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Boukeroui Y, González-Siso MI, DeCastro ME, Arab M, Aissaoui N, Nas F, Saibi ANE, Klouche Khelil N. Characterization, whole-genome sequence analysis, and protease production of a new thermophilic Bacillus licheniformis strain isolated from Debagh hot spring, Algeria. Int Microbiol 2025; 28:667-689. [PMID: 39129036 DOI: 10.1007/s10123-024-00569-9] [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: 05/06/2024] [Revised: 07/26/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
A new thermophilic strain, designated as Bacillus sp. LMB3902, was isolated from Hammam Debagh, the hottest spring in Algeria (up to 98 °C). This isolate showed high protease production in skim milk media at 55 °C and exhibited significant specific protease activity by using azocasein as a substrate (157.50 U/mg). Through conventional methods, chemotaxonomic characteristics, 16S rRNA gene sequencing, and comparative genomic analysis with the closely related strain Bacillus licheniformis DSM 13 (ATCC 14580 T), the isolate Bacillus sp. LMB3902 was identified as a potentially new strain of Bacillus licheniformis. In addition, the gene functions of Bacillus sp. LMB3902 strain were predicted using the Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Clusters of Orthologous Groups, Non-Redundant Protein Sequence Database, Swiss-Prot, and Pfam databases. The results showed that the genome size of Bacillus sp. LMB3902 was 4.279.557 bp, with an average GC content of 46%. The genome contained 4.760 predicted genes, including 8 rRNAs, 78 tRNAs, and 24 sRNAs. A total of 235 protease genes were annotated including 50 proteases with transmembrane helix structures and eight secreted proteases with signal peptides. Additionally, the majority of secondary metabolites found by antiSMASH platform showed low similarity to identified natural products, such as fengicin (53%), lichenysin (57%), and surfactin (34%), suggesting that this strain may encode for novel uncharacterized natural products which can be useful for biotechnological applications. This study is the first report that describes the complete genome sequence, taxono-genomics, and gene annotation as well as protease production of the Bacillus genus in this hydrothermal vent.
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Affiliation(s)
- Yasmina Boukeroui
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE Laboratory), Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, 13000, Tlemcen, Algeria
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro Interdisciplinar de Química E Bioloxía (CICA), Facultade de Ciencias, Universidade da Coruña, 15071 , A Coruña, Spain
| | - María-Eugenia DeCastro
- Grupo EXPRELA, Centro Interdisciplinar de Química E Bioloxía (CICA), Facultade de Ciencias, Universidade da Coruña, 15071 , A Coruña, Spain
| | - Mounia Arab
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE Laboratory), Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, 13000, Tlemcen, Algeria
- Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene, 16000, Algiers, Algeria
| | - Nadia Aissaoui
- Laboratory of Sustainable Management of Natural Resources in Arid and Semi Arid Areas (GDRN), Institute of Sciences, University Center of Naâma, 45000, Naâma, Algeria
| | - Fatima Nas
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE Laboratory), Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, 13000, Tlemcen, Algeria
| | - Amina Nour Elhouda Saibi
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE Laboratory), Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, 13000, Tlemcen, Algeria
| | - Nihel Klouche Khelil
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE Laboratory), Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, 13000, Tlemcen, Algeria.
- Laboratory of Experimental Surgery, Dental Surgery Department, Medical Faculty, University of Tlemcen, 13000, Tlemcen, Algeria.
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Hung SHW, Yeh PH, Huang TC, Huang SY, Wu IC, Liu CH, Lin YH, Chien PR, Huang FC, Ho YN, Kuo CH, Hwang HH, Chiang EPI, Huang CC. A cyclic dipeptide for salinity stress alleviation and the trophic flexibility of endophyte provide insights into saltmarsh plant-microbe interactions. ISME COMMUNICATIONS 2024; 4:ycae041. [PMID: 38707842 PMCID: PMC11070113 DOI: 10.1093/ismeco/ycae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/23/2024] [Accepted: 03/20/2024] [Indexed: 05/07/2024]
Abstract
In response to climate change, the nature of endophytes and their applications in sustainable agriculture have attracted the attention of academics and agro-industries. This work focused on the endophytic halophiles of the endangered Taiwanese salt marsh plant, Bolboschoenus planiculmis, and evaluated the functions of these isolates through in planta salinity stress alleviation assay using Arabidopsis. The endophytic strain Priestia megaterium BP01R2, which can promote plant growth and salinity tolerance, was further characterized through multi-omics approaches. The transcriptomics results suggested that BP01R2 could function by tuning hormone signal transduction, energy-producing metabolism, multiple stress responses, etc. In addition, the cyclodipeptide cyclo(L-Ala-Gly), which was identified by metabolomics analysis, was confirmed to contribute to the alleviation of salinity stress in stressed plants via exogenous supplementation. In this study, we used multi-omics approaches to investigate the genomics, metabolomics, and tropisms of endophytes, as well as the transcriptomics of plants in response to the endophyte. The results revealed the potential molecular mechanisms underlying the occurrence of biostimulant-based plant-endophyte symbioses with possible application in sustainable agriculture.
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Affiliation(s)
- Shih-Hsun Walter Hung
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 402202, Taiwan
| | - Pin-Hsien Yeh
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Tsai-Ching Huang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Shao-Yu Huang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - I-Chen Wu
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Chia-Ho Liu
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Yu-Hsi Lin
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Pei-Ru Chien
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Fan-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Ying-Ning Ho
- Institute of Marine Biology, College of Life Science, National Taiwan Ocean University, Keelung 202301, Taiwan
- Centre of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan
- Taiwan Ocean Genome Center, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 402202, Taiwan
| | - Hau-Hsuan Hwang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 402202, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402202, Taiwan
| | - En-Pei Isabel Chiang
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 402202, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402202, Taiwan
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 402202, Taiwan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 402202, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402202, Taiwan
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Mao Y, Chang D, Cui X, Wu Y, Cai B. Changes in sulfur in soybean rhizosphere soil and the response of microbial flora in a continuous cropping system mediated by Funneliformis mosseae. Front Microbiol 2023; 14:1235736. [PMID: 37692404 PMCID: PMC10484799 DOI: 10.3389/fmicb.2023.1235736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
Soybean is an S-loving crop, and continuous cropping might cause soil sulfur shortage. The primary objectives of this study are to determine whether Funneliformis mosseae (F. mosseae) can enhance the content of available S in S-deficient soil and thereby improve the sulfur utilization rate in soybean. The experiment used Heinong 48 (HN48), a soybean variety with a vast planting area in Heilongjiang Province, and F. mosseae was inoculated in the soil of soybean that had been continuously cropped for 0 and 3 years. The results of the barium sulfur turbidimetric assay show that the sulfur content in the soil and soybean was reduced by continuous cropping and increased by inoculation with F. mosseae; the results of the macro-genome sequencing technology, show that the diversity and abundance of bacteria in the soil was decreased by continuous cropping and increased by inoculation with F. mosseae. The sulfur-oxidizing bacteria (SOB) activity and sulfur-related gene expression levels were lower in the continuous crop group compared to the control group and higher in the F.mosseae-inoculated group compared to the control group. Continuous cropping reduced the sulfur content and ratio of soybean rhizosphere soil, affecting soil flora activity and thus soybean growth; F. mosseae inoculation increased the sulfur content of soybean root-perimeter soil and plants, increased the diversity and abundance of rhizosphere soil microorganisms, increased the expression of genes for sulfur transport systems, sulfur metabolism, and other metabolic functions related to elemental sulfur, and increased the species abundance and metabolic vigor of most SOB. In summary, continuous cropping inhibits soil sulfur uptake and utilization in soybean while the inoculation with F. mosseae can significantly improve this situation. This study offers a theoretical research foundation for using AMF as a bio-fungal agent to enhance soil sulfur use. It also supports the decrease of chemical fertilizers, their substitution, and the protection of native soil.
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Affiliation(s)
- Yizhi Mao
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education and Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region and Key Laboratory of Molecular Biology, College of Heilongjiang Province and School of Life Sciences, Heilongjiang University, Harbin, China
| | - Donghao Chang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education and Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region and Key Laboratory of Molecular Biology, College of Heilongjiang Province and School of Life Sciences, Heilongjiang University, Harbin, China
| | - Xiaoying Cui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education and Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region and Key Laboratory of Molecular Biology, College of Heilongjiang Province and School of Life Sciences, Heilongjiang University, Harbin, China
| | - Yunshu Wu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education and Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region and Key Laboratory of Molecular Biology, College of Heilongjiang Province and School of Life Sciences, Heilongjiang University, Harbin, China
| | - Baiyan Cai
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education and Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region and Key Laboratory of Molecular Biology, College of Heilongjiang Province and School of Life Sciences, Heilongjiang University, Harbin, China
- Hebei Key Laboratory of Agroecological Safety, Hebei University of Environmental Engineering, Qinhuangdao, China
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Rai N, Rai SP, Sarma BK. Prospects for Abiotic Stress Tolerance in Crops Utilizing Phyto- and Bio-Stimulants. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.754853] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Environmental stressors such as salinity, drought, high temperature, high rainfall, etc. have already demonstrated the negative impacts on plant growth and development and thereby limiting productivity of the crops. Therefore, in the time to come, more sustainable efforts are required in agricultural practices to ensure food production and security under such adverse environmental conditions. A most promising and eco-friendly way to achieve this goal would be to apply biostimulants to address the environmental concerns. Non-microbial biostimulants such as humic substances (HA), protein hydrolysate, plant-based products and seaweed extracts (SWE), etc. and/or microbial inoculants comprising of plant growth-promoting microbes such as arbuscular mycorrhizal fungi (AMF), fluorescent and non-fluorescent Pseudomonas, Trichoderma spp., Bacillus spp. etc. have tremendous potentiality to enhance plant growth, flowering, crop productivity, nutrient use efficiency (NUE) and translocation, as well as enhancing tolerance to a wide range of abiotic stresses by modifying physiological, biological and biochemical processes of the crop-plants. Similarly, application techniques and timing are also important to achieve the desired results. In this article we discussed the prospects of using seaweed, microbial, and plant-based biostimulants either individually or in combination for managing environmental stresses to achieve food security in a sustainable way. Particular attention was given to the modifications that take place in plant's physiology under adverse environmental conditions and how different biostimulants re-program the host's physiology to withstand such stresses. Additionally, we also discussed how application of biostimulants can overcome the issue of nutrient deficiency in agricultural lands and improve their use efficiency by crop plants.
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