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Rappaport HB, Oliverio AM. Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life. Genome Biol Evol 2024; 16:evae160. [PMID: 39101574 PMCID: PMC11299111 DOI: 10.1093/gbe/evae160] [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] [Accepted: 07/15/2024] [Indexed: 08/06/2024] Open
Abstract
From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.
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Affiliation(s)
- H B Rappaport
- Department of Biology, Syracuse University, Syracuse, NY, USA
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2
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Rosazza T, Earl C, Eigentler L, Davidson FA, Stanley-Wall NR. Reciprocal sharing of extracellular proteases and extracellular matrix molecules facilitates Bacillus subtilis biofilm formation. Mol Microbiol 2024; 122:184-200. [PMID: 38922753 DOI: 10.1111/mmi.15288] [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: 09/22/2023] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Extracellular proteases are a class of public good that support growth of Bacillus subtilis when nutrients are in a polymeric form. Bacillus subtilis biofilm matrix molecules are another class of public good that are needed for biofilm formation and are prone to exploitation. In this study, we investigated the role of extracellular proteases in B. subtilis biofilm formation and explored interactions between different public good producer strains across various conditions. We confirmed that extracellular proteases support biofilm formation even when glutamic acid provides a freely available nitrogen source. Removal of AprE from the NCIB 3610 secretome adversely affects colony biofilm architecture, while sole induction of WprA activity into an otherwise extracellular protease-free strain is sufficient to promote wrinkle development within the colony biofilm. We found that changing the nutrient source used to support growth affected B. subtilis biofilm structure, hydrophobicity and architecture. We propose that the different phenotypes observed may be due to increased protease dependency for growth when a polymorphic protein presents the sole nitrogen source. We however cannot exclude that the phenotypic changes are due to alternative matrix molecules being made. Co-culture of biofilm matrix and extracellular protease mutants can rescue biofilm structure, yet reliance on extracellular proteases for growth influences population coexistence dynamics. Our findings highlight the intricate interplay between these two classes of public goods, providing insights into microbial social dynamics during biofilm formation across different ecological niches.
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Affiliation(s)
- Thibault Rosazza
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Chris Earl
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lukas Eigentler
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
- Mathematics, School of Science and Engineering, University of Dundee, Dundee, UK
| | - Fordyce A Davidson
- Mathematics, School of Science and Engineering, University of Dundee, Dundee, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
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Maksimova Y, Eliseeva A, Maksimov A. Metabolic and Morphological Aspects of Adaptation of Alkaliphilic Bacillus aequororis 5-DB and Alkali-Tolerant Bacillus subtilis ATCC 6633 to Changes in pH and Mineralization. Int J Microbiol 2024; 2024:3087296. [PMID: 39081933 PMCID: PMC11288695 DOI: 10.1155/2024/3087296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 08/02/2024] Open
Abstract
The goal of the study is to evaluate metabolic and morphological changes of the facultative alkaliphile Bacillus aequororis 5-DB and the weakly alkali-resistant B. subtilis ATCC 6633 in a wide pH range and at different NaCl concentrations. The alkaliphile B. aequororis 5-DB is shown to have a broader general resistance to adverse factors (wide pH range, 50 g/L NaCl) than a weakly alkali-tolerant strain of the same genus. This alkaliphile is also shown to have a significantly greater resistance not only to high pH but also to low pH in comparison with B. subtilis ATCC 6633. The resistance of B. aequororis 5-DB to low pH was expressed in higher metabolic activity, maintenance of ΔpH, and no significant cell damage. The selected set of methods (reduction of resazurin to resorufin by cell dehydrogenases, bioluminescent method for determining ATP, AFM, and measurement of intracellular pH) allows us to adequately assess the ability of microbial cells to withstand harsh environmental factors. Nonspecific resistance of B. aequororis 5-DB was proven using a complex of selected methods. Tolerance to a wide range of pH and high salt concentrations may be useful for biotechnological applications of the strain.
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Affiliation(s)
- Yuliya Maksimova
- Laboratory of Molecular BiotechnologyInstitute of Ecology and Genetics of Microorganisms Ural Branch Russian Academy of Sciences, Golev Str., 13, Perm 614081, Russia
- Department of Microbiology and ImmunologyPerm State University, Bukirev Str., 15, Perm 614990, Russia
| | - Ann Eliseeva
- Laboratory of Molecular BiotechnologyInstitute of Ecology and Genetics of Microorganisms Ural Branch Russian Academy of Sciences, Golev Str., 13, Perm 614081, Russia
| | - Aleksandr Maksimov
- Laboratory of Molecular BiotechnologyInstitute of Ecology and Genetics of Microorganisms Ural Branch Russian Academy of Sciences, Golev Str., 13, Perm 614081, Russia
- Department of Microbiology and ImmunologyPerm State University, Bukirev Str., 15, Perm 614990, Russia
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Sheokand P, Tiwari SK. Characterization of carotenoids extracted from Haloferax larsenii NCIM 5678 isolated from Pachpadra salt lake, Rajasthan. Extremophiles 2024; 28:33. [PMID: 39037576 DOI: 10.1007/s00792-024-01353-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
Carotenoids are a diverse group of pigments known for their broad range of biological functions and applications. This study delves into multifaceted potential of carotenoids extracted from Haloferax larsenii NCIM 5678 previously isolated from Pachpadra Salt Lake in Rajasthan, India. H. larsenii NCIM 5678 was able to grow up to OD600 1.77 ± 0.03 with carotenoid concentration, 3.3 ± 0.03 µg/ml. The spectrophotometric analysis of carotenoid extract indicated the presence of three-fingered peak (460, 490 and 520 nm) which is a characteristic feature of bacterioruberin and its derivatives. The bacterioruberin was purified using silica gel column chromatography and thin layer chromatography. The carotenoid extract showed 12.3 ± 0.09 mm zone of growth inhibition with a minimum inhibitory concentration 546 ng/ml against indicator strain, H. larsenii HA4. The percentage antioxidant activity of carotenoid was found to be 84% which was higher as compared to commercially available ascorbic acid (56.74%). Thus, carotenoid extract from H. larsenii NCIM 5678 possesses unique attributes with compelling evidence of antimicrobial and antioxidant potential for the development of novel pharmaceuticals and nutraceuticals.
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Affiliation(s)
- Pardeep Sheokand
- Department of Genetics, Maharshi Dayanand University, 124001, Rohtak, Haryana, India
| | - Santosh Kumar Tiwari
- Department of Genetics, Maharshi Dayanand University, 124001, Rohtak, Haryana, India.
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Dong Y, Chen R, Graham EB, Yu B, Bao Y, Li X, You X, Feng Y. Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades. Nat Commun 2024; 15:6013. [PMID: 39019914 PMCID: PMC11255312 DOI: 10.1038/s41467-024-50368-z] [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: 09/03/2023] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.
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Affiliation(s)
- Yang Dong
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Ruirui Chen
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China.
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Emily B Graham
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA, 99352, USA.
- School of Biological Sciences, Washington State University, P.O. Box 645910, Pullman, WA, 99164, USA.
| | - Bingqian Yu
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yuanyuan Bao
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xin Li
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiangwei You
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Youzhi Feng
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
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6
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Belkin P, Nechaeva Y, Blinov S, Vaganov S, Perevoshchikov R, Plotnikova E. Sediment microbial communities of a technogenic saline-alkaline reservoir. Heliyon 2024; 10:e33640. [PMID: 39071596 PMCID: PMC11283119 DOI: 10.1016/j.heliyon.2024.e33640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 07/30/2024] Open
Abstract
Various natural saline and alkaline habitats have recently been widely investigated, but knowledge of anthropogenic habitats with more complex environmental conditions is still lacking. This research looks at the structure of microbial communities in 18 bottom sediment samples from a technogenic water body with saline and alkaline composition. The core samples were collected from 2 columns in the western and eastern parts of an artificial water body at the Verkhnekamskoe Salt Deposit (Russia). The microbial community structure was studied using high-throughput 16S rRNA gene sequencing. The bottom sediment composition (salinity, pH, and toxic element content) varies greatly with depth and laterally throughout the study area. The study found a considerable difference in bacterial community diversity between the 2 columns, but no considerable difference was found between the communities at various depths of the studied layers. Proteobacteria, Firmicutes, and Actinobacteria, which are common in both natural and artificial saline and alkaline environments, make up the majority of the bacteria found in the samples. Studies have shown that salinity and total alkalinity are the key factors influencing the formation of microbial communities. Ralstonia and Pseudomonas were the two most common genera in the sediment samples. These two genera are known for having high metabolic flexibility, which means they can survive in extreme environments and use a variety of carbon compounds as energy sources. The study also found that Ralstonia is indicator bacteria in samples with the highest concentrations of toxic elements compared to the other samples. A relatively high microbial diversity was discovered in the studied anthropogenic water reservoir despite the extreme alkaline and saline conditions, but it is considerably lower than that found in natural, less alkaline habitats. This research offers insight into the mechanisms behind microbial community formation in complex anthropogenic environments and covers key factors in microbial community distribution.
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Affiliation(s)
- Pavel Belkin
- Natural Science Institute, Perm State University, 614068, Bukireva st. 15, Perm, Russia
| | - Yulia Nechaeva
- Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Аcademy of Sciences, 614081, Goleva st. 13, Perm, Russia
| | - Sergey Blinov
- Natural Science Institute, Perm State University, 614068, Bukireva st. 15, Perm, Russia
| | - Sergey Vaganov
- Natural Science Institute, Perm State University, 614068, Bukireva st. 15, Perm, Russia
| | - Roman Perevoshchikov
- Natural Science Institute, Perm State University, 614068, Bukireva st. 15, Perm, Russia
| | - Elena Plotnikova
- Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Аcademy of Sciences, 614081, Goleva st. 13, Perm, Russia
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Hour C, Chuon K, Song MC, Shim JG, Cho SG, Kang KW, Kim JH, Jung KH. Unveiling the critical role of K + for xanthorhodopsin expression in E. coli. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 258:112976. [PMID: 39002191 DOI: 10.1016/j.jphotobiol.2024.112976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/19/2024] [Accepted: 07/01/2024] [Indexed: 07/15/2024]
Abstract
Xanthorhodopsin (XR), a retinal-binding 7-transmembrane protein isolated from the eubacterium Salinibacter ruber, utilizes two chromophores (retinal and salinixanthin (SAL)) as an outward proton pump and energy-donating carotenoid. However, research on XR has been impeded owing to limitations in achieving heterogeneous expression of stable forms and high production levels of both wild-type and mutants. We successfully expressed wild-type and mutant XRs in Escherichia coli in the presence of K+. Achieving XR expression requires significant K+ and a low inducer concentration. In particular, we highlight the significance of Ser-159 in helix E located near Gly-156 (a carotenoid-binding position) as a critical site for XR expression. Our findings indicate that replacing Ser-159 with a smaller amino acid, alanine, can enhance XR expression in a manner comparable to K+, implying that Ser-159 poses a steric hindrance for pigment formation in XR. In the presence of K+, the proton pumping and photocycle of the wild-type and mutants were characterized and compared; the wild-type result suggests similar properties to the first reported XR isolation from the S. ruber membrane fraction. We propose that the K+ gradient across the cell membrane of S. ruber serves to uphold the membrane potential of the organism and plays a role in the expression of proteins, such as XR, as demonstrated in our study. Our findings deepen the understanding of adaptive protein expression, particularly in halophilic organisms. We highlight salt selection as a promising strategy for improving protein yield and functionality.
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Affiliation(s)
- Chenda Hour
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Kimleng Chuon
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Myung-Chul Song
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Jin-Gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Shin-Gyu Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea; Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Kun-Wook Kang
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Ji-Hyun Kim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South Korea.
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8
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Martínez-Espinosa RM. Halophilic archaea as tools for bioremediation technologies. Appl Microbiol Biotechnol 2024; 108:401. [PMID: 38951176 PMCID: PMC11217053 DOI: 10.1007/s00253-024-13241-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/16/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024]
Abstract
Haloarchaea are extremophilic microorganisms belonging to the Archaea domain that require high salt concentrations to be alive, thus inhabiting ecosystems like salty ponds, salty marshes, or extremely salty lagoons. They are more abundantly and widely distributed worldwide than initially expected. Most of them are grouped into two families: Halobacteriaceae and Haloferacaceae. The extreme conditions under which haloarchaea survive contribute to their metabolic and molecular adaptations, thus making them good candidates for the design of bioremediation strategies to treat brines, salty water, and saline soils contaminated with toxic compounds such as nitrate, nitrite, oxychlorates such as perchlorate and chlorate, heavy metals, hydrocarbons, and aromatic compounds. New advances in understanding haloarchaea physiology, metabolism, biochemistry, and molecular biology suggest that biochemical pathways related to nitrogen and carbon, metals, hydrocarbons, or aromatic compounds can be used for bioremediation proposals. This review analyses the novelty of the most recent results showing the capability of some haloarchaeal species to assimilate, modify, or degrade toxic compounds for most living beings. Several examples of the role of these microorganisms in the treatment of polluted brine or salty soils are also discussed in connection with circular economy-based processes. KEY POINTS: • Haloarchaea are extremophilic microorganisms showing genuine metabolism • Haloarchaea can metabolise compounds that are highly toxic to most living beings • These metabolic capabilities are useful for designing soil and water bioremediation strategies.
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Affiliation(s)
- Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080, Alicante, Spain.
- Multidisciplinary Institute for Environmental Studies "Ramón Margalef", University of Alicante, Ap. 99, E-03080, Alicante, Spain.
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Galván-Arzola U, Valencia-Vázquez R, Gómez-González R, Alcalá-Rodríguez MM, Loredo-Medrano JÁ, García-Balandrán EE, Rivas-García P. Low-performance diagnosis of covered anaerobic lagoons as a waste management strategy in the intensive dairy industry. ENVIRONMENTAL TECHNOLOGY 2024:1-13. [PMID: 38940278 DOI: 10.1080/09593330.2024.2368688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/26/2024] [Indexed: 06/29/2024]
Abstract
Covered anaerobic lagoons (CALs) are Latin America's main livestock waste treatment systems. Mexico has 680 CALs that present low biogas yields (0.05 m3 m-3 digester d-1) and low COD removal rates (< 60%). This work focused on diagnosing CAL´s low performance in dairy farms by determining and analyzing operational parameters. Seven CALs located in the main dairy basin of Mexico were analyzed. The sampling areas for each CAL were the supernatant, the active zone, settled sludge, and digester inlet and outlet. The variation of the process parameter values corroborated that CALs appeared stratified and not working as expected. The sludge zone, comprising 50-58% of total solids content and 1-15% of total CALs volume, showed an elemental compounds content suitable for organic fertilizer (340, 48, and 5 kg t-1 of C, N, and S, respectively). However, this zone contained, at least, 85% of the slowly hydrolysable material; the methanogenic potential was less than 87 mL CH4 g VS-1, and the C/N ratio ranged from 4.9 to 17, outside of the optimal range. The biogas produced did not exceed 60% of methane content and more than 3000 ppm of H2S. The sludge zone significantly influences the lagoon's dynamics since it is a nutrient sink. Furthermore, the lack of agitation is the leading cause for the low energy yield and the low removal of organic matter rate. This work provides valuable information to address the operational problems within the CALs improving our understanding that shall allow proposing reactivation alternatives.
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Affiliation(s)
- Uriel Galván-Arzola
- Facultad de Ciencias Químicas, Departamento de Ingeniería Química, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Roberto Valencia-Vázquez
- Maestría en Sistemas Ambientales, División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México, Campus Durango, Durango, México
| | - Ricardo Gómez-González
- Facultad de Ciencias Químicas, Departamento de Ingeniería Química, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Mónica María Alcalá-Rodríguez
- Facultad de Ciencias Químicas, Departamento de Ingeniería Química, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - José Ángel Loredo-Medrano
- Facultad de Ciencias Químicas, Departamento de Ingeniería Química, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Ever Efraín García-Balandrán
- Facultad de Ciencias Químicas, Departamento de Ingeniería Química, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Pasiano Rivas-García
- Facultad de Ciencias Químicas, Departamento de Ingeniería Química, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
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Üresin D, Schulte J, Morgner N, Soppa J. C(P)XCG Proteins of Haloferax volcanii with Predicted Zinc Finger Domains: The Majority Bind Zinc, but Several Do Not. Int J Mol Sci 2024; 25:7166. [PMID: 39000272 PMCID: PMC11241148 DOI: 10.3390/ijms25137166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
In recent years, interest in very small proteins (µ-proteins) has increased significantly, and they were found to fulfill important functions in all prokaryotic and eukaryotic species. The halophilic archaeon Haloferax volcanii encodes about 400 µ-proteins of less than 70 amino acids, 49 of which contain at least two C(P)XCG motifs and are, thus, predicted zinc finger proteins. The determination of the NMR solution structure of HVO_2753 revealed that only one of two predicted zinc fingers actually bound zinc, while a second one was metal-free. Therefore, the aim of the current study was the homologous production of additional C(P)XCG proteins and the quantification of their zinc content. Attempts to produce 31 proteins failed, underscoring the particular difficulties of working with µ-proteins. In total, 14 proteins could be produced and purified, and the zinc content was determined. Only nine proteins complexed zinc, while five proteins were zinc-free. Three of the latter could be analyzed using ESI-MS and were found to contain another metal, most likely cobalt or nickel. Therefore, at least in haloarchaea, the variability of predicted C(P)XCG zinc finger motifs is higher than anticipated, and they can be metal-free, bind zinc, or bind another metal. Notably, AlphaFold2 cannot correctly predict whether or not the four cysteines have the tetrahedral configuration that is a prerequisite for metal binding.
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Affiliation(s)
- Deniz Üresin
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt, Germany;
| | - Jonathan Schulte
- Institute of Physical and Theoretical Chemistry, Goethe University, 60438 Frankfurt, Germany; (J.S.); (N.M.)
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University, 60438 Frankfurt, Germany; (J.S.); (N.M.)
| | - Jörg Soppa
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt, Germany;
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11
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Li Y, Wang J, Li E, Yang X, Yang J. Shifts in Microbial Community Structure and Co-occurrence Network along a Wide Soil Salinity Gradient. Microorganisms 2024; 12:1268. [PMID: 39065037 PMCID: PMC11278679 DOI: 10.3390/microorganisms12071268] [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: 05/08/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024] Open
Abstract
The response of microbiomes to salinity has been clarified in different geographic scales or ecosystems. However, how soil microbial community structure and interaction respond to salinity across wide salinity range and climatic region is still unclearly resolved. To address this issue, we examined the microbial community's composition in saline soils from two climatic regions (coastal wetland and arid desert). Our research confirms that soil salinity had a negative effect on soil nutrient content. Salinity decreased the relative abundance of bacteria, but increased archaea abundance, leading to the shifts from bacteria dominant community to archaea dominant community. Low-water medium-salinity soil (LWMS) had the most complex archaeal community network, whereas for bacteria, the most complex bacterial community network was observed in low-water high-salinity soils (LWHS). Key microbial taxa differed in three salinity gradients. Salinity, soil water content, pH, total nitrogen (TN), and soil organic carbon (SOC) were the main driving factors for the composition of archaeal and bacterial community. Salinity directly affected archaeal community, but indirectly influenced bacteria community through SOC; pH affected archaeal community indirectly through TN, but directly affected bacterial community. Our study suggests that soil salinity dramatically influences diversity, composition, and interactions within the microbial community.
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Affiliation(s)
- Yan Li
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China; (Y.L.)
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830017, China
| | - Juan Wang
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China; (Y.L.)
- Chengdu Institute of Biology, Chinese Academy Sciences, Chengdu 610042, China
| | - Eryang Li
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China; (Y.L.)
| | - Xiaodong Yang
- Department of Geography & Spatial Information Technology, Ningbo University, Ningbo 315211, China
| | - Jianjun Yang
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China; (Y.L.)
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830017, China
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Loperena-Barber M, Elizalde-Bielsa A, Salvador-Bescós M, Ruiz-Rodríguez P, Pellegrini JM, Renau-Mínguez C, Lancaster R, Zúñiga-Ripa A, Iriarte M, Bengoechea JA, Coscollá M, Gorvel JP, Moriyón I, Conde-Álvarez R. "Phylogenomic insights into brucellaceae: The Pseudochrobactrum algeriensis case". INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105625. [PMID: 38906517 DOI: 10.1016/j.meegid.2024.105625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
The genus Pseudochrobactrum encompasses free-living bacteria phylogenetically close to Ochrobactrum opportunistic pathogens and to Brucella, facultative intracellular parasites causing brucellosis, a worldwide-extended and grave zoonosis. Recently, Pseudochrobactrum strains were isolated from Brucella natural hosts on Brucella selective media, potentially causing diagnostic confusions. Strikingly, P. algeriensis was isolated from cattle lymph nodes, organs that are inimical to bacteria. Here, we analyse P. algeriensis potential virulence factors in comparison with Ochrobactrum and Brucella. Consistent with genomic analyses, Western-Blot analyses confirmed that P. algeriensis lacks the ability to synthesize the N-formylperosamine O-polysaccharide characteristic of the lipopolysaccharide (LPS) of smooth Brucella core species. However, unlike other Pseudochrobactrum but similar to some early diverging brucellae, P. algeriensis carries genes potentially synthetizing a rhamnose-based O-polysaccharide LPS. Lipid A analysis by MALDI-TOF demonstrated that P. algeriensis LPS bears a lipid A with a reduced pathogen-associated molecular pattern, a trait shared with Ochrobactrum and Brucella that is essential to generate a highly stable outer membrane and to delay immune activation. Also, although not able to multiply intracellularly in macrophages, the analysis of P. algeriensis cell lipid envelope revealed the presence of large amounts of cationic aminolipids, which may account for the extremely high resistance of P. algeriensis to bactericidal peptides and could favor colonization of mucosae and transient survival in Brucella hosts. However, two traits critical in Brucella pathogenicity are either significantly different (T4SS [VirB]) or absent (erythritol catabolic pathway) in P. algeriensis. This work shows that, while diverging in other characteristics, lipidic envelope features relevant in Brucella pathogenicity are conserved in Brucellaceae. The constant presence of these features strongly suggests that reinforcement of the envelope integrity as an adaptive advantage in soil was maintained in Brucella because of the similarity of some environmental challenges, such as the action of cationic peptide antibiotics and host defense peptides. This information adds knowledge about the evolution of Brucellaceae, and also underlines the taxonomical differences of the three genera compared.
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Affiliation(s)
- Maite Loperena-Barber
- Instituto de Investigación Sanitaria de Navarra (IdISNA) and Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Aitor Elizalde-Bielsa
- Instituto de Investigación Sanitaria de Navarra (IdISNA) and Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Miriam Salvador-Bescós
- Instituto de Investigación Sanitaria de Navarra (IdISNA) and Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Paula Ruiz-Rodríguez
- Institute for Integrative Systems Biology, Universidad de Valencia-CSIC, Valencia, Spain
| | | | - Chantal Renau-Mínguez
- Institute for Integrative Systems Biology, Universidad de Valencia-CSIC, Valencia, Spain
| | - Rebecca Lancaster
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
| | - Amaia Zúñiga-Ripa
- Instituto de Investigación Sanitaria de Navarra (IdISNA) and Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Maite Iriarte
- Instituto de Investigación Sanitaria de Navarra (IdISNA) and Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Jose A Bengoechea
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
| | - Mireia Coscollá
- Institute for Integrative Systems Biology, Universidad de Valencia-CSIC, Valencia, Spain
| | - Jean-Pierre Gorvel
- Centre d'Immunologie de Marseille-Luminy, CNRS, INSERM, Aix-Marseille University, Marseille, France
| | - Ignacio Moriyón
- Instituto de Investigación Sanitaria de Navarra (IdISNA) and Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Raquel Conde-Álvarez
- Instituto de Investigación Sanitaria de Navarra (IdISNA) and Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain.
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Arthi R, Parameswari E, Dhevagi P, Janaki P, Parimaladevi R. Microbial alchemists: unveiling the hidden potentials of halophilic organisms for soil restoration. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-33949-9. [PMID: 38877191 DOI: 10.1007/s11356-024-33949-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
Salinity, resulting from various contaminants, is a major concern to global crop cultivation. Soil salinity results in increased osmotic stress, oxidative stress, specific ion toxicity, nutrient deficiency in plants, groundwater contamination, and negative impacts on biogeochemical cycles. Leaching, the prevailing remediation method, is expensive, energy-intensive, demands more fresh water, and also causes nutrient loss which leads to infertile cropland and eutrophication of water bodies. Moreover, in soils co-contaminated with persistent organic pollutants, heavy metals, and textile dyes, leaching techniques may not be effective. It promotes the adoption of microbial remediation as an effective and eco-friendly method. Common microbes such as Pseudomonas, Trichoderma, and Bacillus often struggle to survive in high-saline conditions due to osmotic stress, ion imbalance, and protein denaturation. Halophiles, capable of withstanding high-saline conditions, exhibit a remarkable ability to utilize a broad spectrum of organic pollutants as carbon sources and restore the polluted environment. Furthermore, halophiles can enhance plant growth under stress conditions and produce vital bio-enzymes. Halophilic microorganisms can contribute to increasing soil microbial diversity, pollutant degradation, stabilizing soil structure, participating in nutrient dynamics, bio-geochemical cycles, enhancing soil fertility, and crop growth. This review provides an in-depth analysis of pollutant degradation, salt-tolerating mechanisms, and plant-soil-microbe interaction and offers a holistic perspective on their potential for soil restoration.
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Affiliation(s)
- Ravichandran Arthi
- Department of Environmental Science, Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Periyasamy Dhevagi
- Department of Environmental Science, Tamil Nadu Agricultural University, Coimbatore, India
| | - Ponnusamy Janaki
- Nammazhvar Organic Farming Research Centre, Tamil Nadu Agricultural University, Coimbatore, India
| | - Rathinasamy Parimaladevi
- Department of Bioenergy, Agrl. Engineering College & Research Institute, Tamil Nadu Agricultural University, Coimbatore, India
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Fan M, Tan S, Wang W, Zhang X. Improvement in Salt Tolerance Ability of Pseudomonas putida KT2440. BIOLOGY 2024; 13:404. [PMID: 38927284 PMCID: PMC11200750 DOI: 10.3390/biology13060404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024]
Abstract
Pseudomonas putida KT2440 is a popular platform for bioremediation due to its robust tolerance to environmental stress and strong biodegradation capacity. Limited research on the salt tolerance of P. putida KT2440 has hindered its application. In this study, the strain KT2440 was tested to tolerate a maximum of 4% w/v NaCl cultured with minimal salts medium. Transcriptomic data in a high-salinity environment showed significant expression changes in genes in membrane components, redox processes, chemotaxis, and cellular catabolic processes. betB-encoding betaine-aldehyde dehydrogenase was identified from the transcriptome data to overexpress and enhance growth profile of the strain KT2440 in minimal salts medium containing 4% w/v NaCl. Meanwhile, screening for exogenous salt-tolerant genes revealed that the Na+/H+ antiporter EcnhaA from Escherichia coli significantly increased the growth of the strain KT2440 in 4% w/v NaCl. Then, co-expression of EcnhaA and betB (KT2440-EcnhaA-betB) increased the maximum salt tolerance of strain KT2440 to 5% w/v NaCl. Further addition of betaine and proline improved the salt tolerance of the engineered strain to 6% w/v NaCl. Finally, the engineered strain KT2440-EcnhaA-betB was able to degrade 56.70% of benzoic acid and 95.64% of protocatechuic acid in minimal salt medium containing 4% w/v NaCl in 48 h, while no biodegradation was observed in the normal strain KT2440 in the same conditions. However, the strain KT2440-EcnhaA-betB failed to degrade catechol in minimal salt medium containing 3% w/v NaCl. This study illustrated the improvement in the salt tolerance performance of Pseudomonas putida KT2440 and the feasibility of engineered strain KT2440 as a potential salt-tolerant bioremediation platform.
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Affiliation(s)
| | | | | | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (M.F.); (S.T.); (W.W.)
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15
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Xing Q, Zhang S, Tao X, Mesbah NM, Mao X, Wang H, Wiegel J, Zhao B. The polyextremophile Natranaerobius thermophilus adopts a dual adaptive strategy to long-term salinity stress, simultaneously accumulating compatible solutes and K . Appl Environ Microbiol 2024; 90:e0014524. [PMID: 38578096 PMCID: PMC11107154 DOI: 10.1128/aem.00145-24] [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: 01/25/2024] [Accepted: 03/15/2024] [Indexed: 04/06/2024] Open
Abstract
The bacterium Natranaerobius thermophilus is an extremely halophilic alkalithermophile that can thrive under conditions of high salinity (3.3-3.9 M Na+), alkaline pH (9.5), and elevated temperature (53°C). To understand the molecular mechanisms of salt adaptation in N. thermophilus, it is essential to investigate the protein, mRNA, and key metabolite levels on a molecular basis. Based on proteome profiling of N. thermophilus under 3.1, 3.7, and 4.3 M Na+ conditions compared to 2.5 M Na+ condition, we discovered that a hybrid strategy, combining the "compatible solute" and "salt-in" mechanisms, was utilized for osmotic adjustment dur ing the long-term salinity adaptation of N. thermophilus. The mRNA level of key proteins and the intracellular content of compatible solutes and K+ support this conclusion. Specifically, N. thermophilus employs the glycine betaine ABC transporters (Opu and ProU families), Na+/solute symporters (SSS family), and glutamate and proline synthesis pathways to adapt to high salinity. The intracellular content of compatible solutes, including glycine betaine, glutamate, and proline, increases with rising salinity levels in N. thermophilus. Additionally, the upregulation of Na+/ K+/ H+ transporters facilitates the maintenance of intracellular K+ concentration, ensuring cellular ion homeostasis under varying salinities. Furthermore, N. thermophilus exhibits cytoplasmic acidification in response to high Na+ concentrations. The median isoelectric points of the upregulated proteins decrease with increasing salinity. Amino acid metabolism, carbohydrate and energy metabolism, membrane transport, and bacterial chemotaxis activities contribute to the adaptability of N. thermophilus under high salt stress. This study provides new data that support further elucidating the complex adaptation mechanisms of N. thermophilus under multiple extremes.IMPORTANCEThis study represents the first report of simultaneous utilization of two salt adaptation mechanisms within the Clostridia class in response to long-term salinity stress.
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Affiliation(s)
- Qinghua Xing
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanshan Zhang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
- Luo Yang Branch of Institute of Computing Technology, Chinese Academy of Sciences, Luoyang, China
| | - Xinyi Tao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Noha M. Mesbah
- Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Xinwei Mao
- Department of Civil Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Haisheng Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juergen Wiegel
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Baisuo Zhao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
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Feng Y, Arsenault D, Louyakis AS, Altman-Price N, Gophna U, Papke RT, Gogarten JP. Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense. mBio 2024; 15:e0040824. [PMID: 38619241 PMCID: PMC11078007 DOI: 10.1128/mbio.00408-24] [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: 03/04/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024] Open
Abstract
In this study, we use pan-genomics to characterize the genomic variability of the widely dispersed halophilic archaeal species Halorubrum ezzemoulense (Hez). We include a multi-regional sampling of newly sequenced, high-quality draft genomes. The pan-genome graph of the species reveals 50 genomic islands that represent rare accessory genetic capabilities available to members. Most notably, we observe rearrangements that have led to the insertion/recombination/replacement of mutually exclusive genomic islands in equivalent genome positions ("homeocassettes"). These conflicting islands encode for similar functions, but homologs from islands located between the same core genes exhibit high divergence on the amino acid level, while the neighboring core genes are nearly identical. Both islands of a homeocassette often coexist in the same geographic location, suggesting that either island may be beyond the reach of selective sweeps and that these loci of divergence between Hez members are maintained and persist long term. This implies that subsections of the population have different niche preferences and rare metabolic capabilities. After an evaluation of the gene content in the homeocassettes, we speculate that these islands may play a role in the speciation, niche adaptability, and group selection dynamics in Hez. Though homeocassettes are first described in this study, similar replacements and divergence of genes on genomic islands have been previously reported in other Haloarchaea and distantly related Archaea, suggesting that homeocassettes may be a feature in a wide range of organisms outside of Hez.IMPORTANCEThis study catalogs the rare genes discovered in strains of the species Halorubrum ezzemoulense (Hez), an obligate halophilic archaeon, through the perspective of its pan-genome. These rare genes are often found to be arranged on islands that confer metabolic and transport functions and contain genes that have eluded previous studies. The discovery of divergent, but homologous islands occupying equivalent genome positions ("homeocassettes") in different genomes, reveals significant new information on genome evolution in Hez. Homeocassette pairs encode for similar functions, but their dissimilarity and distribution imply high rates of recombination, different specializations, and niche preferences in Hez. The coexistence of both islands of a homeocassette pair in multiple environments demonstrates that both islands are beyond the reach of selective sweeps and that these genome content differences between strains persist long term. The switch between islands through recombination under different environmental conditions may lead to a greater range of niche adaptability in Hez.
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Affiliation(s)
- Yutian Feng
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Danielle Arsenault
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Artemis S. Louyakis
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Neta Altman-Price
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Avinoam Adam Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - R. Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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17
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Rawat M, Chauhan M, Pandey A. Extremophiles and their expanding biotechnological applications. Arch Microbiol 2024; 206:247. [PMID: 38713374 DOI: 10.1007/s00203-024-03981-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 05/08/2024]
Abstract
Microbial life is not restricted to any particular setting. Over the past several decades, it has been evident that microbial populations can exist in a wide range of environments, including those with extremes in temperature, pressure, salinity, and pH. Bacteria and Archaea are the two most reported types of microbes that can sustain in extreme environments, such as hot springs, ice caves, acid drainage, and salt marshes. Some can even grow in toxic waste, organic solvents, and heavy metals. These microbes are called extremophiles. There exist certain microorganisms that are found capable of thriving in two or more extreme physiological conditions simultaneously, and are regarded as polyextremophiles. Extremophiles possess several physiological and molecular adaptations including production of extremolytes, ice nucleating proteins, pigments, extremozymes and exopolysaccharides. These metabolites are used in many biotechnological industries for making biofuels, developing new medicines, food additives, cryoprotective agents etc. Further, the study of extremophiles holds great significance in astrobiology. The current review summarizes the diversity of microorganisms inhabiting challenging environments and the biotechnological and therapeutic applications of the active metabolites obtained as a response to stress conditions. Bioprospection of extremophiles provides a progressive direction with significant enhancement in economy. Moreover, the introduction to omics approach including whole genome sequencing, single cell genomics, proteomics, metagenomics etc., has made it possible to find many unique microbial communities that could be otherwise difficult to cultivate using traditional methods. These findings might be capable enough to state that discovery of extremophiles can bring evolution to biotechnology.
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Affiliation(s)
- Manvi Rawat
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India
| | - Mansi Chauhan
- Department of Microbiology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India
| | - Anita Pandey
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India.
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Mao YL, Wang BB, Yin XM, Hou J, Cui HL. Halomontanus rarus gen. nov., sp. nov., a novel halophilic archaeon of the family Natrialbaceae from salt lakes on the Qinghai-Xizang Plateau. Syst Appl Microbiol 2024; 47:126500. [PMID: 38417236 DOI: 10.1016/j.syapm.2024.126500] [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: 12/04/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Two halophilic archaeal strains TS33T and KZCA124 were isolated from two distant salt lakes on the Qinghai-Xizang Plateau, respectively. Culture-independent analysis indicated that these two strains were original inhabitants but low abundant taxa in respective salt lakes. Strains TS33T and KZCA124 were able to grow at 20-60 °C (optimum were 42 and 35 °C, respectively), with 0.9-4.8 M NaCl (optimum were 3.0 and 2.6 M, respectively), with 0-0.7 M MgCl2 (optimum, 0.3 M) and at pH 5.0-9.5 (optimum were pH 7.5 and pH 7, respectively). The 16S rRNA and rpoB' gene similarities between these two strains were 99.7% and 99.4%, and these two similarities among strains TS33T, KZCA124, and existing species of the family Natrialbaceae were 90.6-95.5% and 84.4-89.3%, respectively. Phylogenetic and phylogenomic analyses indicated that strains TS33T and KZCA124 formed an independent branch separated from neighboring genera, Saliphagus, Natronosalvus, and Natronobiforma. The averagenucleotideidentity (ANI), digital DNA-DNAhybridization (dDDH), and average amino acid identity (AAI) values between strains TS33T and KZCA124 were 96.4%, 73.1%, and 96.7%, respectively, higher than the thresholds for species demarcation. The overall genome-related indexes between these two strains and existing species of family Natrialbaceae were 73-77%, 21-25%, and 63-70%, respectively, significantly lower than the species boundary thresholds. Strains TS33T and KZCA124 may represent a novel species of a new genus within the family Natrialbaceae judged by the cutoff value of AAI (≤76%) proposed to differentiate genera within the family Natrialbaceae. The major polar lipids of strains TS33T and KZCA124 were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfated mannosyl glucosyl diether, and sulfated galactosyl mannosyl glucosyl diether. These two strains could be distinguished from the related genera according to differential phenotypic characteristics. These phenotypic, phylogenetic, and genomic analyses revealed that strains TS33T (=KCTC 4310T = MCCC 4K00132T) and KZCA124 (=CGMCC 1.17432 = JCM 34316) represent a novel species of a new genus of the family Natrialbaceae and were named Halomontanus rarus gen. nov., sp. nov.
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Affiliation(s)
- Ya-Ling Mao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Bei-Bei Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Xue-Meng Yin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China.
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19
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Zhang G, Bai J, Zhai Y, Jia J, Zhao Q, Wang W, Hu X. Microbial diversity and functions in saline soils: A review from a biogeochemical perspective. J Adv Res 2024; 59:129-140. [PMID: 37392974 PMCID: PMC11081963 DOI: 10.1016/j.jare.2023.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/03/2023] Open
Abstract
BACKGROUND Soil salinization threatens food security and ecosystem health, and is one of the important drivers to the degradation of many ecosystems around the world. Soil microorganisms have extremely high diversity and participate in a variety of key ecological processes. They are important guarantees for soil health and sustainable ecosystem development. However, our understanding of the diversity and function of soil microorganisms under the change of increased soil salinization is fragmented. AIM OF REVIEW Here, we summarize the changes in soil microbial diversity and function under the influence of soil salinization in diverse natural ecosystems. We particularly focus on the diversity of soil bacteria and fungi under salt stress and the changes in their emerging functions (such as their mediated biogeochemical processes). This study also discusses how to use the soil microbiome in saline soils to deal with soil salinization for supporting sustainable ecosystems, and puts forward the knowledge gaps and the research directions that need to be strengthened in the future. KEY SCIENTIFIC CONCEPTS OF REVIEW Due to the rapid development of molecular-based biotechnology (especially high-throughput sequencing technology), the diversity and community composition and functional genes of soil microorganisms have been extensively characterized in different habitats. Clarifying the responding pattern of microbial-mediated nutrient cycling under salt stress and developing and utilizing microorganisms to weaken the adverse effects of salt stress on plants and soil, which are of guiding significance for agricultural production and ecosystem management in saline lands.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China; Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, PR China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China.
| | - Yujia Zhai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Jia Jia
- Henan Key Laboratory of Ecological Environment Protection and Restoration of Yellow River Basin, Yellow River Institute of Hydraulic Research, Zhengzhou 45003, PR China
| | - Qingqing Zhao
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250103, PR China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Xingyun Hu
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350007, PR China
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20
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Thompson TP, Gilmore BF. Exploring halophilic environments as a source of new antibiotics. Crit Rev Microbiol 2024; 50:341-370. [PMID: 37079280 DOI: 10.1080/1040841x.2023.2197491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/25/2023] [Indexed: 04/21/2023]
Abstract
Microbial natural products from microbes in extreme environments, including haloarchaea, and halophilic bacteria, possess a huge capacity to produce novel antibiotics. Additionally, enhanced isolation techniques and improved tools for genomic mining have expanded the efficiencies in the antibiotic discovery process. This review article provides a detailed overview of known antimicrobial compounds produced by halophiles from all three domains of life. We summarize that while halophilic bacteria, in particular actinomycetes, contribute the vast majority of these compounds the importance of understudied halophiles from other domains of life requires additional consideration. Finally, we conclude by discussing upcoming technologies- enhanced isolation and metagenomic screening, as tools that will be required to overcome the barriers to antimicrobial drug discovery. This review highlights the potential of these microbes from extreme environments, and their importance to the wider scientific community, with the hope of provoking discussion and collaborations within halophile biodiscovery. Importantly, we emphasize the importance of bioprospecting from communities of lesser-studied halophilic and halotolerant microorganisms as sources of novel therapeutically relevant chemical diversity to combat the high rediscovery rates. The complexity of halophiles will necessitate a multitude of scientific disciplines to unravel their potential and therefore this review reflects these research communities.
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Affiliation(s)
- Thomas P Thompson
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Brendan F Gilmore
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
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21
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Hackley RK, Hwang S, Herb JT, Bhanap P, Lam K, Vreugdenhil A, Darnell CL, Pastor MM, Martin JH, Maupin-Furlow JA, Schmid AK. TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii. Mol Microbiol 2024; 121:742-766. [PMID: 38204420 PMCID: PMC11023807 DOI: 10.1111/mmi.15225] [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: 06/09/2023] [Revised: 12/09/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt-loving organism Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. However, the mechanisms regulating these lifestyle transitions remain unclear. In prior research, we showed that the transcriptional regulator, TrmB, maintains the rod shape in the related species Halobacterium salinarum by activating the expression of enzyme-coding genes in the gluconeogenesis metabolic pathway. In Hbt. salinarum, TrmB-dependent production of glucose moieties is required for cell surface glycoprotein biogenesis. Here, we use a combination of genetics and quantitative phenotyping assays to demonstrate that TrmB is essential for growth under gluconeogenic conditions in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name trmB suppressor, or TbsP (a.k.a. "tablespoon"). TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild-type cell morphology and motility. We use functional genomics and promoter fusion assays to characterize the regulons controlled by each of TrmB and TbsP, including joint regulation of the glucose-dependent transcription of gapII, which encodes an important gluconeogenic enzyme. We conclude that TrmB and TbsP coregulate gluconeogenesis, with downstream impacts on lifestyle transitions in response to nutrients in Hfx. volcanii.
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Affiliation(s)
- Rylee K. Hackley
- Biology Department, Duke University, Durham, North Carolina, USA
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| | - Sungmin Hwang
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Jake T. Herb
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Preeti Bhanap
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Katie Lam
- Biology Department, Duke University, Durham, North Carolina, USA
| | | | | | | | - Johnathan H. Martin
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Amy K. Schmid
- Biology Department, Duke University, Durham, North Carolina, USA
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
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22
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Narasimman V, Ramachandran S. Purification, structural characterization, and neuroprotective effect of 3,6-diisobutyl-2,5-piperazinedione from Halomonas pacifica CARE-V15 against okadaic acid-induced neurotoxicity in zebrafish model. J Biochem Mol Toxicol 2024; 38:e23708. [PMID: 38597299 DOI: 10.1002/jbt.23708] [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: 10/31/2023] [Revised: 02/26/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Halomonas pacifica CARE-V15 was isolated from the southeastern coast of India to determine its genome sequence. Secondary metabolite gene clusters were identified using an anti-SMASH server. The concentrated crude ethyl acetate extract was evaluated by GC-MS. The bioactive compound from the crude ethyl acetate extract was fractionated by gel column chromatography. HPLC was used to purify the 3,6-diisobutyl-2,5-piperazinedione (DIP), and the structure was determined using FTIR and NMR spectroscopy. Purified DIP was used in an in silico molecular docking analysis. Purified DIP exhibits a stronger affinity for antioxidant genes like glutathione peroxidase (GPx), glutathione-S-transferase (GST), and glutathione reductase (GSR). Using in silco molecular docking analysis, the protein-ligand binding affinities of GSR (-4.70 kcal/mol), GST (-5.27 kcal/mol), and GPx (-5.37 kcal/mol) were measured. The expression of antioxidant genes were investigated by qRT-PCR. The in vivo reactive oxygen species production, lipid peroxidation, and cell death levels were significantly (p ≤ 0.05) increased in OA-induced group, but all these levels were significantly (p ≤ 0.05) decreased in the purified DIP pretreated group. Purified DIP from halophilic bacteria could thus be a useful treatment for neurological disorders associated with oxidative stress.
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Affiliation(s)
- Vignesh Narasimman
- Native Medicine and Marine Pharmacology Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education (Deemed to be University), Chettinad Health City, Kelambakkam, Tamil Nadu, India
| | - Saravanan Ramachandran
- Native Medicine and Marine Pharmacology Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education (Deemed to be University), Chettinad Health City, Kelambakkam, Tamil Nadu, India
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23
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Baker BA, Gutiérrez-Preciado A, Rodríguez Del Río Á, McCarthy CGP, López-García P, Huerta-Cepas J, Susko E, Roger AJ, Eme L, Moreira D. Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments. Nat Microbiol 2024; 9:964-975. [PMID: 38519541 DOI: 10.1038/s41564-024-01647-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/20/2024] [Indexed: 03/25/2024]
Abstract
Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their environment. The evolutionary history of adaptations enabling salt tolerance remains poorly understood, in particular because the phylogeny of several lineages is conflicting. Here we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two uncultured lineages, Afararchaeaceae and Asbonarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. We obtained 13 metagenome-assembled genomes (MAGs) of these archaea from metagenomes of hypersaline aquatic systems of the Danakil Depression (Ethiopia). Our phylogenomic analyses including these taxa show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across extremely halophilic lineages.
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Affiliation(s)
- Brittany A Baker
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Ana Gutiérrez-Preciado
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Álvaro Rodríguez Del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Charley G P McCarthy
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Edward Susko
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew J Roger
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Laura Eme
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
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24
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Young IN, Jimenez VM. Short communication: Investigating optimal laboratory growth conditions of Gracilibacillus halotolerans in media supplemented with salt. J Microbiol Methods 2024; 219:106892. [PMID: 38311183 DOI: 10.1016/j.mimet.2024.106892] [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: 12/22/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Gracilibacillus halotolerans, a new and relatively unstudied extremophile, extracted from the Great Salt Lake USA, survives in an extreme saline environment. Uncovering optimal laboratory growth conditions can be useful to improve treatment strategies against antibiotic resistance and biofilm formation. In the current study, G. halotolerans growth optimization was tested to determine the ideal saline concentration. In addition, a variety of G. halotolerans'-derived survival strategies were reviewed. The major findings of the current study includes the optimal laboratory growth condition for G. halotolerans that requires the supplement of 5% NaCl. In addition, optimal growth was observed up to 72 h in Luria Bertani (LB) broth. Identifying the optimal laboratory growth conditions for G. halotolerans will standardize growth methods, reduce laboratory cost, and can improve future investigations of extremophile bacteria as model organisms to combat antibiotic resistance, biofilm, and other persister cell characteristics that negatively affect research and clinical settings.
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Affiliation(s)
- Isaac N Young
- Department of Biomedical Sciences, Noorda College of Osteopathic Medicine 2162 S 180 E, Provo, UT 84606, United States of America
| | - Victor M Jimenez
- Department of Biomedical Sciences, Noorda College of Osteopathic Medicine 2162 S 180 E, Provo, UT 84606, United States of America; Department of Pharmacy, Roseman University of Health Sciences, 10920 S River Front Pkwy, South Jordan, UT 84095, United States of America.
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25
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Yu J, Zhang Y, Liu H, Liu Y, Mohsin A, Liu Z, Zheng Y, Xing J, Han J, Zhuang Y, Guo M, Wang Z. Temporal dynamics of stress response in Halomonas elongata to NaCl shock: physiological, metabolomic, and transcriptomic insights. Microb Cell Fact 2024; 23:88. [PMID: 38519954 PMCID: PMC10960403 DOI: 10.1186/s12934-024-02358-5] [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: 01/14/2024] [Accepted: 03/06/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND The halophilic bacterium Halomonas elongata is an industrially important strain for ectoine production, with high value and intense research focus. While existing studies primarily delve into the adaptive mechanisms of this bacterium under fixed salt concentrations, there is a notable dearth of attention regarding its response to fluctuating saline environments. Consequently, the stress response of H. elongata to salt shock remains inadequately understood. RESULTS This study investigated the stress response mechanism of H. elongata when exposed to NaCl shock at short- and long-time scales. Results showed that NaCl shock induced two major stresses, namely osmotic stress and oxidative stress. In response to the former, within the cell's tolerable range (1-8% NaCl shock), H. elongata urgently balanced the surging osmotic pressure by uptaking sodium and potassium ions and augmenting intracellular amino acid pools, particularly glutamate and glutamine. However, ectoine content started to increase until 20 min post-shock, rapidly becoming the dominant osmoprotectant, and reaching the maximum productivity (1450 ± 99 mg/L/h). Transcriptomic data also confirmed the delayed response in ectoine biosynthesis, and we speculate that this might be attributed to an intracellular energy crisis caused by NaCl shock. In response to oxidative stress, transcription factor cysB was significantly upregulated, positively regulating the sulfur metabolism and cysteine biosynthesis. Furthermore, the upregulation of the crucial peroxidase gene (HELO_RS18165) and the simultaneous enhancement of peroxidase (POD) and catalase (CAT) activities collectively constitute the antioxidant defense in H. elongata following shock. When exceeding the tolerance threshold of H. elongata (1-13% NaCl shock), the sustained compromised energy status, resulting from the pronounced inhibition of the respiratory chain and ATP synthase, may be a crucial factor leading to the stagnation of both cell growth and ectoine biosynthesis. CONCLUSIONS This study conducted a comprehensive analysis of H. elongata's stress response to NaCl shock at multiple scales. It extends the understanding of stress response of halophilic bacteria to NaCl shock and provides promising theoretical insights to guide future improvements in optimizing industrial ectoine production.
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Affiliation(s)
- Junxiong Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Yue Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Hao Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Yuxuan Liu
- Department of Chemical Engineering for Energy Resources, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Zebo Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Jianmin Xing
- Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China.
| | - Zejian Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China.
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26
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Dindhoria K, Kumar R, Bhargava B, Kumar R. Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils. mSystems 2024; 9:e0105023. [PMID: 38377278 PMCID: PMC10949518 DOI: 10.1128/msystems.01050-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/19/2024] [Indexed: 02/22/2024] Open
Abstract
Climate change is causing unpredictable seasonal variations globally. Due to the continuously increasing earth's surface temperature, the rate of water evaporation is enhanced, conceiving a problem of soil salinization, especially in arid and semi-arid regions. The accumulation of salt degrades soil quality, impairs plant growth, and reduces agricultural yields. Salt-tolerant, plant-growth-promoting microorganisms may offer a solution, enhancing crop productivity and soil fertility in salinized areas. In the current study, genome-resolved metagenomic analysis has been performed to investigate the salt-tolerating and plant growth-promoting potential of two hypersaline ecosystems, Sambhar Lake and Drang Mine. The samples were co-assembled independently by Megahit, MetaSpades, and IDBA-UD tools. A total of 67 metagenomic assembled genomes (MAGs) were reconstructed following the binning process, including 15 from Megahit, 26 from MetaSpades, and 26 from IDBA_UD assembly tools. As compared to other assemblers, the MAGs obtained by MetaSpades were of superior quality, with a completeness range of 12.95%-96.56% and a contamination range of 0%-8.65%. The medium and high-quality MAGs from MetaSpades, upon functional annotation, revealed properties such as salt tolerance (91.3%), heavy metal tolerance (95.6%), exopolysaccharide (95.6%), and antioxidant (60.86%) biosynthesis. Several plant growth-promoting attributes, including phosphate solubilization and indole-3-acetic acid (IAA) production, were consistently identified across all obtained MAGs. Conversely, characteristics such as iron acquisition and potassium solubilization were observed in a substantial majority, specifically 91.3%, of the MAGs. The present study indicates that hypersaline microflora can be used as bio-fertilizing agents for agricultural practices in salinized areas by alleviating prevalent stresses. IMPORTANCE The strategic implementation of metagenomic assembled genomes (MAGs) in exploring the properties and harnessing microorganisms from ecosystems like hypersaline niches has transformative potential in agriculture. This approach promises to redefine our comprehension of microbial diversity and its ecosystem roles. Recovery and decoding of MAGs unlock genetic resources, enabling the development of new solutions for agricultural challenges. Enhanced understanding of these microbial communities can lead to more efficient nutrient cycling, pest control, and soil health maintenance. Consequently, traditional agricultural practices can be improved, resulting in increased yields, reduced environmental impacts, and heightened sustainability. MAGs offer a promising avenue for sustainable agriculture, bridging the gap between cutting-edge genomics and practical field applications.
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Affiliation(s)
- Kiran Dindhoria
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Raghawendra Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Bhavya Bhargava
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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27
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Li Y, Ma G, Xi Y, Wang S, Zeng X, Jia Y. Divergent adaptation strategies of abundant and rare bacteria to salinity stress and metal stress in polluted Jinzhou Bay. ENVIRONMENTAL RESEARCH 2024; 245:118030. [PMID: 38151148 DOI: 10.1016/j.envres.2023.118030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/16/2023] [Accepted: 12/22/2023] [Indexed: 12/29/2023]
Abstract
Understanding how abundant (AT) and rare (RT) taxa adapt to diverse environmental stresses is vital for assessing ecological processes, yet remains understudied. We collected sediment samples from Liaoning Province, China, representing rivers (upstream of wastewater outlet), estuaries (wastewater outlets), and Jinzhou Bay (downstream of wastewater outlets), to comprehensively evaluate AT and RT adaptation strategies to both natural stressors (salinity stress) and anthropogenic stressors (metal stress). Generally, RT displayed higher α- and β-diversities and taxonomic groups compared to AT. Metal and salinity stresses induced distinct α-diversity responses in AT and RT, while β-diversity remained consistent. Both subcommunities were dominated by Woeseia genus. Metal stress emerged as the primary driver of diversity and compositional discrepancies in AT and RT. Notably, AT responded more sensitively to salinity stress than RT. Stress increased topological parameters in the biotic network of AT subcommunities while decreasing values in RT subcommunities, concurrently loosening interactions of AT with other taxa and strengthening interactions of RT with others in biotic networks. RT generally exhibited greater diversity of metal resistance genes compared to AT. Greater numbers of genes related to salinity tolerance was observed for the RT than for AT. Compared to AT, RT demonstrated higher diversity of metal resistance genes and a greater abundance of genes associated with salinity tolerance. Additionally, deterministic processes governed AT community assembly, reinforced by salinity stress. However, the opposite trend was observed in the RT, where the importance of stochastic process gradually increased with metal stresses. The study is centered on exploring the adaptation strategies of both AT and RT to environmental stress. It underscores the importance of future research incorporating diverse ecosystems and a range of environmental stressors to draw broader and more reliable conclusions. This comprehensive approach is essential for gaining a thorough understanding of the adaptive mechanisms employed by these microorganisms.
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Affiliation(s)
- Yongbin Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Guoqing Ma
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yimei Xi
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, 110016, China
| | - Shaofeng Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Xiangfeng Zeng
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, 110016, China.
| | - Yongfeng Jia
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, 110016, China
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28
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Mousa WK, Abu-Izneid T, Salah-Tantawy A. High-throughput sequencing reveals the structure and metabolic resilience of desert microbiome confronting climate change. FRONTIERS IN PLANT SCIENCE 2024; 15:1294173. [PMID: 38510442 PMCID: PMC10953687 DOI: 10.3389/fpls.2024.1294173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Introduction Desert ecosystems harbor a unique microbial diversity that is crucial for ecological stability and biogeochemical cycles. An in-depth understanding of the biodiversity, compositions, and functions of these microbial communities is imperative to navigate global changes and confront potential threats and opportunities applicable to agricultural ecosystems amid climate change. Methods This study explores microbial communities in the rhizosphere and endosphere of desert plants native to the Arabian Peninsula using next-generation sequencing of the 16S rRNA gene (V3-V4 hypervariable region). Results Our results reveal that each microbial community has a diverse and unique microbial composition. Based on alpha and beta diversity indices, the rhizosphere microbiome is significantly diverse and richer in microbial taxa compared to the endosphere. The data reveals a shift towards fast-growing microbes with active metabolism, involvement in nutrient cycling, nitrogen fixation, and defense pathways. Our data reveals the presence of habitat-specific microbial communities in the desert, highlighting their remarkable resilience and adaptability to extreme environmental conditions. Notably, we observed the existence of radiation-resistant microbes such as Deinococcus radiotolerans, Kocuria sp., and Rubrobacter radiotolerans which can tolerate high levels of ionizing radiation. Additionally, examples of microbes exhibiting tolerance to challenging conditions include Nocardioides halotolerans, thriving in high-salinity environments, and hyperthermophilic microbes such as Quasibacillus thermotolerans. Moreover, functional analysis reveals enrichment in chaperon biosynthesis pathways associated with correct protein folding under heat stress conditions. Discussion Our research sheds light on the unique diversity of desert microbes and underscores their potential applications to increase the resilience of agriculture ecosystems, offering a promising strategy to fortify crops against the challenges posed by climate change, ultimately supporting sustainable food production for our ever-expanding global population.
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Affiliation(s)
- Walaa K. Mousa
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
- College of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Tareq Abu-Izneid
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Ahmed Salah-Tantawy
- Institute of Analytical and Environmental Sciences, College of Nuclear Science, National Tsing Hua University, Hsinchu, Taiwan
- Department of Zoology, Marine Science Division, College of Science, Al-Azhar University, Assiut, Egypt
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29
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Thweatt JL, Harman CE, Araújo MN, Marlow JJ, Oliver GC, Sabuda MC, Sevgen S, Wilpiszeki RL. Chapter 6: The Breadth and Limits of Life on Earth. ASTROBIOLOGY 2024; 24:S124-S142. [PMID: 38498824 DOI: 10.1089/ast.2021.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.
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Affiliation(s)
- Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA. (Former)
| | - C E Harman
- Planetary Systems Branch, NASA Ames Research Center, Moffett Field, California, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, USA
| | - Mary C Sabuda
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Serhat Sevgen
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
- Blue Marble Space Institute of Science, Seattle, Washington, USA
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30
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Galisteo C, de la Haba RR, Ventosa A, Sánchez-Porro C. The Hypersaline Soils of the Odiel Saltmarshes Natural Area as a Source for Uncovering a New Taxon: Pseudidiomarina terrestris sp. nov. Microorganisms 2024; 12:375. [PMID: 38399779 PMCID: PMC10893183 DOI: 10.3390/microorganisms12020375] [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: 12/28/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The hypersaline soils of the Odiel Saltmarshes Natural Area are an extreme environment with high levels of some heavy metals; however, it is a relevant source of prokaryotic diversity that we aim to explore. In this study, six strains related to the halophilic genus Pseudidiomarina were isolated from this habitat. The phylogenetic study based on the 16S rRNA gene sequence and the fingerprinting analysis suggested that they constituted a single new species within the genus Pseudidiomarina. Comparative genomic analysis based on the OGRIs indices and the phylogeny inferred from the core genome were performed considering all the members of the family Idiomarinaceae. Additionally, a completed phenotypic characterization, as well as the fatty acid profile, were also carried out. Due to the characteristics of the habitat, genomic functions related to salinity and high heavy metal concentrations were studied, along with the global metabolism of the six isolates. Last, the ecological distribution of the isolates was studied in different hypersaline environments by genome recruitment. To sum up, the six strains constitute a new species within the genus Pseudidiomarina, for which the name Pseudidiomarina terrestris sp. nov. is proposed. The low abundance in all the studied hypersaline habitats indicates that it belongs to the rare biosphere in these habitats. In silico genome functional analysis suggests the presence of heavy metal transporters and pathways for nitrate reduction and nitrogen assimilation in low availability, among other metabolic traits.
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Affiliation(s)
| | | | | | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain; (C.G.); (R.R.d.l.H.); (A.V.)
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Park J, Yoon SG, Lee H, An J, Nam K. Effects of in situ Fe oxide precipitation on As stabilization and soil ecological resilience under salt stress. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132629. [PMID: 37832440 DOI: 10.1016/j.jhazmat.2023.132629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/04/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023]
Abstract
Iron (Fe) oxide precipitation is a promising method for stabilizing arsenic (As) in contaminated soils; however, the addition of salts during the process can negatively affect soil functions. This study investigated the effects of in situ Fe oxide precipitation on As stabilization and the impact of salt stress on soil functions and microbial communities. Fe oxide precipitation reduced the concentration of bioaccessible As by 84% in the stabilized soil, resulting in the formation of ferrihydrite and lepidocrocite, as confirmed by XANES. Nevertheless, an increase in salt stress reduced barley development, microbial enzyme activities, and microbial diversity compared to those in the original soil. Despite this, the stabilized soil exhibited natural resilience and potential for enhanced microbial adaptations, with increased retention of salt-tolerant bacteria. Washing the stabilized soil with water restored EC1:5 to the level of the original soil, resulting in increased barley growth rates and enzyme activities after 5-d and 20-week incubation periods, suggesting soil function recovery. 16 S rRNA sequencing revealed the retention of salt-tolerant bacteria in the stabilized soil, while salt-removed soil exhibited an increase in Proteobacteria, which could facilitate ecological functions. Overall, Fe oxide precipitation effectively stabilized soil As and exhibited potential for restoring the natural resilience and ecological functions of soils through microbial adaptations and salt removal.
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Affiliation(s)
- Jinhee Park
- Department of Civil & Environmental Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Sang-Gyu Yoon
- Department of Smart City Engineering, Hanyang University, Ansan 15588, South Korea
| | - Hosub Lee
- Department of Civil & Environmental Engineering, Seoul National University, Seoul 08826, South Korea
| | - Jinsung An
- Department of Smart City Engineering, Hanyang University, Ansan 15588, South Korea; Department of Civil & Environmental Engineering, Hanyang University, Ansan 15588, South Korea.
| | - Kyoungphile Nam
- Department of Civil & Environmental Engineering, Seoul National University, Seoul 08826, South Korea
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32
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Teles EAP, Xavier JF, Arcênio FS, Amaya RL, Gonçalves JVS, Rouws LFM, Zonta E, Coelho IS. Characterization and evaluation of potential halotolerant phosphate solubilizing bacteria from Salicornia fruticosa rhizosphere. FRONTIERS IN PLANT SCIENCE 2024; 14:1324056. [PMID: 38293620 PMCID: PMC10825674 DOI: 10.3389/fpls.2023.1324056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024]
Abstract
Soil salinization is a significant abiotic factor threatening agricultural production, while the low availability of phosphorus (P) in plants is another worldwide limitation. Approximately 95-99% of the P in soil is unavailable to plants. Phosphate-solubilizing bacteria (PSB) transform insoluble phosphates into soluble forms that plants can utilize. The application of PSB can replace or partially reduce the use of P fertilizers. Therefore, selecting bacteria with high solubilization capacity from extreme environments, such as saline soils, becomes crucial. This study aimed to identify twenty-nine bacterial strains from the rhizosphere of Salicornia fruticosa by sequencing the 16S rDNA gene, evaluate their development in increasing concentrations of NaCl, classify them according to their salinity response, and determine their P solubilization capability. The bacteria were cultivated in nutrient agar medium with NaCl concentrations ranging from 0.5% to 30%. The phosphate solubilization capacity of the bacteria was evaluated in angar and broth National Botanical Research Institute (NBRIP) media supplemented with calcium phosphate (CaHPO4) and aluminum phosphate (AlPO4), and increased with 3% NaCl. All bacterial strains were classified as halotolerant and identified to the genera Bacillus, Enterobacter, Halomonas, Kushneria, Oceanobacillus, Pantoea, Pseudomonas, and Staphylococcus, with only one isolate was not identified. The isolates with the highest ability to solubilize phosphorus from CaHPO4 in the liquid medium were Kushneria sp. (SS102) and Enterobacter sp. (SS186), with 989.53 and 956.37 mg·Kg-1 P content and final pH of 4.1 and 3.9, respectively. For the solubilization of AlPO4, the most effective isolates were Bacillus sp. (SS89) and Oceanobacillus sp. (SS94), which raised soluble P by 61.10 and 45.82 mg·Kg-1 and final pH of 2.9 and 3.6, respectively. These bacteria demonstrated promising results in in vitro P solubilization and can present potential for the development of bioinput. Further analyses, involving different phosphate sources and the composition of produced organic acids, will be conducted to contribute to a comprehensive understanding of their applications in sustainable agriculture.
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Affiliation(s)
- E. A. P. Teles
- Laboratory of Molecular Genetics of Microorganisms, Department of Veterinary Microbiology and Immunology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Seropedica, Brazil
| | - J. F. Xavier
- Laboratory of Molecular Genetics of Microorganisms, Department of Veterinary Microbiology and Immunology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Seropedica, Brazil
| | - F. S. Arcênio
- Laboratory of Molecular Genetics of Microorganisms, Department of Veterinary Microbiology and Immunology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Seropedica, Brazil
| | - R. L. Amaya
- Laboratory of Molecular Genetics of Microorganisms, Department of Veterinary Microbiology and Immunology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Seropedica, Brazil
| | - J. V. S. Gonçalves
- Laboratory of Molecular Genetics of Microorganisms, Department of Veterinary Microbiology and Immunology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Seropedica, Brazil
| | | | - E. Zonta
- Laboratory of Soil-Plant Relationship, Department of Soils, Institute of Agronomy, UFRRJ, Seropedica, Brazil
| | - I. S. Coelho
- Laboratory of Molecular Genetics of Microorganisms, Department of Veterinary Microbiology and Immunology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Seropedica, Brazil
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Ugwuodo CJ, Colosimo F, Adhikari J, Bloodsworth K, Wright SA, Eder J, Mouser PJ. Changes in environmental and engineered conditions alter the plasma membrane lipidome of fractured shale bacteria. Microbiol Spectr 2024; 12:e0233423. [PMID: 38059585 PMCID: PMC10782966 DOI: 10.1128/spectrum.02334-23] [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: 06/05/2023] [Accepted: 10/31/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE Microorganisms inadvertently introduced into the shale reservoir during fracturing face multiple stressors including brine-level salinities and starvation. However, some anaerobic halotolerant bacteria adapt and persist for long periods of time. They produce hydrogen sulfide, which sours the reservoir and corrodes engineering infrastructure. In addition, they form biofilms on rock matrices, which decrease shale permeability and clog fracture networks. These reduce well productivity and increase extraction costs. Under stress, microbes remodel their plasma membrane to optimize its roles in protection and mediating cellular processes such as signaling, transport, and energy metabolism. Hence, by observing changes in the membrane lipidome of model shale bacteria, Halanaerobium congolense WG10, and mixed consortia enriched from produced fluids under varying subsurface conditions and growth modes, we provide insight that advances our knowledge of the fractured shale biosystem. We also offer data-driven recommendations for improving biocontrol efficacy and the efficiency of energy recovery from unconventional formations.
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Affiliation(s)
- Chika Jude Ugwuodo
- Natural Resources and Earth Systems Science, University of New Hampshire, Durham, New Hampshire, USA
- Department of Civil and Environmental Engineering, University of New Hampshire, Durham, New Hampshire, USA
| | | | | | - Kent Bloodsworth
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Stephanie A. Wright
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Josie Eder
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Paula J. Mouser
- Department of Civil and Environmental Engineering, University of New Hampshire, Durham, New Hampshire, USA
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34
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Xing T, Liu K, Ji M, Chen Y, Liu Y. Bacterial diversity in a continuum from supraglacial habitats to a proglacial lake on the Tibetan Plateau. FEMS Microbiol Lett 2024; 371:fnae021. [PMID: 38521984 DOI: 10.1093/femsle/fnae021] [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: 08/23/2023] [Revised: 01/14/2024] [Accepted: 03/22/2024] [Indexed: 03/25/2024] Open
Abstract
Mountain glaciers are frequently assessed for their hydrological connectivity from glaciers to proglacial lakes. Ecological process on glacier surfaces and downstream ecosystems have often been investigated separately, but few studies have focused on the connectivity between the different glacial habitats. Therefore, it remains a limited understanding of bacterial community assembly across different habitats along the glacier hydrological continuum. In this study, we sampled along a glacial catchment from supraglacial snow, cryoconite holes, supraglacial runoff, ice-marginal moraine and proglacial lake on the Tibetan Plateau. The bacterial communities in these habitats were analyzed using high-throughput DNA sequencing of the 16S rRNA gene to determine the bacterial composition and assembly. Our results showed that each habitat hosted unique bacterial communities, with higher bacterial α-diversity in transitional habitats (e.g. runoff and ice-marginal moraine). Null model analysis indicated that deterministic processes predominantly shaped bacterial assembly in snow, cryoconite holes and lake, while stochastic process dominantly governed bacterial community in transitional habitats. Collectively, our findings suggest that local environment play a critical role in filtering bacterial community composition within glacier habitats. This study enhances our understanding of microbial assembly process in glacier environments and provides valuable insights into the factors governing bacterial community compositions across different habitats along the glacial hydrological continuum.
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Affiliation(s)
- Tingting Xing
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Yuying Chen
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
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35
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Kankonkar HT, Khandeparker RS. Halotolerant Bacteria from Genus Nesterenkonia sandarakina VSA9 as a Potential Polyhydroxyalkanoate Producer. Curr Microbiol 2024; 81:53. [PMID: 38172411 DOI: 10.1007/s00284-023-03569-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
Nesterenkonia sandarakina VSA9 pigmented bacteria isolated from Sargassum is being reported to produce polyhydroxyalkanoates (PHA) deduced through detecting the presence of pha C gene using the molecular method. The PHA synthase gene was of type I which has been concluded from the phylogenetic tree and multiple sequence analysis. The amino acid analysis of pha C gene confirms the involvement of the lipase box having a sequence of G-Y-C-I-G-G with cysteine as the active center of the PHA synthase. Homology modeling predicted the 3D protein structure which is similar to the PHA synthase of Chromobacterium sp. USM2. The solvent extract of N. sandarakina VSA9 showed the presence of Carotenoid compound with maximum wavelength at 475 nm. The study's findings could have far-reaching implications, contributing to advancements in the biotechnology, industrial processes, and sustainable practices. The simultaneous production of carotenoids and PHAs by N. sandarakina VSA9 presents exciting opportunities for the development of innovative and environmentally friendly applications.
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Affiliation(s)
- Harshada T Kankonkar
- Microbial Ecology Laboratory, Biological Oceanography Division, CSIR-National Institute of Oceanography, Raj Bhavan Road, Dona Paula, Goa, 403004, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rakhee S Khandeparker
- Microbial Ecology Laboratory, Biological Oceanography Division, CSIR-National Institute of Oceanography, Raj Bhavan Road, Dona Paula, Goa, 403004, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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36
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Zhang Y, Gao H, Zhao D, Chen X, Zhu F, Li Y, Xue S. Microbially-driven alkaline regulation: Organic acid secretion behavior of Penicillium oxalicum and charge neutralization in bauxite residue. ENVIRONMENTAL RESEARCH 2024; 240:117489. [PMID: 37890830 DOI: 10.1016/j.envres.2023.117489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
Microbially-driven alkaline neutralization in bauxite residue by functional microorganisms is a promising approach for the ecological rehabilitation on alkaline disposal areas. However, the alkali resistance and acid secretion mechanism of functional microorganisms are still unknown, which limits their application. Here, saline-alkaline resistance, acid production performance, and differentially expressed genes of Penicillium oxalicum (P. oxalicum, a functional fungus screened from a typical disposal area) were investigated and its bio-neutralization efficiency was evaluated. This fungus exhibited high tolerance to alkalinity (pH 12), and salinity (NaCl 2.0 M), and produced a large amount of oxalic acid to reduce the medium pH to 2.0. Transcriptome showed that alkali stress induced the overexpression of genes related to antioxidant and stress-resistant enzymes (GST, KatE) and glycolytic pathway rate-limiting enzymes (HK). The rate of glycolysis and other organic acid metabolism processes was increased with higher stress resistance of P. oxalicum. The integrated application of P. oxalicum and maize straw accelerated the dissolved organic carbon content and stabilized the leachate pH of bauxite residue at about 7.4. 3DEEM and BIOSEM analysis indicated that P. oxalicum maintained high activity in the residue leachate and continuously decomposed the maize straw for their metabolism. P. oxalicum showed strong alkaline resistance, biomass degradation capacity, and alkaline regulation potential, which should be beneficial for microbial-driven alkaline regulation in bauxite residue.
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Affiliation(s)
- Yifan Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; School of Metallurgy and Environment, Central South University, Changsha 410083, China.
| | - Hui Gao
- China Aluminum Mining Limited Company, Zhengzhou City, Henan Province 450041, China.
| | - Dongliang Zhao
- China Aluminum Mining Limited Company, Zhengzhou City, Henan Province 450041, China.
| | - Xueming Chen
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350108, China.
| | - Feng Zhu
- School of Metallurgy and Environment, Central South University, Changsha 410083, China.
| | - Yinsheng Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Shengguo Xue
- School of Metallurgy and Environment, Central South University, Changsha 410083, China.
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37
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Xu T, Mitra R, Tan D, Li Z, Zhou C, Chen T, Xie Z, Han J. Utilization of gene manipulation system for advancing the biotechnological potential of halophiles: A review. Biotechnol Adv 2024; 70:108302. [PMID: 38101552 DOI: 10.1016/j.biotechadv.2023.108302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/02/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023]
Abstract
Halophiles are salt-loving microorganisms known to have their natural resistance against media contamination even when cultivated in nonsterile and continuous bioprocess system, thus acting as promising cell factories for Next Generation of Industrial Biotechnology (NGIB). NGIB - a successor to the traditional industrial biotechnology, is a more sustainable and efficient bioprocess technology while saving energy and water in a more convenient way as well as reducing the investment cost and skilled workforce requirement. Numerous studies have achieved intriguing outcomes during synthesis of different metabolite using halophiles such as polyhydroxyalkanoates (PHA), ectoine, biosurfactants, and carotenoids. Present-day development in genetic maneuverings have shown optimistic effects on the industrial applications of halophiles. However, viable and competent genetic manipulation system and gene editing tools are critical to accelerate the process of halophile engineering. With the aid of such powerful gene manipulation systems, exclusive microbial chassis are being crafted with desirable features to breed another innovative area of research such as synthetic biology. This review provides an aerial perspective on how the expansion of adaptable gene manipulation toolkits in halophiles are contributing towards biotechnological advancement, and also focusses on their subsequent application for production improvement. This current methodical and comprehensive review will definitely help the scientific fraternity to bridge the gap between challenges and opportunities in halophile engineering.
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Affiliation(s)
- Tong Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Ruchira Mitra
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China; International College, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Dan Tan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Zhengjun Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Cheng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China; College of Biochemical Engineering, Beijing Union University, Beijing 100023, People's Republic of China
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Zhengwei Xie
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing 100191, People's Republic of China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.
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38
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Jaiswal S, Ojha A, Mishra SK. Assessment of Plant Growth-Promoting Parameters of Endophytes Isolated from Calotropis procera and Their Performance Under Irrigated and Non-irrigated Conditions. Curr Microbiol 2023; 81:49. [PMID: 38147132 DOI: 10.1007/s00284-023-03570-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/20/2023] [Indexed: 12/27/2023]
Abstract
In the present study, bacterial and fungal endophytes are isolated from Calotropis procera, a drought-resistant plant and studied for their role in plant growth promotion. Among bacterial sp. Enterobacter cloacae subsp. cloacae strain CPR5B and fungus, Penicillium citrinum strain CPL1F, were identified as potent endophytes as both strains were able to produce Indole Acetic Acid (IAA) and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and solubilize phosphate. Penicillium citrinum CPL1F also been shown to produce siderophore. The IAA production was observed to be 94.28 μg/mL and 17.1 μg/mL for bacterial and fungal sp., respectively. The phosphate solubilization was observed to be 76.41 μg/mL and 114.57 μg/mL, respectively. The in vitro plant treatment studies with bacterium and fungus under irrigated and non-irrigated conditions showed that both strains had promoted plant growth in both conditions with respect to their control. Both the strains showed significant changes in most of the growth parameters under endophyte-treated irrigated and non-irrigated conditions, suggesting their stress-dependent plant growth promotion. The present findings will contribute to exploring endophytes that enhance plant growth in adverse conditions and act as plant growth-promoting endophytes.
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Affiliation(s)
- Sonali Jaiswal
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India.
| | - Anupama Ojha
- Department of Allied Health Science, Mahayogi Gorakhnath University, Gorakhpur, Uttar Pradesh, 273007, India
| | - Sarad Kumar Mishra
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
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Martínez-Alvarez L, Ramond JB, Vikram S, León-Sobrino C, Maggs-Kölling G, Cowan DA. With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities. Appl Environ Microbiol 2023; 89:e0062923. [PMID: 37971255 PMCID: PMC10734447 DOI: 10.1128/aem.00629-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/24/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.
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Affiliation(s)
- Laura Martínez-Alvarez
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | - Jean-Baptiste Ramond
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
- Extreme Ecosystem Microbiomics & Ecogenomics (E²ME) Lab., Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Surendra Vikram
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | - Carlos León-Sobrino
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | | | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
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40
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Nguyen NL, Van Dung V, Van Tung N, Nguyen TKL, Quan ND, Giang TTH, Ngan NTT, Hien NT, Nguyen HH. Draft genome sequencing of halotolerant bacterium Salinicola sp. DM10 unravels plant growth-promoting potentials. 3 Biotech 2023; 13:416. [PMID: 38009164 PMCID: PMC10667196 DOI: 10.1007/s13205-023-03833-3] [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: 09/30/2022] [Accepted: 10/24/2023] [Indexed: 11/28/2023] Open
Abstract
In this study, strain DM10 was isolated from mangrove roots and characterized as a halotolerant plant growth-promoting bacterium. Strain DM10 exhibited the ability to solubilize phosphate, produce siderophore, show 1-aminocyclopropane-1-carboxylic acid deaminase activity, and hydrolyze starch. The rice plants subjected to a treatment of NaCl (200 mM) and inoculated with strain DM10 showed an improvement in the shoot length, root length, and dried weight, when compared to those exposed solely to saline treatment. The comprehensive genome sequencing of strain DM10 revealed a genome spanning of 4,171,745 bp, harboring 3626 protein coding sequences. Within its genome, strain DM10 possesses genes responsible for both salt-in and salt-out strategies, indicative of a robust genetic adaptation aimed at fostering salt tolerance. Additionally, the genome encodes genes involved in phosphate solubilization, such as the synthesis of gluconic acid, high-affinity phosphate transport systems, and alkaline phosphatase. In the genome of DM10, we identified the acdS gene, responsible for encoding 1-aminocyclopropane-1-carboxylate deaminase, as well as the amy1A gene, which encodes α-amylase. Furthermore, the genome of DM10 contains sequences associated with the iron (3+)-hydroxamate and iron uptake clusters, responsible for siderophore production. Such data provide a deep understanding of the mechanism employed by strain DM10 to combat osmotic and salinity stress, facilitate plant growth, and elucidate its molecular-level behaviors.
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Affiliation(s)
- Ngoc-Lan Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Vu Van Dung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Nguyen Van Tung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Thi Kim Lien Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Nguyen Duc Quan
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Tran Thi Huong Giang
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Nguyen Thi Thanh Ngan
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Nguyen Thanh Hien
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Huy-Hoang Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
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41
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Skoog EJ, Fournier GP, Bosak T. Assessing the Influence of HGT on the Evolution of Stress Responses in Microbial Communities from Shark Bay, Western Australia. Genes (Basel) 2023; 14:2168. [PMID: 38136990 PMCID: PMC10742547 DOI: 10.3390/genes14122168] [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: 10/20/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Pustular microbial mats in Shark Bay, Western Australia, are modern analogs of microbial systems that colonized peritidal environments before the evolution of complex life. To understand how these microbial communities evolved to grow and metabolize in the presence of various environmental stresses, the horizontal gene transfer (HGT) detection tool, MetaCHIP, was used to identify the horizontal transfer of genes related to stress response in 83 metagenome-assembled genomes from a Shark Bay pustular mat. Subsequently, maximum-likelihood phylogenies were constructed using these genes and their most closely related homologs from other environments in order to determine the likelihood of these HGT events occurring within the pustular mat. Phylogenies of several stress-related genes-including those involved in response to osmotic stress, oxidative stress and arsenic toxicity-indicate a potentially long history of HGT events and are consistent with these transfers occurring outside of modern pustular mats. The phylogeny of a particular osmoprotectant transport gene reveals relatively recent adaptations and suggests interactions between Planctomycetota and Myxococcota within these pustular mats. Overall, HGT phylogenies support a potentially broad distribution in the relative timing of the HGT events of stress-related genes and demonstrate ongoing microbial adaptations and evolution in these pustular mat communities.
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Affiliation(s)
- Emilie J. Skoog
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (G.P.F.); (T.B.)
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Gregory P. Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (G.P.F.); (T.B.)
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (G.P.F.); (T.B.)
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42
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Akbaba M, Özden E. Salt tolerance of endophytic root bacteria and their effects on seed germination and viability on tomato plants. Braz J Microbiol 2023; 54:3147-3162. [PMID: 37768522 PMCID: PMC10689620 DOI: 10.1007/s42770-023-01127-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Salinity is one of the most brutal environmental factors limiting the productivity of agricultural lands worldwide. It is considered that the salinity may be one of the important reasons for the low yield in Iğdır of the tomato plants, which is medium resistant (3-5 dS.m-1) among vegetables. Eco-friendly techniques such as endophytic root bacteria treatments (ERB) are needed to restore saline soils to agriculture and also to increase the yield of tomatoes. Endophytic bacteria colonizing the inside of plants increase plant growth by various mechanisms and also mitigate the adverse effects of biotic and abiotic stresses on plants. In this study, endophytic bacteria were isolated from the roots of tomato plants exposed to salt stress. Then, these isolates' tolerance levels to different NaCl (0, 0.1, 0.2, 0.4, 0.8 M) concentrations and their potential to promote plant growth (PGP) traits were determined. It was recorded that 14.8% of the isolates whose salt tolerance was tested were highly tolerant to NaCl and 18.5% were highly susceptible. The tested ERB isolates exhibited typical PGP characteristics such as siderophore production (4-30 mm diameter), phosphate solubilizing activity (6-16 mm diameter), and IAA production activity (24.9-171.6 µg/ml). Moreover, it was determined that the nitrogen fixation potential is high 55.7% of the isolates tested, and 11.1% low. In addition, the effects of ERB treatments on germination and vigor index in two tomato cultivars under standard and saline conditions in the lab were evaluated. Some ERB isolates in tomato plants under standard and saline conditions increased seed viability, hypocotyl length, root length, and seedling fresh weight, and also accelerated germination.
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Affiliation(s)
- Mustafa Akbaba
- Plant Protection, Faculty of Agriculture, Igdir University, Igdir, Turkey.
| | - Eren Özden
- Horticulture, Faculty of Agriculture, Igdir University, Igdir, Turkey
- Horticulture and Agronomy, Faculty of Agriculture, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyz Republic
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43
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Hernández-Soto LM, Martínez-Abarca F, Ramírez-Saad H, López-Pérez M, Aguirre-Garrido JF. Genome analysis of haloalkaline isolates from the soda saline crater lake of Isabel Island; comparative genomics and potential metabolic analysis within the genus Halomonas. BMC Genomics 2023; 24:696. [PMID: 37986038 PMCID: PMC10662389 DOI: 10.1186/s12864-023-09800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Isabel Island is a Mexican volcanic island primarily composed of basaltic stones. It features a maar known as Laguna Fragatas, which is classified as a meromictic thalassohaline lake. The constant deposition of guano in this maar results in increased levels of phosphorus, nitrogen, and carbon. The aim of this study was to utilize high-quality genomes from the genus Halomonas found in specialized databases as a reference for genome mining of moderately halophilic bacteria isolated from Laguna Fragatas. This research involved genomic comparisons employing phylogenetic, pangenomic, and metabolic-inference approaches. RESULTS The Halomonas genus exhibited a large open pangenome, but several genes associated with salt metabolism and homeostatic regulation (ectABC and betABC), nitrogen intake through nitrate and nitrite transporters (nasA, and narGI), and phosphorus uptake (pstABCS) were shared among the Halomonas isolates. CONCLUSIONS The isolated bacteria demonstrate consistent adaptation to high salt concentrations, and their nitrogen and phosphorus uptake mechanisms are highly optimized. This optimization is expected in an extremophile environment characterized by minimal disturbances or abrupt seasonal variations. The primary significance of this study lies in the dearth of genomic information available for this saline and low-disturbance environment. This makes it important for ecosystem conservation and enabling an exploration of its biotechnological potential. Additionally, the study presents the first two draft genomes of H. janggokensis.
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Affiliation(s)
- Luis Mario Hernández-Soto
- Doctorado en Ciencias Biológicas y de La Salud, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Francisco Martínez-Abarca
- Estructura, Dinámica y Función de Genomas de Rizobacterias, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - Hugo Ramírez-Saad
- Departamento Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de Mexico, México
| | - Marcos López-Pérez
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana-Lerma, Estado de México, Lerma, México
| | - José Félix Aguirre-Garrido
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana-Lerma, Estado de México, Lerma, México.
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Font-Verdera F, Liébana R, Rossello-Mora R, Viver T. Impact of dilution on stochastically driven methanogenic microbial communities of hypersaline anoxic sediments. FEMS Microbiol Ecol 2023; 99:fiad146. [PMID: 37989854 PMCID: PMC10673710 DOI: 10.1093/femsec/fiad146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/02/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023] Open
Abstract
Sediments underlying the solar salterns of S'Avall are anoxic hypersaline ecosystems dominated by anaerobic prokaryotes, and with the especial relevance of putative methanogenic archaea. Slurries from salt-saturated sediments, diluted in a gradient of salinity and incubated for > 4 years revealed that salt concentration was the major selection force that deterministically structured microbial communities. The dominant archaea in the original communities showed a decrease in alpha diversity with dilution accompanied by the increase of bacterial alpha diversity, being highest at 5% salts. Correspondingly, methanogens decreased and in turn sulfate reducers increased with decreasing salt concentrations. Methanogens especially dominated at 25%. Different concentrations of litter of Posidonia oceanica seagrass added as a carbon substrate, did not promote any clear relevant effect. However, the addition of ampicillin as selection pressure exerted important effects on the assemblage probably due to the removal of competitors or enhancers. The amended antibiotic enhanced methanogenesis in the concentrations ≤ 15% of salts, whereas it was depleted at salinities ≥ 20% revealing key roles of ampicillin-sensitive bacteria.
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Affiliation(s)
- Francisca Font-Verdera
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
| | - Raquel Liébana
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
- AZTI, Basque Research Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, 48395 Sukarrieta, Bizkaia, Spain
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
| | - Tomeu Viver
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
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Coker JA. 'All About' Extremophiles. Fac Rev 2023; 12:27. [PMID: 38027090 PMCID: PMC10630985 DOI: 10.12703/r/12-27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Despite common perception, most of Earth is what is often referred to as an 'extreme environment.' Yet to the organisms that call these places home, it is simply that (home). They have adapted to thrive in these environments and, in the process, have evolved many unique adaptations at the molecular- and 'omic-level. Scientists' interest in these organisms has typically been in how they and their products can be harnessed for biotechnological applications and the environments where they are found, while the general public's veers more toward a fascination with their deviation from the 'norm'. However, these organisms have so much more to tell us about Life and the myriad ways there are to perform 'simple' biological processes.
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Affiliation(s)
- James A Coker
- Center for Biotechnology Education, Advanced Academic Programs, Krieger School of Arts and Sciences, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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Kowalewicz-Kulbat M, Krawczyk KT, Szulc-Kielbik I, Rykowski S, Denel-Bobrowska M, Olejniczak AB, Locht C, Klink M. Cytotoxic effects of halophilic archaea metabolites on ovarian cancer cell lines. Microb Cell Fact 2023; 22:197. [PMID: 37759261 PMCID: PMC10537157 DOI: 10.1186/s12934-023-02206-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Ovarian cancer is one of the most frequent and deadly gynaecological cancers, often resistant to platinum-based chemotherapy, the current standard of care. Halophilic microorganisms have been shown to produce a large variety of metabolites, some of which show toxicity to various cancer cell lines. However, none have yet been shown to be active against ovarian cancer cells. Here, we examined the effects of metabolites secreted by the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae on various cancer cell lines, including ovarian cancer cell lines. RESULTS 1H NMR analyses of Hrd. rudnickae and Nnm. salaciae culture supernatants contain a complex mixture of metabolites that differ between species, and even between two different strains of the same species, such as Hrd. rudnickae strains 64T and 66. By using the MTT and the xCELLigence RTCA assays, we found that the secreted metabolites of all three halophilic strains expressed cytotoxicity to the ovarian cancer cell lines, especially A2780, as well as its cisplatin-resistant derivative A2780cis, in a dose-dependent manner. The other tested cell lines A549, HepG2, SK-OV-3 and HeLa were only minimally, or not at all affected by the archaeal metabolites, and this was only seen with the MTT assay. CONCLUSIONS The halophilic archaea Hrd. rudnickae and Nnm. salaciae, isolated from a Polish salt mine and Lake Medee in the Mediterranean Sea, respectively, secrete metabolites that are active against ovarian cancer cells, including those that are resistant to cisplatin. This opens potential new possibilities for the treatment of these frequent and deadly gynaecological cancers.
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Affiliation(s)
- Magdalena Kowalewicz-Kulbat
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
| | - Krzysztof T Krawczyk
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | | | | | | | | | - Camille Locht
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Magdalena Klink
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland.
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Wang YH, Liu JC, Du YH, Xu JH, Du ZJ, Ye MQ. Psychromarinibacter sediminicola sp. nov., a novel moderately halophilic, metabolically diverse bacterium isolated from a solar saltern sediment, and comparison between members of family Roseobacteraceae. Arch Microbiol 2023; 205:331. [PMID: 37698663 DOI: 10.1007/s00203-023-03672-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/13/2023]
Abstract
Known for its species abundance and evolutionary status complexity, family Roseobacteraceae is an important subject of many studies on the discovery, identification, taxonomic status, and ecological properties of marine bacteria. This study compared and analyzed the phylogenetic, genomic, biochemical, and chemo taxonomical properties of seven species from three genera (Psychromarinibacter, Lutimaribacter, and Maritimibacter) of the family Roseobacteraceae. Moreover, a novel strain, named C21-152T was isolated from solar saltern sediment in Weihai, China. The values of 16S rRNA gene sequence similarity, the average nucleotide identity (ANI), the average amino acid identity (AAI), and the digital DNA-DNA hybridization (dDDH) between genomes of the novel strain and Psychromarinibacter halotolerans MCCC 1K03203T were 97.19, 78.49, 73.45, and 21.90%, respectively. Genome sequencing of strain C21-152T revealed a complete Sox enzyme system related to thiosulfate oxidization as well as a complete pathway for the final conversion of hydroxyproline to α-ketoglutarate. In addition, strain C21-152T was resistant to many antibiotics and had the ability to survive below 13% salinity. This strain had versatile survival strategies in saline environments including salt-in, compatible solute production and compatible solute transport. Some of its physiological features enriched and complemented the knowledge of the characteristics of the genus Psychromarinibacter. Optimum growth of strain C21-152T occurred at 37 ℃, with 5-6% (w/v) NaCl and at pH 7.5. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain C21-152T should represent a novel specie of the genus Psychromarinibacter, for which the name Psychromarinibacter sediminicola sp. nov. is proposed. The type strain is C21-152T (= MCCC 1H00808T = KCTC 92746T = SDUM1063002T).
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Affiliation(s)
- Yu-Hui Wang
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Jun-Cheng Liu
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Yi-Heng Du
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Jin-Hao Xu
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Meng-Qi Ye
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China.
- Shenzhen Research Institute of Shandong University, Shenzhen, 518057, Guangdong, People's Republic of China.
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, People's Republic of China.
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Jia H, Dantuluri S, Margulies S, Smith V, Lever R, Allers T, Koh J, Chen S, Maupin-Furlow JA. RecJ3/4-aRNase J form a Ubl-associated nuclease complex functioning in survival against DNA damage in Haloferax volcanii. mBio 2023; 14:e0085223. [PMID: 37458473 PMCID: PMC10470531 DOI: 10.1128/mbio.00852-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/02/2023] [Indexed: 09/02/2023] Open
Abstract
Nucleases are strictly regulated and often localized in the cell to avoid the uncontrolled degradation of DNA and RNA. Here, a new type of nuclease complex, composed of RecJ3, RecJ4, and aRNase J, was identified through its ATP-dependent association with the ubiquitin-like SAMP1 and AAA-ATPase Cdc48a. The complex was discovered in Haloferax volcanii, an archaeon lacking an RNA exosome. Genetic analysis revealed aRNase J to be essential and RecJ3, RecJ4, and Cdc48a to function in the recovery from DNA damage including genotoxic agents that generate double-strand breaks. The RecJ3:RecJ4:aRNase J complex (isolated in 2:2:1 stoichiometry) functioned primarily as a 3'-5' exonuclease in hydrolyzing RNA and ssDNA, with the mechanism non-processive for ssDNA. aRNase J could also be purified as a homodimer that catalyzed endoribonuclease activity and, thus, was not restricted to the 5'-3' exonuclease activity typical of aRNase J homologs. Moreover, RecJ3 and RecJ4 could be purified as a 560-kDa subcomplex in equimolar subunit ratio with nuclease activities mirroring the full RecJ3/4-aRNase J complex. These findings prompted reconstitution assays that suggested RecJ3/4 could suppress, alter, and/or outcompete the nuclease activities of aRNase J. Based on the phenotypic results, this control mechanism of aRNase J by RecJ3/4 is not necessary for cell growth but instead appears important for DNA repair. IMPORTANCE Nucleases are critical for various cellular processes including DNA replication and repair. Here, a dynamic type of nuclease complex is newly identified in the archaeon Haloferax volcanii, which is missing the canonical RNA exosome. The complex, composed of RecJ3, RecJ4, and aRNase J, functions primarily as a 3'-5' exonuclease and was discovered through its ATP-dependent association with the ubiquitin-like SAMP1 and Cdc48a. aRNase J alone forms a homodimer that has endonuclease function and, thus, is not restricted to 5'-3' exonuclease activity typical of other aRNase J enzymes. RecJ3/4 appears to suppress, alter, and/or outcompete the nuclease activities of aRNase J. While aRNase J is essential for growth, RecJ3/4, Cdc48a, and SAMPs are important for recovery against DNA damage. These biological distinctions may correlate with the regulated nuclease activity of aRNase J in the RecJ3/4-aRNaseJ complex.
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Affiliation(s)
- Huiyong Jia
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Swathi Dantuluri
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Shae Margulies
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Victoria Smith
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Rebecca Lever
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Sixue Chen
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
- Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, Florida, USA
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
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49
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Naamala J, Subramanian S, Msimbira LA, Smith DL. Effect of NaCl stress on exoproteome profiles of Bacillus amyloliquefaciens EB2003A and Lactobacillus helveticus EL2006H. Front Microbiol 2023; 14:1206152. [PMID: 37700863 PMCID: PMC10493332 DOI: 10.3389/fmicb.2023.1206152] [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: 04/17/2023] [Accepted: 07/31/2023] [Indexed: 09/14/2023] Open
Abstract
Salt stress can affect survival, multiplication and ability of plant growth promoting microorganisms to enhance plant growth. Changes in a microbe's proteome profile is one of the mechanisms employed by PGPM to enhance tolerance of salt stress. This study was focused on understanding changes in the exoproteome profile of Bacillus amyloliquefaciens EB2003A and Lactobacillus helveticus EL2006H when exposed to salt stress. The strains were cultured in 100 mL M13 (B. amyloliquefaciens) and 100 mL De man, Rogosa and Sharpe (MRS) (L. helveticus) media, supplemented with 200 and 0 mM NaCl (control), at pH 7.0. The strains were then incubated for 48 h (late exponential growth phase), at 120 rpm and 30 (B. amyloliquefaciens) and 37 (L. helveticus) °C. The microbial cultures were then centrifuged and filtered sterilized, to obtain cell free supernatants whose proteome profiles were studied using LC-MS/MS analysis and quantified using scaffold. Results of the study revealed that treatment with 200 mM NaCl negatively affected the quantity of identified proteins in comparison to the control, for both strains. There was upregulation and downregulation of some proteins, even up to 100%, which resulted in identification of proteins significantly unique between the control or 200 mM NaCl (p ≤ 0.05), for both microbial species. Proteins unique to 200 mM NaCl were mostly those involved in cell wall metabolism, substrate transport, oxidative stress tolerance, gene expression and DNA replication and repair. Some of the identified unique proteins have also been reported to enhance plant growth. In conclusion, based on the results of the work described here, PGPM alter their exoproteome profile when exposed to salt stress, potentially upregulating proteins that enhance their tolerance to this stress.
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Affiliation(s)
| | | | | | - Donald L. Smith
- Department of Plant Science, McGill University, Montreal, QC, Canada
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Rappaport HB, Oliverio AM. Extreme environments offer an unprecedented opportunity to understand microbial eukaryotic ecology, evolution, and genome biology. Nat Commun 2023; 14:4959. [PMID: 37587119 PMCID: PMC10432404 DOI: 10.1038/s41467-023-40657-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
Research in extreme environments has substantially expanded our understanding of the ecology and evolution of life on Earth, but a major group of organisms has been largely overlooked: microbial eukaryotes (i.e., protists). In this Perspective, we summarize data from over 80 studies of protists in extreme environments and identify focal lineages that are of significant interest for further study, including clades within Echinamoebida, Heterolobosea, Radiolaria, Haptophyta, Oomycota, and Cryptophyta. We argue that extreme environments are prime sampling targets to fill gaps in the eukaryotic tree of life and to increase our understanding of the ecology, metabolism, genome architecture, and evolution of eukaryotic life.
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Affiliation(s)
| | - Angela M Oliverio
- Department of Biology, Syracuse University, Syracuse, NY, 13210, USA.
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