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Rangel LI, Leveau JHJ. Applied microbiology of the phyllosphere. Appl Microbiol Biotechnol 2024; 108:211. [PMID: 38358509 PMCID: PMC10869387 DOI: 10.1007/s00253-024-13042-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024]
Abstract
The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.
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Affiliation(s)
- Lorena I Rangel
- Cell & Molecular Sciences, The James Hutton Institute, Dundee, Scotland, UK.
- Department of Plant Pathology, University of California, Davis, CA, USA.
| | - Johan H J Leveau
- Department of Plant Pathology, University of California, Davis, CA, USA.
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Xu L, Li K, Bai X, Zhang G, Tian X, Tang Q, Zhang M, Hu M, Huang Y. Microplastics in the atmosphere: Adsorb on leaves and their effects on the phyllosphere bacterial community. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132789. [PMID: 37862903 DOI: 10.1016/j.jhazmat.2023.132789] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/02/2023] [Accepted: 10/13/2023] [Indexed: 10/22/2023]
Abstract
Phyllosphere is the largest interface between the atmosphere and terrestrial ecosystems and serves as a major sink for atmospheric microplastics (MPs). It is also a unique habitat for microbiota with diverse ecological functions. This field study investigated the characteristics of atmospheric MPs adsorbed on leaves with automatic technology, and found their abundance was 3.62 ± 1.29 items cm-2. MPs on leaves were mainly below 80 µm, and dominated by polyamide, polyethene, and rubber. MPs on leaves correlated significantly with the structure and functions of the phyllosphere bacterial community (PBC). Both the MPs abundance and size distribution (MSD) were positively correlated with the α diversity and negatively correlated with the β diversity and network complexity of PBC. PBC functions of environmental and genetic information process were negatively correlated with MPs abundance, and functions related to human diseases and cellular process were positively correlated with MSD significantly. The relative abundance of Sphingomonas was significantly correlated with the MSD, suggesting that Sphingomonas might emerge as the key genus involved in the pathogenicity of PBC mediated by MPs. These results highlighted the ecological health risks of atmospheric MPs as they can be transferred anywhere and potentially increase the pathogenicity of local phyllosphere microflora.
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Affiliation(s)
- Libo Xu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Kang Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xinyi Bai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Guangbao Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xudong Tian
- Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control of Zhejiang, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, China
| | - Qian Tang
- Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control of Zhejiang, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, China
| | - Mengjun Zhang
- Peking University Shenzhen Institute, Shenzhen, Guangdong 518057, China; PKU-HKUST Shenzhen-Hongkong Institution, Shenzhen, Guangdong 518057, China.
| | - Min Hu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Peking University Shenzhen Institute, Shenzhen, Guangdong 518057, China.
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Gottel NR, Hill MS, Neal MJ, Allard SM, Zengler K, Gilbert JA. Biocontrol in built environments to reduce pathogen exposure and infection risk. THE ISME JOURNAL 2024; 18:wrad024. [PMID: 38365248 PMCID: PMC10848226 DOI: 10.1093/ismejo/wrad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.
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Affiliation(s)
- Neil R Gottel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
| | - Megan S Hill
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Maxwell J Neal
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, United States
| | - Sarah M Allard
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Karsten Zengler
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, United States
| | - Jack A Gilbert
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, United States
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Zhou JC, Wang YF, Zhu D, Zhu YG. Deciphering the distribution of microbial communities and potential pathogens in the household dust. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162250. [PMID: 36804982 DOI: 10.1016/j.scitotenv.2023.162250] [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: 11/27/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
The reliance of modern society on indoor environments increasing has made them crucial sites for human exposure to microbes. Extensive research has identified ecological drivers that influence indoor microbial assemblages. However, few studies have examined the dispersion of microbes in different locations of identical indoor environments. In this study, we employed PacBio Sequel full-length amplicon sequencing to examine the distribution of microbes at distinct locations in a single home and to identify the potential pathogens and microbial functions. Microbial communities differed considerably among the indoor sampling sites (P < 0.05). In addition, bacterial diversity was influenced by human activities and contact with the external environment at different sites, whereas fungal diversity did not significantly differ among the sites. Potential pathogens, including bacteria and fungi, were significantly enriched on the door handle (P < 0.05), suggesting that door handles may be hotpots for potential pathogens in the household. A high proportion of fungal allergens (34.37 %-56.50 %), which can cause skin diseases and asthma, were observed. Co-occurrence network analysis revealed the essential ecological role of microbial interactions in the development of a healthy immune system. Overall, we revealed the differences in microbial communities at different sampling sites within a single indoor environment, highlighting the distribution of potential pathogens and ecological functions of microbes, and providing a new perspective and information for assessing indoor health from a microbiological viewpoint.
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Affiliation(s)
- Jia-Cheng Zhou
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; International School of Beijing, Beijing 101318, China
| | - Yi-Fei Wang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of the Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Wicaksono WA, Morauf C, Müller H, Abdelfattah A, Donat C, Berg G. The mature phyllosphere microbiome of grapevine is associated with resistance against Plasmopara viticola. Front Microbiol 2023; 14:1149307. [PMID: 37113228 PMCID: PMC10127535 DOI: 10.3389/fmicb.2023.1149307] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/15/2023] [Indexed: 04/29/2023] Open
Abstract
Phyllosphere microbiota represents a substantial but hardly explored reservoir for disease resistance mechanisms. The goal of our study was to understand the link between grapevine cultivars susceptibility to Plasmopara viticola, one of the most devastating leaf pathogens in viticulture, and the phyllosphere microbiota. Therefore, we analyzed a 16S rRNA gene library for the dominant phyllosphere bacterial phyla Alphaproteobacteria of seven Vitis genotypes at different developmental stages, i.e., flowering and harvesting, via amplicon sequencing. Young leaves had significantly higher Alphaproteobacterial richness and diversity without significant host-specificity. In contrast, the microbial communities of mature leaves were structurally distinct in accordance with P. viticola resistance levels. This statistically significant link between mature bacterial phyllosphere communities and resistant phenotypes was corroborated by beta diversity metrics and network analysis. Beyond direct host-driven effects via the provision of microhabitats, we found evidence that plants recruit for specific bacterial taxa that were likely playing a fundamental role in mediating microbe-microbe interactions and structuring clusters within mature communities. Our results on grape-microbiota interaction provide insights for targeted biocontrol and breeding strategies.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- *Correspondence: Wisnu Adi Wicaksono,
| | | | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Graz, Austria
- Gabriele Berg,
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The Microbiome of the Built Environment: The Nexus for Urban Regeneration for the Cities of Tomorrow. Microorganisms 2022; 10:microorganisms10122311. [PMID: 36557564 PMCID: PMC9783557 DOI: 10.3390/microorganisms10122311] [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: 10/17/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Built environments are, for most of us, our natural habitat. In the last 50 years, the built-up area has more than doubled, with a massive biodiversity loss. The undeniable benefits of a city providing all the basic needs to a growing population showed longer-term and less obvious costs to human health: autoimmune and non-communicable diseases, as well as antimicrobial resistance, have reached unprecedented and alarming levels. Humans coevolved with microbes, and this long-lasting alliance is affected by the loss of connection with natural environments, misuse of antibiotics, and highly sanitized environments. Our aim is to direct the focus onto the microbial communities harbored by the built environments we live in. They represent the nexus for urban regeneration, which starts from a healthy environment. Planning a city means considering, in a two-fold way, the ecosystem health and the multidimensional aspects of wellbeing, including social, cultural, and aesthetic values. The significance of this perspective is inspiring guidelines and strategies for the urban regeneration of the cities of tomorrow, exploiting the invaluable role of microbial biodiversity and the ecosystem services that it could provide to create the robust scientific knowledge that is necessary for a bioinformed design of buildings and cities for healthy and sustainable living.
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