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Sharma P, Mahongnao S, Ahamad A, Gupta R, Goel A, Kumar N, Nanda S. 16S rRNA metagenomic profiling of red amaranth grown organically with different composts and soils. Appl Microbiol Biotechnol 2024; 108:129. [PMID: 38229333 DOI: 10.1007/s00253-023-12982-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/14/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024]
Abstract
In recent years organic food is gaining popularity as it is believed to promote better human health and improve soil sustainability, but there are apprehensions about pathogens in organic produces. This study was designed to understand the effect of different composts and soils on the status of the microbiome present in organically grown leafy vegetables. 16S rRNA metagenomic profiling of the leaves was done, and data were analyzed. It was found that by adding composts, the OTU of the microbiome in the organic produce was higher than in the conventional produce. The beneficial genera identified across the samples included plant growth promoters (Achromobacter, Paenibacillus, Pseudomonas, Sphingobacterium) and probiotics (Lactobacillus), which were higher in the organic produce. Some pathogenic genera, viz., plant pathogenic bacteria (Cellvibrio, Georgenia) and human pathogenic bacteria (Corynebacterium, Acinetobacter, Streptococcus, Streptomyces) were also found but with relatively low counts in the organic produce. Thus, the present study highlights that organic produce has lesser pathogen contamination than the conventional produce. KEY POINTS: • 16S rRNA metagenomics profiling done for organic red amaranth cultivar • Microbial richness varied with respect to the soil and compost type used • The ratio of beneficial to pathogenic genera improves with the addition of compost.
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Affiliation(s)
- Pooja Sharma
- Department of Biochemistry, Daulat Ram College, University of Delhi, 4, Patel Marg, Maurice Nagar, Delhi, 110007, India
| | - Sophayo Mahongnao
- Department of Biochemistry, Daulat Ram College, University of Delhi, 4, Patel Marg, Maurice Nagar, Delhi, 110007, India
| | - Arif Ahamad
- Department of Environmental Science, Jamia Millia Islamia University, New Delhi, 110025, India
| | - Radhika Gupta
- Department of Biochemistry, Daulat Ram College, University of Delhi, 4, Patel Marg, Maurice Nagar, Delhi, 110007, India
| | - Anita Goel
- Department of Biochemistry, Daulat Ram College, University of Delhi, 4, Patel Marg, Maurice Nagar, Delhi, 110007, India
| | - Narendra Kumar
- Department of Biochemistry, Daulat Ram College, University of Delhi, 4, Patel Marg, Maurice Nagar, Delhi, 110007, India
| | - Sarita Nanda
- Department of Biochemistry, Daulat Ram College, University of Delhi, 4, Patel Marg, Maurice Nagar, Delhi, 110007, India.
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Cuartero J, Querejeta JI, Prieto I, Frey B, Alguacil MM. Warming and rainfall reduction alter soil microbial diversity and co-occurrence networks and enhance pathogenic fungi in dryland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175006. [PMID: 39069184 DOI: 10.1016/j.scitotenv.2024.175006] [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: 06/03/2024] [Revised: 07/10/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
In this 9-year manipulative field experiment, we examined the impacts of experimental warming (2 °C, W), rainfall reduction (30 % decrease in annual rainfall, RR), and their combination (W + RR) on soil microbial communities and native vegetation in a semi-arid shrubland in south-eastern Spain. Warming had strong negative effects on plant performance across five coexisting native shrub species, consistently reducing their aboveground biomass growth and long-term survival. The impacts of rainfall reduction on plant growth and survival were species-specific and more variable. Warming strongly altered the soil microbial community alpha-diversity and changed the co-occurrence network structure. The relative abundance of symbiotic arbuscular mycorrhizal fungi (AMF) increased under W and W + RR, which could help buffer the direct negative impacts of climate change on their host plants nutrition and enhance their resistance to heat and drought stress. Indicator microbial taxa analyses evidenced that the marked sequence abundance of many plant pathogenic fungi, such as Phaeoacremonium, Cyberlindnera, Acremonium, Occultifur, Neodevriesia and Stagonosporopsis, increased significantly in the W and W + RR treatments. Moreover, the relative abundance of fungal animal pathogens and mycoparasites in soil also increased significantly under climate warming. Our findings indicate that warmer and drier conditions sustained over several years can alter the soil microbial community structure, composition, and network topology. The projected warmer and drier climate favours pathogenic fungi, which could offset the benefits of increased AMF abundance under warming and further aggravate the severe detrimental impacts of increased abiotic stress on native vegetation performance and ecosystem services in drylands.
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Affiliation(s)
- J Cuartero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland.
| | - J I Querejeta
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | - I Prieto
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain; Area de Ecología, Facultad de Ciencias Biológicas y Ambientales, Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - B Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - M M Alguacil
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain
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Hemapriya M, Nataraja KN, Suryanarayanan TS, Uma Shaanker R. Comparative Metagenomic Analysis of Seed Endobiome of Domesticated and Wild Finger Millet Species (Eleusine spp.): Unveiling Microbial Diversity and Composition. Curr Microbiol 2024; 81:373. [PMID: 39313592 DOI: 10.1007/s00284-024-03891-7] [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: 02/29/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024]
Abstract
Domestication, which involves selective breeding, modern agricultural practices, and specific growing conditions, can influence the microbial and endophytic communities in crop plants. In this study, we examined the microbial diversity and community composition in the seeds of wild and domesticated finger millet species. We employed a metagenomic approach to investigate the seed microbial diversity and community composition of wild (Eleusine africana) and domesticated finger millet species (Eleusine coracana (L.) Gaertn) grown in the same habitat. While our findings indicated no significant change in seed endobiome diversity due to domestication, there were differences in microbial community composition between wild and domesticated species. Seeds of domesticated species had higher relative abundance of certain bacterial genera including Helicobacter, Akkermansia, Streptococcus, Bacteroides, and Pseudomonas, whereas seeds of wild species had higher relative abundance of unclassified Streptophyta. The seed-associated microbiota also varied among domesticated finger millet accessions. Co-occurrence network analysis revealed a strong relationship between bacteria and fungi in domesticated compared to wild species. We discuss the results obtained in the larger context of the importance of seed endobiome and how domestication processes in crop plants may have impacted the seed endobiome diversity, composition, and function compared to their wild counterparts.
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Affiliation(s)
- M Hemapriya
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, 560 065, India
| | - K N Nataraja
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, 560 065, India
| | - T S Suryanarayanan
- Vivekananda Institute of Tropical Mycology, Ramakrishna Mission Vidyapith, Chennai, 600 004, India
| | - R Uma Shaanker
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, 560 065, India.
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jammu, 181221, India.
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Saarenpää S, Shalev O, Ashkenazy H, Carlos V, Lundberg DS, Weigel D, Giacomello S. Spatial metatranscriptomics resolves host-bacteria-fungi interactomes. Nat Biotechnol 2024; 42:1384-1393. [PMID: 37985875 PMCID: PMC11392817 DOI: 10.1038/s41587-023-01979-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/06/2023] [Indexed: 11/22/2023]
Abstract
The interactions of microorganisms among themselves and with their multicellular host take place at the microscale, forming complex networks and spatial patterns. Existing technology does not allow the simultaneous investigation of spatial interactions between a host and the multitude of its colonizing microorganisms, which limits our understanding of host-microorganism interactions within a plant or animal tissue. Here we present spatial metatranscriptomics (SmT), a sequencing-based approach that leverages 16S/18S/ITS/poly-d(T) multimodal arrays for simultaneous host transcriptome- and microbiome-wide characterization of tissues at 55-µm resolution. We showcase SmT in outdoor-grown Arabidopsis thaliana leaves as a model system, and find tissue-scale bacterial and fungal hotspots. By network analysis, we study inter- and intrakingdom spatial interactions among microorganisms, as well as the host response to microbial hotspots. SmT provides an approach for answering fundamental questions on host-microbiome interplay.
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Affiliation(s)
- Sami Saarenpää
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Or Shalev
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Systems Biology of Microbial Communities, University of Tübingen, Tübingen, Germany
| | - Haim Ashkenazy
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Vanessa Carlos
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Derek Severi Lundberg
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Detlef Weigel
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Stefania Giacomello
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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Li S, Yin Y, Zhang R, Wang C. The Impacts of Cellulose on Volatile Fatty Acid Production and the Microbial Community in Anaerobic Fermentation of Sludge at High and Medium Temperatures. Appl Biochem Biotechnol 2024:10.1007/s12010-024-05052-9. [PMID: 39212899 DOI: 10.1007/s12010-024-05052-9] [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] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
During large-scale sewage treatment, a large amount of excessive sludge is produced, which will cause serious pollution in the environment. In recent years, anaerobic digestion technology has been widely promoted because it can achieve better sludge reduction, and the products and byproducts after anaerobic digestion can be fully utilized as resources. In this study, cellulose was added as the co-fermentation substrate during the fermentation process at 30 ℃ and 50 ℃ to enhance the production of VFAs. The result indicated that cellulose could significantly increase the yield of VFAs in both 30 ℃ and 50 ℃. Meanwhile, COD and reducing sugar generation in the fermentation process were also measure. Analysis of the microbial community structure at the class and genus levels revealed that the proportion of several genus closely related with cellulose degradation such as Cellvibrio, Fibrobacter, and Sporocytophaga were significantly increased with the addition of cellulose. Co-fermentation was recognized as an economic and environmental friendly strategy for sludge and other solid waste treatment. The analysis of the effect of cellulose as a substrate on the production of VFAs at high and medium temperatures is highly important for exploring ways to increase the production of VFAs in anaerobic fermentation.
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Affiliation(s)
- Suyu Li
- Miami College, Henan University, Henan Province, Kaifeng, 475000, China
| | - Yilong Yin
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Ruyan Zhang
- Miami College, Henan University, Henan Province, Kaifeng, 475000, China
| | - Chongyang Wang
- Miami College, Henan University, Henan Province, Kaifeng, 475000, China.
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Xu X, Ding Z, Pu C, Kong C, Chen S, Lu W, Zhang J. The structural characterization and UV-protective properties of an exopolysaccharide from a Paenibacillus isolate. Front Pharmacol 2024; 15:1434136. [PMID: 39185320 PMCID: PMC11341463 DOI: 10.3389/fphar.2024.1434136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 07/29/2024] [Indexed: 08/27/2024] Open
Abstract
Introduction Overexposure to ultraviolet (UV) light is known to cause damage to the skin, leading to sunburn and photo-aging. Chemical sunscreen products may give rise to health risks including phototoxicity, photosensitivity, and photosensitivity. Natural polysaccharides have attracted considerable interests due to diverse biological activities. Methods A novel polysaccharide isolated was purified and structurally characterized using chemical methods followed by HPLC, GLC-MS, as well as 1D and 2D NMR spectroscopy. The photoprotective effect of the EPS on UVB-induced damage was assessed in vitro using cultured keratinocytes and in vivo using C57BL/6 mouse models. Results The average molecular weight of the EPS was 5.48 × 106 Da, composed of glucose, mannose and galactose residues at a ratio of 2:2:1. The repeating units of the EPS were →3)-β-D-Glcp (1→3) [β-D-Galp (1→2)-α-D-Glcp (1→2)]-α-D-Manp (1→3)-α-D-Manp (1→. In cultured keratinocytes, the EPS reduced cytotoxicity and excessive ROS production induced by UVB irradiation. The EPS also exhibits an inhibitory effect on oxidative stress, inflammation, and collagen degradation found in the photodamage in mice. 1H NMR-based metabolomics analysis for skin suggested that the EPS partly reversed the shifts of metabolic profiles of the skin in UVB-exposed mice. Conclusion The EPS exhibits skin photoprotective effects through regulating oxidative stress both in vivo and in vitro. Our findings highlight that the EPS is a potential candidate in sunscreen formulations for an efficient solution to UVB radiation.
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Affiliation(s)
- Xiaodong Xu
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
| | - Zhao Ding
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
| | - Chunlin Pu
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
| | - Changchang Kong
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
| | - Shijunyin Chen
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
| | - Weiling Lu
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
| | - Jianfa Zhang
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
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Kaur H, Mir RA, Hussain SJ, Prasad B, Kumar P, Aloo BN, Sharma CM, Dubey RC. Prospects of phosphate solubilizing microorganisms in sustainable agriculture. World J Microbiol Biotechnol 2024; 40:291. [PMID: 39105959 DOI: 10.1007/s11274-024-04086-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/16/2024] [Indexed: 08/07/2024]
Abstract
Phosphorus (P), an essential macronutrient for various plant processes, is generally a limiting soil component for crop growth and yields. Organic and inorganic types of P are copious in soils, but their phyto-availability is limited as it is present largely in insoluble forms. Although phosphate fertilizers are applied in P-deficit soils, their undue use negatively impacts soil quality and the environment. Moreover, many P fertilizers are lost because of adsorption and fixation mechanisms, further reducing fertilizer efficiencies. The application of phosphate-solubilizing microorganisms (PSMs) is an environmentally friendly, low-budget, and biologically efficient method for sustainable agriculture without causing environmental hazards. These beneficial microorganisms are widely distributed in the rhizosphere and can hydrolyze inorganic and organic insoluble P substances to soluble P forms which are directly assimilated by plants. The present review summarizes and discusses our existing understanding related to various forms and sources of P in soils, the importance and P utilization by plants and microbes,, the diversification of PSMs along with mixed consortia of diverse PSMs including endophytic PSMs, the mechanism of P solubilization, and lastly constraints being faced in terms of production and adoption of PSMs on large scale have also been discussed.
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Affiliation(s)
- Harmanjit Kaur
- Department of Botany, University of Allahabad, Prayagraj, Uttar Pradesh, 211002, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, Jammu, Kashmir, 191201, India
| | - Sofi Javed Hussain
- Department of Botany, Central University of Kashmir, Ganderbal, Jammu, Kashmir, 191201, India
| | - Bhairav Prasad
- Department of Biotechnology, Chandigarh Group of Colleges, SAS Nagar, Landran, Punjab, 140307, India
| | - Pankaj Kumar
- Department of Botany and Microbiology, School of Life Sciences, H.N.B. Garhwal University (A Central University), Srinagar Garhwal, Uttarakhand, 246174, India.
| | - Becky N Aloo
- Department of Biological Sciences, University of Eldoret, P. O. Box 1125-30100, Eldoret, Kenya
| | - Chandra Mohan Sharma
- Department of Botany and Microbiology, School of Life Sciences, H.N.B. Garhwal University (A Central University), Srinagar Garhwal, Uttarakhand, 246174, India
| | - Ramesh Chandra Dubey
- Department of Botany and Microbiology, Gurukul Kangri Vishwavidyalaya, Haridwar, Uttarakhand, 249404, India
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Ravagnan G, Schmid J. Promising non-model microbial cell factories obtained by genome reduction. Front Bioeng Biotechnol 2024; 12:1427248. [PMID: 39161352 PMCID: PMC11330790 DOI: 10.3389/fbioe.2024.1427248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 06/12/2024] [Indexed: 08/21/2024] Open
Abstract
The development of sustainable processes is the most important basis to realize the shift from the fossil-fuel based industry to bio-based production. Non-model microbes represent a great resource due to their advantageous traits and unique repertoire of bioproducts. However, most of these microbes require modifications to improve their growth and production capacities as well as robustness in terms of genetic stability. For this, genome reduction is a valuable and powerful approach to meet industry requirements and to design highly efficient production strains. Here, we provide an overview of various genome reduction approaches in prokaryotic microorganisms, with a focus on non-model organisms, and highlight the example of a successful genome-reduced model organism chassis. Furthermore, we discuss the advances and challenges of promising non-model microbial chassis.
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Affiliation(s)
| | - Jochen Schmid
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
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9
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Berdaguer R, van der Wielen N, Lorenzo ZC, Testerink C, Karlova R. The bryophyte rhizoid-sphere microbiome responds to water deficit. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39078220 DOI: 10.1111/pce.15063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/31/2024]
Abstract
The roots of vascular plants are colonised by a multitude of microbes, which play an important role in plant health and stress resilience. Drought stress in particular is devastating for crop yield and causes major shifts in the rhizosphere microbial communities. However, the microbiome associated to the rhizoids (hereafter termed rhizoid-sphere) of the nonvascular bryophytes remains largely unexplored. Here, we use amplicon sequencing to explore the rhizoid-sphere microbiome of three bryophyte species under drought and well-watered conditions. Comparing rhizoid-sphere microbial communities associated with the two liverworts Marchantia polymorpha and Marchantia paleacea and the moss Physcomitrium patens showed characteristic differences in composition between host species and both conserved and unique changes under drought. At phylum level, these changes were similar to changes in the rhizosphere of angiosperms under drought. Furthermore, we observed strong differences in rhizoid-sphere colonisation between bryophyte species for taxa known for nitrogen fixation and plant growth promotion. Interestingly, M. polymorpha prioritised the growth of belowground organs under osmotic stress, as is the case for angiosperms under drought. Taken together, our results show interesting parallels between bryophytes and angiosperms in the relation with their rhizo(id-)sphere, suggesting evolutionary conservation among land plants in their response to drought stress.
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Affiliation(s)
- Roland Berdaguer
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | | | - Zulema Carracedo Lorenzo
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
- Laboratory of Entomology, Wageningen University, Wageningen, Netherlands
| | - Christa Testerink
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | - Rumyana Karlova
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
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Rizzo G, Choudoir M, Simoes R, Dayarathne N, DeAngelis KM. High-quality draft genome sequence of Paenibacillus sp. RC80, a candidate for biofuel production. Microbiol Resour Announc 2024; 13:e0106723. [PMID: 38847544 PMCID: PMC11256801 DOI: 10.1128/mra.01067-23] [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: 11/30/2023] [Accepted: 05/10/2024] [Indexed: 07/19/2024] Open
Abstract
Paenibacillus sp. RC80 was isolated from temperate deciduous forest soil in New England. The assembled genome is a single contig with 5,977,337 bp and 97.15% estimated completion. RC80 contains features for 2,3-butanediol dehydrogenase production and pathways involved in ethanol production.
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Affiliation(s)
- Gabriella Rizzo
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Mallory Choudoir
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Rachel Simoes
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Nipuni Dayarathne
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Kristen M. DeAngelis
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
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Tyborski N, Koehler T, Steiner FA, Tung SY, Wild AJ, Carminati A, Mueller CW, Vidal A, Wolfrum S, Pausch J, Lueders T. Consistent prokaryotic community patterns along the radial root axis of two Zea mays L. landraces across two distinct field locations. Front Microbiol 2024; 15:1386476. [PMID: 39091306 PMCID: PMC11292614 DOI: 10.3389/fmicb.2024.1386476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
The close interconnection of plants with rhizosphere- and root-associated microorganisms is well recognized, and high expectations are raised for considering their symbioses in the breeding of future crop varieties. However, it is unclear how consistently plant-mediated selection, a potential target in crop breeding, influences microbiome members compared to selection imposed by the agricultural environment. Landraces may have traits shaping their microbiome, which were lost during the breeding of modern varieties, but knowledge about this is scarce. We investigated prokaryotic community composition along the radial root axis of two European maize (Zea mays L.) landraces. A sampling gradient included bulk soil, a distal and proximal rhizosphere fraction, and the root compartment. Our study was replicated at two field locations with differing edaphic and climatic conditions. Further, we tested for differences between two plant developmental stages and two precipitation treatments. Community data were generated by metabarcoding of the V4 SSU rRNA region. While communities were generally distinct between field sites, the effects of landrace variety, developmental stage, and precipitation treatment were comparatively weak and not statistically significant. Under all conditions, patterns in community composition corresponded strongly to the distance to the root. Changes in α- and β-diversity, as well as abundance shifts of many taxa along this gradient, were similar for both landraces and field locations. Most affected taxa belonged to a core microbiome present in all investigated samples. Remarkably, we observed consistent enrichment of Actinobacteriota (particularly Streptomyces, Lechevalieria) and Pseudomonadota (particularly Sphingobium) toward the root. Further, we report a depletion of ammonia-oxidizers along this axis at both field sites. We identified clear enrichment and depletion patterns in microbiome composition along the radial root axis of Z. mays. Many of these were consistent across two distinct field locations, plant developmental stages, precipitation treatments, and for both landraces. This suggests a considerable influence of plant-mediated effects on the microbiome. We propose that the affected taxa have key roles in the rhizosphere and root microbiome of Z. mays. Understanding the functions of these taxa appears highly relevant for the development of methods aiming to promote microbiome services for crops.
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Affiliation(s)
- Nicolas Tyborski
- Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Tina Koehler
- Root-Soil Interaction, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Franziska A. Steiner
- Soil Science, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Shu-Yin Tung
- Institute for Agroecology and Organic Farming, Bavarian State Research Center for Agriculture (LfL), Freising, Germany
- TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Andreas J. Wild
- Agroecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Andrea Carminati
- Physics of Soils and Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Carsten W. Mueller
- Soil Science, Institute of Ecology, Technical University of Berlin, Berlin, Germany
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Alix Vidal
- Soil Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Sebastian Wolfrum
- Institute for Agroecology and Organic Farming, Bavarian State Research Center for Agriculture (LfL), Freising, Germany
| | - Johanna Pausch
- Agroecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Tillmann Lueders
- Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
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Zeng C, Liu Y, Zhang B, Zhang C, Li N, Ji L, Lan C, Qin B, Yang Y, Wang J, Chen T, Fang C, Lin W. The functional identification and evaluation of endophytic bacteria sourced from the roots of tolerant Achyranthes bidentata to overcome monoculture problems of Rehmannia glutinosa. Front Microbiol 2024; 15:1399406. [PMID: 39081886 PMCID: PMC11286500 DOI: 10.3389/fmicb.2024.1399406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/21/2024] [Indexed: 08/02/2024] Open
Abstract
The isolation and identification of plant growth-promoting endophytic bacteria (PGPEB) from Achyranthes bidentata roots have profound theoretical and practical implications in ecological agriculture, particularly as bio-inoculants to address challenges associated with continuous monoculture. Our research revealed a significant increase in the abundance of these beneficial bacteria in A. bidentata rhizosphere soil under prolonged monoculture conditions, as shown by bioinformatics analysis. Subsequently, we isolated 563 strains of endophytic bacteria from A. bidentata roots. Functional characterization highlighted diverse plant growth-promoting traits among these bacteria, including the secretion of indole-3-acetic acid (IAA) ranging from 68.01 to 73.25 mg/L, phosphorus and potassium solubilization capacities, and antagonistic activity against pathogenic fungi (21.54%-50.81%). Through 16S rDNA sequencing, we identified nine strains exhibiting biocontrol and growth-promoting potential. Introduction of a synthetic microbial consortium (SMC) in pot experiments significantly increased root biomass by 48.19% in A. bidentata and 27.01% in replanted Rehmannia glutinosa. These findings provide innovative insights and strategies for addressing continuous cropping challenges, highlighting the practical promise of PGPEB from A. bidentata in ecological agriculture to overcome replanting obstacles for non-host plants like R. glutinosa, thereby promoting robust growth in medicinal plants.
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Affiliation(s)
- Chunli Zeng
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yazhou Liu
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Bianhong Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chenjing Zhang
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Niu Li
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Leshan Ji
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chaojie Lan
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Bin Qin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuncheng Yang
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Juanying Wang
- College of Life Science, Guizhou University, Guiyang, Guizhou, China
| | - Ting Chen
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Changxun Fang
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wenxiong Lin
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Topalian J, Navas L, Ontañon O, Valacco MP, Noseda DG, Blasco M, Peña MJ, Urbanowicz BR, Campos E. Production of a bacterial secretome highly efficient for the deconstruction of xylans. World J Microbiol Biotechnol 2024; 40:266. [PMID: 38997527 DOI: 10.1007/s11274-024-04075-y] [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: 05/10/2024] [Accepted: 07/06/2024] [Indexed: 07/14/2024]
Abstract
Bacteria within the Paenibacillus genus are known to secrete a diverse array of enzymes capable of breaking down plant cell wall polysaccharides. We studied the extracellular xylanolytic activity of Paenibacillus xylanivorans and examined the complete range of secreted proteins when grown on carbohydrate-based carbon sources of increasing complexity, including wheat bran, sugar cane straw, beechwood xylan and sucrose, as control. Our data showed that the relative abundances of secreted proteins varied depending on the carbon source used. Extracellular enzymatic extracts from wheat bran (WB) or sugar cane straw (SCR) cultures had the highest xylanolytic activity, coincidently with the largest representation of carbohydrate active enzymes (CAZymes). Scaling-up to a benchtop bioreactor using WB resulted in a significant enhancement in productivity and in the overall volumetric extracellular xylanase activity, that was further concentrated by freeze-drying. The enzymatic extract was efficient in the deconstruction of xylans from different sources as well as sugar cane straw pretreated by alkali extrusion (SCRe), resulting in xylobiose and xylose, as primary products. The overall yield of xylose released from SCRe was improved by supplementing the enzymatic extract with a recombinant GH43 β-xylosidase (EcXyl43) and a GH62 α-L-arabinofuranosidase (CsAbf62A), two activities that were under-represented. Overall, we showed that the extracellular enzymatic extract from P. xylanivorans, supplemented with specific enzymatic activities, is an effective approach for targeting xylan within lignocellulosic biomass.
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Affiliation(s)
- Juliana Topalian
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto s/n, Hurlingham, Buenos Aires, B1686IGC, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Laura Navas
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto s/n, Hurlingham, Buenos Aires, B1686IGC, Argentina
| | - Ornella Ontañon
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto s/n, Hurlingham, Buenos Aires, B1686IGC, Argentina
| | - Maria Pia Valacco
- Centro de Estudios Químicos y Biológicos por Espectrometría de Masa (CEQUIBIEM-FCEN), Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires (UBA-IQUIBICEN), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego Gabriel Noseda
- Instituto de Investigaciones Biotecnológicas (IIBio), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Martín Blasco
- Departamento de Bioprocesos, Instituto Nacional de Tecnología Industrial (INTI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Maria Jesus Peña
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA, USA
| | - Breeanna R Urbanowicz
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA, USA
| | - Eleonora Campos
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto s/n, Hurlingham, Buenos Aires, B1686IGC, Argentina.
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14
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Haidar R, Compant S, Robert C, Antonielli L, Yacoub A, Grélard A, Loquet A, Brader G, Guyoneaud R, Attard E, Rey P. Two Paenibacillus spp. strains promote grapevine wood degradation by the fungus Fomitiporia mediterranea: from degradation experiments to genome analyses. Sci Rep 2024; 14:15779. [PMID: 38982270 PMCID: PMC11233627 DOI: 10.1038/s41598-024-66620-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: 01/11/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
Ascomycetes, basidiomycetes and deuteromycetes can degrade wood, but less attention has been paid to basidiomycetes involved in Esca, a major Grapevine Trunk Disease. Using a wood sawdust microcosm system, we compared the wood degradation of three grapevine cultivars inoculated with Fomitiporia mediterranea M. Fisch, a basidiomycete responsible for white-rot development and involved in Esca disease. The grapevine cultivar Ugni blanc was more susceptible to wood degradation caused by F. mediterranea than the cultivars Cabernet Sauvignon and Merlot. Solid-state Nuclear Magnetic Resonance (NMR) spectroscopy showed that F. mediterranea preferentially degrades lignin and hemicellulose over cellulose (preferential, successive or sequential white-rot). In addition, co-inoculation of sawdust with two cellulolytic and xylanolytic bacterial strains of Paenibacillus (Nakamura) Ash (Paenibacillus sp. (S231-2) and P. amylolyticus (S293)), enhanced F. mediterranea ability to degrade Ugni blanc. The NMR data further showed that the increase in Ugni blanc sawdust degradation products was greater when bacteria and fungi were inoculated together. We also demonstrated that these two bacterial strains could degrade the wood components of Ugni blanc sawdust. Genome analysis of these bacterial strains revealed numerous genes predicted to be involved in cellulose, hemicellulose, and lignin degradation, as well as several other genes related to bacteria-fungi interactions and endophytism inside the plant. The occurrence of this type of bacteria-fungus interaction could explain, at least in part, why necrosis develops extensively in certain grapevine varieties such as Ugni blanc.
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Affiliation(s)
- Rana Haidar
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France.
- INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883, Villenave d'Ornon, France.
| | - Stéphane Compant
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Coralie Robert
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, 33607, Pessac, France
| | - Livio Antonielli
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Amira Yacoub
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
- INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883, Villenave d'Ornon, France
| | - Axelle Grélard
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, 33607, Pessac, France
| | - Antoine Loquet
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, 33607, Pessac, France
| | - Günter Brader
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Rémy Guyoneaud
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Eléonore Attard
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Patrice Rey
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
- INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883, Villenave d'Ornon, France
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Funnicelli MIG, de Carvalho LAL, Teheran-Sierra LG, Dibelli SC, Lemos EGDM, Pinheiro DG. Unveiling genomic features linked to traits of plant growth-promoting bacterial communities from sugarcane. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174577. [PMID: 38981540 DOI: 10.1016/j.scitotenv.2024.174577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024]
Abstract
Microorganisms are ubiquitous, and those inhabiting plants have been the subject of several studies. Plant-associated bacteria exhibit various biological mechanisms that enable them to colonize host plants and, in some cases, enhance their fitness. In this study, we describe the genomic features predicted to be associated with plant growth-promoting traits in six bacterial communities isolated from sugarcane. The use of highly accurate single-molecule real-time sequencing technology for metagenomic samples from these bacterial communities allowed us to recover 17 genomes. The taxonomic assignments for the binned genomes were performed, revealing taxa distributed across three main phyla: Bacillota, Bacteroidota, and Pseudomonadota, with the latter being the most representative. Subsequently, we functionally annotated the metagenome-assembled genomes (MAGs) to characterize their metabolic pathways related to plant growth-promoting traits. Our study successfully identified the enrichment of important functions related to phosphate and potassium acquisition, modulation of phytohormones, and mechanisms for coping with abiotic stress. These findings could be linked to the robust colonization of these sugarcane endophytes.
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Affiliation(s)
- Michelli Inácio Gonçalves Funnicelli
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Lucas Amoroso Lopes de Carvalho
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Luis Guillermo Teheran-Sierra
- Agronomy Research Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, Bogotá 111121, Colombia
| | - Sabrina Custodio Dibelli
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Eliana Gertrudes de Macedo Lemos
- Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Molecular Biology Laboratory, Institute for Research in Bioenergy (IPBEN), São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Daniel Guariz Pinheiro
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil.
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16
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Boie F, Ducey TF, Xing Y, Wang J, Rinklebe J. Field-aged rice hull biochar stimulated the methylation of mercury and altered the microbial community in a paddy soil under controlled redox condition changes. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134446. [PMID: 38696958 DOI: 10.1016/j.jhazmat.2024.134446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/25/2024] [Accepted: 04/25/2024] [Indexed: 05/04/2024]
Abstract
Mercury (Hg) contaminated paddy soils are hot spots for methylmercury (MeHg) which can enter the food chain via rice plants causing high risks for human health. Biochar can immobilize Hg and reduce plant uptake of MeHg. However, the effects of biochar on the microbial community and Hg (de)methylation under dynamic redox conditions in paddy soils are unclear. Therefore, we determined the microbial community in an Hg contaminated paddy soil non-treated and treated with rice hull biochar under controlled redox conditions (< 0 mV to 600 mV) using a biogeochemical microcosm system. Hg methylation exceeded demethylation in the biochar-treated soil. The aromatic hydrocarbon degraders Phenylobacterium and Novosphingobium provided electron donors stimulating Hg methylation. MeHg demethylation exceeded methylation in the non-treated soil and was associated with lower available organic matter. Actinobacteria were involved in MeHg demethylation and interlinked with nitrifying bacteria and nitrogen-fixing genus Hyphomicrobium. Microbial assemblages seem more important than single species in Hg transformation. For future directions, the demethylation potential of Hyphomicrobium assemblages and other nitrogen-fixing bacteria should be elucidated. Additionally, different organic matter inputs on paddy soils under constant and dynamic redox conditions could unravel the relationship between Hg (de)methylation, microbial carbon utilization and nitrogen cycling.
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Affiliation(s)
- Felizitas Boie
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water and Waste Management, Laboratory of Soil and Groundwater Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany
| | - Thomas F Ducey
- US Department of Agriculture, Coastal Plains Soil, Water, Plant Research Center, 2611 West Lucas Street, Florence, SC, USA
| | - Ying Xing
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water and Waste Management, Laboratory of Soil and Groundwater Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany; School of Chemistry and Materials Science, Guizhou Normal University, Guiyang 550002, PR China
| | - Jianxu Wang
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water and Waste Management, Laboratory of Soil and Groundwater Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany; State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, 550082 Guiyang, P.R. China
| | - Jörg Rinklebe
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water and Waste Management, Laboratory of Soil and Groundwater Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany.
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Ali MA, Ahmed T, Ibrahim E, Rizwan M, Chong KP, Yong JWH. A review on mechanisms and prospects of endophytic bacteria in biocontrol of plant pathogenic fungi and their plant growth-promoting activities. Heliyon 2024; 10:e31573. [PMID: 38841467 PMCID: PMC11152693 DOI: 10.1016/j.heliyon.2024.e31573] [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: 01/15/2024] [Revised: 05/08/2024] [Accepted: 05/19/2024] [Indexed: 06/07/2024] Open
Abstract
Endophytic bacteria, living inside plants, are competent plant colonizers, capable of enhancing immune responses in plants and establishing a symbiotic relationship with them. Endophytic bacteria are able to control phytopathogenic fungi while exhibiting plant growth-promoting activity. Here, we discussed the mechanisms of phytopathogenic fungi control and plant growth-promoting actions discovered in some major groups of beneficial endophytic bacteria such as Bacillus, Paenibacillus, and Pseudomonas. Most of the studied strains in these genera were isolated from the rhizosphere and soils, and a more extensive study of these endophytic bacteria is needed. It is essential to understand the underlying biocontrol and plant growth-promoting mechanisms and to develop an effective screening approach for selecting potential endophytic bacteria for various applications. We have suggested a screening strategy to identify potentially useful endophytic bacteria based on mechanistic phenomena. The discovery of endophytic bacteria with useful biocontrol and plant growth-promoting characteristics is essential for developing sustainable agriculture.
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Affiliation(s)
- Md. Arshad Ali
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, 88400, Sabah, Malaysia
| | - Temoor Ahmed
- Xianghu Laboratory, Hangzhou, 311231, China
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- MEU Research Unit, Middle East University, Amman, Jordan
| | - Ezzeldin Ibrahim
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Department of Vegetable Diseases Research, Plant Pathology Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Muhammad Rizwan
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Khim Phin Chong
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, 88400, Sabah, Malaysia
| | - Jean Wan Hong Yong
- Department of Biosystems and Technology, Swedish University of Agricultural Sciences, 23456, Alnarp, Sweden
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18
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Garcia A, Rivera R, Simpson AC, Singh NK, Green S, Venkateswaran K. Whole-genome sequencing of Paenibacillus phoenicis isolated from the Phoenix Mars Lander spacecraft assembly facility. Microbiol Resour Announc 2024; 13:e0126523. [PMID: 38742883 PMCID: PMC11237736 DOI: 10.1128/mra.01265-23] [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: 12/25/2023] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
The genome of Paenibacillus phoenicis, a spore-forming bacterium isolated from the spacecraft assembly facility of the Phoenix mission, was generated via hybrid assembly by merging short and long reads. Examining this genome may shed light on strategies to minimize the risk of contaminating extraterrestrial environments with Earth-based microorganisms.
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Affiliation(s)
- Andrew Garcia
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Oregon State University, Corvallis, Oregon, USA
| | - Romar Rivera
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Anna C. Simpson
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Nitin K. Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Stefan Green
- Rush University Medical Center, Genomics and Microbiome Core Facility, Chicago, Illinois, USA
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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19
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Jung HK, Kim DG, Zin H, Park J, Jung H, Kim YO, Kong HJ, Kim JW, Kim YS. Paenibacillus hexagrammi sp. nov., a novel bacterium isolated from the gut content of Hexagrammos agrammus. Int J Syst Evol Microbiol 2024; 74. [PMID: 38869487 DOI: 10.1099/ijsem.0.006419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
A Gram-stain-positive, aerobic bacterium, designated as YPD9-1T, was isolated from the gut contents of a spotty belly greenling, Hexagrammos agrammus, collected near Dokdo island, South Korea. The rod-shaped cells were oxidase-positive, and catalase-negative. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C16 : 0 and iso-C17: 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The DNA G+C content was 47.6 mol% and the predominant respiratory quinone was menaquinone MK-7. The 16S rRNA gene sequence of YPD9-1T showed low sequence similarities to species of the genus Paenibacillus, Paenibacillus pocheonensis Gsoil 1138T (97.21 % of sequence similarity), Paenibacillus aestuarii CJ25T (97.12 %) and Paenibacillus allorhizoplanae JJ-42T (96.89 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that YPD9-1T formed a distinct branch among other species of the genus Paenibacillus. The digital DNA-DNA hybridisation, average nucleotide identity, and average amino acid identity values between YPD9-1T and the related species were in the ranges of 15.3-16.2 %, 74.1-78.4 %, and 71.1-71.9 %, respectively, which are below the species cutoff values. On the basis of the results of the polyphasic analysis, we conclude that strain YPD9-1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus hexagrammi sp. nov. is proposed. The type strain of Paenibacillus hexagrammi is YPD9-1T (=KCTC 43424T =LMG 32988T).
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Affiliation(s)
- Hyun-Kyoung Jung
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Dong-Gyun Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Hyunwoo Zin
- Food Safety and Processing Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Jungwook Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Hyejung Jung
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Ju-Won Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Young-Sam Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
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Rimoldi S, Di Rosa AR, Oteri M, Chiofalo B, Hasan I, Saroglia M, Terova G. The impact of diets containing Hermetia illucens meal on the growth, intestinal health, and microbiota of gilthead seabream (Sparus aurata). FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:1003-1024. [PMID: 38386264 PMCID: PMC11213805 DOI: 10.1007/s10695-024-01314-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 01/29/2024] [Indexed: 02/23/2024]
Abstract
The present study investigated the effect of replacing fishmeal (FM) with insect meal of Hermetia illucens (HI) in the diet of Sparus aurata farmed inshore on growth, gut health, and microbiota composition. Two isolipidic (18% as fed) and isoproteic (42% as fed) diets were tested at the farm scale: a control diet without HI meal and an experimental diet with 11% HI meal replacing FM. At the end of the 25-week feeding trial, final body weight, specific growth rate, feed conversion rate, and hepatosomatic index were not affected by the diet. Gross morphology of the gastrointestinal tract and the liver was unchanged and showed no obvious signs of inflammation. High-throughput sequencing of 16S rRNA gene amplicons (MiSeq platform, Illumina) used to characterize the gut microbial community profile showed that Proteobacteria, Fusobacteria, and Firmicutes were the dominant phyla of the gut microbiota of gilthead seabream, regardless of diet. Dietary inclusion of HI meal altered the gut microbiota by significantly decreasing the abundance of Cetobacterium and increasing the relative abundance of the Oceanobacillus and Paenibacillus genera. Our results clearly indicate that the inclusion of HI meal as an alternative animal protein source positively affects the gut microbiota of seabream by increasing the abundance of beneficial genera, thereby improving gut health and maintaining growth performance of S. aurata from coastal farms.
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Affiliation(s)
- Simona Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100, Varese, Italy
| | - Ambra Rita Di Rosa
- Department of Veterinary Sciences, University of Messina, Messina, Italy.
| | - Marianna Oteri
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Biagina Chiofalo
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Imam Hasan
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100, Varese, Italy
| | - Marco Saroglia
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100, Varese, Italy
| | - Genciana Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100, Varese, Italy.
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21
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Li Z, Lin Y, Song F, Zheng R, Huang Q. Isolation and characterization of Paenibacillus peoriae JC-3jx from Dendrobium nobile. Biotechniques 2024; 76:192-202. [PMID: 38469872 DOI: 10.2144/btn-2023-0083] [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] [Indexed: 03/13/2024] Open
Abstract
Dendrobium is a rich source of high-value natural components. Endophytic fungi are well studied, yet bacteria research is limited. In this study, endophytic bacteria from Dendrobium nobile were isolated using an improved method, showing inhibition of pathogens and growth promotion. JC-3jx, identified as Paenibacillus peoriae, exhibited significant inhibitory activity against tested fungi and bacteria, including Escherichia coli. JC-3jx also promoted corn seed rooting and Dendrobium growth, highlighting its excellent biocontrol and growth-promoting potential.
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Affiliation(s)
- ZhiPing Li
- Department of Health Food, Fujian Vocational College of Bioengineering, Fuzhou, 350000, PR China
| | - Yuan Lin
- Department of Health Food, Fujian Vocational College of Bioengineering, Fuzhou, 350000, PR China
| | - FeiFei Song
- Department of Health Food, Fujian Vocational College of Bioengineering, Fuzhou, 350000, PR China
| | - RuoNan Zheng
- Department of Health Food, Fujian Vocational College of Bioengineering, Fuzhou, 350000, PR China
| | - QinGeng Huang
- Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou, 350108, PR China
- Qingyuan One Alive Institute of Biological Research Co., Ltd, Qingyuan, 500112, PR China
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22
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Wang A, Zhang S, Liang Z, Zeng Z, Ma Y, Zhang Z, Yang Y, He Z, Yu G, Liang Y. Response of microbial communities to exogenous nitrate nitrogen input in black and odorous sediment. ENVIRONMENTAL RESEARCH 2024; 248:118137. [PMID: 38295972 DOI: 10.1016/j.envres.2024.118137] [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: 11/27/2023] [Revised: 12/30/2023] [Accepted: 01/05/2024] [Indexed: 02/10/2024]
Abstract
Since nitrate nitrogen (NO3--N) input has proved an effective approach for the treatment of black and odorous river waterbody, it was controversial whether the total nitrogen concentration standard should be raised when the effluent from the sewage treatment plant is discharged into the polluted river. To reveal the effect of exogenous nitrate (NO3--N) on black odorous waterbody, sediments with different features from contaminated rivers were collected, and the changes of physical and chemical characteristics and microbial community structure in sediments before and after the addition of exogenous NO3--N were investigated. The results showed that after the input of NO3--N, reducing substances such as acid volatile sulfide (AVS) in the sediment decreased by 80 % on average, ferrous (Fe2+) decreased by 50 %, yet the changing trend of ammonia nitrogen (NH4+-N) in some sediment samples increased while others decreased. High-throughput sequencing results showed that the abundance of Thiobacillus at most sites increased significantly, becoming the dominant genus in the sediment, and the abundance of functional genes in the metabolome increased, such as soxA, soxX, soxY, soxZ. Network analysis showed that sediment microorganisms evolved from a single sulfur oxidation ecological function to diverse ecological functions, such as nitrogen cycle nirB, nirD, nirK, nosZ, and aerobic decomposition. In summary, inputting an appropriate amount of exogenous NO3--N is beneficial for restoring and maintaining the oxidation states of river sediment ecosystems.
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Affiliation(s)
- Ao Wang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Shengrui Zhang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Ziyang Liang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Zhanqin Zeng
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Yingshi Ma
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiang Zhang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Ying Yang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Zihao He
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Guangwei Yu
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China.
| | - Yuhai Liang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China.
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Islam T, Haque MA, Barai HR, Istiaq A, Kim JJ. Antibiotic Resistance in Plant Pathogenic Bacteria: Recent Data and Environmental Impact of Unchecked Use and the Potential of Biocontrol Agents as an Eco-Friendly Alternative. PLANTS (BASEL, SWITZERLAND) 2024; 13:1135. [PMID: 38674544 PMCID: PMC11054394 DOI: 10.3390/plants13081135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024]
Abstract
The economic impact of phytopathogenic bacteria on agriculture is staggering, costing billions of US dollars globally. Pseudomonas syringae is the top most phytopathogenic bacteria, having more than 60 pathovars, which cause bacteria speck in tomatoes, halo blight in beans, and so on. Although antibiotics or a combination of antibiotics are used to manage infectious diseases in plants, they are employed far less in agriculture compared to human and animal populations. Moreover, the majority of antibiotics used in plants are immediately washed away, leading to environmental damage to ecosystems and food chains. Due to the serious risk of antibiotic resistance (AR) and the potential for environmental contamination with antibiotic residues and resistance genes, the use of unchecked antibiotics against phytopathogenic bacteria is not advisable. Despite the significant concern regarding AR in the world today, there are inadequate and outdated data on the AR of phytopathogenic bacteria. This review presents recent AR data on plant pathogenic bacteria (PPB), along with their environmental impact. In light of these findings, we suggest the use of biocontrol agents as a sustainable, eco-friendly, and effective alternative to controlling phytopathogenic bacteria.
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Affiliation(s)
- Tarequl Islam
- Department of Microbiology, Noakhali Science and Technology University, Sonapur, Noakhali 3814, Bangladesh;
| | - Md Azizul Haque
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea;
| | - Hasi Rani Barai
- School of Mechanical and IT Engineering, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea;
| | - Arif Istiaq
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St Louis, MO 63110-1010, USA
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea;
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24
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Shih SY, Huang YS, Chou KR, Wu HY, Tsai H. Isolation and genome characterization of Paenibacillus polymyxa 188, a potential biocontrol agent against fungi. J Appl Microbiol 2024; 135:lxae075. [PMID: 38509027 DOI: 10.1093/jambio/lxae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/04/2024] [Accepted: 03/19/2024] [Indexed: 03/22/2024]
Abstract
AIMS In this work, we aimed to isolate marine bacteria that produce metabolites with antifungal properties. METHODS AND RESULTS Paenibacillus polymyxa 188 was isolated from a marine sediment sample, and it showed excellent antifungal activity against many fungi pathogenic to plants (Fusarium tricinctum, Pestalotiopsis clavispora, Fusarium oxysporum, F. oxysporum f. sp. Cubense (Foc), Curvularia plantarum, and Talaromyces pinophilus) and to humans (Aspergillus terreus, Penicillium oxalicum, and Microsphaeropsis arundinis). The antifungal compounds produced by P. polymyxa 188 were extracted and analyzed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The complete genome sequence and biosynthetic gene clusters of P. polymyxa 188 were characterized and compared with those of other strains. A total of 238 carbohydrate-active enzymes (CAZymes) were identified in P. polymyxa 188. Two antibiotic gene clusters, fusaricidin and tridecaptin, exist in P. polymyxa 188, which is different from other strains that typically have multiple antibiotic gene clusters. CONCLUSIONS Paenibacilluspolymyxa 188 was identified with numerous biosynthetic gene clusters, and its antifungal ability against pathogenic fungi was verified.
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Affiliation(s)
- Sra-Yh Shih
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
| | - You-Syu Huang
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
- Eastern Marine Biology Research Center, Taitung City, 950, Taiwan
| | - Ker-Rui Chou
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
| | - Hung-Yi Wu
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
| | - HsinYuan Tsai
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
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25
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Guo C, Liu J, Wei Y, Du W, Li S. Comparison of the gastrointestinal bacterial microbiota between dairy cows with and without mastitis. Front Microbiol 2024; 15:1332497. [PMID: 38585704 PMCID: PMC10996066 DOI: 10.3389/fmicb.2024.1332497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/14/2024] [Indexed: 04/09/2024] Open
Abstract
Mastitis causes significant losses in the global dairy industry, and the health of animals has been linked to their intestinal microbiota. To better understand the relationship between gastrointestinal microbiota and mastitis in dairy cows, we collected blood, rumen fluid, and fecal samples from 23 dairy cows, including 13 cows with mastitis and 10 healthy cows. Using ELISA kit and high-throughput sequencing, we found that cows with mastitis had higher concentrations of TNF-α, IL-1, and LPS than healthy cows (p < 0.05), but no significant differences in microbiota abundance or diversity (p > 0.05). Principal coordinate analysis (PCOA) revealed significant differences in rumen microbial structure between the two groups (p < 0.05), with Moryella as the signature for rumen in cows with mastitis. In contrast, fecal microbial structure showed no significant differences (p > 0.05), with Aeriscardovia, Lactococcus, and Bacillus as the signature for feces in healthy cows. Furthermore, the results showed distinct microbial interaction patterns in the rumen and feces of cows with mastitis compared to healthy cows. Additionally, we observed correlations between the microbiota in both the rumen and feces of cows and blood inflammatory indicators. Our study sheds new light on the prevention of mastitis in dairy cows by highlighting the relationship between gastrointestinal microbiota and mastitis.
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Affiliation(s)
- Chunyan Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Jinzhong Vocational and Technical College, Jinzhong, China
| | - Jingjing Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yong Wei
- Xinjiang Agricultural University, Urumuqi, China
| | - Wen Du
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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26
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Ribeiro IDA, Paes JA, Wendisch VF, Ferreira HB, Passaglia LMP. Proteome profiling of Paenibacillus sonchi genomovar Riograndensis SBR5 T under conventional and alternative nitrogen fixation. J Proteomics 2024; 294:105061. [PMID: 38154550 DOI: 10.1016/j.jprot.2023.105061] [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: 08/21/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/30/2023]
Abstract
Paenibacillus sonchi SBR5T is a Gram-positive, endospore-forming facultative aerobic diazotrophic bacterium that can fix nitrogen via an alternative Fe-only nitrogenase (AnfHDGK). In several bacteria, this alternative system is expressed under molybdenum (Mo)-limiting conditions when the conventional Mo-dependent nitrogenase (NifHDK) production is impaired. The regulatory mechanisms, metabolic processes, and cellular functions of N2 fixation by alternative and/or conventional systems are poorly understood in the Paenibacillus genus. We conducted a comparative proteomic profiling study of P. sonchi SBR5T grown under N2-fixing conditions with and without Mo supply through an LC-MS/MS and label-free quantification analysis to address this gap. Protein abundances revealed overrepresented processes related to anaerobiosis growth adaption, Fe-S cluster biosynthesis, ammonia assimilation, electron transfer, and sporulation under N2-fixing conditions compared to non-fixing control. Under Mo limitation, the Fe-only nitrogenase components were overrepresented together with the Mo-transporter system, while the dinitrogenase component (NifDK) of Mo‑nitrogenase was underrepresented. The dinitrogenase reductase component (NifH) and accessory proteins encoded by the nif operon had no significant differential expression, suggesting post-transcriptional regulation of nif gene products in this strain. Overall, this was the first comprehensive proteomic analysis of a diazotrophic strain from the Paenibacillaceae family, and it provided insights related to alternative N2-fixation by Fe-only nitrogenase. SIGNIFICANCE: In this work, we try to understand how the alternative nitrogen fixation system, presented by some diazotrophic bacteria, works. For this, we used the SBR5 lineage of P. sonchi, which presents the alternative system in which the nitrogenase cofactor is composed only of iron. In addition, we tried to unravel the proteome of this strain in different situations of nitrogen fixation, since, for Gram-positive bacteria, these systems are little known. The results achieved, through LC-MS/MS and label-free quantitative analysis, showed an overrepresentation of proteins related to different processes involved with growth under stressful conditions in situations of nitrogen deficiency, in addition to suggesting that some encoded proteins by the nif operon may be regulated at post-transcriptional levels. Our findings represent important steps toward the elucidation of nitrogen fixation systems in Gram-positive diazotrophic bacteria.
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Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43312, Porto Alegre, RS, Brazil
| | - Jéssica Andrade Paes
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves, 9500 Porto Alegre, RS, Brazil
| | - Volker F Wendisch
- Institute for Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Henrique Bunselmeyer Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves, 9500 Porto Alegre, RS, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43312, Porto Alegre, RS, Brazil.
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Fernandes P, Pinto R, Correia C, Mourão I, Moura L, Brito LM. Valorization of kiwi waste through composting. ENVIRONMENTAL TECHNOLOGY 2024:1-15. [PMID: 38471044 DOI: 10.1080/09593330.2024.2326797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Kiwi waste from the calibration process is a major environmental problem of kiwi production due to landfill deposition. This work aims to contribute to the agronomic use of recycled kiwi waste through composting. With this objective, a composting experiment was carried out with kiwi fruit waste mixed with 5%, 10% and 20% (fresh weight) of wheat straw from bundles used to protect kiwifruit trunks from frost, as abulking agent to increase aeration, in the piles 5S, 10S and 20S, respectively. The highest temperatures for piles 5S and 10S were above 60°C, whereas the temperature did not reach 40°C in the pile with the highest straw content (20S) because the aeration increased heat loss in addition to increased C/N ratio of this pile. Also, the amount of organic matter mineralized decreased with increasing amount of straw because of the high C/N ratio of the straw. The highest total N (29.7 g kg-1) and the lowest C/N ratio (13) of the compost with 5% of straw is important from the agricultural point of view to promote N availability. In contrast, the high electrical conductivity (4.6 dS m-1) of this compost increases the risk of salt accumulation in the soil. Our results show that the compost with 10% straw, with high degree of maturation, absence of poor hygiene indicators as coliforms and pathogens as Salmonella sp., high organic matter content and rich in nutrients, together with the adequate compost pH and low electrical conductivity improves compost quality.
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Affiliation(s)
- Paulo Fernandes
- Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial de Nun'Álvares, Viana do Castelo, Portugal
- Centro de Investigação e Desenvolvimento em Sistemas Agroalimentares e Sustentabilidade (CISAS), R. Escola Industrial e Comercial de Nun'Álvares, Viana do Castelo, Portugal
| | - Rui Pinto
- Centro de Investigação e Desenvolvimento em Sistemas Agroalimentares e Sustentabilidade (CISAS), R. Escola Industrial e Comercial de Nun'Álvares, Viana do Castelo, Portugal
| | - Cláudia Correia
- Escola Superior Agrária, Instituto Politécnico de Viana do Castelo, Ponte de Lima, Portugal
| | - Isabel Mourão
- Escola Superior Agrária, Instituto Politécnico de Viana do Castelo, Ponte de Lima, Portugal
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus Santa Apolónia, Bragança, Portugal
| | - Luísa Moura
- Centro de Investigação e Desenvolvimento em Sistemas Agroalimentares e Sustentabilidade (CISAS), R. Escola Industrial e Comercial de Nun'Álvares, Viana do Castelo, Portugal
- Escola Superior Agrária, Instituto Politécnico de Viana do Castelo, Ponte de Lima, Portugal
| | - Luis Miguel Brito
- Centro de Investigação e Desenvolvimento em Sistemas Agroalimentares e Sustentabilidade (CISAS), R. Escola Industrial e Comercial de Nun'Álvares, Viana do Castelo, Portugal
- Escola Superior Agrária, Instituto Politécnico de Viana do Castelo, Ponte de Lima, Portugal
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus Santa Apolónia, Bragança, Portugal
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Huang XY, Ye XP, Hu YY, Tang ZX, Zhang T, Zhou H, Zhou T, Bai XL, Pi EX, Xie BH, Shi LE. Exopolysaccharides of Paenibacillus polymyxa: A review. Int J Biol Macromol 2024; 261:129663. [PMID: 38278396 DOI: 10.1016/j.ijbiomac.2024.129663] [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: 11/08/2023] [Revised: 12/30/2023] [Accepted: 01/19/2024] [Indexed: 01/28/2024]
Abstract
Paenibacillus polymyxa (P. polymyxa) is a member of the genus Paenibacillus, which is a rod-shaped, spore-forming gram-positive bacterium. P. polymyxa is a source of many metabolically active substances, including polypeptides, volatile organic compounds, phytohormone, hydrolytic enzymes, exopolysaccharide (EPS), etc. Due to the wide range of compounds that it produces, P. polymyxa has been extensively studied as a plant growth promoting bacterium which provides a direct benefit to plants through the improvement of N fixation from the atmosphere and enhancement of the solubilization of phosphorus and the uptake of iron in the soil, and phytohormones production. Among the metabolites from P. polymyxa, EPS exhibits many activities, for example, antioxidant, immunomodulating, anti-tumor and many others. EPS has various applications in food, agriculture, environmental protection. Particularly, in the field of sustainable agriculture, P. polymyxa EPS can be served as a biofilm to colonize microbes, and also can act as a nutrient sink on the roots of plants in the rhizosphere. Therefore, this paper would provide a comprehensive review of the advancements of diverse aspects of EPS from P. polymyxa, including the production, extraction, structure, biosynthesis, bioactivity and applications, etc. It would provide a direction for future research on P. polymyxa EPS.
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Affiliation(s)
- Xuan-Ya Huang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Xin-Pei Ye
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Yan-Yu Hu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Zhen-Xing Tang
- School of Culinary Art, Tourism College of Zhejiang, Hangzhou, Zhejiang 311231, China
| | - Tian Zhang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Hai Zhou
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Ting Zhou
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Xue-Lian Bai
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Er-Xu Pi
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Bing-Hua Xie
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.
| | - Lu-E Shi
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.
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29
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Valdez-Nuñez LF, Rivera-Jacinto MA. Thermophilic bacteria from Peruvian hot springs with high potential application in environmental biotechnology. ENVIRONMENTAL TECHNOLOGY 2024; 45:1420-1435. [PMID: 36356186 DOI: 10.1080/09593330.2022.2143293] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Hot springs are extreme environments in which well-adapted microorganisms with biotechnological applications can thrive naturally. These thermal environments across Peruvian territory have, until now, remained poorly investigated. In this study, two hot springs, El Tragadero and Quilcate, located in Cajamarca (Peru) were selected in order to investigate the biotechnological potential of indigenous thermophilic bacteria. Enrichment and isolation processes were carried out using microbial mats, sediments, biofilms, and plastic polymers as samples. Screening for biosurfactants and siderophores production, as well as for polyethylene terephthalate (PET) hydrolysis was done using culture-dependent techniques. After molecular identification, Bacillus was found as the most abundant genus in both hot springs. Bacillus velezensis was found producing biosurfactants under high-level temperature. Anoxybacillus species (A. salavatliensis and A. gonensis) are here reported as siderophore-producing bacteria for the first time. Additionally, Brevibacillus and the less-known bacterium Tistrella mobilis were found demonstrating PET hydrolysis activity. Our study provides the first report of thermophilic bacteria isolated from Peruvian hot springs with biotechnological potential for the bioremediation of oil-, metal- and plastic-polluted environments.
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Affiliation(s)
- Luis Felipe Valdez-Nuñez
- Laboratorio de Microbiología, Departamento de Ciencias Biológicas, Universidad Nacional de Cajamarca, Cajamarca, Peru
| | - Marco A Rivera-Jacinto
- Laboratorio de Microbiología, Departamento de Ciencias Biológicas, Universidad Nacional de Cajamarca, Cajamarca, Peru
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30
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Saikh SR, Mushtaque MA, Pramanick A, Prasad JK, Roy D, Saha S, Das SK. Fog caused distinct diversity of airborne bacterial communities enriched with pathogens over central Indo-Gangetic plain in India. Heliyon 2024; 10:e26370. [PMID: 38420377 PMCID: PMC10901028 DOI: 10.1016/j.heliyon.2024.e26370] [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: 08/14/2023] [Revised: 11/30/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Fog causes enhancement of bacterial loading in the atmosphere. Current study represents the impact of occurrences of fog on the alteration of diversity of airborne bacteria and their network computed from metagenomic data of airborne samples collected at Arthauli (25.95°N, 85.10°E) situated at central Indo-Gangetic Plain (IGP) during 1-14 January 2021. A distinct bacterial diversity with a complex network is identified in foggy condition due to the enrichment of unique types of bacteria. Present investigation highlights a statistically significant enrichment of airborne pathogenic bacteria found in a unique ecosystem within air evolved due to the occurrences of fog over central IGP. In the foggy network, Cutibacterium, an opportunistic pathogen, is identified to be interacting maximum (21 edges) with other bacteria with statistically significant copresence relation, which are responsible for various infections for human beings. A 40-60% increase (p < 0.01) in the abundance of pathogenic bacteria for respiratory and skin diseases is noticed in fog period. Among the fog-enriched bacteria, Cutibacterium, Herbaspirillum, Paenibacillus, and Tsukamurella are examples of opportunistic bacteria causing various respiratory diseases, while Paenibacillus can even cause skin cancer and acute lymphoblastic leukemia.
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Affiliation(s)
- Shahina Raushan Saikh
- Department of Physical Sciences, Bose Institute, Kolkata, India
- Department of Life Science & Bio-technology, Jadavpur University, Kolkata, India
| | | | | | | | - Dibakar Roy
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Sudipto Saha
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Sanat Kumar Das
- Department of Physical Sciences, Bose Institute, Kolkata, India
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31
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Xu Y, Liang X, Hyun CG. Isolation, Characterization, Genome Annotation, and Evaluation of Tyrosinase Inhibitory Activity in Secondary Metabolites of Paenibacillus sp. JNUCC32: A Comprehensive Analysis through Molecular Docking and Molecular Dynamics Simulation. Int J Mol Sci 2024; 25:2213. [PMID: 38396889 PMCID: PMC10889091 DOI: 10.3390/ijms25042213] [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: 01/12/2024] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
A potential strain, Paenibacillus sp. JNUCC32, was isolated and subjected to whole-genome sequencing. Genome functional annotation revealed its active metabolic capabilities. This study aimed to investigate the pivotal secondary metabolites in the biological system. Fermentation and extraction were performed, resulting in the isolation of seven known compounds: tryptophol (1), 3-(4-hydroxyphenyl)propionic acid (2), ferulic acid (3), maculosin (4), brevianamide F (5), indole-3-acetic acid (6), and butyric acid (7). Tryptophol exhibited favorable pharmacokinetic properties and demonstrated certain tyrosinase inhibitory activity (IC50 = 999 μM). For further analysis of its inhibition mechanism through molecular docking and molecular dynamics (MD) simulation, tryptophol formed three hydrogen bonds and a pro-Michaelis complex with tyrosinase (binding energy = -5.3 kcal/mol). The MD simulation indicated favorable stability for the tryptophol-mushroom tyrosinase complex, primarily governed by hydrogen bond interactions. The crucial residues VAL-283 and HIS-263 in the docking were also validated. This study suggests tryptophol as a potential candidate for antibrowning agents and dermatological research.
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Affiliation(s)
| | | | - Chang-Gu Hyun
- Department of Beauty and Cosmetology, Jeju Inside Agency and Cosmetic Science Center, Jeju National University, Jeju 63243, Republic of Korea; (Y.X.); (X.L.)
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Zhao T, Ma J, Lin M, Gao C, Zhao Y, Li X, Sun W. Isolation and Characterization of Paenibacillus polymyxa B7 and Inhibition of Aspergillus tubingensis A1 by Its Antifungal Substances. Int J Mol Sci 2024; 25:2195. [PMID: 38396880 PMCID: PMC10889487 DOI: 10.3390/ijms25042195] [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: 01/09/2024] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Screening of Bacillus with antagonistic effects on paddy mold pathogens to provide strain resources for biological control of mold in Oryza sativa L. screening of Bacillus isolates antagonistic towards Aspergillus tubingensis from rhizosphere soil of healthy paddy; classification and identification of antagonistic strains by biological characteristics and 16S rDNA sequence analysis; transcriptome sequencing after RNA extraction from Bacillus-treated Aspergillus tubingensis; and extraction of inhibitory crude proteins of Bacillus by ammonium sulfate precipitation; inhibitory crude protein and Bacillus spp. were treated separately for A. tubingensis and observed by scanning electron microscopy (SEM). An antagonistic strain of Bacillus, named B7, was identified as Paenibacillus polymyxa by 16S rDNA identification and phylogenetic evolutionary tree comparison analysis. Analysis of the transcriptome results showed that genes related to secondary metabolite biosynthesis such as antifungal protein were significantly downregulated. SEM results showed that the mycelium of A. tubingensis underwent severe rupture after treatment with P. polymyxa and antifungal proteins, respectively. In addition, the sporocarp changed less after treatment with P. polymyxa, and the sporangium stalks had obvious folds. P. polymyxa B7 has a good antagonistic effect against A. tubingensis and has potential for biocontrol applications of paddy mold pathogens.
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Affiliation(s)
| | | | | | | | | | | | - Weihong Sun
- College of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China; (T.Z.); (J.M.); (M.L.); (C.G.); (Y.Z.); (X.L.)
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Miyata A, Ito S, Fujinami D. Structure Prediction and Genome Mining-Aided Discovery of the Bacterial C-Terminal Tryptophan Prenyltransferase PalQ. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307372. [PMID: 38059776 PMCID: PMC10853753 DOI: 10.1002/advs.202307372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/13/2023] [Indexed: 12/08/2023]
Abstract
Post-translational prenylations, found in eukaryotic primary metabolites and bacterial secondary metabolites, play crucial roles in biomolecular interactions. Employing genome mining methods combined with AlphaFold2-based predictions of protein interactions, PalQ , a prenyltransferase responsible for the tryptophan prenylation of RiPPs produced by Paenibacillus alvei, is identified. PalQ differs from cyanobactin prenyltransferases because of its evolutionary relationship to isoprene synthases, which enables PalQ to transfer extended prenyl chains to the indole C3 position. This prenylation introduces structural diversity to the tryptophan side chain and also leads to conformational dynamics in the peptide backbone, attributed to the cis/trans isomerization that arises from the formation of a pyrrolidine ring. Additionally, PalQ exhibited pronounced positional selectivity for the C-terminal tryptophan. Such enzymatic characteristics offer a toolkit for peptide therapeutic lipidation.
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Affiliation(s)
- Azusa Miyata
- Graduate Division of Nutritional and Environmental SciencesUniversity of Shizuoka52‐1 Yada, Suruga‐kuShizuoka422‐8526Japan
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental SciencesUniversity of Shizuoka52‐1 Yada, Suruga‐kuShizuoka422‐8526Japan
| | - Daisuke Fujinami
- Graduate Division of Nutritional and Environmental SciencesUniversity of Shizuoka52‐1 Yada, Suruga‐kuShizuoka422‐8526Japan
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34
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Nanfack AD, Nguefack J, Musonerimana S, La China S, Giovanardi D, Stefani E. Exploiting the microbiome associated with normal and abnormal sprouting rice (Oryza sativa L.) seed phenotypes through a metabarcoding approach. Microbiol Res 2024; 279:127546. [PMID: 37992468 DOI: 10.1016/j.micres.2023.127546] [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: 08/29/2023] [Revised: 10/16/2023] [Accepted: 11/07/2023] [Indexed: 11/24/2023]
Abstract
Rice germination and seedlings' growth are crucial stages that influence crop establishment and productivity. These performances depend on several factors, including the abundance and diversity of seed microbial endophytes. Two popular rainfed rice varieties cultivated in Cameroon, NERICA 3 and NERICA 8, were used for investigating the seed-associated microbiome using the Illumina-based 16 S rRNA gene. Significant differences were observed in terms of richness index between normal and abnormal seedlings developed from sprouting seeds, although no significant species evenness index was assessed within either phenotype. Two hundred ninety-two bacterial amplicon sequence variants were identified in seed microbiome of the rice varieties, and principal coordinate analysis revealed that microbial communities formed two distinct clusters in normal and abnormal seedling phenotypes. Overall, 38 bacteria genera were identified, belonging to 6 main phyla. Furthermore, the core microbiome was defined, and the differential abundance of 28 bacteria genera was assessed. Based on the collected results, putative bacterial genera were directly correlated with the development of normal seedlings. For most genera that are recognised to include beneficial species, such as Brevundimonas, Sphingomonas, Exiguobacterium, Luteibacter, Microbacterium and Streptomyces, a significant increase of their relative abundance was found in normal seedlings. Additionally, in abnormal seedlings, we also observed an increased abundance of the genera Kosakonia and Paenibacillus, which might have controversial aspects (beneficial or pathogenic), together with the presence of some genera (Clostridium sensu stricto) that are commonly correlated to sick plants. The putative functional gene annotation revealed the higher abundance of genes related to the metabolic biosynthesis of soluble carbohydrates and starch, tryptophan, nucleotides and ABC transporters in normal seedlings. Data presented in this study may help in further understanding the importance of the seed endophyte microbiome for driving a correct development of rice plants at the early stages and to identify possible beneficial bacteria for technological applications aimed to increase seed quality and crop productivity.
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Affiliation(s)
- Albert Dongmo Nanfack
- Department of Biochemistry, University of Yaoundé 1, Yaoundé, Cameroon; Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy
| | - Julienne Nguefack
- Department of Biochemistry, University of Yaoundé 1, Yaoundé, Cameroon
| | - Samson Musonerimana
- International Centre for Genetic Engineering and Biotechnology, Padriciano, TS, Italy; Burundi University, Faculty of Agronomy and Bio-Engineering 2, UNESCO Avenue, P.O. Box 2940, Bujumbura, Burundi
| | - Salvatore La China
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy
| | - Davide Giovanardi
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy.
| | - Emilio Stefani
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; University Centre for International Cooperation and Development (CUSCOS), via Università 4, 41121 Modena, Italy
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35
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Ritz NL, Draper LA, Bastiaanssen TFS, Turkington CJR, Peterson VL, van de Wouw M, Vlckova K, Fülling C, Guzzetta KE, Burokas A, Harris H, Dalmasso M, Crispie F, Cotter PD, Shkoporov AN, Moloney GM, Dinan TG, Hill C, Cryan JF. The gut virome is associated with stress-induced changes in behaviour and immune responses in mice. Nat Microbiol 2024; 9:359-376. [PMID: 38316929 PMCID: PMC10847049 DOI: 10.1038/s41564-023-01564-y] [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: 03/09/2023] [Accepted: 11/17/2023] [Indexed: 02/07/2024]
Abstract
The microbiota-gut-brain axis has been shown to play an important role in the stress response, but previous work has focused primarily on the role of the bacteriome. The gut virome constitutes a major portion of the microbiome, with bacteriophages having the potential to remodel bacteriome structure and activity. Here we use a mouse model of chronic social stress, and employ 16S rRNA and whole metagenomic sequencing on faecal pellets to determine how the virome is modulated by and contributes to the effects of stress. We found that chronic stress led to behavioural, immune and bacteriome alterations in mice that were associated with changes in the bacteriophage class Caudoviricetes and unassigned viral taxa. To determine whether these changes were causally related to stress-associated behavioural or physiological outcomes, we conducted a faecal virome transplant from mice before stress and autochthonously transferred it to mice undergoing chronic social stress. The transfer of the faecal virome protected against stress-associated behaviour sequelae and restored stress-induced changes in select circulating immune cell populations, cytokine release, bacteriome alterations and gene expression in the amygdala. These data provide evidence that the virome plays a role in the modulation of the microbiota-gut-brain axis during stress, indicating that these viral populations should be considered when designing future microbiome-directed therapies.
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Affiliation(s)
- Nathaniel L Ritz
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Thomaz F S Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Christopher J R Turkington
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Veronica L Peterson
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Marcel van de Wouw
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- Department of Pediatrics, University of Calgary, Calgary, Canada
| | - Klara Vlckova
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Katherine E Guzzetta
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Aurelijus Burokas
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Hugh Harris
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Marion Dalmasso
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Normandie Univ, UNICAEN, UNIROUEN, ABTE, 14000, Caen, France
| | - Fiona Crispie
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Andrey N Shkoporov
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Gerard M Moloney
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Corke, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
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36
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Lebano I, Fracchetti F, Vigni ML, Mejia JF, Felis G, Lampis S. MALDI-TOF as a powerful tool for identifying and differentiating closely related microorganisms: the strange case of three reference strains of Paenibacillus polymyxa. Sci Rep 2024; 14:2585. [PMID: 38297004 PMCID: PMC10831075 DOI: 10.1038/s41598-023-50010-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/14/2023] [Indexed: 02/02/2024] Open
Abstract
Accurate identification and typing of microbes are crucial steps in gaining an awareness of the biological heterogeneity and reliability of microbial material within any proprietary or public collection. Paenibacillus polymyxa is a bacterial species of great agricultural and industrial importance due to its plant growth-promoting activities and production of several relevant secondary metabolites. In recent years, matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used as an alternative rapid tool for identifying, typing, and differentiating closely related strains. In this study, we investigated the diversity of three P. polymyxa strains. The mass spectra of ATCC 842T, DSM 292, and DSM 365 were obtained, analysed, and compared to select discriminant peaks using ClinProTools software and generate classification models. MALDI-TOF MS analysis showed inconsistent results in identifying DSM 292 and DSM 365 as belonging to P. polimixa species, and comparative analysis of mass spectra revealed the presence of highly discriminatory biomarkers among the three strains. 16S rRNA sequencing and Average Nucleotide Identity (ANI) confirmed the discrepancies found in the proteomic analysis. The case study presented here suggests the enormous potential of the proteomic-based approach, combined with statistical tools, to predict and explore differences between closely related strains in large microbial datasets.
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Affiliation(s)
- Ilaria Lebano
- Syngenta Biologicals (Valagro SpA), 66041, Atessa, CH, Italy.
| | | | - Mario Li Vigni
- Syngenta Biologicals (Valagro SpA), 66041, Atessa, CH, Italy
| | | | - Giovanna Felis
- Department of Biotechnology and VUCC-DBT Verona University Culture Collection, University of Verona, 37154, Verona, VR, Italy
| | - Silvia Lampis
- Department of Biotechnology and VUCC-DBT Verona University Culture Collection, University of Verona, 37154, Verona, VR, Italy.
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Wang L, Nabi F, Yi W, Wang D, Zhu Y, Jiang X. Low-dose thiram exposure elicits dysregulation of the gut microbial ecology in broiler chickens. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 270:115879. [PMID: 38157796 DOI: 10.1016/j.ecoenv.2023.115879] [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: 10/05/2023] [Revised: 12/17/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Thiram, a typical fungicide pesticide, is widely used in agricultural production. The presence of thiram residues is not only due to over-utilization, but is also primarily attributed to long-term accumulation. However, there is a paucity of information regarding the impact of prolonged utilization of thiram at low doses on the gut microbiota, particularly with respect to gut fungi. Our objective is to explore the effect of thiram on broilers from the perspective of gut microbiota, which includes both bacteria and fungi. We developed a long-term low-dose thiram model to simulate thiram residue and employed 16 S rRNA and ITS gene sequencing to investigate the diversity and profile of gut microbiota between group CC (normal diet) and TC (normal diet supplemented with 5 mg/kg thiram). The results revealed that low doses of thiram had a detrimental effect on broiler's growth performance, resulting in an approximate reduction of 669.33 g in their final body weight at day 45. Our findings indicated that low-dose thiram had a negative impact on the gut bacterial composition, leading to a notable reduction in the abundance of Merdibacter, Paenibacillus, Macrococcus, Fournierella, and Anaeroplasma (p < 0.05) compared to the CC group. Conversely, the relative level of Myroides was significantly increased (p < 0.05) in response to thiram exposure. In gut fungi, thiram significantly enhanced the diversity and richness of gut fungal populations (p < 0.05), as evidenced by the notable increase in alpha indices, i.e. ACE (CC: 346.49 ± 117.27 vs TC: 787.27 ± 379.14, p < 0.05), Chao 1 (CC: 317.63 ± 69.13 vs TC: 504.85 ± 104.50, p < 0.05), Shannon (CC: 1.28 ± 1.19 vs TC: 5.39 ± 2.66, p < 0.05), Simpson (CC: 0.21 ± 0.21 vs TC: 0.78 ± 0.34, p < 0.05). Furthermore, the abundance of Ascomycota, Kickxellomycota, and Glomeromycota were significantly increased (p < 0.05) by exposure to thiram, conversely, the level of Basidiomycota was decreased (p < 0.05) in the TC group compared to the CC group. Overall, this study demonstrated that low doses of thiram induced significant changes in the composition and abundance of gut microbiota in broilers, with more pronounced changes observed in the gut fungal community as compared to the gut bacterial community. Importantly, our findings further emphasize the potential risks associated with low dose thiram exposure and have revealed a novel discovery indicating that significant alterations in gut fungi may serve as the crucial factor contributing to the detrimental effects exerted by thiram residues.
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Affiliation(s)
- Lei Wang
- Hubei Three Gorges Polytechnic, Yichang 443000, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430000, China
| | - Fazul Nabi
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China
| | - Weixue Yi
- Hubei Three Gorges Polytechnic, Yichang 443000, China
| | - Dongjing Wang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Autonomous Region Academy of Agriculture and Animal Science, Lasa 850009, China
| | - Ying Zhu
- Animal Husbandry Station of Bijie City, Bijie 551700, China
| | - Xiong Jiang
- Hubei Three Gorges Polytechnic, Yichang 443000, China.
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Liu X, Wang A, Zhu L, Guo W, Guo X, Zhu B, Yang M. Effect of additive cellulase on fermentation quality of whole-plant corn silage ensiling by a Bacillus inoculant and dynamic microbial community analysis. Front Microbiol 2024; 14:1330538. [PMID: 38264477 PMCID: PMC10803609 DOI: 10.3389/fmicb.2023.1330538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
Whole-plant corn silage (WPCS) has been widely used as the main roughage for ruminant, which promoted the utilization of corn stover for animal feed production. However, rigid cell wall structure of corn stover limits the fiber digestion and nutrients adsorption of WPCS. This study investigated the effect of adding cellulase on improving the fermentation quality of WPCS ensiling with a Bacillus complex inoculant. With the Bacillus (BA), the lactic acid accumulation in the WPCS was significantly higher than that in control (CK). The additive cellulase (BC) increased the lactic acid content to the highest of 8.2% DW at 60 days, which was significantly higher than that in the CK and BA groups, and it reduced the neutral detergent fiber (NDF) and acid detergent fiber (ADF) contents from 42.5 to 31.7% DW and 28.4 to 20.3% DW, respectively, which were significantly lower than that in the CK and BA groups. The crude protein and starch were not obviously lost. Dynamic microbial community analysis showed that the Bacillus inoculant promoted the lactic acid bacteria (LAB) fermentation, because higher abundance of Lactobacillus as the dominant bacteria was observed in BA group. Although the addition of cellulase slowed the Lactobacillus fermentation, it increased the bacterial community, where potential lignocellulolytic microorganisms and more functional enzymes were observed, thus leading to the significant degradation of NDF and ADF. The results revealed the mechanism behind the degradation of NDF and ADF in corn stover, and also suggested the potential of cellulase for improving the nutritional quality of WPCS.
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Affiliation(s)
- Xudong Liu
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Aifang Wang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Liqi Zhu
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Wei Guo
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Engineering Research Center for Agricultural Waste Resource Utilization, Baoding, China
| | - Xiaojun Guo
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Engineering Research Center for Agricultural Waste Resource Utilization, Baoding, China
| | - Baocheng Zhu
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Engineering Research Center for Agricultural Waste Resource Utilization, Baoding, China
| | - Ming Yang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Engineering Research Center for Agricultural Waste Resource Utilization, Baoding, China
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39
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Chen E, Yang C, Tao W, Li S. Polysaccharides Produced by Plant Growth-Promoting Rhizobacteria Strain Burkholderia sp. BK01 Enhance Salt Stress Tolerance to Arabidopsis thaliana. Polymers (Basel) 2024; 16:145. [PMID: 38201810 PMCID: PMC10780357 DOI: 10.3390/polym16010145] [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: 11/16/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Salt stress is one of the most serious abiotic stresses leading to reduced agricultural productivity. Polysaccharides from seaweed have been used as biostimulants to promote crop growth and improve plant resistance to abiotic stress. In this study, PGPR strain Burkholderia sp. BK01 was isolated from the rhizosphere of wheat, and it was characterized for phosphorus (Pi) dissolution, indole-3-acetic acid (IAA) production, ammonia (NH3) and exopolysaccharides (EPS). In particular, strain BK01 can efficiently produce extracellular polysaccharide with a yield of 12.86 g/L, using sorbitol as carbon source. BK01 EPS was identified as an heteropolysaccharide with Mw 3.559 × 106 Da, composed of (D)-galactose (75.3%), (D)-glucose (5.5%), (L)-rhamnose (5.5%), (D)-galactouronic acid (4.9%) and (D)-glucuronic acid (8.8%). The present work aims to highlight the effect of the BK01 EPS on growth and biochemical changes in Arabidopsis thaliana under salt stress (100 mM). The purified BK01 EPS at a concentration of 100 mg/L efficiently promoted the growth of plants in pot assays, improved the chlorophyll content, enhanced the activities of SOD, POD and CAT, and decreased the content of MDA. This results suggested that the polysaccharides produced by PGPR strain Burkholderia sp. BK01 can be used as biostimulants to promote plant growth and improve plant resistance to salt stress.
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Affiliation(s)
- Enni Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; (E.C.); (C.Y.)
| | - Changsheng Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; (E.C.); (C.Y.)
| | - Weiyi Tao
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China;
| | - Shuang Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; (E.C.); (C.Y.)
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40
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Sliti A, Singh V, Ibal JC, Jeong M, Shin JH. Impact of propiconazole fungicide on soil microbiome (bacterial and fungal) diversity, functional profile, and associated dehydrogenase activity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:8240-8253. [PMID: 38175519 DOI: 10.1007/s11356-023-31643-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024]
Abstract
Pesticides, protect crops but can harm the environment and human health when used without caution. This study evaluated the impact of propiconazole, a fungicide that acts on fungal cell membranes, on soil microbiome abundance, diversity, and functional profile, as well as soil dehydrogenase activity (DHA). The study conducted microcosm experiments using soil samples treated with propiconazole and employed next-generation sequencing (MiSeq) and chromatographic approaches (GC-MS/MS) to analyze the shift in microbial communities and propiconazole level, respectively. The results showed that propiconazole significantly altered the distribution of microbial communities, with notable changes in the abundance of various bacterial and fungal taxa. Among soil bacterial communities, the relative abundance of Proteobacteria and Planctomycetota increased, while that of Acidobacteria decreased after propiconazole treatment. In the fungal communities, propiconazole increased the abundance of Ascomycota and Basidiomycota in the treated soil, while that of Mortierellomycota was reduced. Fungicide application further triggered a significant decrease in DHA over time. Analysis of the functional profile of bacterial communities showed that propiconazole significantly affected bacterial cellular and metabolic pathways. The carbon degradation pathway was upregulated, indicating the microbial detoxification of the contaminant in the treated soil. Our findings suggest that propiconazole application has a discernible impact on soil microbial communities, which could have long-term consequences for soil health, quality, and function.
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Affiliation(s)
- Amani Sliti
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Vineet Singh
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jerald Conrad Ibal
- Department of Biological Sciences, Idaho State University, Pocatello, ID, 83209, USA
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
- NGS Core Facility, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Department of Integrative Biotechnology, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Ma S, Shen Y, Ding J, Cheng H, Zhou H, Ge M, Wang J, Cheng Q, Zhang D, Zhang Y, Xu P, Zhang P. Effects of biochar and volcanic rock addition on humification and microbial community during aerobic composting of cow manure. BIORESOURCE TECHNOLOGY 2024; 391:129973. [PMID: 37931759 DOI: 10.1016/j.biortech.2023.129973] [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: 08/06/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]
Abstract
Additives are important for accelerating humification during aerobic composting. The impacts of porous additives biochar and volcanic rock on the physicochemical parameters, maturity indicators, microbial communities, and bacterial functional metabolism during the aerobic composting of cow manure were investigated in this study. The results showed that the biochar addition decreased the E4/E6 value by 10.42% and increased the abundance of Geobacillus (1.69 times), and volcanic rock addition decreased the E4/E6 value by 11.31% and increased the abundance of Thermobacillus (1.29 times) and Paenibacillus (1.72 times). The network analysis demonstrated that biochar promoted maturity by reducing the abundance of Pseudomonas and increasing the abundance of genes related to the metabolism of other amino acids, while volcanic rock promoted maturity by reducing the abundance of genes related to nucleotide metabolism. These results provided data and theoretical justification for the selection of porous additives for composting.
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Affiliation(s)
- Shuangshuang Ma
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China; Key Laboratory of Technologies and Models for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Yujun Shen
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China; Key Laboratory of Technologies and Models for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Jingtao Ding
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China; Key Laboratory of Technologies and Models for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Hongsheng Cheng
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China; Key Laboratory of Technologies and Models for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Haibin Zhou
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China; Key Laboratory of Technologies and Models for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China.
| | - Mianshen Ge
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China; Key Laboratory of Technologies and Models for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Jian Wang
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China; Key Laboratory of Technologies and Models for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Qiongyi Cheng
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China; Key Laboratory of Technologies and Models for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Dongli Zhang
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China; Key Laboratory of Technologies and Models for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Yun Zhang
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China; Key Laboratory of Technologies and Models for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Pengxiang Xu
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China; Key Laboratory of Technologies and Models for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Pengyue Zhang
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China; Key Laboratory of Technologies and Models for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
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Firincă C, Zamfir LG, Constantin M, Răut I, Capră L, Popa D, Jinga ML, Baroi AM, Fierăscu RC, Corneli NO, Postolache C, Doni M, Gurban AM, Jecu L, Șesan TE. Microbial Removal of Heavy Metals from Contaminated Environments Using Metal-Resistant Indigenous Strains. J Xenobiot 2023; 14:51-78. [PMID: 38249101 PMCID: PMC10801475 DOI: 10.3390/jox14010004] [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: 11/15/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024] Open
Abstract
Contamination of soil with heavy metals has become a matter of global importance due to its impact on agriculture, environmental integrity, and therefore human health and safety. Several microbial strains isolated from soil contaminated by long-term chemical and petrochemical activities were found to manifest various levels of tolerance to Cr, Pb, and Zn, out of which Bacillus marisflavi and Trichoderma longibrachiatum exhibited above-moderate tolerance. The concentrations of target heavy metals before and after bioremediation were determined using electrochemical screen-printed electrodes (SPE) modified with different nanomaterials. The morpho-structural SEM/EDX analyses confirmed the presence of metal ions on the surface of the cell, with metal uptake being mediated by biosorption with hydroxyl, carboxyl, and amino groups as per FTIR observations. T. longibrachiatum was observed to pose a higher bioremediation potential compared to B. marisflavi, removing 87% of Cr and 67% of Zn, respectively. Conversely, B. marisflavi removed 86% of Pb from the solution, compared to 48% by T. longibrachiatum. Therefore, the fungal strain T. longibrachiatum could represent a viable option for Cr and Zn bioremediation strategies, whereas the bacterial strain B. marisflavi may be used in Pb bioremediation applications.
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Affiliation(s)
- Cristina Firincă
- Biotechnology and Bioanalysis Departments, National Institute of Research and Development in Chemistry and Petrochemistry—ICECHIM, 202 Spl. Independenței, 060021 Bucharest, Romania; (C.F.); (M.D.)
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 91–95 Spl. Independenței, 050095 Bucharest, Romania
| | - Lucian-Gabriel Zamfir
- Biotechnology and Bioanalysis Departments, National Institute of Research and Development in Chemistry and Petrochemistry—ICECHIM, 202 Spl. Independenței, 060021 Bucharest, Romania; (C.F.); (M.D.)
| | - Mariana Constantin
- Biotechnology and Bioanalysis Departments, National Institute of Research and Development in Chemistry and Petrochemistry—ICECHIM, 202 Spl. Independenței, 060021 Bucharest, Romania; (C.F.); (M.D.)
- Department of Pharmacy, Faculty of Pharmacy, University Titu Maiorescu of Bucharest, 040441 Bucharest, Romania
| | - Iuliana Răut
- Biotechnology and Bioanalysis Departments, National Institute of Research and Development in Chemistry and Petrochemistry—ICECHIM, 202 Spl. Independenței, 060021 Bucharest, Romania; (C.F.); (M.D.)
| | - Luiza Capră
- Biotechnology and Bioanalysis Departments, National Institute of Research and Development in Chemistry and Petrochemistry—ICECHIM, 202 Spl. Independenței, 060021 Bucharest, Romania; (C.F.); (M.D.)
| | - Diana Popa
- Biotechnology and Bioanalysis Departments, National Institute of Research and Development in Chemistry and Petrochemistry—ICECHIM, 202 Spl. Independenței, 060021 Bucharest, Romania; (C.F.); (M.D.)
| | - Maria-Lorena Jinga
- Biotechnology and Bioanalysis Departments, National Institute of Research and Development in Chemistry and Petrochemistry—ICECHIM, 202 Spl. Independenței, 060021 Bucharest, Romania; (C.F.); (M.D.)
| | - Anda Maria Baroi
- Biotechnology and Bioanalysis Departments, National Institute of Research and Development in Chemistry and Petrochemistry—ICECHIM, 202 Spl. Independenței, 060021 Bucharest, Romania; (C.F.); (M.D.)
| | - Radu Claudiu Fierăscu
- Biotechnology and Bioanalysis Departments, National Institute of Research and Development in Chemistry and Petrochemistry—ICECHIM, 202 Spl. Independenței, 060021 Bucharest, Romania; (C.F.); (M.D.)
| | - Nicoleta Olguța Corneli
- National Institute of Research and Development for Microbiology and Immunology—Cantacuzino, 103 Spl. Independenței, 050096 Bucharest, Romania
| | - Carmen Postolache
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 91–95 Spl. Independenței, 050095 Bucharest, Romania
| | - Mihaela Doni
- Biotechnology and Bioanalysis Departments, National Institute of Research and Development in Chemistry and Petrochemistry—ICECHIM, 202 Spl. Independenței, 060021 Bucharest, Romania; (C.F.); (M.D.)
| | - Ana-Maria Gurban
- Biotechnology and Bioanalysis Departments, National Institute of Research and Development in Chemistry and Petrochemistry—ICECHIM, 202 Spl. Independenței, 060021 Bucharest, Romania; (C.F.); (M.D.)
| | - Luiza Jecu
- Biotechnology and Bioanalysis Departments, National Institute of Research and Development in Chemistry and Petrochemistry—ICECHIM, 202 Spl. Independenței, 060021 Bucharest, Romania; (C.F.); (M.D.)
| | - Tatiana Eugenia Șesan
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 91–95 Spl. Independenței, 050095 Bucharest, Romania
- Field Crop Section, Academy of Agricultural and Forestry Sciences, Bd Mărăști 61, 011464 Bucharest, Romania
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Erhunmwunse AS, Guerra VA, Liu JC, Mackowiak CL, Blount ARS, Dubeux JCB, Liao HL. Soil Bacterial Diversity Responds to Long-Term Establishment of Perennial Legumes in Warm-Season Grassland at Two Soil Depths. Microorganisms 2023; 11:3002. [PMID: 38138146 PMCID: PMC10745480 DOI: 10.3390/microorganisms11123002] [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: 10/31/2023] [Revised: 11/24/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
The introduction of rhizoma peanut (RP Arachis glabrata Benth) into bahiagrass (Paspalum notatum Flüggé) may require time to develop stable plant-soil microbe interactions as the microbial legacy of the previous plant community may be long-lasting. A previous study showed that <2 years of introducing rhizoma peanut into bahiagrass pastures minimally affected soil bacterial diversity and community composition. In this study, we compared the effects of the long-term inclusion of rhizoma peanut (>8 years) into bahiagrass on soil bacterial diversity and community composition against their monocultures at 0 to 15 and 15 to 30 cm soil depths using next-generation sequencing to target bacterial 16S V3-V4 regions. We observed that a well-established RP-bahiagrass mixed stand led to a 36% increase in bacterial alpha diversity compared to the bahiagrass monoculture. There was a shift from a soil bacterial community dominated by Proteobacteria (~26%) reported in other bahiagrass and rhizoma peanut studies to a soil bacterial community dominated by Firmicutes (39%) in our study. The relative abundance of the bacterial genus Crossiella, known for its antimicrobial traits, was enhanced in the presence of RP. Differences in soil bacterial diversity and community composition were substantial between 0 to 15 and 15 to 30 cm soil layers, with N2-fixing bacteria belonging to the phylum Proteobacteria concentrated in 0 to 15 cm. Introducing RP into bahiagrass pastures is a highly sustainable alternative to mineral N fertilizer inputs. Our results provide evidence that this system also promotes greater soil microbial diversity and is associated with unique taxa that require further study to better understand their contributions to healthy pastures.
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Affiliation(s)
- Adesuwa Sylvia Erhunmwunse
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Victor Alonso Guerra
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Jung-Chen Liu
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Cheryl L. Mackowiak
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Ann Rachel Soffes Blount
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
| | - José Carlos Batista Dubeux
- North Florida Research and Education Center, University of Florida, 3925 Highway 71, Marianna, FL 32446, USA;
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
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Cismasiu RS, Birlutiu RM, Preoțescu LL. Uncommon Septic Arthritis of the Hip Joint in an Immunocompetent Adult Patient Due to Bacillus pumilus and Paenibacillus barengoltzii Managed with Long-Term Treatment with Linezolid: A Case Report and Short Literature Review. Pharmaceuticals (Basel) 2023; 16:1743. [PMID: 38139869 PMCID: PMC10747381 DOI: 10.3390/ph16121743] [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: 11/29/2023] [Revised: 12/07/2023] [Accepted: 12/17/2023] [Indexed: 12/24/2023] Open
Abstract
The Bacillus and Paenibacillus genera are diverse soil-related bacterial pathogens. In this case report, we describe, to our knowledge, the first report of septic arthritis in a native hip joint in an immunocompetent adult patient caused by Bacillus pumilus and Paenibacillus barengoltzii. We describe the case of a 39-year-old Caucasian male patient who sought medical advice for chronic pain on the mobilization of the right hip, decreased range of motion, and physical asthenia. The patient underwent a surgical intervention (core decompression) for a right osteonecrosis of the femoral head, with a slightly favorable postoperative evolution after surgery for one month. Surgical treatment was planned on the basis of clinical and paraclinical investigations and the joint damage. The hip was explored using an anterior approach under spinal anesthesia and standard antibiotic prophylaxis. After resection of the femoral head, meticulous debridement of all inflammatory tissues was performed, and a preformed temporary spacer was inserted into the femoral canal. Bacteriological laboratory studies identified Bacillus pumilus and Paenibacillus barengoltzii via matrix-assisted laser desorption-ionization time-of-flight mass spectrometry analysis. The patient initially received nine days of empirical therapy with intravenous antibiotics (linezolid and meropenem). After the bacterial strains were identified, the patient received organism-specific antibiotic therapy with the same antibiotics and dose for eight days until discharge. After discharge, the patient was referred to another hospital, where he continued treatment with linezolid for seven weeks and, after that, four weeks of oral therapy with cotrimoxazole and rifampicin. During this period, no severe or potentially life-threatening adverse events were recorded during long-term treatment with linezolid or with the two oral antibiotics. In conclusion, our findings suggest that long-term treatment with linezolid may be a viable option for the management of bone and joint infections caused by Bacillus pumilus and Paenibacillus barengoltzii.
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Affiliation(s)
- Razvan Silviu Cismasiu
- Clinical Hospital of Orthopedics, Traumatology, and Osteoarticular TB Bucharest, B-dul Ferdinand 35-37, Sector 2, 021382 Bucharest, Romania;
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, 050474 Bucharest, Romania;
| | - Rares-Mircea Birlutiu
- Clinical Hospital of Orthopedics, Traumatology, and Osteoarticular TB Bucharest, B-dul Ferdinand 35-37, Sector 2, 021382 Bucharest, Romania;
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, 050474 Bucharest, Romania;
| | - Liliana Lucia Preoțescu
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, 050474 Bucharest, Romania;
- National Institute for Infectious Diseases “Prof. Dr. Matei Bals”, 021105 Bucharest, Romania
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45
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Yuan P, Chen Z, Xu M, Cai W, Liu Z, Sun D. Microbial cell factories using Paenibacillus: status and perspectives. Crit Rev Biotechnol 2023:1-17. [PMID: 38105503 DOI: 10.1080/07388551.2023.2289342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/22/2023] [Indexed: 12/19/2023]
Abstract
Considered a "Generally Recognized As Safe" (GRAS) bacterium, the plant growth-promoting rhizobacterium Paenibacillus has been widely applied in: agriculture, medicine, industry, and environmental remediation. Paenibacillus species not only accelerate plant growth and degrade toxic substances in wastewater and soil but also produce industrially-relevant enzymes and antimicrobial peptides. Due to a lack of genetic manipulation tools and methods, exploitation of the bioresources of naturally isolated Paenibacillus species has long been limited. Genetic manipulation tools and methods continue to improve in Paenibacillus, such as shuttle plasmids, promoters, and genetic tools of CRISPR. Furthermore, genetic transformation systems develop gradually, including: penicillin-mediated transformation, electroporation, and magnesium amino acid-mediated transformation. As genetic manipulation methods of homologous recombination and CRISPR-mediated editing system have developed gradually, Paenibacillus has come to be regarded as a promising microbial chassis for biomanufacturing, expanding its application scope, such as: industrial enzymes, bioremediation and bioadsorption, surfactants, and antibacterial agents. In this review, we describe the applications of Paenibacillus bioproducts, and then discuss recent advances and future challenges in the development of genetic manipulation systems in this genus. This work highlights the potential of Paenibacillus as a new microbial chassis for mining bioresources.
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Affiliation(s)
- Panhong Yuan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Ziyan Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Mengtao Xu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Wenfeng Cai
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Zhizhi Liu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
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Venkatachalam J, Mohan H, Seralathan KK. Significance of Herbaspirillum sp. in biodegradation and biodetoxification of herbicides, pesticides, hydrocarbons and heavy metals - A review. ENVIRONMENTAL RESEARCH 2023; 239:117367. [PMID: 37827364 DOI: 10.1016/j.envres.2023.117367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
In today's industrialized world, contamination of soil and water with various substances has emerged as a pressing concern. Bioremediation, with its advantages of degradation or detoxification, non-polluting nature, and cost-effectiveness, has become a promising method due to technological advancements. Among the bioremediation agents, bacteria have been highly explored and documented as a productive organism. Recently, few studies have reported on the significance of Herbaspirillum sp., a Gram-negative bacterium, in bioremediating herbicides, pesticides, polycyclic aromatic hydrocarbons, metalloids, and heavy metals, as well as its role in augmenting phytoremediation efforts. Herbaspirillum sp. GW103 leached 66% of Cu from ore materials and significantly enhanced the phytoaccumulation of Pb and Zn in plumule and radical tissues of Zea mays L. plants. Additionally, Herbaspirillum sp. WT00C reduced Se6+ into Se0, resulting in an increased Se0 content in tea plants. Also, Herbaspirillum sp. proved effective in degrading 0.6 mM of 4-chlorophenol, 92.8% of pyrene, 77.4% of fluoranthene, and 16.4% of trifluralin from aqueous solution and soil-water system. Considering these findings, this review underscores the need for further exploration into the pathways of pollutant degradation, the enzymes pivotal in the degradation or detoxification processes, the influence of abiotic factors and pollutants on crucial gene expression, and the potential toxicity of intermediate products generated during the degradation process. This perspective reframes the numerical data to underscore the underutilized potential of Herbaspirillum sp. within the broader context of addressing a significant research gap. This shift in emphasis aligns more closely with the problem-necessity for solution-existing unexplored solution framework.
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Affiliation(s)
- Janaki Venkatachalam
- PG and Research Department of Chemistry, Sri Sarada College for Women, Salem, 636016, Tamil Nadu, India
| | - Harshavardhan Mohan
- Division of Biotechnology, Advanced Institute of Environment and Bioscience, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan, 54596, South Korea
| | - Kamala-Kannan Seralathan
- Division of Biotechnology, Advanced Institute of Environment and Bioscience, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan, 54596, South Korea.
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Gao Y, Zhao Y, Li P, Qi X. Responses of the maize rhizosphere soil environment to drought-flood abrupt alternation stress. Front Microbiol 2023; 14:1295376. [PMID: 38170081 PMCID: PMC10760638 DOI: 10.3389/fmicb.2023.1295376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
Changes in the soil environment in the root zone will affect the growth, development and resistance of plants. The mechanism underlying the effect of drought and flood stress on rhizosphere bacterial diversity, soil metabolites and soil enzyme activity is not clear and needs further study. To analyze the dynamic changes in bacteria, metabolites and enzyme activities in the rhizosphere soil of maize under different drought-flood abrupt alternation (DFAA) stresses, the barrel test method was used to set up the 'sporadic light rain' to flooding (referring to trace rainfall to heavy rain) (DFAA1) group, 'continuous drought' to flooding (DFAA2) group and normal irrigation (CK) group from the jointing to the tassel flowering stage of maize. The results showed that Actinobacteria was the most dominant phylum in the two DFAA groups during the drought period and the rewatering period, and Proteobacteria was the most dominant phylum during the flooding period and the harvest period. The alpha diversity index of rhizosphere bacteria in the DFAA2 group during the flooding period was significantly lower than that in other stages, and the relative abundance of Chloroflexi was higher. The correlation analysis between the differential genera and soil metabolites of the two DFAA groups showed that the relative abundance of Paenibacillus in the DFAA1 group was higher during the drought period, and it was significantly positively correlated with the bioactive lipid metabolites. The differential SJA-15 bacterium was enriched in the DFAA2 group during the flooding period and were strongly correlated with biogenic amine metabolites. The relative abundances of Arthrobacter, Alphaproteobacteria and Brevibacillus in the DFAA2 group were higher compared with DFAA1 group from rewatering to harvest and were significantly positively correlated with hydrocarbon compounds and steroid hormone metabolites. The acid phosphatase activity of the DFAA1 group was significantly higher than that of the DFAA2 group during the flooding period. The study suggests that there is a yield compensation phenomenon in the conversion of 'continuous drought' to flooding compared with 'sporadic light rain', which is related to the improvement in the flooding tolerance of maize by the dominant bacteria Chloroflexi, bacterium SJA-15 and biogenic amine metabolites. These rhizosphere bacteria and soil metabolites may have the potential function of helping plants adapt to the DFAA environment. The study revealed the response of the maize rhizosphere soil environment to DFAA stress and provided new ideas for exploring the potential mechanism of crop yield compensation under DFAA.
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Affiliation(s)
| | - Yulong Zhao
- Farmland Irrigation Research Institute of CAAS, Xinxiang, China
| | | | - Xuebin Qi
- Farmland Irrigation Research Institute of CAAS, Xinxiang, China
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Weigh KV, Batista BD, Hoang H, Dennis PG. Characterisation of Soil Bacterial Communities That Exhibit Chemotaxis to Root Exudates from Phosphorus-Limited Plants. Microorganisms 2023; 11:2984. [PMID: 38138128 PMCID: PMC10745596 DOI: 10.3390/microorganisms11122984] [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: 11/24/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
The ability to sense and direct movement along chemical gradients is known as 'chemotaxis' and is a common trait among rhizosphere microorganisms, which are attracted to organic compounds released from plant roots. In response to stress, the compounds released from roots can change and may recruit symbionts that enhance host stress tolerance. Decoding this language of attraction could support the development of microbiome management strategies that would enhance agricultural production and sustainability. In this study, we employ a culture-independent bait-trap chemotaxis assay to capture microbial communities attracted to root exudates from phosphorus (P)-sufficient and P-deficient Arabidopsis thaliana Col-0 plants. The captured populations were then enumerated and characterised using flow cytometry and phylogenetic marker gene sequencing, respectively. Exudates attracted significantly more cells than the control but did not differ between P treatments. Relative to exudates from P-sufficient plants, those collected from P-deficient plants attracted a significantly less diverse bacterial community that was dominated by members of the Paenibacillus, which is a genus known to include powerful phosphate solubilisers and plant growth promoters. These results suggest that in response to P deficiency, Arabidopsis exudates attract organisms that could help to alleviate nutrient stress.
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Affiliation(s)
| | | | | | - Paul G. Dennis
- School of the Environment, The University of Queensland, Brisbane, QLD 4072, Australia (B.D.B.)
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49
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Shankar N, Shetty P, Melo TC, Kesseli R. Multi-Generation Ecosystem Selection of Rhizosphere Microbial Communities Associated with Plant Genotype and Biomass in Arabidopsis thaliana. Microorganisms 2023; 11:2932. [PMID: 38138075 PMCID: PMC10745315 DOI: 10.3390/microorganisms11122932] [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: 11/02/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
The role of the microbiome in shaping the host's phenotype has emerged as a critical area of investigation, with implications in ecology, evolution, and host health. The complex and dynamic interactions involving plants and their diverse rhizospheres' microbial communities are influenced by a multitude of factors, including but not limited to soil type, environment, and plant genotype. Understanding the impact of these factors on microbial community assembly is key to yielding host-specific and robust benefits for plants, yet it remains challenging. Here, we conducted an artificial ecosystem selection experiment for eight generations of Arabidopsis thaliana Ler and Cvi to select soil microbiomes associated with a higher or lower biomass of the host. This resulted in divergent microbial communities shaped by a complex interplay between random environmental variations, plant genotypes, and biomass selection pressures. In the initial phases of the experiment, the genotype and the biomass selection treatment had modest but significant impacts. Over time, the plant genotype and biomass treatments gained more influence, explaining ~40% of the variation in the microbial community's composition. Furthermore, a genotype-specific association of plant-growth-promoting rhizobacterial taxa, Labraceae with Ler and Rhizobiaceae with Cvi, was observed under selection for high biomass.
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Affiliation(s)
- Nachiket Shankar
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA (R.K.)
| | - Prateek Shetty
- Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary;
| | - Tatiana C. Melo
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA (R.K.)
| | - Rick Kesseli
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA (R.K.)
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Yang X, Tan AJ, Zheng MM, Feng D, Mao K, Yang GL. Physiological response, microbial diversity characterization, and endophytic bacteria isolation of duckweed under cadmium stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166056. [PMID: 37558073 DOI: 10.1016/j.scitotenv.2023.166056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/17/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
Duckweed is a cadmium (Cd) hyperaccumulator. However, its enrichment characteristics and physiological responses to Cd have not been systematically studied. The physiological responses, enrichment characteristics, diversity of endophytic bacterial communities, and isolation of Cd-resistant endophytes in duckweed (Lemna minor 0014) were studied for different durations and Cd concentrations. The results indicated that peroxidase (POD) and catalase (CAT) activities decreased while superoxide dismutase activity first increased and then decreased with increasing Cd stress duration. POD activities, CAT activities, and O2- increased as Cd concentrations increased. Malondialdehyde content and Cd accumulation in duckweed increased with increasing concentrations and time. This endophytic diversity study identified 488 operational taxonomic units, with the dominant groups being Proteobacteria, Firmicutes, and Actinobacteria. Paenibacillus sp. Y11, a strain tolerant to high concentrations of Cd and capable of significantly promoting duckweed growth, was isolated from the plant. Our study revealed the effects of heavy metals on aquatic plants, providing a theoretical basis for the application of duckweed in water pollution.
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Affiliation(s)
- Xiao Yang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Ai-Juan Tan
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Meng-Meng Zheng
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Dan Feng
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Kang Mao
- Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, Guizhou Province, China
| | - Gui-Li Yang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China; Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, Guizhou Province, China.
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