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Jagadesh M, Dash M, Kumari A, Singh SK, Verma KK, Kumar P, Bhatt R, Sharma SK. Revealing the hidden world of soil microbes: Metagenomic insights into plant, bacteria, and fungi interactions for sustainable agriculture and ecosystem restoration. Microbiol Res 2024; 285:127764. [PMID: 38805978 DOI: 10.1016/j.micres.2024.127764] [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: 11/30/2023] [Revised: 03/10/2024] [Accepted: 05/11/2024] [Indexed: 05/30/2024]
Abstract
The future of agriculture is questionable under the current climate change scenario. Climate change and climate-related calamities directly influence biotic and abiotic factors that control agroecosystems, endangering the safety of the world's food supply. The intricate interactions between soil microorganisms, including plants, bacteria, and fungi, play a pivotal role in promoting sustainable agriculture and ecosystem restoration. Soil microbes play a major part in nutrient cycling, including soil organic carbon (SOC), and play a pivotal function in the emission and depletion of greenhouse gases, including CH4, CO2, and N2O, which can impact the climate. At this juncture, developing a triumphant metagenomics approach has greatly increased our knowledge of the makeup, functionality, and dynamics of the soil microbiome. Currently, the involvement of plants in climate change indicates that they can interact with the microbial communities in their environment to relieve various stresses through the innate microbiome assortment of focused strains, a phenomenon dubbed "Cry for Help." The metagenomics method has lately appeared as a new platform to adjust and encourage beneficial communications between plants and microbes and improve plant fitness. The metagenomics of soil microbes can provide a powerful tool for designing and evaluating ecosystem restoration strategies that promote sustainable agriculture under a changing climate. By identifying the specific functions and activities of soil microbes, we can develop restoration programs that support these critical components of healthy ecosystems while providing economic benefits through ecosystem services. In the current review, we highlight the innate functions of microbiomes to maintain the sustainability of agriculture and ecosystem restoration. Through this insight study of soil microbe metagenomics, we pave the way for innovative strategies to address the pressing challenges of food security and environmental conservation. The present article elucidates the mechanisms through which plants and microbes communicate to enhance plant resilience and ecosystem restoration and to leverage metagenomics to identify and promote beneficial plant-microbe interactions. Key findings reveal that soil microbes are pivotal in nutrient cycling, greenhouse gas modulation, and overall ecosystem health, offering novel insights into designing ecosystem restoration strategies that bolster sustainable agriculture. As this is a topic many are grappling with, hope these musings will provide people alike with some food for thought.
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Affiliation(s)
- M Jagadesh
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Munmun Dash
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Aradhna Kumari
- College of Agriculture, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Ganj Basoda, Vidisha, Madhya Pradesh, India.
| | - Santosh Kumar Singh
- Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, India.
| | - Krishan K Verma
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi 530007, China.
| | - Prasann Kumar
- Department of Agronomy, School of Agriculture, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Rajan Bhatt
- Krishi Vigyan Kendra, Amritsar, Punjab Agricultural University (PAU), Ludhiana, Punjab 144601, India
| | - Satish Kumar Sharma
- College of Agriculture, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Ganj Basoda, Vidisha, Madhya Pradesh, India
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Bing H, Qi C, Gu J, Zhao T, Yu X, Cai Y, Zhang Y, Li A, Wang X, Zhao J, Xiang W. Isolation and identification of NEAU-CP5: A seed-endophytic strain of B. velezensis that controls tomato bacterial wilt. Microb Pathog 2024; 192:106707. [PMID: 38777241 DOI: 10.1016/j.micpath.2024.106707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/29/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
Bacterial wilt of tomato caused by Ralstonia solanacearum is a critical soilborne disease that drastically reduces yield. In the current study, an endophytic strain NEAU-CP5 with strong antagonistic activity against R. solanacearum was isolated from tomato seeds and characterized. The strain was identified as Bacillus velezensis based on 16S rRNA gene and whole genome sequence analysis. NEAU-CP5 can secrete amylase, protease, and cellulase, and also produce known antibacterial metabolites, including cyclo (leucylprolyl), cyclo (phenylalanyl-prolyl), cyclo (Pro-Gly), 3-benzyl-2,5-piperazinedione, pentadecanoic acid, eicosane, 2-methyoic acid, isovaleric acid, dibuty phthalate, and esters of fatty acids (HFDU), which may be responsible for its strong antibacterial activity. Fourteen gene clusters associated with antibacterial properties were also identified in the whole genome sequence of NEAU-CP5. Pot experiment demonstrated that the application of 108 CFU/mL NEAU-CP5 on tomato plants significantly reduced the incidence of tomato bacterial wilt by 68.36 ± 1.67 %. NEAU-CP5 also increased the activity of defense-related enzymes (CAT, POD, PPO, SOD, and PAL) in tomato plants. This is the first report of an effective control of bacterial wilt on tomato plants by B. velezensis and highlights the potential of NEAU-CP5 as a potential biocontrol agent for the management of tomato bacterial wilt.
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Affiliation(s)
- Hui Bing
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Cuiping Qi
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Jinzhao Gu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Tianxin Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Xiaoyan Yu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Yang Cai
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Yance Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Ailin Li
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China.
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China.
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Williams A, Sinanaj B, Hoysted GA. Plant-microbe interactions through a lens: tales from the mycorrhizosphere. ANNALS OF BOTANY 2024; 133:399-412. [PMID: 38085925 PMCID: PMC11006548 DOI: 10.1093/aob/mcad191] [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: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 04/12/2024]
Abstract
BACKGROUND The soil microbiome plays a pivotal role in maintaining ecological balance, supporting food production, preserving water quality and safeguarding human health. Understanding the intricate dynamics within the soil microbiome necessitates unravelling complex bacterial-fungal interactions (BFIs). BFIs occur in diverse habitats, such as the phyllosphere, rhizosphere and bulk soil, where they exert substantial influence on plant-microbe associations, nutrient cycling and overall ecosystem functions. In various symbiotic associations, fungi form mycorrhizal connections with plant roots, enhancing nutrient uptake through the root and mycorrhizal pathways. Concurrently, specific soil bacteria, including mycorrhiza helper bacteria, play a pivotal role in nutrient acquisition and promoting plant growth. Chemical communication and biofilm formation further shape plant-microbial interactions, affecting plant growth, disease resistance and nutrient acquisition processes. SCOPE Promoting synergistic interactions between mycorrhizal fungi and soil microbes holds immense potential for advancing ecological knowledge and conservation. However, despite the significant progress, gaps remain in our understanding of the evolutionary significance, perception, functional traits and ecological relevance of BFIs. Here we review recent findings obtained with respect to complex microbial communities - particularly in the mycorrhizosphere - and include the latest advances in the field, outlining their profound impacts on our understanding of ecosystem dynamics and plant physiology and function. CONCLUSIONS Deepening our understanding of plant BFIs can help assess their capabilities with regard to ecological and agricultural safe-guarding, in particular buffering soil stresses, and ensuring sustainable land management practices. Preserving and enhancing soil biodiversity emerge as critical imperatives in sustaining life on Earth amidst pressures of anthropogenic climate change. A holistic approach integrates scientific knowledge on bacteria and fungi, which includes their potential to foster resilient soil ecosystems for present and future generations.
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Affiliation(s)
- Alex Williams
- Plants, Photosynthesis and Soil, School of Bioscience, University of Sheffield, Sheffield, S10 2TN, UK
| | - Besiana Sinanaj
- Plants, Photosynthesis and Soil, School of Bioscience, University of Sheffield, Sheffield, S10 2TN, UK
| | - Grace A Hoysted
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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Cantor-Vásquez S, Silva Lima CD, Alves IA, Aragón DM. Plant-based compositions for the treatment of local and topical bacterial infections: a patent review. Future Microbiol 2024; 19:535-557. [PMID: 38530361 DOI: 10.2217/fmb-2023-0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/23/2023] [Indexed: 03/27/2024] Open
Abstract
Aim: To examine recent patents related to plants with antimicrobial effects. Methods: Our investigation was carried out using the Espacenet database, searching patents related to International Patent Classification (IPC) codes A61P31/04, and A61K36/00 between 2008 and 2023. Results: The study began with 360 patents, of which 15 were found to be duplicates; 144 were not related to the research topic and six were not available. Then, 48 patents were related to other administration routes. The final selection was 47 patents related to local administration compositions. The potential for these herbal compositions to be marketed as over-the-counter medicines was evident. Conclusion: Developing new plant-origin anti-infective agents could provide promising solutions for combating resistant infections and offer accessible treatment options.
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Affiliation(s)
- Sergio Cantor-Vásquez
- Departamento de Farmacia, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Camila da Silva Lima
- Programa de pós graduação em Ciências Farmacêuticas, Universidade do Estado da Bahia, Brasil
| | | | - Diana Marcela Aragón
- Departamento de Farmacia, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
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Cuervo L, Méndez C, Olano C, Malmierca MG. Volatilome: Smells like microbial spirit. ADVANCES IN APPLIED MICROBIOLOGY 2024; 127:1-43. [PMID: 38763526 DOI: 10.1016/bs.aambs.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
In recent years, the study of volatile compounds has sparked interest due to their implications in signaling and the enormous variety of bioactive properties attributed to them. Despite the absence of analysis methods standardization, there are a multitude of tools and databases that allow the identification and quantification of volatile compounds. These compounds are chemically heterogeneous and their diverse properties are exploited by various fields such as cosmetics, the food industry, agriculture and medicine, some of which will be discussed here. In virtue of volatile compounds being ubiquitous and fast chemical messengers, these molecules mediate a large number of interspecific and intraspecific interactions, which are key at an ecological level to maintaining the balance and correct functioning of ecosystems. This review briefly summarized the role of volatile compounds in inter- and intra-specific relationships as well as industrial applications associated with the use of these compounds that is emerging as a promising field of study.
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Affiliation(s)
- Lorena Cuervo
- Functional Biology Department, University of Oviedo, Oviedo, Spain; University Institute of Oncology of Asturias, University of Oviedo, Oviedo, Spain; Health Research Institute of Asturias, Av. del Hospital Universitario, s/n, Oviedo, Spain
| | - Carmen Méndez
- Functional Biology Department, University of Oviedo, Oviedo, Spain; University Institute of Oncology of Asturias, University of Oviedo, Oviedo, Spain; Health Research Institute of Asturias, Av. del Hospital Universitario, s/n, Oviedo, Spain
| | - Carlos Olano
- Functional Biology Department, University of Oviedo, Oviedo, Spain; University Institute of Oncology of Asturias, University of Oviedo, Oviedo, Spain; Health Research Institute of Asturias, Av. del Hospital Universitario, s/n, Oviedo, Spain
| | - Mónica G Malmierca
- Functional Biology Department, University of Oviedo, Oviedo, Spain; University Institute of Oncology of Asturias, University of Oviedo, Oviedo, Spain; Health Research Institute of Asturias, Av. del Hospital Universitario, s/n, Oviedo, Spain.
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Geesink P, ter Horst J, Ettema TJG. More than the sum of its parts: uncovering emerging effects of microbial interactions in complex communities. FEMS Microbiol Ecol 2024; 100:fiae029. [PMID: 38444203 PMCID: PMC10950044 DOI: 10.1093/femsec/fiae029] [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: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024] Open
Abstract
Microbial communities are not only shaped by the diversity of microorganisms and their individual metabolic potential, but also by the vast amount of intra- and interspecies interactions that can occur pairwise interactions among microorganisms, we suggest that more attention should be drawn towards the effects on the entire microbiome that emerge from individual interactions between community members. The production of certain metabolites that can be tied to a specific microbe-microbe interaction might subsequently influence the physicochemical parameters of the habitat, stimulate a change in the trophic network of the community or create new micro-habitats through the formation of biofilms, similar to the production of antimicrobial substances which might negatively affect only one microorganism but cause a ripple effect on the abundance of other community members. Here, we argue that combining established as well as innovative laboratory and computational methods is needed to predict novel interactions and assess their secondary effects. Such efforts will enable future microbiome studies to expand our knowledge on the dynamics of complex microbial communities.
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Affiliation(s)
- Patricia Geesink
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jolanda ter Horst
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Wan Y, Zhang L, Xu Z, Su Q, Leung TF, Chan D, Wong OWH, Chan S, Chan FKL, Tun HM, Ng SC. Alterations in fecal virome and bacteriome virome interplay in children with autism spectrum disorder. Cell Rep Med 2024; 5:101409. [PMID: 38307030 PMCID: PMC10897546 DOI: 10.1016/j.xcrm.2024.101409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/10/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024]
Abstract
Emerging evidence suggests autism spectrum disorder (ASD) is associated with altered gut bacteria. However, less is known about the gut viral community and its role in shaping microbiota in neurodevelopmental disorders. Herein, we perform a metagenomic analysis of gut-DNA viruses in 60 children with ASD and 64 age- and gender-matched typically developing children to investigate the effect of the gut virome on host bacteria in children with ASD. ASD is associated with altered gut virome composition accompanied by the enrichment of Clostridium phage, Bacillus phage, and Enterobacteria phage. These ASD-enriched phages are largely associated with disrupted viral ecology in ASD. Importantly, changes in the interplay between the gut bacteriome and virome seen in ASD may influence the encoding capacity of microbial pathways for neuroactive metabolite biosynthesis. These findings suggest an impaired bacteriome-virome ecology in ASD, which sheds light on the importance of bacteriophages in pathogenesis and the development of microbial therapeutics in ASD.
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Affiliation(s)
- Yating Wan
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lin Zhang
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhilu Xu
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qi Su
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ting-Fan Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Dorothy Chan
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Oscar W H Wong
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sandra Chan
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Francis K L Chan
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hein M Tun
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; The D.H. Chen Foundation Hub of Advanced Technology for Child Health (HATCH), The Chinese University of Hong Kong, Hong Kong SAR, China.
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Diabankana RGC, Frolov M, Islamov B, Shulga E, Filimonova MN, Afordoanyi DM, Validov S. Identification and Aggressiveness of Fusarium Species Associated with Onion Bulb ( Allium cepa L.) during Storage. J Fungi (Basel) 2024; 10:161. [PMID: 38392833 PMCID: PMC10890437 DOI: 10.3390/jof10020161] [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] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/24/2024] Open
Abstract
Plant pathogens present a major challenge to crop production, leading to decreased yield and quality during growth and storage. During long-term storage, healthy onions can develop diseases from latent pathogen infections. This poses a challenge for onion growers because infected bulbs without visible symptoms can lead to significant crop losses during the growing season. In this study, we aimed to isolate and identify Fusarium species from yellow onion bulbs (Allium cepa L.) that developed disease symptoms during storage. The aggressiveness of these strains against onion bulbs and seedlings was also evaluated. The isolated strains were further subjected to morphological and molecular differentiation. The results revealed that all 16 isolated strains belonged to the Fusarium complex species incarnatum-equiseti and Fusarium fujikuroi, namely, F. proliferatum (98%), F. oxysporum (1%), and Fusarium sp. (1%). Koch's postulate analysis of isolated strains revealed varying aggressiveness on onion bulbs and plants depending on fungal species. Disease symptoms developed more slowly on plants than on onion bulb plants according to Koch's postulates. Moreover, the results revealed that Fusarium strains that can infect onion plants were less pathogenic to onion bulbs and vice versa. In addition, three isolates were found to be non-pathogenic to onions. Furthermore, the in vitro control of Fusarium species through Bacillus velezensis KS04-AU and Streptomyces albidoflavus MGMM6 showed high potential for controlling the growth of these pathogenic fungi. These results may contribute to the development of environmentally friendly approaches for controlling onion spoilage caused by pathogens during storage.
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Affiliation(s)
- Roderic Gilles Claret Diabankana
- Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of the Russian Academy of Sciences, 420111 Kazan, Russia
| | - Mikhail Frolov
- Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of the Russian Academy of Sciences, 420111 Kazan, Russia
| | - Bakhtiyar Islamov
- Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of the Russian Academy of Sciences, 420111 Kazan, Russia
| | - Elena Shulga
- Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of the Russian Academy of Sciences, 420111 Kazan, Russia
| | - Maria Nikolaevna Filimonova
- Academic and Research Centre, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Daniel Mawuena Afordoanyi
- Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of the Russian Academy of Sciences, 420111 Kazan, Russia
| | - Shamil Validov
- Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of the Russian Academy of Sciences, 420111 Kazan, Russia
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Dragičević P, Rosado D, Bielen A, Hudina S. Host-related traits influence the microbial diversity of the invasive signal crayfish Pacifastacus leniusculus. J Invertebr Pathol 2024; 202:108039. [PMID: 38097037 DOI: 10.1016/j.jip.2023.108039] [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: 08/30/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 12/22/2023]
Abstract
The microbiome influences a variety of host-environment interactions, and there is mounting evidence of its significant role in biological invasions. During invasion, shifts in microbial diversity and function can occur due to both changing characteristics of the novel environment and physiological condition of the host. The signal crayfish (Pacifastacus leniusculus) is one of the most successful crayfish invaders in Europe. During range expansion, its populations often exhibit differences in many traits along the invasion range, including sex-composition, size-structure and aggressiveness, but to date it was not studied whether crayfish traits can also drive changes in the host microbiome. Thus, we used 16S rRNA gene amplicon sequencing to examine the effects of host-related traits, namely total length (TL), body condition index (FCF), hepatosomatic index (HSI) and sex on the microbial diversity of the signal crayfish. We examined both external (exoskeletal) and internal (intestinal, hepatopancreatic, hemolymph) microbiomes of 110 signal crayfish individuals from four sites along its invasion range in the Korana River, Croatia. While sex did not exhibit a significant effect on the microbial diversity in any of the examined tissues, exoskeletal, intestinal and hemolymph microbial diversity significantly decreased with increasing crayfish size. Additionally, significant effects of signal crayfish condition (FCF, HSI) on microbial diversity were recorded in the hepatopancreas, a main energy storage organ in crayfish that supports reproduction and growth and also regulates immune response. Our findings provide a baseline for evaluating the contribution of microbiome to an invader's overall health, fitness and subsequent invasion success.
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Affiliation(s)
- Paula Dragičević
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Daniela Rosado
- S2AQUA - Collaborative Laboratory, Association for a Sustainable and Smart Aquaculture, Avenida Parque Natural da Ria Formosa s/n, 8700-194 Olhão, Portugal
| | - Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Kršnjavoga 25, Zagreb, Croatia
| | - Sandra Hudina
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia.
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Zulfiqar M, Singh V, Steinbeck C, Sorokina M. Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. Crit Rev Microbiol 2024:1-40. [PMID: 38270170 DOI: 10.1080/1040841x.2024.2306465] [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: 03/13/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Vinay Singh
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Data Science and Artificial Intelligence, Research and Development, Pharmaceuticals, Bayer, Berlin, Germany
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Reyes-Ardila WL, Rugeles-Silva PA, Duque-Zapata JD, Vélez-Martínez GA, Tarazona Pulido L, Cardona Tobar KM, Díaz Gallo SA, Muñoz Flórez JE, Díaz-Ariza LA, López-Alvarez D. Exploring Genomics and Microbial Ecology: Analysis of Bidens pilosa L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding. PLANTS (BASEL, SWITZERLAND) 2024; 13:221. [PMID: 38256774 PMCID: PMC10818919 DOI: 10.3390/plants13020221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
Bidens pilosa L., native to South America and commonly used for medicinal purposes, has been understudied at molecular and genomic levels and in its relationship with soil microorganisms. In this study, restriction site-associated DNA markers (RADseq) techniques were implemented to analyze genetic diversity and population structure, and metabarcoding to examine microbial composition in soils from Palmira, Sibundoy, and Bogotá, Colombia. A total of 2,984,123 loci and 3485 single nucleotide polymorphisms (SNPs) were identified, revealing a genetic variation of 12% between populations and 88% within individuals, and distributing the population into three main genetic groups, FST = 0.115 (p < 0.001) and FIT = 0.013 (p > 0.05). In the soil analysis, significant correlations were found between effective cation exchange capacity (ECEC) and apparent density, soil texture, and levels of Mg and Fe, as well as negative correlations between ECEC and Mg, and Mg, Fe, and Ca. Proteobacteria and Ascomycota emerged as the predominant bacterial and fungal phyla, respectively. Analyses of alpha, beta, and multifactorial diversity highlight the influence of ecological and environmental factors on these microbial communities, revealing specific patterns of clustering and association between bacteria and fungi in the studied locations.
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Affiliation(s)
- Wendy Lorena Reyes-Ardila
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, Colombia; (P.A.R.-S.); (J.D.D.-Z.); (G.A.V.-M.)
- Grupo de Investigación en Agricultura Biológica, Departamento de Biología, Pontificia Universidad Javeriana, Sede Bogotá, Bogotá D.C. 110231, Colombia;
| | - Paula Andrea Rugeles-Silva
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, Colombia; (P.A.R.-S.); (J.D.D.-Z.); (G.A.V.-M.)
- Grupo de Investigación en Agricultura Biológica, Departamento de Biología, Pontificia Universidad Javeriana, Sede Bogotá, Bogotá D.C. 110231, Colombia;
| | - Juan Diego Duque-Zapata
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, Colombia; (P.A.R.-S.); (J.D.D.-Z.); (G.A.V.-M.)
- Grupo de Investigación en Agricultura Biológica, Departamento de Biología, Pontificia Universidad Javeriana, Sede Bogotá, Bogotá D.C. 110231, Colombia;
| | - Glever Alexander Vélez-Martínez
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, Colombia; (P.A.R.-S.); (J.D.D.-Z.); (G.A.V.-M.)
- Grupo de Investigación en Agricultura Biológica, Departamento de Biología, Pontificia Universidad Javeriana, Sede Bogotá, Bogotá D.C. 110231, Colombia;
| | - Lina Tarazona Pulido
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, Colombia; (P.A.R.-S.); (J.D.D.-Z.); (G.A.V.-M.)
- Grupo de Investigación en Agricultura Biológica, Departamento de Biología, Pontificia Universidad Javeriana, Sede Bogotá, Bogotá D.C. 110231, Colombia;
| | - Karen Melissa Cardona Tobar
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, Colombia; (P.A.R.-S.); (J.D.D.-Z.); (G.A.V.-M.)
- Grupo de Investigación en Agricultura Biológica, Departamento de Biología, Pontificia Universidad Javeriana, Sede Bogotá, Bogotá D.C. 110231, Colombia;
| | - Sergio Alberto Díaz Gallo
- Grupo de Investigación en Agricultura Biológica, Departamento de Biología, Pontificia Universidad Javeriana, Sede Bogotá, Bogotá D.C. 110231, Colombia;
| | - Jaime Eduardo Muñoz Flórez
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, Colombia; (P.A.R.-S.); (J.D.D.-Z.); (G.A.V.-M.)
| | - Lucia Ana Díaz-Ariza
- Grupo de Investigación en Agricultura Biológica, Departamento de Biología, Pontificia Universidad Javeriana, Sede Bogotá, Bogotá D.C. 110231, Colombia;
| | - Diana López-Alvarez
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Sede Palmira, Palmira 763533, Colombia; (P.A.R.-S.); (J.D.D.-Z.); (G.A.V.-M.)
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12
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Ahmed AAQ, McKay TJM. Environmental and ecological importance of bacterial extracellular vesicles (BEVs). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:168098. [PMID: 37884154 DOI: 10.1016/j.scitotenv.2023.168098] [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: 05/10/2023] [Revised: 09/24/2023] [Accepted: 10/22/2023] [Indexed: 10/28/2023]
Abstract
Extracellular vesicles are unique structures released by the cells of all life forms. Bacterial extracellular vesicles (BEVs) were found in various ecosystems and natural habitats. They are associated with bacterial-bacterial interactions as well as host-bacterial interactions in the environment. Moreover, BEVs facilitate bacterial adaptation to a variety of environmental conditions. BEVs were found to be abundant in the environment, and therefore they can regulate a broad range of environmental processes. In the environment, BEVs can serve as tools for cell-to-cell interaction, secreting mechanism of unwanted materials, transportation, genetic materials exchange and storage, defense and protection, growth support, electron transfer, and cell-surface interplay regulation. Thus, BEVs have a great potential to be used in a variety of environmental applications such as serving as bioremediating reagents for environmental disaster mitigation as well as removing problematic biofilms and waste treatment. This research area needs to be investigated further to disclose the full environmental and ecological importance of BEVs as well as to investigate how to harness BEVs as effective tools in a variety of environmental applications.
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Affiliation(s)
- Abeer Ahmed Qaed Ahmed
- Department of Environmental Sciences, School of Ecological and Human Sustainability, College of Agriculture and Environmental Sciences, University of South Africa, P.O. Box 392, Florida, Johannesburg 1710, South Africa.
| | - Tracey Jill Morton McKay
- Department of Environmental Sciences, School of Ecological and Human Sustainability, College of Agriculture and Environmental Sciences, University of South Africa, P.O. Box 392, Florida, Johannesburg 1710, South Africa
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13
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de Oliveira KB, Goes AC, Silva AD, Vieira PC, Rodrigues A. Fungal Cultivars of Higher Attine Ants Promote Escovopsis Chemotropism. Curr Microbiol 2023; 81:37. [PMID: 38063979 DOI: 10.1007/s00284-023-03552-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023]
Abstract
In varied environments, microorganisms search for partners or nutritional resources using chemical signals. Microbes are drawn (chemotaxis) or grow directionally (chemotropism) towards the chemical source, enabling them to establish and maintain symbiosis. The hypocrealean fungi Escovopsis enhance their growth towards the basidiomycete fungus Leucoagaricus gongylophorus, which is cultivated by leaf-cutting attine ants for food. Although directional growth is well documented in this symbiosis, it is unclear whether non-volatile or volatile organic compounds participate in the interaction between cultivar and Escovopsis, and which specific chemical compounds might attract and induce chemotropism. In this study, we examined the growth responses of Escovopsis isolates to non-volatile and volatile organic compounds produced by fungal cultivars of higher attine ants. We also isolated and identified molecules released by the ant-cultivar and assessed the chemotropism of Escovopsis towards them. Our results indicate that the growth of Escovopsis is stimulated in the presence of both non-volatile and volatile compounds from fungal cultivars. We also identified three isomeric diketopiperazines molecules from crude extracts of the ant cultivar, suggesting that these might play a role in Escovopsis chemotropism. Our findings provide insights into the complex chemical interactions that govern the association between Escovopsis and fungal cultivars.
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Affiliation(s)
- Karina B de Oliveira
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP, Brazil
| | - Aryel C Goes
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP, Brazil
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Airton D Silva
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Paulo C Vieira
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Andre Rodrigues
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP, Brazil.
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Lawrence P, Padamsee M, Lee K, Lacap-Bugler DC. Soil microbial functional gene dataset associated with Agathis australis. Data Brief 2023; 51:109791. [PMID: 38053586 PMCID: PMC10694058 DOI: 10.1016/j.dib.2023.109791] [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: 08/01/2023] [Revised: 09/19/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023] Open
Abstract
Agathis australis (New Zealand kauri) is a significant and iconic native tree of Aotearoa New Zealand. Currently, Phytophthora agathidicida that causes kauri-dieback disease is killing kauri trees. Only 1% of the New Zealand virgin kauri forest remains [1,2]. Recent studies revealed that many soil-borne microorganisms had been found to systemically boost the defensive capacity of the trees by providing competition to pathogens for nutrient intake, thus preventing pathogen colonization and modulating plant immunity [3,4]. In addition, the root microbiome consists of an entire complex rhizosphere-associated microbes with their genetic elements and interactions that have influenced plant health. To date, very few studies have been conducted to investigate the microorganisms in the kauri soil and possible environmental drivers. To characterize the functional gene profile in relation to soil microbial diversity of the kauri trees at Auckland Botanic Gardens (ABG), Auckland, New Zealand the GeoChip 5.0 M (Glomics Inc. USA), a microarray-based metagenomics tool, was used. GeoChip 5.0 M comprises of 162,000 probes from 365,000 target genes (coding DNA sequence - CDS), which covers all taxonomic groups (archaea, bacteria, fungi, protists, algae, and viruses) [5]. The ABG has kauri trees that are approximately 20 years old, located in three distinct man-made environments: Native Forest, Kauri Grove, and Rose Garden. We selected two trees from the Native Forest and two from the Kauri Grove for our experiment. Soil samples were collected from the four cardinal points of each tree, at 10 cm depth. Pooled environmental DNA was sent to Glomics (USA) and the data were preprocessed using GeoChip data analysis pipeline described in http://www.ou.edu/ieg/tools/data-analysispipeline.html. Based on the GeoChip data generated from the soil samples, we have detected a total of 946 genes, 4342 taxa, 102 phyla, and 995 genera. The data presented here provide an overview of functional genes associated with kauri soil, which can serve as baseline for other kauri soil microbiome analysis at forest-scale studies. The raw data has been uploaded to Mendeley Data https://doi.org/10.17632/T22NNN385K.1.
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Affiliation(s)
- Praveenth Lawrence
- School of Science, Faculty of Health and Environmental Science, Auckland University of Technology, Auckland 1010, New Zealand
| | - Mahajabeen Padamsee
- Manaaki Whenua Landcare Research, 231 Morrin Road, Auckland 1072, New Zealand
| | - Kevin Lee
- School of Science, Faculty of Health and Environmental Science, Auckland University of Technology, Auckland 1010, New Zealand
| | - Donnabella C. Lacap-Bugler
- School of Science, Faculty of Health and Environmental Science, Auckland University of Technology, Auckland 1010, New Zealand
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15
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Savytska M, Kyriienko D, Komisarenko I, Kovalchuk O, Falalyeyeva T, Kobyliak N. Probiotic for Pancreatic β-Cell Function in Type 2 Diabetes: A Randomized, Double-Blinded, Placebo-Controlled Clinical Trial. Diabetes Ther 2023; 14:1915-1931. [PMID: 37713103 PMCID: PMC10570251 DOI: 10.1007/s13300-023-01474-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
INTRODUCTION Many clinical studies have proved the effectiveness of probiotics in metabolic disorders associated with insulin resistance. However, the impact of probiotic therapy on pancreatic β-cell function is ambiguous. The influence of probiotic supplementation vs. placebo on β-cell function in people with type 2 diabetes (T2D) was assessed in a double-blind, single-center, randomized, placebo-controlled trial (RCT). METHODS Sixty-eight patients with T2D were selected for participation in the RCT. Patients were randomly allocated to consumption of live multistrain probiotics or a placebo for 8 weeks, administered as a sachet formulation in double-blind treatment. The primary main outcome was the assessment of β-cell function as change in C-peptide and HOMA-β (homeostasis model assessment-estimated β-cell function), which was calculated using the HOMA2 calculator (Diabetes Trials Unit, University of Oxford). Secondary outcomes were the changes in glycemic control-related parameters, anthropomorphic variables, and cytokines levels. Analysis of covariance was used to assess the difference between groups. RESULTS Supplementation with live multiprobiotic was associated with slight significant improvement of β-cell function (HOMA-β increased from 32.48 ± 13.12 to 45.71 ± 25.18; p = 0.003) and reduction of fasting glucose level (13.03 ± 3.46 vs 10.66 ± 2.63 mmol/L and 234.63 ± 62.36 vs 192.07 ± 47.46 mg/dL; p < 0.001) and HbA1c (8.86 ± 1.28 vs 8.48 ± 1.22; p = 0.043) as compared to placebo. Probiotic therapy significantly affects chronic systemic inflammation in people with T2D by reducing pro-inflammatory cytokine levels. CONCLUSIONS Probiotic therapies modestly improved β-cell function in patients with T2D. Modulating the gut microbiota represents a new diabetes treatment and should be tested in more extensive studies. TRIAL REGISTRATION NCT05765292.
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Affiliation(s)
- Maryana Savytska
- Normal Physiology Department, Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | | | - Iuliia Komisarenko
- Endocrinology Department, Bogomolets National Medical University, Kyiv, Ukraine
| | | | - Tetyana Falalyeyeva
- Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
- Medical Laboratory CSD, Kyiv, Ukraine
| | - Nazarii Kobyliak
- Endocrinology Department, Bogomolets National Medical University, Kyiv, Ukraine.
- Medical Laboratory CSD, Kyiv, Ukraine.
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Wang D, Chen L, Tang G, Yu J, Chen J, Li Z, Cao Y, Lei X, Deng L, Wu S, Guan LL, Yao J. Multi-omics revealed the long-term effect of ruminal keystone bacteria and the microbial metabolome on lactation performance in adult dairy goats. MICROBIOME 2023; 11:215. [PMID: 37773207 PMCID: PMC10540338 DOI: 10.1186/s40168-023-01652-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/23/2023] [Indexed: 10/01/2023]
Abstract
BACKGROUND The increased growth rate of young animals can lead to higher lactation performance in adult goats; however, the effects of the ruminal microbiome on the growth of young goats, and the contribution of the early-life rumen microbiome to lifelong growth and lactation performance in goats has not yet been well defined. Hence, this study assessed the rumen microbiome in young goats with different average daily gains (ADG) and evaluated its contribution to growth and lactation performance during the first lactation period. RESULTS Based on monitoring of a cohort of 99 goats from youth to first lactation, the 15 highest ADG (HADG) goats and 15 lowest ADG (LADG) goats were subjected to rumen fluid microbiome and metabolome profiling. The comparison of the rumen metagenome of HADG and LADG goats revealed that ruminal carbohydrate metabolism and amino acid metabolism function were enhanced in HADG goats, suggesting that the rumen fluid microbiome of HADG goats has higher feed fermentation ability. Co-occurrence network and correlation analysis revealed that Streptococcus, Candidatus Saccharimonans, and Succinivibrionaceae UCG-001 were significantly positively correlated with young goats' growth rates and some HADG-enriched carbohydrate and protein metabolites, such as propionate, butyrate, maltoriose, and amino acids, while several genera and species of Prevotella and Methanogens exhibited a negative relationship with young goats' growth rates and correlated with LADG-enriched metabolites, such as rumen acetate as well as methane. Additionally, some functional keystone bacterial taxa, such as Prevotella, in the rumen of young goats were significantly correlated with the same taxa in the rumen of adult lactation goats. Prevotella also enriched the rumen of LADG lactating goats and had a negative effect on rumen fermentation efficiency in lactating goats. Additional analysis using random forest machine learning showed that rumen fluid microbiota and their metabolites of young goats, such as Prevotellaceae UCG-003, acetate to propionate ratio could be potential microbial markers that can potentially classify high or low ADG goats with an accuracy of prediction of > 81.3%. Similarly, the abundance of Streptococcus in the rumen of young goats could be predictive of milk yield in adult goats with high accuracy (area under the curve 91.7%). CONCLUSIONS This study identified the keystone bacterial taxa that influence carbohydrate and amino acid metabolic functions and shape the rumen fluid microbiota in the rumen of adult animals. Keystone bacteria and their effects on rumen fluid microbiota and metabolome composition during early life can lead to higher lactation performance in adult ruminants. These findings suggest that the rumen microbiome together with their metabolites in young ruminants have long-term effect on feed efficiency and animal performance. The fundamental knowledge may allow us to develop advanced methods to manipulate the rumen microbiome and improve production efficiency of ruminants. Video Abstract.
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Affiliation(s)
- Dangdang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Luyu Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Guangfu Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Junjian Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jie Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Zongjun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yangchun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xinjian Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lu Deng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 116 St. and 85 Ave, Edmonton, AB, Canada.
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Lei HM, Wang JT, Hu QY, Li CQ, Mo MH, Zhang KQ, Li GH, Zhao PJ. 2-Furoic acid associated with the infection of nematodes by Dactylellina haptotyla and its biocontrol potential on plant root-knot nematodes. Microbiol Spectr 2023; 11:e0189623. [PMID: 37754836 PMCID: PMC10580851 DOI: 10.1128/spectrum.01896-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/05/2023] [Indexed: 09/28/2023] Open
Abstract
Dactylellina haptotyla is a typical nematode-trapping fungus that has garnered the attention of many scholars for its highly effective lethal potential for nematodes. Secondary metabolites play an important role in D. haptotyla-nematode interactions, but which metabolites perform which function remains unclear. We report the metabolic functions based on high-quality, chromosome-level genome assembly of wild D. haptotyla YMF1.03409. The results indicate that a large variety of secondary metabolites and their biosynthetic genes were significantly upregulated during the nematode-trapping stage. In parallel, we identified that 2-furoic acid was specifically produced during nematode trapping by D. haptotyla YMF1.03409 and isolated it from fermentation production. 2-Furoic acid demonstrated strong nematicidal activity with an LD50 value of 55.05 µg/mL against Meloidogyne incognita at 48 h. Furthermore, the pot experiment showed that the number of galls of tomato root was significantly reduced in the experimental group treated with 2-furoic acid. The considerable increase in the 2-furoic acid content during the infection process and its virulent nematicidal activity revealed an essential synergistic effect during the process of nematode-trapping fungal infection. IMPORTANCE Dactylellina haptotyla have significant application potential in nematode biocontrol. In this study, we determined the chromosome-level genome sequence of D. haptotyla YMF1.03409 by long-read sequencing technology. Comparative genomic analysis identified a series of pathogenesis-related genes and revealed significant gene family contraction events during the evolution of D. haptotyla YMF1.03409. Combining transcriptomic and metabolomic data as well as in vitro activity test results, a compound with important application potential in nematode biocontrol, 2-furoic acid, was identified. Our result expanded the genetic resource of D. haptotyla and identified a previously unreported nematicidal small molecule, which provides new options for the development of plant biocontrol agents.
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Affiliation(s)
- Hong-Mei Lei
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Jun-Tao Wang
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Qian-Yi Hu
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Chun-Qiang Li
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Ming-He Mo
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Ke-Qin Zhang
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Guo-Hong Li
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Pei-Ji Zhao
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
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18
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Lim JJ, Diener C, Wilson J, Valenzuela JJ, Baliga NS, Gibbons SM. Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes. Nat Commun 2023; 14:5682. [PMID: 37709733 PMCID: PMC10502120 DOI: 10.1038/s41467-023-41424-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/04/2023] [Indexed: 09/16/2023] Open
Abstract
Longitudinal sampling of the stool has yielded important insights into the ecological dynamics of the human gut microbiome. However, human stool samples are available approximately once per day, while commensal population doubling times are likely on the order of minutes-to-hours. Despite this mismatch in timescales, much of the prior work on human gut microbiome time series modeling has assumed that day-to-day fluctuations in taxon abundances are related to population growth or death rates, which is likely not the case. Here, we propose an alternative model of the human gut as a stationary system, where population dynamics occur internally and the bacterial population sizes measured in a bolus of stool represent a steady-state endpoint of these dynamics. We formalize this idea as stochastic logistic growth. We show how this model provides a path toward estimating the growth phases of gut bacterial populations in situ. We validate our model predictions using an in vitro Escherichia coli growth experiment. Finally, we show how this method can be applied to densely-sampled human stool metagenomic time series data. We discuss how these growth phase estimates may be used to better inform metabolic modeling in flow-through ecosystems, like animal guts or industrial bioreactors.
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Affiliation(s)
- Joe J Lim
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA, 98105, USA
| | | | - James Wilson
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Departments of Biology and Microbiology, University of Washington, Seattle, WA, 98105, USA
- Lawrence Berkeley National Laboratory, CA, 94720, Berkeley, USA
- Molecular and Cellular Biology Program, University of Washington, WA, 98105, Seattle, USA
- Molecular Engineering Graduate Program, University of Washington, WA, 98105, Seattle, USA
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, 98109, USA.
- Molecular Engineering Graduate Program, University of Washington, WA, 98105, Seattle, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, 98105, USA.
- eScience Institute, University of Washington, Seattle, WA, 98105, USA.
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19
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Tang S, Mao S, Chen Y, Tan F, Duan L, Pian C, Zeng X. LRBmat: A novel gut microbial interaction and individual heterogeneity inference method for colorectal cancer. J Theor Biol 2023; 571:111538. [PMID: 37257720 DOI: 10.1016/j.jtbi.2023.111538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/18/2023] [Indexed: 06/02/2023]
Abstract
The gut microbial community has been shown to play a significant role in various diseases, including colorectal cancer (CRC), which is a major public health concern worldwide. The accurate diagnosis and etiological analysis of CRC are crucial issues. Numerous methods have utilized gut microbiota to address these challenges; however, few have considered the complex interactions and individual heterogeneity of the gut microbiota, which are important issues in genetics and intestinal microbiology, particularly in high-dimensional cases. This paper presents a novel method called Binary matrix based on Logistic Regression (LRBmat) to address these concerns. The binary matrix in LRBmat can directly mitigate or eliminate the influence of heterogeneity, while also capturing information on gut microbial interactions with any order. LRBmat is highly adaptable and can be combined with any machine learning method to enhance its capabilities. The proposed method was evaluated using real CRC data and demonstrated superior classification performance compared to state-of-the-art methods. Furthermore, the association rules extracted from the binary matrix of the real data align well with biological properties and existing literature, thereby aiding in the etiological analysis of CRC.
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Affiliation(s)
- Shan Tang
- Department of Statistics, Hunan University, Changsha 410006, China
| | - Shanjun Mao
- Department of Statistics, Hunan University, Changsha 410006, China.
| | - Yangyang Chen
- Department of Computer Science, University of Tsukuba, Tsukuba 3058577, Japan
| | - Falong Tan
- Department of Statistics, Hunan University, Changsha 410006, China
| | - Lihua Duan
- Department of Rheumatology and Clinical Immunology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Cong Pian
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiangxiang Zeng
- Department of Computer Science, Hunan University, Changsha 410086, China
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20
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Yan C, Owen JS, Seo EY, Jung D, He S. Microbial Interaction is Among the Key Factors for Isolation of Previous Uncultured Microbes. J Microbiol 2023; 61:655-662. [PMID: 37589838 PMCID: PMC10477116 DOI: 10.1007/s12275-023-00063-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/13/2023] [Accepted: 06/18/2023] [Indexed: 08/18/2023]
Abstract
Pure cultivation of microbes is still limited by the challenges of microbial uncultivability, with most microbial strains unable to be cultivated under standard laboratory conditions. The experience accumulated from advanced techniques such as in situ cultivation has identified that microbial interactions exist in natural habitats but are absent in laboratory cultures. These microbial interactions are likely one of the key factors in isolating previously uncultured microbes. The need for better knowledge of the mechanisms operating in microbial interactions has led to various experiments that have utilized microbial interactions in different approaches to microbial cultivation. These new attempts to understand microbial interactions not only present a new perspective on microbial uncultivability but also provide an opportunity to access uncultured phylogenetically novel microbes with their potential biotechnology applications. In this review, we focus on studies of the mechanisms of microbial interaction where the growth of other microbes is affected. Additionally, we review some successful applications of microbial interactions in cultivation methods, an approach that can play an important role in the bioprospecting of untapped microbial resources.
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Affiliation(s)
- Chang Yan
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315832, People's Republic of China
- Ningbo Institute of Marine Medicine, Peking University, Ningbo, 315832, People's Republic of China
| | - Jeffrey S Owen
- Department of Environmental Science, Hankuk University of Foreign Studies, Yongin, 17035, Republic of Korea
| | - Eun-Young Seo
- Ningbo Institute of Marine Medicine, Peking University, Ningbo, 315832, People's Republic of China
| | - Dawoon Jung
- Ningbo Institute of Marine Medicine, Peking University, Ningbo, 315832, People's Republic of China.
| | - Shan He
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315832, People's Republic of China.
- Ningbo Institute of Marine Medicine, Peking University, Ningbo, 315832, People's Republic of China.
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21
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Wang M, Zeng J, Zhu Y, Chen X, Guo Q, Tan H, Cui B, Song S, Deng Y. A 4-Hydroxybenzoic Acid-Mediated Signaling System Controls the Physiology and Virulence of Shigella sonnei. Microbiol Spectr 2023; 11:e0483522. [PMID: 37036340 PMCID: PMC10269604 DOI: 10.1128/spectrum.04835-22] [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: 11/24/2022] [Accepted: 03/15/2023] [Indexed: 04/11/2023] Open
Abstract
Many bacteria use small molecules, such as quorum sensing (QS) signals, to perform intraspecies signaling and interspecies or interkingdom communication. Previous studies demonstrated that some bacteria regulate their physiology and pathogenicity by employing 4-hydroxybenzoic acid (4-HBA). Here, we report that 4-HBA controls biological functions, virulence, and anthranilic acid production in Shigella sonnei. The biosynthesis of 4-HBA is performed by UbiC (SSON_4219), which is a chorismate pyruvate-lyase that catalyzes the conversion of chorismate to 4-HBA. Deletion of ubiC caused S. sonnei to exhibit impaired phenotypes, including impaired biofilm formation, extracellular polysaccharide (EPS) production, and virulence. In addition, we found that 4-HBA controls the physiology and virulence of S. sonnei through the response regulator AaeR (SSON_3385), which contains a helix-turn-helix (HTH) domain and a LysR substrate-binding (LysR_substrate) domain. The same biological functions are controlled by AaeR and the 4-HBA signal, and 4-HBA-deficient mutant phenotypes were rescued by in trans expression of AaeR. We found that 4-HBA binds to AaeR and then enhances the binding of AaeR to the promoter DNA regions in target genes. Moreover, we revealed that 4-HBA from S. sonnei reduces the competitive fitness of Candida albicans by interfering with morphological transition. Together, our results suggested that the 4-HBA signaling system plays crucial roles in bacterial physiology and interkingdom communication. IMPORTANCE Shigella sonnei is an important pathogen in human intestines. Following previous findings that some bacteria employ 4-HBA as a QS signal to regulate biological functions, we demonstrate that 4-HBA controls the physiology and virulence of S. sonnei. This study is significant because it identifies both the signal synthase UbiC and receptor AaeR and unveils the signaling pathway of 4-HBA in S. sonnei. In addition, this study also supports the important role of 4-HBA in microbial cross talk, as 4-HBA strongly inhibits hyphal formation by Candida albicans. Together, our findings describe the dual roles of 4-HBA in both intraspecies signaling and interkingdom communication.
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Affiliation(s)
- Mingfang Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Jia Zeng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yu Zhu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Xiayu Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Quan Guo
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Huihui Tan
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Binbin Cui
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Shihao Song
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- School of Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Yinyue Deng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- School of Pharmaceutical Sciences, Hainan University, Haikou, China
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22
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Campos EVR, Pereira ADES, Aleksieienko I, do Carmo GC, Gohari G, Santaella C, Fraceto LF, Oliveira HC. Encapsulated plant growth regulators and associative microorganisms: Nature-based solutions to mitigate the effects of climate change on plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 331:111688. [PMID: 36963636 DOI: 10.1016/j.plantsci.2023.111688] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/16/2023] [Accepted: 03/19/2023] [Indexed: 06/18/2023]
Abstract
Over the past decades, the atmospheric CO2 concentration and global average temperature have been increasing, and this trend is projected to soon become more severe. This scenario of climate change intensifies abiotic stress factors (such as drought, flooding, salinity, and ultraviolet radiation) that threaten forest and associated ecosystems as well as crop production. These factors can negatively affect plant growth and development with a consequent reduction in plant biomass accumulation and yield, in addition to increasing plant susceptibility to biotic stresses. Recently, biostimulants have become a hotspot as an effective and sustainable alternative to alleviate the negative effects of stresses on plants. However, the majority of biostimulants have poor stability under environmental conditions, which leads to premature degradation, shortening their biological activity. To solve these bottlenecks, micro- and nano-based formulations containing biostimulant molecules and/or microorganisms are gaining attention, as they demonstrate several advantages over their conventional formulations. In this review, we focus on the encapsulation of plant growth regulators and plant associative microorganisms as a strategy to boost their application for plant protection against abiotic stresses. We also address the potential limitations and challenges faced for the implementation of this technology, as well as possibilities regarding future research.
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Affiliation(s)
- Estefânia V R Campos
- Institute of Science and Technology of Sorocaba, São Paulo State University (UNESP), Av. Três de Março 511, 18087-180 Sorocaba, São Paulo, Brazil; B.Nano Soluções Tecnológicas Ltda, Rua Dr. Júlio Prestes, 355,18230-000 São Miguel Arcanjo, São Paulo, Brazil.
| | - Anderson do E S Pereira
- Institute of Science and Technology of Sorocaba, São Paulo State University (UNESP), Av. Três de Março 511, 18087-180 Sorocaba, São Paulo, Brazil; B.Nano Soluções Tecnológicas Ltda, Rua Dr. Júlio Prestes, 355,18230-000 São Miguel Arcanjo, São Paulo, Brazil
| | - Ivan Aleksieienko
- Aix Marseille University, CEA, CNRS, BIAM, LEMiRE, Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France
| | - Giovanna C do Carmo
- Department of Animal and Plant Biology, State University of Londrina (UEL), PR 445, Km 380, 86057-970 Londrina, Paraná, Brazil
| | - Gholamreza Gohari
- Department of Horticultural Science, Faculty of Agriculture, University of Maragheh, Maragheh, Iran
| | - Catherine Santaella
- Aix Marseille University, CEA, CNRS, BIAM, LEMiRE, Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France
| | - Leonardo F Fraceto
- Institute of Science and Technology of Sorocaba, São Paulo State University (UNESP), Av. Três de Março 511, 18087-180 Sorocaba, São Paulo, Brazil
| | - Halley C Oliveira
- Department of Animal and Plant Biology, State University of Londrina (UEL), PR 445, Km 380, 86057-970 Londrina, Paraná, Brazil.
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23
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Wong SK, Cui Y, Chun SJ, Kaneko R, Masumoto S, Kitagawa R, Mori AS, Lim AS, Uchida M. Vegetation as a key driver of the distribution of microbial generalists that in turn shapes the overall microbial community structure in the low Arctic tundra. ENVIRONMENTAL MICROBIOME 2023; 18:41. [PMID: 37165459 PMCID: PMC10173506 DOI: 10.1186/s40793-023-00498-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/27/2023] [Indexed: 05/12/2023]
Abstract
Understanding the variability of microbial niches and their interaction with abiotic and biotic factors in the Arctic can provide valuable insights into microbial adaptations to extreme environments. This study investigates the structure and diversity of soil bacterial communities obtained from sites with varying vegetation coverage and soil biogeochemical properties in the low Arctic tundra and explores how bacteria interact under different environmental parameters. Our findings reveal differences in bacterial composition and abundance among three bacterial niche breadths (specialists, common taxa, and generalists). Co-occurrence network analysis revealed Rhizobiales and Ktedonobacterales as keystone taxa that connect and support other microbes in the habitat. Low-elevation indicators, such as vascular plants and moisture content, were correlated with two out of three generalist modular hubs and were linked to a large proportion of generalists' distribution (18%). Structural equation modeling revealed that generalists' distribution, which influenced the remaining microbial communities, was mainly regulated by vegetation coverage as well as other abiotic and biotic factors. These results suggest that elevation-dependent environmental factors directly influence microbial community structure and module formation through the regulation of generalists' distribution. Furthermore, the distribution of generalists was mainly affected by macroenvironment filtering, whereas the distribution of specialists was mainly affected by microenvironment filtering (species-engineered microbial niche construction). In summary, our findings highlight the strong top-down control exerted by vegetation on generalists' distribution, which in turn shapes the overall microbial community structure in the low Arctic tundra.
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Affiliation(s)
- Shu-Kuan Wong
- Research Organization of Information and Systems, National Institute of Polar Research, 10-3, Midori-cho, Tachikawa, Tokyo, Japan
| | - Yingshun Cui
- Division of Life Science and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Seong-Jun Chun
- LMO Team, National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon, Republic of Korea.
| | - Ryo Kaneko
- Research Organization of Information and Systems, National Institute of Polar Research, 10-3, Midori-cho, Tachikawa, Tokyo, Japan
| | - Shota Masumoto
- Graduate School of Environment and Information Sciences, Yokohama National University, 79-7, Tokiwadai, Hodogaya, Yokohama, Japan
| | - Ryo Kitagawa
- Kansai Research Center, Forestry and Forest Products Research Institute, 68, Nagaikyutaroh, Momoyama, Fushimi, Kyoto, Japan
| | - Akira S Mori
- Graduate School of Environment and Information Sciences, Yokohama National University, 79-7, Tokiwadai, Hodogaya, Yokohama, Japan
| | - An Suk Lim
- Division of Life Science and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Masaki Uchida
- Research Organization of Information and Systems, National Institute of Polar Research, 10-3, Midori-cho, Tachikawa, Tokyo, Japan.
- Department of Polar Science, School of Multidisciplinary Sciences, The Graduate University for Advanced Studies, SOKENDAI, 10-3, Midori-cho, Tachikawa, Tokyo, Japan.
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24
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Lyu D, Backer R, Berrué F, Martinez-Farina C, Hui JPM, Smith DL. Plant Growth-Promoting Rhizobacteria (PGPR) with Microbial Growth Broth Improve Biomass and Secondary Metabolite Accumulation of Cannabis sativa L. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7268-7277. [PMID: 37130078 DOI: 10.1021/acs.jafc.2c06961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) are a sustainable crop production input; some show positive effects under laboratory conditions but poorly colonize host field-grown plants. Inoculating with PGPR in microbial growth medium (e.g., King's B) could overcome this. We evaluated cannabis plant (cv. CBD Kush) growth promotion by inoculating three PGPR (Bacillus sp., Mucilaginibacter sp., and Pseudomonas sp.) in King's B at vegetative and flower stages. At the vegetative stage, Mucilaginibacter sp. inoculation increased flower dry weight (24%), total CBD (11.1%), and THC (11.6%); Pseudomonas sp. increased stem (28%) dry matter, total CBD (7.2%), and THC (5.9%); and Bacillus sp. increased total THC by 4.8%. Inoculation with Mucilaginibacter sp. and Pseudomonas sp. at the flowering stage led to 23 and 18% increases in total terpene accumulation, respectively. Overall, vegetative inoculation with PGPR enhanced cannabis yield attributes and chemical profiles. Further research into PGPR inoculation onto cannabis and the subsequent level of colonization could provide key insights regarding PGPR-host interactions.
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Affiliation(s)
- Dongmei Lyu
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue H9X3V9, Quebec, Canada
| | - Rachel Backer
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue H9X3V9, Quebec, Canada
| | - Fabrice Berrué
- National Research Council Canada, Halifax B3H 3Z1, Nova Scotia, Canada
| | | | - Joseph P M Hui
- National Research Council Canada, Halifax B3H 3Z1, Nova Scotia, Canada
| | - Donald Lawrence Smith
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue H9X3V9, Quebec, Canada
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25
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Zhang D, Zhang J, Kalimuthu S, Liu J, Song ZM, He BB, Cai P, Zhong Z, Feng C, Neelakantan P, Li YX. A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome. MICROBIOME 2023; 11:91. [PMID: 37101246 PMCID: PMC10134562 DOI: 10.1186/s40168-023-01540-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 03/31/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Lactic acid bacteria (LAB) produce various bioactive secondary metabolites (SMs), which endow LAB with a protective role for the host. However, the biosynthetic potentials of LAB-derived SMs remain elusive, particularly in their diversity, abundance, and distribution in the human microbiome. Thus, it is still unknown to what extent LAB-derived SMs are involved in microbiome homeostasis. RESULTS Here, we systematically investigate the biosynthetic potential of LAB from 31,977 LAB genomes, identifying 130,051 secondary metabolite biosynthetic gene clusters (BGCs) of 2,849 gene cluster families (GCFs). Most of these GCFs are species-specific or even strain-specific and uncharacterized yet. Analyzing 748 human-associated metagenomes, we gain an insight into the profile of LAB BGCs, which are highly diverse and niche-specific in the human microbiome. We discover that most LAB BGCs may encode bacteriocins with pervasive antagonistic activities predicted by machine learning models, potentially playing protective roles in the human microbiome. Class II bacteriocins, one of the most abundant and diverse LAB SMs, are particularly enriched and predominant in the vaginal microbiome. We utilized metagenomic and metatranscriptomic analyses to guide our discovery of functional class II bacteriocins. Our findings suggest that these antibacterial bacteriocins have the potential to regulate microbial communities in the vagina, thereby contributing to the maintenance of microbiome homeostasis. CONCLUSIONS Our study systematically investigates LAB biosynthetic potential and their profiles in the human microbiome, linking them to the antagonistic contributions to microbiome homeostasis via omics analysis. These discoveries of the diverse and prevalent antagonistic SMs are expected to stimulate the mechanism study of LAB's protective roles for the microbiome and host, highlighting the potential of LAB and their bacteriocins as therapeutic alternatives. Video Abstract.
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Affiliation(s)
- Dengwei Zhang
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jian Zhang
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Shanthini Kalimuthu
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Jing Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhi-Man Song
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Bei-Bei He
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Peiyan Cai
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zheng Zhong
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chenchen Feng
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Prasanna Neelakantan
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Yong-Xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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26
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Rozaliyani A, Antariksa B, Nurwidya F, Zaini J, Setianingrum F, Hasan F, Nugrahapraja H, Yusva H, Wibowo H, Bowolaksono A, Kosmidis C. The Fungal and Bacterial Interface in the Respiratory Mycobiome with a Focus on Aspergillus spp. Life (Basel) 2023; 13:life13041017. [PMID: 37109545 PMCID: PMC10142979 DOI: 10.3390/life13041017] [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: 02/27/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The heterogeneity of the lung microbiome and its alteration are prevalently seen among chronic lung diseases patients. However, studies to date have primarily focused on the bacterial microbiome in the lung rather than fungal composition, which might play an essential role in the mechanisms of several chronic lung diseases. It is now well established that Aspergillus spp. colonies may induce various unfavorable inflammatory responses. Furthermore, bacterial microbiomes such as Pseudomonas aeruginosa provide several mechanisms that inhibit or stimulate Aspergillus spp. life cycles. In this review, we highlighted fungal and bacterial microbiome interactions in the respiratory tract, with a focus on Aspergillus spp.
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Affiliation(s)
- Anna Rozaliyani
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Budhi Antariksa
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Fariz Nurwidya
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Jamal Zaini
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Findra Setianingrum
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Firman Hasan
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Husna Nugrahapraja
- Life Science and Biotechnology, Bandung Institute of Technology, Bandung 40312, Indonesia
| | - Humaira Yusva
- Magister Program of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Heri Wibowo
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Anom Bowolaksono
- Department of Biology, Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Indonesia, Depok 16424, Indonesia
| | - Chris Kosmidis
- Manchester Academic Health Science Centre, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK
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27
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Dragičević P, Bielen A, Žučko J, Hudina S. The mycobiome of a successful crayfish invader and its changes along the environmental gradient. Anim Microbiome 2023; 5:23. [PMID: 37041598 PMCID: PMC10088235 DOI: 10.1186/s42523-023-00245-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/26/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND The microbiome plays an important role in biological invasions, since it affects various interactions between host and environment. However, most studies focus on the bacteriome, insufficiently addressing other components of the microbiome such as the mycobiome. Microbial fungi are among the most damaging pathogens in freshwater crayfish populations, colonizing and infecting both native and invasive crayfish species. Invading crayfish may transmit novel fungal species to native populations, but also, dispersal process and characteristics of the novel environment may affect the invaders' mycobiome composition, directly and indirectly affecting their fitness and invasion success. This study analyzes the mycobiome of a successful invader in Europe, the signal crayfish, using the ITS rRNA amplicon sequencing approach. We explored the mycobiomes of crayfish samples (exoskeletal biofilm, hemolymph, hepatopancreas, intestine), compared them to environmental samples (water, sediment), and examined the differences in fungal diversity and abundance between upstream and downstream segments of the signal crayfish invasion range in the Korana River, Croatia. RESULTS A low number of ASVs (indicating low abundance and/or diversity of fungal taxa) was obtained in hemolymph and hepatopancreas samples. Thus, only exoskeleton, intestine, sediment and water samples were analyzed further. Significant differences were recorded between their mycobiomes, confirming their uniqueness. Generally, environmental mycobiomes showed higher diversity than crayfish-associated mycobiomes. The intestinal mycobiome showed significantly lower richness compared to other mycobiomes. Significant differences in the diversity of sediment and exoskeletal mycobiomes were recorded between different river segments (but not for water and intestinal mycobiomes). Together with the high observed portion of shared ASVs between sediment and exoskeleton, this indicates that the environment (i.e. sediment mycobiome) at least partly shapes the exoskeletal mycobiome of crayfish. CONCLUSION This study presents the first data on crayfish-associated fungal communities across different tissues, which is valuable given the lack of studies on the crayfish mycobiome. We demonstrate significant differences in the crayfish exoskeletal mycobiome along the invasion range, suggesting that different local environmental conditions may shape the exoskeletal mycobiome during range expansion, while the mycobiome of the internal organ (intestine) remained more stable. Our results provide a basis for assessing how the mycobiome contributes to the overall health of the signal crayfish and its further invasion success.
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Affiliation(s)
- Paula Dragičević
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia.
| | - Ana Bielen
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, Zagreb, Croatia
| | - Jurica Žučko
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, Zagreb, Croatia
| | - Sandra Hudina
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
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28
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Sahoo B, Chaudhuri S. Removal of lindane in liquid culture using soil bacteria and toxicity assessment in human skin fibroblast and HCT116 cell lines. ENVIRONMENTAL TECHNOLOGY 2023; 44:1213-1227. [PMID: 34694963 DOI: 10.1080/09593330.2021.1998229] [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: 07/23/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
The development of effective measures for the remediation of lindane contaminated sites is the need of the hour. In this study, a potent lindane degrading bacteria, identified as Rhodococcus rhodochrous NITDBS9 was isolated from an agricultural field of Odisha that could utilize up to 87% of 100 mg L-1 lindane when grown under liquid culture conditions in mineral salt media in 10 days. The bacteria could produce biofilm in lindane-containing media. Rhodococcus rhodochrous NITDBS9 was further characterized for its plant growth-promoting properties and it was found that the bacteria showed abilities for phytohormone, ammonia and biosurfactant production, etc. This could be beneficial for the bioremediation and improvement of crop production in contaminated sites. Ecotoxicity studies carried out for lindane, and its degradation products in mung bean and mustard seeds showed a reduction in toxicity of lindane after treatment with NITDBS9. NITDBS9 was used with a previously isolated potent lindane degrading strain Paracoccus sp. NITDBR1 in a dual mixed culture for the enhanced removal of lindane in the liquid system i.e. up to 93% in 10 days. Cytotoxicity studies were conducted with lindane before and after treatment with the single and dual mixed cultures on human skin fibroblast and HCT116 cell lines. They revealed a significant reduction in toxicity of lindane after it was bioremediated with the single and dual mixed cultures. Therefore, our proposed strategy could be efficiently used for the detoxification of the lindane-contaminated system, and further work should be done to study the use of these cultures in the contaminated soil system.
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Affiliation(s)
- Banishree Sahoo
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, India
| | - Surabhi Chaudhuri
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, India
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Aldirawi H, Morales FG. Univariate and Multivariate Statistical Analysis of Microbiome Data: An Overview. Appl Microbiol 2023. [DOI: 10.3390/applmicrobiol3020023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Microbiome data is high dimensional, sparse, compositional, and over-dispersed. Therefore, modeling microbiome data is very challenging and it is an active research area. Microbiome analysis has become a progressing area of research as microorganisms constitute a large part of life. Since many methods of microbiome data analysis have been presented, this review summarizes the challenges, methods used, and the advantages and disadvantages of those methods, to serve as an updated guide for those in the field. This review also compared different methods of analysis to progress the development of newer methods.
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Tian C, Jiang D, Hammer A, Sharpton T, Jiang Y. Compositional Graphical Lasso Resolves the Impact of Parasitic Infection on Gut Microbial Interaction Networks in a Zebrafish Model. J Am Stat Assoc 2023; 118:1500-1514. [PMID: 38143789 PMCID: PMC10746147 DOI: 10.1080/01621459.2022.2164287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/23/2022] [Indexed: 01/07/2023]
Abstract
Understanding how microbes interact with each other is key to revealing the underlying role that microorganisms play in the host or environment and to identifying microorganisms as an agent that can potentially alter the host or environment. For example, understanding how the microbial interactions associate with parasitic infection can help resolve potential drug or diagnostic test for parasitic infection. To unravel the microbial interactions, existing tools often rely on graphical models to infer the conditional dependence of microbial abundances to represent their interactions. However, current methods do not simultaneously account for the discreteness, compositionality, and heterogeneity inherent to microbiome data. Thus, we build a new approach called "compositional graphical lasso" upon existing tools by incorporating the above characteristics into the graphical model explicitly. We illustrate the advantage of compositional graphical lasso over current methods under a variety of simulation scenarios and on a benchmark study, the Tara Oceans Project. Moreover, we present our results from the analysis of a dataset from the Zebrafish Parasite Infection Study, which aims to gain insight into how the gut microbiome and parasite burden covary during infection, thus uncovering novel putative methods of disrupting parasite success. Our approach identifies changes in interaction degree between infected and uninfected individuals for three taxa, Photobacterium, Gemmobacter, and Paucibacter, which are inversely predicted by other methods. Further investigation of these method-specific taxa interaction changes reveals their biological plausibility. In particular, we speculate on the potential pathobiotic roles of Photobacterium and Gemmobacter in the zebrafish gut, and the potential probiotic role of Paucibacter. Collectively, our analyses demonstrate that compositional graphical lasso provides a powerful means of accurately resolving interactions between microbiota and can thus drive novel biological discovery.
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Affiliation(s)
- Chuan Tian
- Department of Statistics, Oregon State University, Corvallis, OR
| | - Duo Jiang
- Department of Statistics, Oregon State University, Corvallis, OR
| | - Austin Hammer
- Department of Microbiology, Oregon State University, Corvallis, OR
| | - Thomas Sharpton
- Department of Statistics, Oregon State University, Corvallis, OR
- Department of Microbiology, Oregon State University, Corvallis, OR
| | - Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, OR
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Tanoeyadi S, Tsunoda T, Ito T, Philmus B, Mahmud T. Acarbose May Function as a Competitive Exclusion Agent for the Producing Bacteria. ACS Chem Biol 2023; 18:367-376. [PMID: 36648321 PMCID: PMC9957957 DOI: 10.1021/acschembio.2c00795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Acarbose is a well-known microbial specialized metabolite used clinically to treat type 2 diabetes. This natural pseudo-oligosaccharide (PsOS) shows potent inhibitory activity toward various glycosyl hydrolases, including α-glucosidases and α-amylases. While acarbose and other PsOSs are produced by many different bacteria, their ecological or biological role in microbial communities is still an open question. Here, we show that several PsOS-producing actinobacteria, i.e., Actinoplanes sp. SE50/110 (acarbose producer), Streptomyces glaucescens GLA.O (acarbose producer), and Streptomyces dimorphogenes ATCC 31484 (trestatin producer), can grow in the presence of acarbose, while the growth of the non-PsOS-producing organism Streptomyces coelicolor M1152 was suppressed when starch is the main source of energy. Further investigations using recombinant α-amylases from S. coelicolor M1152 and the PsOS-producing actinobacteria revealed that the S. coelicolor α-amylase was inhibited by acarbose, whereas those from the PsOS-producing bacteria were not inhibited by acarbose. Bioinformatic and protein modeling studies suggested that a point mutation in the α-amylases of the PsOS-producing actinobacteria is responsible for the resistance of those enzymes toward acarbose. Converting the acarbose-resistant α-amylase AcbE to its A304H variant diminished its acarbose-resistance property. Taken together, the results suggest that acarbose is used by the producing bacteria as a competitive exclusion agent to suppress the growth of other microorganisms in their natural environment, while the producing organisms equip themselves with α-amylase variants that are resistant to acarbose.
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Affiliation(s)
- Samuel Tanoeyadi
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Takeshi Tsunoda
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Takuya Ito
- Laboratory of Natural Medicines, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nisikiorikita, Tondabayashi 584-8540 (Japan)
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
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Marine Fungi Select and Transport Aerobic and Anaerobic Bacterial Populations from Polycyclic Aromatic Hydrocarbon-Contaminated Sediments. mBio 2023; 14:e0276122. [PMID: 36786561 PMCID: PMC10127579 DOI: 10.1128/mbio.02761-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
The organization of microbial communities in marine sediment relies on complex biotic and abiotic interactions. Among them, the interaction between fungi and bacteria plays a crucial role building specific microbial assemblages, resulting in metabolic networks adapted to environmental conditions. The fungal-bacterial interaction (FBI) includes bacterial translocation via fungal mycelia, allowing bacterial dispersion, and ecological niche colonization. In order to demonstrate that the translocation of bacteria through fungal mycelia involves bacterial selection, the mycelia of two fungi isolated from marine coastal sediment, Alternaria destruens F10.81 and Fusarium pseudonygamai F5.76, showing different strategies for uptake of polycyclic aromatic hydrocarbon (PAH), homogenous internalization and vacuole forming respectively, were used to translocate bacteria through hydrophobic hydrocarbon contaminated sediments. A. destruens F10.81 selected four specific bacteria, while bacterial selection by F. pseudonygamai F5.76 was not evident. Among the bacteria selected by A. destruens F10.81, Spirochaeta litoralis, known as strictly anaerobic bacterium, was identified, indicating that A. destruens F10.81 selects and transports both aerobic and anaerobic bacteria. Such a result is consistent with the observed formation of anoxic micro-niches in areas surrounding and affected by fungal hyphae. Our findings provide new insights on the selection and dispersion of bacterial communities by fungi, which are crucial for the organization of microbial communities and their functioning in coastal PAH-contaminated sediments. IMPORTANCE The study provides advances for understanding fungal-bacterial relationships, particularly on the selection and dispersion of bacterial communities by fungi, which are crucial for the organization of microbial communities and their functioning in coastal PAH-contaminated sediments. The transportation of bacteria via fungal hyphae (fungal highway) results in bacterial selection; in particular, fungal hyphae offer adequate conditions for the transport of both aerobic and anaerobic bacteria through hydrophobic patches for the colonization of novel niches.
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Moshe M, Gupta CL, Sela N, Minz D, Banin E, Frenkel O, Cytryn E. Comparative genomics of Bacillus cereus sensu lato spp. biocontrol strains in correlation to in-vitro phenotypes and plant pathogen antagonistic capacity. Front Microbiol 2023; 14:996287. [PMID: 36846749 PMCID: PMC9947482 DOI: 10.3389/fmicb.2023.996287] [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: 07/17/2022] [Accepted: 01/12/2023] [Indexed: 02/11/2023] Open
Abstract
Bacillus cereus sensu lato (Bcsl) strains are widely explored due to their capacity to antagonize a broad range of plant pathogens. These include B. cereus sp. UW85, whose antagonistic capacity is attributed to the secondary metabolite Zwittermicin A (ZwA). We recently isolated four soil and root-associated Bcsl strains (MO2, S-10, S-25, LSTW-24) that displayed different growth profiles and in-vitro antagonistic effects against three soilborne plant pathogens models: Pythium aphanidermatum (oomycete) Rhizoctonia solani (basidiomycete), and Fusarium oxysporum (ascomycete). To identify genetic mechanisms potentially responsible for the differences in growth and antagonistic phenotypes of these Bcsl strains, we sequenced and compared their genomes, and that of strain UW85 using a hybrid sequencing pipeline. Despite similarities, specific Bcsl strains had unique secondary metabolite and chitinase-encoding genes that could potentially explain observed differences in in-vitro chitinolytic potential and anti-fungal activity. Strains UW85, S-10 and S-25 contained a (~500 Kbp) mega-plasmid that harbored the ZwA biosynthetic gene cluster. The UW85 mega-plasmid contained more ABC transporters than the other two strains, whereas the S-25 mega-plasmid carried a unique cluster containing cellulose and chitin degrading genes. Collectively, comparative genomics revealed several mechanisms that can potentially explain differences in in-vitro antagonism of Bcsl strains toward fungal plant pathogens.
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Affiliation(s)
- Maya Moshe
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
- Institute of Plant Pathology and Weed Research, Agricultural Research Organization, Rishon-Lezion, Israel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Chhedi Lal Gupta
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Noa Sela
- Institute of Plant Pathology and Weed Research, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Ehud Banin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Omer Frenkel
- Institute of Plant Pathology and Weed Research, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
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Xu Y, Wu M, Zhao D, Zheng J, Dai M, Li X, Li W, Zhang C, Sun B. Simulated Fermentation of Strong-Flavor Baijiu through Functional Microbial Combination to Realize the Stable Synthesis of Important Flavor Chemicals. Foods 2023; 12:foods12030644. [PMID: 36766173 PMCID: PMC9913964 DOI: 10.3390/foods12030644] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The solid-state fermentation of Baijiu is complicated by the co-fermentation of many microorganisms. The instability of the composition and abundance of the microorganisms in the fermentation process leads to fluctuations of product quality, which is one of the bottleneck problems faced by the Strong-flavor Baijiu industry. In this study, we established a combination of functional microorganisms for the stable fermentation of the main flavor compounds of Baijiu, including medium and long-chain fatty acid ethyl esters such as hexanoic acid, ethyl ester; butanoic acid, ethyl ester; octanoic acid, ethyl ester; acetic acid, ethyl ester; 9,12-octadecadienoic acid, ethyl ester; and decanoic acid, ethyl ester in the fermented grains. Our study investigated the effects of microbial combinations on the fermentation from three aspects: microbial composition, microbial interactions, and microbial association with flavor compounds. The results showed that the added functional microorganisms (Lactobacillus, Clostridium, Caproiciproducens, Saccharomyces, and Aspergillus) became the dominant species in the fermentation system and formed positive interactions with other microorganisms, while the negative interactions between microorganisms were significantly reduced in the fermentation systems that contained both Daqu and functional microorganisms. The redundancy analysis showed that the functional microorganisms (Lactobacillus, Saccharomyces, Clostridium, Cloacibacterium, Chaenothecopsis, Anaerosporobacter, and Sporolactobacillus) showed strong positive correlations with the main flavor compounds (hexanoic acid, ethyl ester; lactic acid, ethyl ester; butanoic acid, ethyl ester; acetic acid, ethyl ester; and octanoic acid, ethyl ester). These results indicated that it was feasible to produce Baijiu with a functional microbial combination, and that this could promote stable Baijiu production.
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Affiliation(s)
- Youqiang Xu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Correspondence: (Y.X.); (X.L.)
| | - Mengqin Wu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Dong Zhao
- Wuliangye Yibin Co., Ltd., Yibin 644000, China
| | - Jia Zheng
- Wuliangye Yibin Co., Ltd., Yibin 644000, China
| | - Mengqi Dai
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Xiuting Li
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 102401, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Correspondence: (Y.X.); (X.L.)
| | - Weiwei Li
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Chengnan Zhang
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Baoguo Sun
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 102401, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University (BTBU), Beijing 100048, China
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Selegato DM, Castro-Gamboa I. Enhancing chemical and biological diversity by co-cultivation. Front Microbiol 2023; 14:1117559. [PMID: 36819067 PMCID: PMC9928954 DOI: 10.3389/fmicb.2023.1117559] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023] Open
Abstract
In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.
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Ibrahimi M, Loqman S, Jemo M, Hafidi M, Lemee L, Ouhdouch Y. The potential of facultative predatory Actinomycetota spp. and prospects in agricultural sustainability. Front Microbiol 2023; 13:1081815. [PMID: 36762097 PMCID: PMC9905845 DOI: 10.3389/fmicb.2022.1081815] [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: 10/27/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023] Open
Abstract
Actinomycetota in the phylum of bacteria has been explored extensively as a source of antibiotics and secondary metabolites. In addition to acting as plant growth-promoting agents, they also possess the potential to control various plant pathogens; however, there are limited studies that report the facultative predatory ability of Actinomycetota spp. Furthermore, the mechanisms that underline predation are poorly understood. We assessed the diversity of strategies employed by predatory bacteria to attack and subsequently induce the cell lysing of their prey. We revisited the diversity and abundance of secondary metabolite molecules linked to the different predation strategies by bacteria species. We analyzed the pros and cons of the distinctive predation mechanisms and explored their potential for the development of new biocontrol agents. The facultative predatory behaviors diverge from group attack "wolfpack," cell-to-cell proximity "epibiotic," periplasmic penetration, and endobiotic invasion to degrade host-cellular content. The epibiotic represents the dominant facultative mode of predation, irrespective of the habitat origins. The wolfpack is the second-used approach among the Actinomycetota harboring predatory traits. The secondary molecules as chemical weapons engaged in the respective attacks were reviewed. We finally explored the use of predatory Actinomycetota as a new cost-effective and sustainable biocontrol agent against plant pathogens.
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Affiliation(s)
- Manar Ibrahimi
- Laboratory of Molecular Chemistry, Materials and Catalysis, Faculty of Sciences and Technics, Sultan Moulay Slimane University, Beni-Mellal, Morocco,Higher School of Technology Fkih Ben Salah, Sultan Moulay Slimane University, Fkih Ben Salah, Morocco
| | - Souad Loqman
- Laboratory of Microbiology and Virology, Faculty of Medicine and Pharmacy, Cadi Ayyad University, Marrakesh, Morocco
| | - Martin Jemo
- AgroBiosciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Mohamed Hafidi
- AgroBiosciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco,Labelled Research Unit N°4 CNRST, Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco
| | - Laurent Lemee
- Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP–CNRS UMR 7285), Université de Poitiers, Poitiers, France
| | - Yedir Ouhdouch
- AgroBiosciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco,Labelled Research Unit N°4 CNRST, Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco,*Correspondence: Yedir Ouhdouch,
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Enespa, Chandra P. Tool and techniques study to plant microbiome current understanding and future needs: an overview. Commun Integr Biol 2022; 15:209-225. [PMID: 35967908 PMCID: PMC9367660 DOI: 10.1080/19420889.2022.2082736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Microorganisms are present in the universe and they play role in beneficial and harmful to human life, society, and environments. Plant microbiome is a broad term in which microbes are present in the rhizo, phyllo, or endophytic region and play several beneficial and harmful roles with the plant. To know of these microorganisms, it is essential to be able to isolate purification and identify them quickly under laboratory conditions. So, to improve the microbial study, several tools and techniques such as microscopy, rRNA, or rDNA sequencing, fingerprinting, probing, clone libraries, chips, and metagenomics have been developed. The major benefits of these techniques are the identification of microbial community through direct analysis as well as it can apply in situ. Without tools and techniques, we cannot understand the roles of microbiomes. This review explains the tools and their roles in the understanding of microbiomes and their ecological diversity in environments.
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Affiliation(s)
- Enespa
- Department of Plant Pathology, School of Agriculture, SMPDC, University of Lucknow, Lucknow, India
| | - Prem Chandra
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (A Central) University, Lucknow, India
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Melayah D, Bontemps Z, Bruto M, Nguyen A, Oger P, Hugoni M. Metabarcoding of the Three Domains of Life in Aquatic Saline Ecosystems. Methods Mol Biol 2022; 2605:17-35. [PMID: 36520387 DOI: 10.1007/978-1-0716-2871-3_2] [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: 12/23/2022]
Abstract
High-throughput amplicon sequencing, known as metabarcoding, is a powerful technique to decipher exhaustive microbial diversity considering specific gene markers. While most of the studies investigating ecosystem functioning through microbial diversity targeted only one domain of life, either bacteria, or archaea or microeukaryotes, the remaining challenge in microbial ecology is to uncover the integrated view of microbial diversity occurring in ecosystems. Indeed, interactions occurring between the different microbial counterparts are now recognized having a great impact on stability and resilience of ecosystems. Here, we summarize protocols describing sampling, molecular, and simultaneous metabarcoding of bacteria, archaea, and microeukaryotes, as well as a bioinformatic pipeline allowing the study of exhaustive microbial diversity in natural aquatic saline samples.
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Affiliation(s)
- Delphine Melayah
- Université de Lyon, INSA Lyon, CNRS, UMR5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
| | - Zélia Bontemps
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Maxime Bruto
- Université de Lyon, VetAgro Sup, Anses, UMR Mycoplasmoses Animales, Marcy l'Etoile, France
| | | | - Philippe Oger
- Université de Lyon, INSA Lyon, CNRS, UMR5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
| | - Mylène Hugoni
- Université de Lyon, INSA Lyon, CNRS, UMR5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France.
- Institut Universitaire de France (IUF), Paris, France.
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Xing J, Chen M, Deng X, Chen J, Jiang P, Qin H. Resilience of soil microbial metabolic functions to temporary E. coli invasion. CHEMOSPHERE 2022; 307:135906. [PMID: 35944672 DOI: 10.1016/j.chemosphere.2022.135906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/23/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Due to the globalization and increasing human activities, there is a significant increase in bacterial invasions to the soil ecosystems. Soil resident communities are vulnerable to bacterial invasion and suffered legacy effects after unsuccessful invasion. However, whether such changes in the soil ecosystems are permanent or temporary remains unclear. Here, we investigated the functional resilience of soil ecosystems to bacterial invasion and intensive managements. We used Escherichia coli O157:H7 (E. coli) as model strain examined the soil microbial metabolic functions, including enzyme activities, nitrogen and carbon use efficiency, community niche, and carbon metabolic potential, as well as soil physicochemical properties and microbial invader survival in 8 soil samples, 4 from natural hardwood forests and 4 from intensively managed Moso bamboo forests. The results showed that soil ecosystems were not resistant to E. coli invasion regardless of the intensity of management, which the finding was significantly reflected in the nutrient-acquiring activities or carbon utilization, or both. Besides, the invasion legacy effect (the effect after invader apoptosis) was positively related to E. coli survival time. However, most of the metabolic functions could recover almost to the initial state after 135 days of incubation, suggesting a strong recovery capacity of the soil ecosystems. These data indicate that E. coli invasion has a legacy effect on the functions of soil resident communities. However, soil ecosystems are highly resilient even under intensive human management.
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Affiliation(s)
- Jiajia Xing
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Min Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junhui Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Peikun Jiang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Hua Qin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China.
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Sridhar S, Ajo-Franklin CM, Masiello CA. A Framework for the Systematic Selection of Biosensor Chassis for Environmental Synthetic Biology. ACS Synth Biol 2022; 11:2909-2916. [PMID: 35961652 PMCID: PMC9486965 DOI: 10.1021/acssynbio.2c00079] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Microbial biosensors sense and report exposures to stimuli, thereby facilitating our understanding of environmental processes. Successful design and deployment of biosensors hinge on the persistence of the microbial host of the genetic circuit, termed the chassis. However, model chassis organisms may persist poorly in environmental conditions. In contrast, non-model organisms persist better in environmental conditions but are limited by other challenges, such as genetic intractability and part unavailability. Here we identify ecological, metabolic, and genetic constraints for chassis development and propose a conceptual framework for the systematic selection of environmental biosensor chassis. We identify key challenges with using current model chassis and delineate major points of conflict in choosing the most suitable organisms as chassis for environmental biosensing. This framework provides a way forward in the selection of biosensor chassis for environmental synthetic biology.
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Affiliation(s)
- Swetha Sridhar
- Systems,
Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, Texas 77005, United
States,Tel: 713-348-2565.
| | - Caroline M. Ajo-Franklin
- Department
of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Caroline A. Masiello
- Department
of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States,Department
of Earth, Environmental, and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United
States
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41
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Tang J, Chen J, Chen D, Li Z, Huang D, Luo H. Structural Characteristics and Formation Mechanism of Microbiota Related to Fermentation Ability and Alcohol Production Ability in Nongxiang Daqu. Foods 2022; 11:foods11172602. [PMID: 36076788 PMCID: PMC9455232 DOI: 10.3390/foods11172602] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 12/04/2022] Open
Abstract
Fermentation ability and alcohol production ability are important quality indicators of Chinese liquor Daqu, reflecting microbial growth and metabolic capacity and ethanol production capacity of Daqu microbiota, respectively. However, information on the microbial community related to the fermentation ability and alcohol production ability is unclear. In this study, fermentation functional microbiota (FFM) and alcohol functional microbiota (AFM) were obtained by correlating fermentation ability and alcohol production ability with Daqu microbiota. FFM and AFM consisted of 50 and 49 genera, respectively, which were basically the same at the phylum level but differed at the genus level. Correlation analysis showed that FFM and AFM were mainly affected by moisture, acidity, and humidity in the early stage of Daqu fermentation, and oxygen content was a critical factor for microbial succession in the middle stage of fermentation. FFM and AFM had commensal or synergistic interactions with multiple microbes. Function predictions indicated that fermentation functional bacterial microbiota was active in product synthesis and transport-related metabolic functions, and alcohol functional bacterial microbiota was very active in raw material utilization and its own metabolic synthesis. This study reveals the structural characteristics and formation mechanism of FFM and AFM, which is important for control of Daqu quality.
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Affiliation(s)
- Jie Tang
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong 643000, China
| | - Jie Chen
- Yibin Nanxi Wine Co., Ltd., Yibin 644000, China
| | - Deming Chen
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong 643000, China
| | - Zijian Li
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong 643000, China
- Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Yibin 644000, China
| | - Dan Huang
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong 643000, China
- Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Yibin 644000, China
| | - Huibo Luo
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong 643000, China
- Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Yibin 644000, China
- Correspondence: or
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42
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Xing G, Lu J, Xuan L, Chen J, Xiong J. Sediment prokaryotic assembly, methane cycling, and ammonia oxidation potentials in response to increasing antibiotic pollution at shrimp aquafarm. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128885. [PMID: 35421673 DOI: 10.1016/j.jhazmat.2022.128885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/30/2022] [Accepted: 04/07/2022] [Indexed: 05/28/2023]
Abstract
Antibiotic pollution poses serious threats to public health and ecological processes. However, systematic research regarding the interactive effects of increasing nutrient and antibiotic pollutions on the prokaryotic community, particularly taxa that contribute to greenhouse gas emissions, is lacking. By exploring the complex interactions that occur between interkingdom bacteria and archaea, biotic and abiotic factors, the responses of sediment prokaryotic assembly were determined along a significant antibiotic pollution gradient. Bacterial and archaeal communities were primarily governed by sediment antibiotic pollution, ammonia, phosphate, and redox potential, which further affected enzyme activities. The two communities nonlinearly responded to increasing antibiotic pollution, with significant tipping points of 3.906 and 0.979 mg/kg antibiotics, respectively. The combined antibiotic concentration-discriminatory taxa of bacteria and archaea accurately (98.0% accuracy) diagnosed in situ antibiotic concentrations. Co-abundance analysis revealed that the methanogens, methanotrophs, sulfate-reducing bacteria, and novel players synergistically contributed to methane cycling. Antibiotic pollution caused the dominant role of ammonia-oxidizing archaea in ammonia oxidation at these alkaline sediments. Collectively, the significant tipping points and bio-indicators afford indexes for regime shift and quantitative diagnosis of antibiotic pollution, respectively. Antibiotic pollution could expedite methane cycling and mitigate nitrous oxide yield, which are previously unrecognized ecological effects. These findings provide new insights into the interactive biological and ecological consequences of increasing nutrient and antibiotic pollutions.
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Affiliation(s)
- Guorui Xing
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Lixia Xuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China.
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China.
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43
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Fang Y, Yang Y, Liu C. Evolutionary Relationships Between Dysregulated Genes in Oral Squamous Cell Carcinoma and Oral Microbiota. Front Cell Infect Microbiol 2022; 12:931011. [PMID: 35909962 PMCID: PMC9328420 DOI: 10.3389/fcimb.2022.931011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/20/2022] [Indexed: 11/30/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is one of the most prevalent cancers in the world. Changes in the composition and abundance of oral microbiota are associated with the development and metastasis of OSCC. To elucidate the exact roles of the oral microbiota in OSCC, it is essential to reveal the evolutionary relationships between the dysregulated genes in OSCC progression and the oral microbiota. Thus, we interrogated the microarray and high-throughput sequencing datasets to obtain the transcriptional landscape of OSCC. After identifying differentially expressed genes (DEGs) with three different methods, pathway and functional analyses were also performed. A total of 127 genes were identified as common DEGs, which were enriched in extracellular matrix organization and cytokine related pathways. Furthermore, we established a predictive pipeline for detecting the coevolutionary of dysregulated host genes and microbial proteomes based on the homology method, and this pipeline was employed to analyze the evolutionary relations between the seven most dysregulated genes (MMP13, MMP7, MMP1, CXCL13, CRISPO3, CYP3A4, and CRNN) and microbiota obtained from the eHOMD database. We found that cytochrome P450 3A4 (CYP3A4), a member of the cytochrome P450 family of oxidizing enzymes, was associated with 45 microbes from the eHOMD database and involved in the oral habitat of Comamonas testosteroni and Arachnia rubra. The peptidase M10 family of matrix metalloproteinases (MMP13, MMP7, and MMP1) was associated with Lacticaseibacillus paracasei, Lacticaseibacillus rhamnosus, Streptococcus salivarius, Tannerella sp._HMT_286, and Streptococcus infantis in the oral cavity. Overall, this study revealed the dysregulated genes in OSCC and explored their evolutionary relationship with oral microbiota, which provides new insight for exploring the microbiota–host interactions in diseases.
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Affiliation(s)
- Yang Fang
- Department of Laboratory Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yi Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontics, West China School and Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chengcheng Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontics, West China School and Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Chengcheng Liu,
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44
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Nwachukwu BC, Babalola OO. Metagenomics: A Tool for Exploring Key Microbiome With the Potentials for Improving Sustainable Agriculture. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.886987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are immense in nature and exist in every imaginable ecological niche, performing a wide range of metabolic processes. Unfortunately, using traditional microbiological methods, most microorganisms remain unculturable. The emergence of metagenomics has resolved the challenge of capturing the entire microbial community in an environmental sample by enabling the analysis of whole genomes without requiring culturing. Metagenomics as a non-culture approach encompasses a greater amount of genetic information than traditional approaches. The plant root-associated microbial community is essential for plant growth and development, hence the interactions between microorganisms, soil, and plants is essential to understand and improve crop yields in rural and urban agriculture. Although some of these microorganisms are currently unculturable in the laboratory, metagenomic techniques may nevertheless be used to identify the microorganisms and their functional traits. A detailed understanding of these organisms and their interactions should facilitate an improvement of plant growth and sustainable crop production in soil and soilless agriculture. Therefore, the objective of this review is to provide insights into metagenomic techniques to study plant root-associated microbiota and microbial ecology. In addition, the different DNA-based techniques and their role in elaborating plant microbiomes are discussed. As an understanding of these microorganisms and their biotechnological potentials are unlocked through metagenomics, they can be used to develop new, useful and unique bio-fertilizers and bio-pesticides that are not harmful to the environment.
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45
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Research Progress and Hopeful Strategies of Application of Quorum Sensing in Food, Agriculture and Nanomedicine. Microorganisms 2022; 10:microorganisms10061192. [PMID: 35744710 PMCID: PMC9229978 DOI: 10.3390/microorganisms10061192] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 02/06/2023] Open
Abstract
Quorum sensing (QS) regulates the expression of several genes including motility, biofilm development, virulence expression, population density detection and plasmid conjugation. It is based on “autoinducers”, small molecules that microorganisms produce and release in the extracellular milieu. The biochemistry of quorum sensing is widely discussed and numerous papers are available to scientists. The main purpose of this research is to understand how knowledge about this mechanism can be exploited for the benefit of humans and the environment. Here, we report the most promising studies on QS and their resulting applications in different fields of global interest: food, agriculture and nanomedicine.
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Maldonado JE, Gaete A, Mandakovic D, Aguado-Norese C, Aguilar M, Gutiérrez RA, González M. Partners to survive: Hoffmannseggia doellii root-associated microbiome at the Atacama Desert. THE NEW PHYTOLOGIST 2022; 234:2126-2139. [PMID: 35274744 DOI: 10.1111/nph.18080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
The discovery and characterization of plant species adapted to extreme environmental conditions have become increasingly important. Hoffmannseggia doellii is a perennial herb endemic to the Chilean Atacama Desert that grows in the western Andes between 2800 and 3600 m above sea level. Its growing habitat is characterized by high radiation and low water and nutrient availability. Under these conditions, H. doellii can grow, reproduce, and develop an edible tuberous root. We characterized the H. doellii soil-associated microbiomes to understand the biotic factors that could influence their surprising ability to survive. We found an increased number of observed species and higher phylogenetic diversity of bacteria and fungi on H. doellii root soils compared with bare soil (BS) along different sites and to soil microbiomes of other plant species. Also, the H. doellii-associated microbiome had a higher incidence of overall positive interactions and fungal within-kingdom interactions than their corresponding BS network. These findings suggest a microbial diversity soil modulation mechanism that may be a characteristic of highly tolerant plants to diverse and extreme environments. Furthermore, since H. doellii is related to important cultivated crops, our results create an opportunity for future studies on climate change adaptation of crop plants.
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Affiliation(s)
- Jonathan E Maldonado
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Departamento de Genética Molecular y Microbiología, ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 7500565, Chile
- Laboratorio de Multiómica Vegetal y Bioinformática, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile
| | - Alexis Gaete
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, 7830490, Chile
| | - Dinka Mandakovic
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, 8580745, Chile
| | - Constanza Aguado-Norese
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, 7830490, Chile
| | - Melissa Aguilar
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Departamento de Genética Molecular y Microbiología, ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 7500565, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Departamento de Genética Molecular y Microbiología, ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 7500565, Chile
| | - Mauricio González
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, 7830490, Chile
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Zhou Y, Wang H, Xu S, Liu K, Qi H, Wang M, Chen X, Berg G, Ma Z, Cernava T, Chen Y. Bacterial-fungal interactions under agricultural settings: from physical to chemical interactions. STRESS BIOLOGY 2022; 2:22. [PMID: 37676347 PMCID: PMC10442017 DOI: 10.1007/s44154-022-00046-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/17/2022] [Indexed: 09/08/2023]
Abstract
Bacteria and fungi are dominant members of environmental microbiomes. Various bacterial-fungal interactions (BFIs) and their mutual regulation are important factors for ecosystem functioning and health. Such interactions can be highly dynamic, and often require spatiotemporally resolved assessments to understand the interplay which ranges from antagonism to mutualism. Many of these interactions are still poorly understood, especially in terms of the underlying chemical and molecular interplay, which is crucial for inter-kingdom communication and interference. BFIs are highly relevant under agricultural settings; they can be determinative for crop health. Advancing our knowledge related to mechanisms underpinning the interactions between bacteria and fungi will provide an extended basis for biological control of pests and pathogens in agriculture. Moreover, it will facilitate a better understanding of complex microbial community networks that commonly occur in nature. This will allow us to determine factors that are crucial for community assembly under different environmental conditions and pave the way for constructing synthetic communities for various biotechnological applications. Here, we summarize the current advances in the field of BFIs with an emphasis on agriculture.
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Affiliation(s)
- Yaqi Zhou
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Hongkai Wang
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Sunde Xu
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Kai Liu
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Hao Qi
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Mengcen Wang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Xiaoyulong Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria
- Leibniz-Institute for Agricultural Engineering and Bioeconomy, Potsdam, Germany
- University of Potsdam, Potsdam, Germany
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria.
| | - Yun Chen
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
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48
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Wan Y, Zuo T, Xu Z, Zhang F, Zhan H, Chan D, Leung TF, Yeoh YK, Chan FKL, Chan R, Ng SC. Underdevelopment of the gut microbiota and bacteria species as non-invasive markers of prediction in children with autism spectrum disorder. Gut 2022; 71:910-918. [PMID: 34312160 DOI: 10.1136/gutjnl-2020-324015] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/20/2021] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The gut microbiota has been suggested to play a role in autism spectrum disorder (ASD). We postulate that children with ASD harbour an altered developmental profile of the gut microbiota distinct from that of typically developing (TD) children. Here, we aimed to characterise compositional and functional alterations in gut microbiome in association with age in children with ASD and to identify novel faecal bacterial markers for predicting ASD. DESIGN We performed deep metagenomic sequencing in faecal samples of 146 Chinese children (72 ASD and 74 TD children). We compared gut microbial composition and functions between children with ASD and TD children. Candidate bacteria markers were identified and validated by metagenomic analysis. Gut microbiota development in relation to chronological age was assessed using random forest model. RESULTS ASD and chronological age had the most significant and largest impacts on children's faecal microbiome while diet showed no correlation. Children with ASD had significant alterations in faecal microbiome composition compared with TD children characterised by increased bacterial richness (p=0.021) and altered microbiome composition (p<0.05). Five bacterial species were identified to distinguish gut microbes in ASD and TD children, with areas under the receiver operating curve (AUC) of 82.6% and 76.2% in the discovery cohort and validation cohort, respectively. Multiple neurotransmitter biosynthesis related pathways in the gut microbiome were depleted in children with ASD compared with TD children (p<0.05). Developing dynamics of growth-associated gut bacteria (age-discriminatory species) seen in TD children were lost in children with ASD across the early-life age spectrum. CONCLUSIONS Gut microbiome in Chinese children with ASD was altered in composition, ecological network and functionality compared with TD children. We identified novel bacterial markers for prediction of ASD and demonstrated persistent underdevelopment of the gut microbiota in children with ASD which lagged behind their respective age-matched peers.
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Affiliation(s)
- Yating Wan
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Microbiota I-Center (MagIC), Hong Kong, China
| | - Tao Zuo
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhilu Xu
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Microbiota I-Center (MagIC), Hong Kong, China
| | - Fen Zhang
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Microbiota I-Center (MagIC), Hong Kong, China
| | - Hui Zhan
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Microbiota I-Center (MagIC), Hong Kong, China
| | - Dorothy Chan
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Ting-Fan Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun Kit Yeoh
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Microbiota I-Center (MagIC), Hong Kong, China.,Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Francis K L Chan
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Microbiota I-Center (MagIC), Hong Kong, China
| | - Ruth Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Siew C Ng
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China .,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Microbiota I-Center (MagIC), Hong Kong, China
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Fessia A, Barra P, Barros G, Nesci A. Could Bacillus biofilms enhance the effectivity of biocontrol strategies in the phyllosphere? J Appl Microbiol 2022; 133:2148-2166. [PMID: 35476896 DOI: 10.1111/jam.15596] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 11/30/2022]
Abstract
Maize (Zea mays L.), a major crop in Argentina and a staple food around the world, is affected by the emergence and re-emergence of foliar diseases. Agrochemicals are the main control strategy nowadays, but they can cause resistance in insects and microbial pathogens and have negative effects on the environment and human health. An emerging alternative is the use of living organisms, i.e. microbial biocontrol agents, to suppress plant pathogen populations. This is a risk-free approach when the organisms acting as biocontrol agents come from the same ecosystem as the foliar pathogens they are meant to antagonize. Some epiphytic microorganisms may form biofilm by becoming aggregated and attached to a surface, as is the case of spore-forming bacteria from the genus Bacillus. Their ability to sporulate and their tolerance to long storage periods make them a frequently used biocontrol agent. Moreover, the biofilm that they create protects them against different abiotic and biotic factors and helps them to acquire nutrients, which ensures their survival on the plants they protect. This review analyzes the interactions that the phyllosphere-inhabiting Bacillus genus establishes with its environment through biofilm, and how this lifestyle could serve to design effective biological control strategies.
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Affiliation(s)
- Aluminé Fessia
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina
| | - Paula Barra
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina
| | - Germán Barros
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina
| | - Andrea Nesci
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina
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Inhibitory Bacterial Diversity and Mucosome Function Differentiate Susceptibility of Appalachian Salamanders to Chytrid Fungal Infection. Appl Environ Microbiol 2022; 88:e0181821. [PMID: 35348389 PMCID: PMC9040618 DOI: 10.1128/aem.01818-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Mucosal defenses are crucial in animals for protection against pathogens and predators. Host defense peptides (antimicrobial peptides, AMPs) as well as skin-associated microbes are key components of mucosal immunity, particularly in amphibians. We integrate microbiology, molecular biology, network-thinking, and proteomics to understand how host and microbially derived products on amphibian skin (referred to as the mucosome) serve as pathogen defenses. We studied defense mechanisms against chytrid pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), in four salamander species with different Batrachochytrium susceptibilities. Bd infection was quantified using qPCR, mucosome function (i.e., ability to kill Bd or Bsal zoospores in vitro), skin bacterial communities using 16S rRNA gene amplicon sequencing, and the role of Bd-inhibitory bacteria in microbial networks across all species. We explored the presence of candidate-AMPs in eastern newts and red-backed salamanders. Eastern newts had the highest Bd prevalence and mucosome function, while red-back salamanders had the lowest Bd prevalence and mucosome function, and two-lined salamanders and seal salamanders were intermediates. Salamanders with highest Bd infection intensity showed greater mucosome function. Bd infection prevalence significantly decreased as putative Bd-inhibitory bacterial richness and relative abundance increased on hosts. In co-occurrence networks, some putative Bd-inhibitory bacteria were found as hub-taxa, with red-backs having the highest proportion of protective hubs and positive associations related to putative Bd-inhibitory hub bacteria. We found more AMP candidates on salamanders with lower Bd susceptibility. These findings suggest that salamanders possess distinct innate mechanisms that affect chytrid fungi. IMPORTANCE How host mucosal defenses interact, and influence disease outcome is critical in understanding host defenses against pathogens. A more detailed understanding is needed of the interactions between the host and the functioning of its mucosal defenses in pathogen defense. This study investigates the variability of chytrid susceptibility in salamanders and the innate defenses each species possesses to mediate pathogens, thus advancing the knowledge toward a deeper understanding of the microbial ecology of skin-associated bacteria and contributing to the development of bioaugmentation strategies to mediate pathogen infection and disease. This study improves the understanding of complex immune defense mechanisms in salamanders and highlights the potential role of the mucosome to reduce the probability of Bd disease development and that putative protective bacteria may reduce likelihood of Bd infecting skin.
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