistical approach for taxonomic hierarchy data was introduced, both for the assessment of diversity within microbial communities and the comparison between different microbiotas. In general, diversity and similarity indices are more informative when computed at the lowest level of the taxonomic hierarchy, the species level. This is not the case with microbial data, for which the species level is not necessarily the most informative. Indeed, the possibility to detect a large number of unclassified records at every level of the hierarchy (even at the top) is very realistic due to both the partial knowledge about the cultivable fraction of microbial communities and limitations to taxonomic assignment connected to the quality and completeness of the 16S rRNA gene reference databases. Thus, a global approach considering information from the whole taxonomic hierarchy was adopted in order to obtain a more consistent assessment of the biodiversity.
Result
The main phyla retrieved in the investigated snow samples were Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Interestingly, DNA from bacteria adapted to thrive at low temperatures, but also from microorganisms normally associated with other habitats, whose presence in the snow could be justified by wind-transport, was found. Biomolecular investigations and statistical data analysis showed relevant differences in terms of biodiversity, composition, and distribution of bacterial species between the studied snow samples.
Conclusion
The relevance of this research lies in the expansion of knowledge about microorganisms associated with cold environments in contexts poorly investigated such as the Italian Apennines, and in the development of a global statistical approach for the assessment of biological diversity and similarity of microbial communities as an additional tool to be usefully combined with the barcoding methods.
Collapse
|
32
|
Liu T, Liu X, Zhu J, Tang Q, Wang W, Zhu L, Zhang Z, Zhang Z, Jiang L, Huang H. Characterization of Radiation-Resistant Yeast Isolated from Radiation-Polluted Areas and Its Potential Application in Bioremediation. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820050117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
33
|
Bruckbauer ST, Martin J, Minkoff BB, Veling MT, Lancaster I, Liu J, Trimarco JD, Bushnell B, Lipzen A, Wood EA, Sussman MR, Pennacchio C, Cox MM. Physiology of Highly Radioresistant Escherichia coli After Experimental Evolution for 100 Cycles of Selection. Front Microbiol 2020; 11:582590. [PMID: 33072055 PMCID: PMC7536353 DOI: 10.3389/fmicb.2020.582590] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/26/2020] [Indexed: 11/13/2022] Open
Abstract
Ionizing radiation (IR) is lethal to most organisms at high doses, damaging every cellular macromolecule via induction of reactive oxygen species (ROS). Utilizing experimental evolution and continuing previous work, we have generated the most IR-resistant Escherichia coli populations developed to date. After 100 cycles of selection, the dose required to kill 99% the four replicate populations (IR9-100, IR10-100, IR11-100, and IR12-100) has increased from 750 Gy to approximately 3,000 Gy. Fitness trade-offs, specialization, and clonal interference are evident. Long-lived competing sub-populations are present in three of the four lineages. In IR9, one lineage accumulates the heme precursor, porphyrin, leading to generation of yellow-brown colonies. Major genomic alterations are present. IR9 and IR10 exhibit major deletions and/or duplications proximal to the chromosome replication terminus. Contributions to IR resistance have expanded beyond the alterations in DNA repair systems documented previously. Variants of proteins involved in ATP synthesis (AtpA), iron-sulfur cluster biogenesis (SufD) and cadaverine synthesis (CadA) each contribute to IR resistance in IR9-100. Major genomic and physiological changes are emerging. An isolate from IR10 exhibits protein protection from ROS similar to the extremely radiation resistant bacterium Deinococcus radiodurans, without evident changes in cellular metal homeostasis. Selection is continuing with no limit to IR resistance in evidence as our E. coli populations approach levels of IR resistance typical of D. radiodurans.
Collapse
Affiliation(s)
- Steven T Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Joel Martin
- DOE Joint Genome Institute, Berkeley, CA, United States
| | - Benjamin B Minkoff
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States.,Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Mike T Veling
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States
| | - Illissa Lancaster
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Jessica Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Joseph D Trimarco
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Anna Lipzen
- DOE Joint Genome Institute, Berkeley, CA, United States
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Michael R Sussman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States.,Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | | | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| |
Collapse
|
34
|
Wang JJ, Wu SG, Chen Q, Sheng DH, Du ZJ, Li YZ. Deinococcus terrestris sp. nov., a gamma ray- and ultraviolet-resistant bacterium isolated from soil. Int J Syst Evol Microbiol 2020; 70:4993-5000. [PMID: 32776869 DOI: 10.1099/ijsem.0.004369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain SDU3-2T was isolated from a soil sample collected in Shandong Province, PR China. Cells of SDU3-2T were spherical, Gram-stain-positive, aerobic and non-motile. Cellular growth of the strain occurred at 25-45 °C, pH 5.5-8.5 and with 0-1.5 % (w/v) of NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SDU3-2T was closest to the type strain Deinococcus murrayi ALT-1bT with a similarity of 95.2 %. The draft genome was 3.49 Mbp long with 69.2 mol% G+C content. Strain SDU3-2T exhibited high resistance to gamma radiation (D10 >12 kGy) and UV (D10 >900 J m-2). The strain encoded many genes for resistance to radiation and oxidative stress, which were highly conserved with other Deinococcus species, but possessed interspecific properties. The major fatty acids of SDU3-2T cells were C15 : 1 ω6c, C16 : 1 ω7c/C16 : 1 ω6c, and C17 : 1 ω8c, the major menaquinone was menaquinone-8, and the major polar lipids were an unidentified phosphoglycolipid, four unidentified glycolipids and an unidentified phospholipid. The average nucleotide identity and DNA-DNA hybridization results further indicated that strain SDU3-2T represents a new species in the genus Deinococcus, for which the name Deinococcus terrestris sp. nov. is proposed. The type strain is SDU3-2T (=CGMCC 1.17147T=KCTC 43098T).
Collapse
Affiliation(s)
- Jing-Jing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Shu-Ge Wu
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Qi Chen
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Duo-Hong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Zong-Jun Du
- College of Marine Science, Shandong University, Weihai 264209, PR China.,State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| |
Collapse
|
35
|
Xing J, Sun S, Wang H, Brookes PC, Xu J. Response of soil native microbial community to Eschericia coli O157:H7 invasion. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 261:114225. [PMID: 32220754 DOI: 10.1016/j.envpol.2020.114225] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/31/2020] [Accepted: 02/16/2020] [Indexed: 06/10/2023]
Abstract
The presence of Eschericia coli O157:H7 in the natural environment is a serious threat to human health. The native microbial community in soil plays an important role in resisting E. coli O157:H7 invasion. This study examined the responses of soil microbial community to E. coli O157:H7 invasion during a 32-day incubation. The E. coli O157:H7 persisted longer in γ-irradiated soil than non-irradiated soil while glucose addition decreased its persistence in the irradiated soil which was associated with an increasing recovery of the native community. The invasion of E. coli O157:H7 increased soil organic carbon mineralization, an indicator of microbial activity, in both non-irradiated and irradiated soils, while glucose addition significantly promoted the carbon mineralization process. The 16S rRNA sequencing data showed the gradual recovery of the native bacterial population including specific taxa such as proteobacteria and actinobacteria following irradiation. It is concluded that soil microbial function and structure can affect persistence of E. coli O157:H7 and that lower biodiversity of the native community favors its persistence.
Collapse
Affiliation(s)
- Jiajia Xing
- Institute of Soil and Water Resources and Environmental Science, College of Environment and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Substrates and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Shanshan Sun
- Institute of Soil and Water Resources and Environmental Science, College of Environment and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Substrates and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Haizhen Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environment and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Substrates and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Philip C Brookes
- Institute of Soil and Water Resources and Environmental Science, College of Environment and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Substrates and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environment and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Substrates and Environment, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
36
|
González-Toril E, Osuna S, Viúdez-Moreiras D, Navarro-Cid I, Toro SDD, Sor S, Bardera R, Puente-Sánchez F, de Diego-Castilla G, Aguilera Á. Impacts of Saharan Dust Intrusions on Bacterial Communities of the Low Troposphere. Sci Rep 2020; 10:6837. [PMID: 32321958 PMCID: PMC7176723 DOI: 10.1038/s41598-020-63797-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/31/2020] [Indexed: 11/30/2022] Open
Abstract
We have analyzed the bacterial community of a large Saharan dust event in the Iberian Peninsula and, for the first time, we offer new insights regarding the bacterial distribution at different altitudes of the lower troposphere and the replacement of the microbial airborne structure as the dust event receeds. Samples from different open-air altitudes (surface, 100 m and 3 km), were obtained onboard the National Institute for Aerospace Technology (INTA) C-212 aircrafts. Samples were collected during dust and dust-free air masses as well two weeks after the dust event. Samples related in height or time scale seems to show more similar community composition patterns compared with unrelated samples. The most abundant bacterial species during the dust event, grouped in three different phyla: (a) Proteobacteria: Rhizobiales, Sphingomonadales, Rhodobacterales, (b) Actinobacteria: Geodermatophilaceae; (c) Firmicutes: Bacillaceae. Most of these taxa are well known for being extremely stress-resistant. After the dust intrusion, Rhizobium was the most abundant genus, (40-90% total sequences). Samples taken during the flights carried out 15 days after the dust event were much more similar to the dust event samples compared with the remaining samples. In this case, Brevundimonas, and Methylobacterium as well as Cupriavidus and Mesorizobium were the most abundant genera.
Collapse
Affiliation(s)
- Elena González-Toril
- Centro de Astrobiología (CSIC-INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Susana Osuna
- Centro de Astrobiología (CSIC-INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Daniel Viúdez-Moreiras
- Centro de Astrobiología (CSIC-INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Ivan Navarro-Cid
- Centro de Astrobiología (CSIC-INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Silvia Díaz Del Toro
- Department of Genetics, Physiology and Microbiology. Biology Faculty. C/José Antonio Novais, 12, Universidad Complutense de Madrid (UCM), 28040, Madrid, Spain
| | - Suthyvann Sor
- Aerodinamic Department (INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Rafael Bardera
- Aerodinamic Department (INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Fernando Puente-Sánchez
- Systems Biology Program. Centro Nacional de Biotecnología. C/ Darwin n° 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | | | - Ángeles Aguilera
- Centro de Astrobiología (CSIC-INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain.
| |
Collapse
|
37
|
Shifts in microbial community composition in tannery-contaminated soil in response to increased gamma radiation. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01541-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Abstract
Purpose
Contaminated sites from man-made activities such as old-fashioned tanneries are inhabited by virulent microorganisms that exhibit more resistance against extreme and toxic environmental conditions. We investigated the effect of different Gamma radiation doses on microbial community composition in the sediment of an old-fashioned tannery.
Methods
Seven samples collected from the contaminated sites received different gamma radiation doses (I = 0.0, II = 5, III = 10, VI = 15, V = 20, VI = 25, and VII = 30 kGy) as an acute exposure. The shift in microbial community structure was assessed using the high throughput 454 pyrosequencing. Variations in diversity, richness, and the shift in operational taxonomic units (OTUs) were investigated using statistical analysis.
Result
Our results showed that the control sample (I) had the highest diversity, richness, and OTUs when compared with the irradiated samples. Species of Halocella, Parasporobacterium, and Anaerosporobacter had the highest relative abundance at the highest radiation dose of 30 kGy. Members of the Firmicutes also increased by 20% at the highest radiation dose when compared with the control sample (0.0 kGy). Representatives of Synergistetes decreased by 25% while Bacteroidetes retained a steady distribution across the range of gamma radiation intensities.
Conclusion
This study provides information about potential “radioresistant” and/or “radiotolerant” microbial species that are adapted to elevated level of chemical toxicity such as Cr and Sr in tannery. These species can be of a high biotechnological and environmental importance.
Collapse
|
38
|
Choi JY, Lee K, Lee PC. Characterization of Carotenoid Biosynthesis in Newly Isolated Deinococcus sp. AJ005 and Investigation of the Effects of Environmental Conditions on Cell Growth and Carotenoid Biosynthesis. Mar Drugs 2019; 17:md17120705. [PMID: 31847382 PMCID: PMC6950390 DOI: 10.3390/md17120705] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/08/2019] [Accepted: 12/11/2019] [Indexed: 12/30/2022] Open
Abstract
Our purpose was to characterize the structures of deinoxanthin from Deinococcus sp. AJ005. The latter is a novel reddish strain and was found to synthesize two main acyclic carotenoids: deinoxanthin and its derivative. The derivative (2-keto-deinoxanthin) contains a 2-keto functional group instead of a 2-hydroxyl group on a β-ionone ring. A deinoxanthin biosynthesis pathway of Deinococcus sp. AJ005 involving eight putative enzymes was proposed according to genome annotation analysis and chemical identification of deinoxanthin. Optimal culture pH and temperature for Deinococcus sp. AJ005 growth were pH 7.4 and 20 °C. Sucrose as a carbon source significantly enhanced the cell growth in comparison with glucose, glycerol, maltose, lactose, and galactose. When batch fermentation was performed in a bioreactor containing 40g/L sucrose, total carotenoid production was 650% higher than that in a medium without sucrose supplementation. The culture conditions found in this study should provide the basis for the development of fermentation strategies for the production of deinoxanthin and of its derivative by means of Deinococcus sp. AJ005.
Collapse
|
39
|
Bastian FO, Lynch J, Wang WH. Novel Spiroplasma sp. Isolated From CWD Is an Extreme Bacterial Thermoacidophile That Survives Autoclaving, Boiling, Formalin Treatment, and Significant Gamma Irradiation. J Neuropathol Exp Neurol 2019; 78:993-1001. [PMID: 31512718 DOI: 10.1093/jnen/nlz081] [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: 05/11/2019] [Revised: 07/12/2019] [Accepted: 08/05/2019] [Indexed: 11/14/2022] Open
Abstract
Rapid spreading of chronic wasting disease (CWD) in wildlife and captive cervid populations has exposed lack of progress in dealing with the transmissible spongiform encephalopathies (TSE) of man and animals. Since the TSE transmissible agent was resistant to extremes in environmental and chemical treatments, focus was on an unconventional agent including the prion theory. Recent breakthrough research has revealed consistent isolation of a novel Spiroplasma sp. from TSE-affected tissues that propagates in cell-free media and on agar. Here, we developed a live culture assay to test whether the CWD spiroplasma isolate possessed unconventional biologic properties akin to those of the transmissible agent of TSE. The CWD spiroplasma isolate survived boiling for 1 hour, standard liquid autoclaving, 10% formalin treatment overnight, and gamma irradiation of 20 kGy. The CWD spiroplasma isolate is an acidophile, growing best at pH 2. The biologic resistance of the CWD spiroplasma isolate may be due to unusual phage-like viruses found in the bacterial pellet or to DNA-protein binding. Because the CWD spiroplasma isolate has biologic properties consistent with the causal agent of the TSEs, TSE research focus should be redirected to development of diagnostic tests and preventive vaccines for control of CWD based upon the bacterium.
Collapse
Affiliation(s)
- Frank O Bastian
- Bastian Laboratory for Neurological Disease Research, New Orleans, Louisiana.,Texas Tech University, Department of Environmental Toxicology, Lubbock, Texas.,Tulane Medical School Department of Pathology, New Orleans, Louisiana
| | - James Lynch
- Bastian Laboratory for Neurological Disease Research, New Orleans, Louisiana
| | - Wei-Hsung Wang
- Radiation Safety Office/Center for Energy Studies, Louisiana State University, Louisiana
| |
Collapse
|
40
|
Ogwu MC, Srinivasan S, Dong K, Ramasamy D, Waldman B, Adams JM. Community Ecology of Deinococcus in Irradiated Soil. MICROBIAL ECOLOGY 2019; 78:855-872. [PMID: 30980101 DOI: 10.1007/s00248-019-01343-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/12/2019] [Indexed: 05/24/2023]
Abstract
Deinococcus is a genus of soil bacteria known for radiation resistance. However, the effects of radiation exposure on its community structure are unknown. We exposed soil to three levels of gamma radiation, 0.1 kGy/h (low), 1 kGy/h (medium), and 3 kGy/h (high), once a week for 6 weeks and then extracted soil DNA for 16S rRNA amplicon sequencing. We found the following: (1) Increasing radiation dose produced a major increase in relative abundance of Deinococcus, reaching ~ 80% of reads at the highest doses. Differing abundances of the various Deinococcus species in relation to exposure levels indicate distinct "radiation niches." At 3 kGy/h, a single OTU identified as D. ficus overwhelmingly dominated the mesocosms. (2) Corresponding published genome data show that the dominant species at 3 kGy/h, D. ficus, has a larger and more complex genome than other Deinococcus species with a greater proportion of genes related to DNA and nucleotide metabolism, cell wall, membrane, and envelope biogenesis as well as more cell cycle control, cell division, and chromosome partitioning-related genes. Deinococcus ficus also has a higher guanine-cytosine ratio than most other Deinococcus. These features may be linked to genome stability and may explain its greater abundance in this apparently competitive system, under high-radiation exposures. (3) Genomic analysis suggests that Deinococcus, including D. ficus, are capable of utilizing diverse carbon sources derived from both microbial cells killed by the radiation (including C5-C12-containing compounds, like arabinose, lactose, N-acetyl-D-glucosamine) and plant-derived organic matter in the soil (e.g., cellulose and hemicellulose). (4) Overall, based on its metagenome, even the most highly irradiated (3 kGy/h) soil possesses a wide range of the activities necessary for a functional soil system. Future studies may consider the resilience and sustainability of such soils in a high-radiation environment.
Collapse
Affiliation(s)
- Matthew Chidozie Ogwu
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- Department of Plant Biology and Biotechnology, University of Benin, PMB 1154, Ugbowo, Benin City, Edo State, Nigeria
| | - Sathiyaraj Srinivasan
- Department of Bio and Environmental Technology, Division of Environmental and Life Science, College of Natural Science, Seoul Women's University, 623 Hwarangno, Nowon-gu, Seoul, 139-774, Republic of Korea
| | - Ke Dong
- Department of Life Sciences, Kyonggi University, Suwon, 443-760, Republic of Korea
| | - Dhamodharan Ramasamy
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Bruce Waldman
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
- Department of Integrative Biology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK, 74078, USA.
| | - Jonathan M Adams
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210023, Qixia District, Jiangsu Province, People's Republic of China.
| |
Collapse
|
41
|
Yamanouchi K, Tsujiguchi T, Shiroma Y, Suzuki T, Tamakuma Y, Yamaguchi M, Sakamoto Y, Hegedűs M, Iwaoka K, Hosoda M, Kashiwakura I, Miura T, Tokonami S. COMPARISON OF BACTERIAL FLORA IN RIVER SEDIMENTS FROM FUKUSHIMA AND AOMORI PREFECTURES BY 16S RDNA SEQUENCE ANALYSIS. RADIATION PROTECTION DOSIMETRY 2019; 184:504-509. [PMID: 31038686 DOI: 10.1093/rpd/ncz114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Monitoring of radioactive materials has been reported in rivers and soil in Fukushima post the Fukushima Daiichi Nuclear Power Plant accident in March 2011. However, there are few reports on the influence of this event on bacteria in forest soils and rivers. Therefore, through amplicon sequencing of 16S rDNA we compared the bacterial flora in river sediment soils from Fukushima prefecture and from an area not exposed to radioactive contamination, Aomori prefecture. The bacterial composition in the Aomori prefecture soil and Fukushima soil were found to be very similar at the phylum level. However, Fukushima soil had significantly fewer Bacteroidetes than the Aomori soil (p = 0.014), while the content of Firmicutes and Latescibacteria (WS3) was significantly higher (p = 0.001, 0.013 respectively). However, no increase in the content of radioactive-resistant bacteria was observed. In future studies, it is necessary to standardise the conditions for soil collection to assess its content of radioactive substances.
Collapse
Affiliation(s)
- K Yamanouchi
- Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan
| | - T Tsujiguchi
- Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan
| | - Y Shiroma
- Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan
| | - T Suzuki
- Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan
| | - Y Tamakuma
- Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan
| | - M Yamaguchi
- Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan
| | - Y Sakamoto
- Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan
| | - M Hegedűs
- Institute of Radiation Emergency Medicine, Hirosaki University, Hirosaki, Japan
| | - K Iwaoka
- Institute of Radiation Emergency Medicine, Hirosaki University, Hirosaki, Japan
- National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - M Hosoda
- Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan
| | - I Kashiwakura
- Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan
| | - T Miura
- Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan
| | - S Tokonami
- Institute of Radiation Emergency Medicine, Hirosaki University, Hirosaki, Japan
| |
Collapse
|
42
|
Holmes CJ, Jennings EC, Gantz JD, Spacht D, Spangler AA, Denlinger DL, Lee RE, Hamilton TL, Benoit JB. The Antarctic mite, Alaskozetes antarcticus, shares bacterial microbiome community membership but not abundance between adults and tritonymphs. Polar Biol 2019. [DOI: 10.1007/s00300-019-02582-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
43
|
Seasonal diversity of the bacterial communities associated with petroglyphs sites from the Negev Desert, Israel. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01509-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
44
|
Ravindran R, Jaiswal AK. Wholesomeness and safety aspects of irradiated foods. Food Chem 2019; 285:363-368. [DOI: 10.1016/j.foodchem.2019.02.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/25/2018] [Accepted: 02/04/2019] [Indexed: 11/26/2022]
|
45
|
Temporal changes of geochemistry and microbial community in low and intermediate level waste (LILW) repository, South Korea. ANN NUCL ENERGY 2019. [DOI: 10.1016/j.anucene.2019.01.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
46
|
Gamma-radiation combined with tricycloazole to protect tempera paintings in ancient Egyptian tombs (Nile Delta, Lower Egypt). J Radioanal Nucl Chem 2019. [DOI: 10.1007/s10967-019-06580-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
47
|
León-Sobrino C, Ramond JB, Maggs-Kölling G, Cowan DA. Nutrient Acquisition, Rather Than Stress Response Over Diel Cycles, Drives Microbial Transcription in a Hyper-Arid Namib Desert Soil. Front Microbiol 2019; 10:1054. [PMID: 31139170 PMCID: PMC6527771 DOI: 10.3389/fmicb.2019.01054] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/26/2019] [Indexed: 11/13/2022] Open
Abstract
Hot desert surface soils are characterized by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over 3 days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.
Collapse
Affiliation(s)
- Carlos León-Sobrino
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | | | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
48
|
Merino N, Aronson HS, Bojanova DP, Feyhl-Buska J, Wong ML, Zhang S, Giovannelli D. Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context. Front Microbiol 2019; 10:780. [PMID: 31037068 PMCID: PMC6476344 DOI: 10.3389/fmicb.2019.00780] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/27/2019] [Indexed: 01/21/2023] Open
Abstract
Prokaryotic life has dominated most of the evolutionary history of our planet, evolving to occupy virtually all available environmental niches. Extremophiles, especially those thriving under multiple extremes, represent a key area of research for multiple disciplines, spanning from the study of adaptations to harsh conditions, to the biogeochemical cycling of elements. Extremophile research also has implications for origin of life studies and the search for life on other planetary and celestial bodies. In this article, we will review the current state of knowledge for the biospace in which life operates on Earth and will discuss it in a planetary context, highlighting knowledge gaps and areas of opportunity.
Collapse
Affiliation(s)
- Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, United States
| | - Heidi S Aronson
- Department of Biology, University of Southern California, Los Angeles, CA, United States
| | - Diana P Bojanova
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jayme Feyhl-Buska
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Michael L Wong
- Department of Astronomy - Astrobiology Program, University of Washington, Seattle, WA, United States.,NASA Astrobiology Institute's Virtual Planetary Laboratory, University of Washington, Seattle, WA, United States
| | - Shu Zhang
- Section of Infection and Immunity, Herman Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA, United States
| | - Donato Giovannelli
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Biology, University of Naples "Federico II", Naples, Italy.,Department of Marine and Coastal Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.,Institute for Biological Resources and Marine Biotechnology, National Research Council of Italy, Ancona, Italy
| |
Collapse
|
49
|
Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample. GEOSCIENCES 2019. [DOI: 10.3390/geosciences9040166] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The arid Mojave Desert is one of the most significant terrestrial analogue objects for astrobiological research due to its genesis, mineralogy, and climate. However, the knowledge of culturable bacterial communities found in this extreme ecotope’s soil is yet insufficient. Therefore, our research has been aimed to fulfil this lack of knowledge and improve the understanding of functioning of edaphic bacterial communities of the Central Mojave Desert soil. We characterized aerobic heterotrophic soil bacterial communities of the central region of the Mojave Desert. A high total number of prokaryotic cells and a high proportion of culturable forms in the soil studied were observed. Prevalence of Actinobacteria, Proteobacteria, and Firmicutes was discovered. The dominance of pigmented strains in culturable communities and high proportion of thermotolerant and pH-tolerant bacteria were detected. Resistance to a number of salts, including the ones found in Martian regolith, as well as antibiotic resistance, were also estimated.
Collapse
|
50
|
Experimental Evolution of Extreme Resistance to Ionizing Radiation in Escherichia coli after 50 Cycles of Selection. J Bacteriol 2019; 201:JB.00784-18. [PMID: 30692176 DOI: 10.1128/jb.00784-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/24/2019] [Indexed: 02/06/2023] Open
Abstract
In previous work (D. R. Harris et al., J Bacteriol 191:5240-5252, 2009, https://doi.org/10.1128/JB.00502-09; B. T. Byrne et al., Elife 3:e01322, 2014, https://doi.org/10.7554/eLife.01322), we demonstrated that Escherichia coli could acquire substantial levels of resistance to ionizing radiation (IR) via directed evolution. Major phenotypic contributions involved adaptation of organic systems for DNA repair. We have now undertaken an extended effort to generate E. coli populations that are as resistant to IR as Deinococcus radiodurans After an initial 50 cycles of selection using high-energy electron beam IR, four replicate populations exhibit major increases in IR resistance but have not yet reached IR resistance equivalent to D. radiodurans Regular deep sequencing reveals complex evolutionary patterns with abundant clonal interference. Prominent IR resistance mechanisms involve novel adaptations to DNA repair systems and alterations in RNA polymerase. Adaptation is highly specialized to resist IR exposure, since isolates from the evolved populations exhibit highly variable patterns of resistance to other forms of DNA damage. Sequenced isolates from the populations possess between 184 and 280 mutations. IR resistance in one isolate, IR9-50-1, is derived largely from four novel mutations affecting DNA and RNA metabolism: RecD A90E, RecN K429Q, and RpoB S72N/RpoC K1172I. Additional mechanisms of IR resistance are evident.IMPORTANCE Some bacterial species exhibit astonishing resistance to ionizing radiation, with Deinococcus radiodurans being the archetype. As natural IR sources rarely exceed mGy levels, the capacity of Deinococcus to survive 5,000 Gy has been attributed to desiccation resistance. To understand the molecular basis of true extreme IR resistance, we are using experimental evolution to generate strains of Escherichia coli with IR resistance levels comparable to Deinococcus Experimental evolution has previously generated moderate radioresistance for multiple bacterial species. However, these efforts could not take advantage of modern genomic sequencing technologies. In this report, we examine four replicate bacterial populations after 50 selection cycles. Genomic sequencing allows us to follow the genesis of mutations in populations throughout selection. Novel mutations affecting genes encoding DNA repair proteins and RNA polymerase enhance radioresistance. However, more contributors are apparent.
Collapse
|