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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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Fuentes-Quiroz A, Herrera H, Alvarado R, Rabert C, Arriagada C, Valadares RBDS. Functional differences of cultivable leaf-associated microorganisms in the native Andean tree Gevuina avellana Mol. (Proteaceae) exposed to atmospheric contamination. J Appl Microbiol 2024; 135:lxae041. [PMID: 38364303 DOI: 10.1093/jambio/lxae041] [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: 12/12/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
AIMS This study aimed to evaluate and describe the functional differences of cultivable bacteria and fungi inhabiting the leaves of Gevuina avellana Mol. (Proteaceae) in an urban area with high levels of air pollution and in a native forest in the southern Andes. METHODS AND RESULTS Phyllosphere microorganisms were isolated from the leaves of G. avellana, their plant growth-promoting capabilities were estimated along with their biocontrol potential and tolerance to metal(loid)s. Notably, plants from the urban area showed contrasting culturable leaf-associated microorganisms compared to those from the native area. The tolerance to metal(loid)s in bacteria range from 15 to 450 mg l-1 of metal(loid)s, while fungal strains showed tolerance from 15 to 625 mg l-1, being especially higher in the isolates from the urban area. Notably, the bacterial strain Curtobacterium flaccumfaciens and the fungal strain Cladosporium sp. exhibited several plant-growth-promoting properties along with the ability to inhibit the growth of phytopathogenic fungi. CONCLUSIONS Overall, our study provides evidence that culturable taxa in G. avellana leaves is directly influenced by the sampling area. This change is likely due to the presence of atmospheric pollutants and diverse microbial symbionts that can be horizontally acquired from the environment.
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Affiliation(s)
- Alejandra Fuentes-Quiroz
- Laboratorio de Silvicultura, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile
| | - Héctor Herrera
- Laboratorio de Silvicultura, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile
| | - Roxana Alvarado
- Laboratorio de Silvicultura, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile
| | - Claudia Rabert
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Avenida Alemania 01090, Temuco, Chile
| | - Cesar Arriagada
- Laboratorio de Biorremediación, Departamento de Ciencias Forestales, Universidad de La Frontera, Temuco 4811230, Chile
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Wang W, Hu C, Chang Y, Wang L, Bi Q, Lu X, Zheng Z, Zheng X, Wu D, Niu B. Differentiated responses of the phyllosphere bacterial community of the yellowhorn tree to precipitation and temperature regimes across Northern China. FRONTIERS IN PLANT SCIENCE 2023; 14:1265362. [PMID: 37954985 PMCID: PMC10634255 DOI: 10.3389/fpls.2023.1265362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/10/2023] [Indexed: 11/14/2023]
Abstract
Introduction As an ephemeral and oligotrophic environment, the phyllosphere harbors many highly diverse microorganisms. Importantly, it is known that their colonization of plant leaf surfaces is considerably influenced by a few abiotic factors related to climatic conditions. Yet how the dynamics of phyllosphere bacterial community assembly are shaped by detailed climatological elements, such as various bioclimatic variables, remains poorly understood. Methods Using high-throughput 16S rRNA gene amplicon sequencing technology, we analyzed the bacterial communities inhabiting the leaf surfaces of an oilseed tree, yellowhorn (Xanthoceras sorbifolium), grown at four sites (Yinchuan, Otogqianqi, Tongliao, and Zhangwu) whose climatic status differs in northern China. Results and Discussion We found that the yellowhorn phyllosphere's bacterial community was generally dominated by four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Nevertheless, bacterial community composition differed significantly among the four sampled site regions, indicating the possible impact of climatological factors upon the phyllosphere microbiome. Interestingly, we also noted that the α-diversities of phyllosphere microbiota showed strong positive or negative correlation with 13 bioclimatic factors (including 7 precipitation factors and 6 temperature factors). Furthermore, the relative abundances of 55 amplicon sequence variants (ASVs), including three ASVs representing two keystone taxa (the genera Curtobacterium and Streptomyces), exhibited significant yet contrary responses to the precipitation and temperature climatic variables. That pattern was consistent with all ASVs' trends of possessing opposite correlations to those two parameter classes. In addition, the total number of links and nodes, which conveys community network complexity, increased with rising values of most temperature variables. Besides that, remarkably positive relevance was found between average clustering coefficient and most precipitation variables. Altogether, these results suggest the yellowhorn phyllosphere bacterial community is capable of responding to variation in rainfall and temperature regimes in distinctive ways.
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Affiliation(s)
- Weixiong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Congcong Hu
- Department of Mathematics, Shanghai Normal University, Shanghai, China
| | - Yu Chang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Libing Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Quanxin Bi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xin Lu
- Chifeng Research Institute of Forestry Science, Chifeng, China
- National Forestry and Grassland Shiny-Leaved Yellowhorn Engineering and Technology Research Center, Chifeng, China
| | - Zhimin Zheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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Genomic, Molecular, and Phenotypic Characterization of Arthrobacter sp. OVS8, an Endophytic Bacterium Isolated from and Contributing to the Bioactive Compound Content of the Essential Oil of the Medicinal Plant Origanum vulgare L. Int J Mol Sci 2023; 24:ijms24054845. [PMID: 36902273 PMCID: PMC10002853 DOI: 10.3390/ijms24054845] [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: 02/03/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
Medicinal plants play an important role in the discovery of new bioactive compounds with antimicrobial activity, thanks to their pharmacological properties. However, members of their microbiota can also synthesize bioactive molecules. Among these, strains belonging to the genera Arthrobacter are commonly found associated with the plant's microenvironments, showing plant growth-promoting (PGP) activity and bioremediation properties. However, their role as antimicrobial secondary metabolite producers has not been fully explored. The aim of this work was to characterize the Arthrobacter sp. OVS8 endophytic strain, isolated from the medicinal plant Origanum vulgare L., from molecular and phenotypic viewpoints to evaluate its adaptation and influence on the plant internal microenvironments and its potential as a producer of antibacterial volatile molecules (VOCs). Results obtained from the phenotypic and genomic characterization highlight its ability to produce volatile antimicrobials effective against multidrug-resistant (MDR) human pathogens and its putative PGP role as a producer of siderophores and degrader of organic and inorganic pollutants. The outcomes presented in this work identify Arthrobacter sp. OVS8 as an excellent starting point toward the exploitation of bacterial endophytes as antibiotics sources.
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Çelik T, Sevim A. Bacterial pathogens from Diprion pini L. (Hymenoptera: Diprionidae) and their biocontrol potential. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01161-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Bashir I, War AF, Rafiq I, Reshi ZA, Rashid I, Shouche YS. Phyllosphere microbiome: Diversity and functions. Microbiol Res 2021; 254:126888. [PMID: 34700185 DOI: 10.1016/j.micres.2021.126888] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.
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Affiliation(s)
- Iqra Bashir
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India.
| | - Aadil Farooq War
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Iflah Rafiq
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Irfan Rashid
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
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Palmer JL, Hilton S, Picot E, Bending GD, Schäfer H. Tree phyllospheres are a habitat for diverse populations of CO-oxidizing bacteria. Environ Microbiol 2021; 23:6309-6327. [PMID: 34523801 DOI: 10.1111/1462-2920.15770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/21/2021] [Accepted: 09/08/2021] [Indexed: 11/28/2022]
Abstract
Carbon monoxide (CO) is both a ubiquitous atmospheric trace gas and an air pollutant. While aerobic CO-degrading microorganisms in soils and oceans are estimated to remove ~370 Tg of CO per year, the presence of CO-degrading microorganisms in above-ground habitats, such as the phyllosphere, and their potential role in CO cycling remains unknown. CO-degradation by leaf washes of two common British trees, Ilex aquifolium and Crataegus monogyna, demonstrated CO uptake in all samples investigated. Based on the analyses of taxonomic and functional genes, diverse communities of candidate CO-oxidizing taxa were identified, including members of Rhizobiales and Burkholderiales which were abundant in the phyllosphere at the time of sampling. Based on predicted genomes of phyllosphere community members, an estimated 21% of phyllosphere bacteria contained CoxL, the large subunit of CO-dehydrogenase. In support of this, data mining of publicly available phyllosphere metagenomes for genes encoding CO-dehydrogenase subunits demonstrated that, on average, 25% of phyllosphere bacteria contained CO-dehydrogenase gene homologues. A CO-oxidizing Phyllobacteriaceae strain was also isolated from phyllosphere samples which contains genes encoding both CO-dehydrogenase as well as a ribulose-1,5-bisphosphate carboxylase-oxygenase. These results suggest that the phyllosphere supports diverse and potentially abundant CO-oxidizing bacteria, which are a potential sink for atmospheric CO.
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Affiliation(s)
- Jess L Palmer
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Emma Picot
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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Aghdam SA, Brown AMV. Deep learning approaches for natural product discovery from plant endophytic microbiomes. ENVIRONMENTAL MICROBIOME 2021; 16:6. [PMID: 33758794 PMCID: PMC7972023 DOI: 10.1186/s40793-021-00375-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/21/2021] [Indexed: 05/10/2023]
Abstract
Plant microbiomes are not only diverse, but also appear to host a vast pool of secondary metabolites holding great promise for bioactive natural products and drug discovery. Yet, most microbes within plants appear to be uncultivable, and for those that can be cultivated, their metabolic potential lies largely hidden through regulatory silencing of biosynthetic genes. The recent explosion of powerful interdisciplinary approaches, including multi-omics methods to address multi-trophic interactions and artificial intelligence-based computational approaches to infer distribution of function, together present a paradigm shift in high-throughput approaches to natural product discovery from plant-associated microbes. Arguably, the key to characterizing and harnessing this biochemical capacity depends on a novel, systematic approach to characterize the triggers that turn on secondary metabolite biosynthesis through molecular or genetic signals from the host plant, members of the rich 'in planta' community, or from the environment. This review explores breakthrough approaches for natural product discovery from plant microbiomes, emphasizing the promise of deep learning as a tool for endophyte bioprospecting, endophyte biochemical novelty prediction, and endophyte regulatory control. It concludes with a proposed pipeline to harness global databases (genomic, metabolomic, regulomic, and chemical) to uncover and unsilence desirable natural products. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s40793-021-00375-0.
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Affiliation(s)
- Shiva Abdollahi Aghdam
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX 79409 USA
| | - Amanda May Vivian Brown
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX 79409 USA
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Chen X, Wicaksono WA, Berg G, Cernava T. Bacterial communities in the plant phyllosphere harbour distinct responders to a broad-spectrum pesticide. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141799. [PMID: 32889475 DOI: 10.1016/j.scitotenv.2020.141799] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/29/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Pesticide application can be accompanied by harmful non-target effects that affect humans, animals, as well as whole ecosystems. However, such effects remain mainly unaddressed in connection with microorganisms, and especially bacteria therein, which are essential for ecosystem functioning and host health. We analysed bacterial communities by sequencing 16S rRNA gene fragment amplicons following spray application of a broad-spectrum fungicide based on the active ingredient N-(3,5-dichlorophenyl) succinimide on Nicotiana tabacum L. leaves. The plant's phyllosphere was predominantly colonized by Proteobacteria, with Alphaproteobacteria accounting for up to 33.8% of the indigenous bacterial community. Bioinformatic analyses indicated that pesticide applications had an effect on the core microbiome as well as the rare microbiome. Moreover, the interference of the pesticide with phyllosphere bacteria was found to be selective. We have identified four positive responders including an ASV assigned to the genus Acinetobacter and 12 negative responders mainly assigned to bacterial genera known for beneficial plant-microbe interactions, including Stenotrophomonas, Sphingomonas, Flavobacterium and Serratia. Complementary inference of bacterial functioning on community level indicated that microbes with distinct stress response systems were likely enriched in the conducted treatments. The overall findings confirmed that pesticide treatments can induce measureable shifts in non-target bacterial communities colonizing the plant phyllosphere. They also indicate that potentially beneficial bacteria, which are known for their intrinsic association with plants, are among the most sensitive responders to the employed fungicide and thus highlight the importance of off-target studies in the context of the plant microbiome.
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Affiliation(s)
- Xiaoyulong Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, 550025 Guiyang, China; College of Tobacco Science, Guizhou University, 550025 Guiyang, China; Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, 550025 Guiyang, China
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria.
| | - Tomislav Cernava
- College of Tobacco Science, Guizhou University, 550025 Guiyang, China; Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, 550025 Guiyang, China; Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria.
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Katsoula A, Vasileiadis S, Sapountzi M, Karpouzas DG. The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: accelerated biodegradation or toxicity? FEMS Microbiol Ecol 2020; 96:5813261. [PMID: 32221586 DOI: 10.1093/femsec/fiaa056] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/23/2020] [Indexed: 12/30/2022] Open
Abstract
Pesticides interact with microorganisms in various ways with the outcome being negative or positive for the soil microbiota. Pesticides' effects on soil microorganisms have been studied extensively in soil but not in other pesticides-exposed microbial habitats like the phyllosphere. We tested the hypothesis that soil and phyllosphere support distinct microbial communities, but exhibit a similar response (accelerated biodegradation or toxicity) to repeated exposure to the fungicide iprodione. Pepper plants received four repeated foliage or soil applications of iprodione, which accelerated its degradation in soil (DT50_1st = 1.23 and DT50_4th = 0.48 days) and on plant leaves (DT50_1st > 365 and DT50_4th = 5.95 days). The composition of the epiphytic and soil bacterial and fungal communities, determined by amplicon sequencing, was significantly altered by iprodione. The archaeal epiphytic and soil communities responded differently; the former showed no response to iprodione. Three iprodione-degrading Paenarthrobacter strains were isolated from soil and phyllosphere. They hydrolyzed iprodione to 3,5-dichloraniline via the formation of 3,5-dichlorophenyl-carboxiamide and 3,5-dichlorophenylurea-acetate, a pathway shared by other soil-derived arthrobacters implying a phylogenetic specialization in iprodione biotransformation. Our results suggest that iprodione-repeated application could affect soil and epiphytic microbial communities with implications for the homeostasis of the plant-soil system and agricultural production.
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Affiliation(s)
- A Katsoula
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis 41500, Larissa, Greece
| | - S Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis 41500, Larissa, Greece
| | - M Sapountzi
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis 41500, Larissa, Greece
| | - Dimitrios G Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis 41500, Larissa, Greece
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Khodadad CLM, Hummerick ME, Spencer LE, Dixit AR, Richards JT, Romeyn MW, Smith TM, Wheeler RM, Massa GD. Microbiological and Nutritional Analysis of Lettuce Crops Grown on the International Space Station. FRONTIERS IN PLANT SCIENCE 2020; 11:199. [PMID: 32210992 PMCID: PMC7067979 DOI: 10.3389/fpls.2020.00199] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/11/2020] [Indexed: 05/07/2023]
Abstract
The ability to grow safe, fresh food to supplement packaged foods of astronauts in space has been an important goal for NASA. Food crops grown in space experience different environmental conditions than plants grown on Earth (e.g., reduced gravity, elevated radiation levels). To study the effects of space conditions, red romaine lettuce, Lactuca sativa cv 'Outredgeous,' plants were grown in Veggie plant growth chambers on the International Space Station (ISS) and compared with ground-grown plants. Multiple plantings were grown on ISS and harvested using either a single, final harvest, or sequential harvests in which several mature leaves were removed from the plants at weekly intervals. Ground controls were grown simultaneously with a 24-72 h delay using ISS environmental data. Food safety of the plants was determined by heterotrophic plate counts for bacteria and fungi, as well as isolate identification using samples taken from the leaves and roots. Molecular characterization was conducted using Next Generation Sequencing (NGS) to provide taxonomic composition and phylogenetic structure of the community. Leaves were also analyzed for elemental composition, as well as levels of phenolics, anthocyanins, and Oxygen Radical Absorbance Capacity (ORAC). Comparison of flight and ground tissues showed some differences in total counts for bacteria and yeast/molds (2.14 - 4.86 log10 CFU/g), while screening for select human pathogens yielded negative results. Bacterial and fungal isolate identification and community characterization indicated variation in the diversity of genera between leaf and root tissue with diversity being higher in root tissue, and included differences in the dominant genera. The only difference between ground and flight experiments was seen in the third experiment, VEG-03A, with significant differences in the genera from leaf tissue. Flight and ground tissue showed differences in Fe, K, Na, P, S, and Zn content and total phenolic levels, but no differences in anthocyanin and ORAC levels. This study indicated that leafy vegetable crops can produce safe, edible, fresh food to supplement to the astronauts' diet, and provide baseline data for continual operation of the Veggie plant growth units on ISS.
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Affiliation(s)
| | - Mary E. Hummerick
- AECOM Management Services, Inc., LASSO, Kennedy Space Center, Merritt Island, FL, United States
| | - LaShelle E. Spencer
- AECOM Management Services, Inc., LASSO, Kennedy Space Center, Merritt Island, FL, United States
| | - Anirudha R. Dixit
- AECOM Management Services, Inc., LASSO, Kennedy Space Center, Merritt Island, FL, United States
| | - Jeffrey T. Richards
- AECOM Management Services, Inc., LASSO, Kennedy Space Center, Merritt Island, FL, United States
| | | | - Trent M. Smith
- NASA UB, Kennedy Space Center, Merritt Island, FL, United States
| | | | - Gioia D. Massa
- NASA UB, Kennedy Space Center, Merritt Island, FL, United States
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Biodegradation of Ephedrine Isomers by Arthrobacter sp. Strain TS-15: Discovery of Novel Ephedrine and Pseudoephedrine Dehydrogenases. Appl Environ Microbiol 2020; 86:AEM.02487-19. [PMID: 31900306 DOI: 10.1128/aem.02487-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/18/2019] [Indexed: 11/20/2022] Open
Abstract
The Gram-positive soil bacterium Arthrobacter sp. strain TS-15 (DSM 32400), which is capable of metabolizing ephedrine as a sole source of carbon and energy, was isolated. According to 16S rRNA gene sequences and comparative genomic analysis, Arthrobacter sp. TS-15 is closely related to Arthrobacter aurescens Distinct from all known physiological paths, ephedrine metabolism by Arthrobacter sp. TS-15 is initiated by the selective oxidation of the hydroxyl function at the α-C atom, yielding methcathinone as the primary degradation product. Rational genome mining revealed a gene cluster potentially encoding the novel pathway. Two genes from the cluster, which encoded putative short-chain dehydrogenases, were cloned and expressed in Escherichia coli The obtained enzymes were strictly NAD+ dependent and catalyzed the oxidation of ephedrine to methcathinone. Pseudoephedrine dehydrogenase (PseDH) selectively converted (S,S)-(+)-pseudoephedrine and (S,R)-(+)-ephedrine to (S)- and (R)-methcathinone, respectively. Ephedrine dehydrogenase (EDH) exhibited strict selectivity for the oxidation of the diastereomers (R,S)-(-)-ephedrine and (R,R)-(-)-pseudoephedrine.IMPORTANCE Arthrobacter sp. TS-15 is a newly isolated bacterium with the unique ability to degrade ephedrine isomers. The initiating steps of the novel metabolic pathway are described. Arthrobacter sp. TS-15 and its isolated ephedrine-oxidizing enzymes have potential for use in decontamination and synthetic applications.
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Bie J, Tong Q, Liu X, Zhang X, Wang H. Comparative analysis of cutaneous bacterial communities of farmed Rana dybowskii after gentamycin bath. PeerJ 2020; 8:e8430. [PMID: 31998565 PMCID: PMC6977512 DOI: 10.7717/peerj.8430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/18/2019] [Indexed: 12/17/2022] Open
Abstract
Introduction Pathogenic bacteria limit the success of Rana dybowskii breeding. Gentamicin is used to treat R. dybowskii disease. To understand the effects of gentamicin on the composition and structure of the cutaneous bacterial community of R. dybowskii, three groups (control, gentamicin and recovery) were established in this study. Materials & Methods The V3-V4 hypervariable region of the 16S rRNA gene was analyzed in samples by high-throughput sequencing. Alpha diversity and beta diversity were evaluated to compare the cutaneous bacterial community diversity. Results A total of 1,159,668 valid sequences and 3,132 operational taxonomic units (OTUs) were obtained from these three experimental groups. The number of OTUs obtained in the control group, gentamicin group and recovery group were 2,194, 2,288, and 2,047, respectively, and the number of shared OTUs was 1,313. The alpha diversity of the cutaneous bacterial community was not significantly affected by gentamicin, while beta diversity was significantly affected. Discussion & Conclusions The effect of a gentamicin bath on relative species abundance was greater than the effect on the species composition. The changes in Proteobacteria, Acinetobacter, and Chryseobacterium were significant, and reductions were observed after the recovery period. Six potentially pathogenic genera were detected, including Aeromonas, Citrobacter, Chryseobacterium, Pseudomonas, Staphylococcus, and Streptococcus. Among them, Aeromonas and Chryseobacterium were significantly inhibited by the gentamicin bath. The results of this study provide a theoretical basis for the application of gentamicin in R. dybowskii breeding.
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Affiliation(s)
- Jia Bie
- Northeast Agricultural University, Harbin, China
| | - Qing Tong
- Northeast Agricultural University, Harbin, China
| | - Xiaoning Liu
- Northeast Agricultural University, Harbin, China
| | | | - Hongbin Wang
- Northeast Agricultural University, Harbin, China
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Liang S, Liu H, Wu S, Xu S, Jin D, Faiola F, Zhuang X, Zhuang G, Qu D, Fan H, Bai Z. Genetic diversity of diazotrophs and total bacteria in the phyllosphere of Pyrus serotina, Prunus armeniaca, Prunus avium, and Vitis vinifera. Can J Microbiol 2019; 65:642-652. [PMID: 31241350 DOI: 10.1139/cjm-2018-0588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The phyllosphere, which supports a large number of microorganisms, represents the interface between the aboveground parts of plants and air. In this study, four nifH clone libraries were constructed from the phyllosphere of Pyrus serotina (L), Vitis vinifera (P), Prunus armeniaca (X), and Prunus avium (Y). Clones related to Skermanella (L, 12.1%; X, 15.6%; Y, 62.5%; P 70.8%), Bradyrhizobium (X, 2.1%; P, 15.1%; L, 63.7%), Erwinia (X, 68.8%), Pseudomonas (L, 3.3%; P, 7.6%), and Chroococcidiopsis (P, 0.9%; L, 4.4%, X; 5.2%, Y; 19.6%) were present at high percentages, highlighting their critical role in contributing nitrogen to the phyllosphere ecosystem. The 16S rDNA sequence analysis suggested that phyllosphere-associated bacteria were affiliated with a wide range of taxa, encompassing members from Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Tenericutes, and Deinococcus-Thermus. Additionally, the abundance of the nifH gene and 16S rDNA was assessed with quantitative PCR. The number of copies of nifH and 16S rDNA ranged from 1.14 × 103 to 1.49 × 104 and from 3.72 × 106 to 7.02 × 107 copies/g fresh leaf sample, respectively. In conclusion, our work sheds light on the microbial communities of the phyllosphere that are important for plant growth. Moreover, we observed a unique composition of nitrogen-fixing bacteria in each phyllosphere sample, suggesting the existence of specific interactions between these functional microorganism and plants, which may provide information or be a reference for the development of bacterial fertilizers.
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Affiliation(s)
- Shengxian Liang
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.,College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Hao Liu
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Natural Resources and Environment, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Shanghua Wu
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengjun Xu
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Decai Jin
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Francesco Faiola
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoqiang Zhuang
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Qu
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Haiyan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhihui Bai
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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15
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Shrestha RG, Tanaka Y, Malla B, Tandukar S, Bhandari D, Inoue D, Sei K, Sherchand JB, Haramoto E. Development of a Quantitative PCR Assay for Arcobacter spp. and its Application to Environmental Water Samples. Microbes Environ 2018; 33:309-316. [PMID: 30185726 PMCID: PMC6167121 DOI: 10.1264/jsme2.me18052] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Arcobacter spp. are emerging pathogens associated with gastroenteritis in humans. The objective of this study was to develop a highly sensitive and broadly reactive quantitative PCR (qPCR) assay for Arcobacter spp. and to apply the developed assay to different water sources in the Kathmandu Valley, Nepal. Fifteen samples to be analyzed by next-generation sequencing were collected from 13 shallow dug wells, a deep tube well, and a river in the Kathmandu Valley in August 2015. Among the 86 potential pathogenic bacterial genera identified, Acinetobacter, Pseudomonas, Flavobacterium, and Arcobacter were detected with relatively high abundance in 15, 14, 12, and 8 samples, respectively. A primer pair was designed with maximal nucleotide homologies among Arcobacter spp. by comparing the sequences of 16S rRNA genes. These primers were highly specific to most of the known species of Arcobacter and quantified between 1.0×101 and 6.4×106 copies reaction−1 and sometimes detected as few as 3 copies reaction−1. The qPCR assay was used to quantify Arcobacter spp. in bacterial DNA in not only the above 15 water samples, but also in 33 other samples collected from 15 shallow dug wells, 6 shallow tube wells, 5 stone spouts, 4 deep tube wells, and 3 springs. Thirteen (27%) out of 48 samples tested were positive for Arcobacter spp., with concentrations of 5.3–9.1 log copies 100 mL−1. This qPCR assay represents a powerful new tool to assess the prevalence of Arcobacter spp. in environmental water samples.
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Affiliation(s)
- Rajani Ghaju Shrestha
- Department of Natural, Biotic and Social Environment Engineering, University of Yamanashi
| | - Yasuhiro Tanaka
- Department of Environmental Sciences, University of Yamanashi
| | - Bikash Malla
- Department of Natural, Biotic and Social Environment Engineering, University of Yamanashi
| | - Sarmila Tandukar
- Department of Natural, Biotic and Social Environment Engineering, University of Yamanashi
| | | | - Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Osaka University
| | - Kazunari Sei
- Department of Health Science, Kitasato University
| | | | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi
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Dobrovol’skaya TG, Khusnetdinova KA, Manucharova NA, Yakushev AV, Khusnetdinova TI. Comparison of Diversity and Functions of Epiphytic Bacteria from Cultivated and Weed Plants in Agrocenoses. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718040057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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17
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Bjerketorp J, Röling WFM, Feng XM, Garcia AH, Heipieper HJ, Håkansson S. Formulation and stabilization of an Arthrobacter strain with good storage stability and 4-chlorophenol-degradation activity for bioremediation. Appl Microbiol Biotechnol 2018; 102:2031-2040. [PMID: 29349491 PMCID: PMC5794804 DOI: 10.1007/s00253-017-8706-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/08/2017] [Accepted: 12/11/2017] [Indexed: 10/27/2022]
Abstract
Chlorophenols are widespread and of environmental concern due to their toxic and carcinogenic properties. Development of less costly and less technically challenging remediation methods are needed; therefore, we developed a formulation based on micronized vermiculite that, when air-dried, resulted in a granular product containing the 4-chlorophenol (4-CP)-degrading Gram-positive bacterium Arthrobacter chlorophenolicus A6. This formulation and stabilization method yielded survival rates of about 60% that remained stable in storage for at least 3 months at 4 °C. The 4-CP degradation by the formulated and desiccated A. chlorophenolicus A6 cells was compared to that of freshly grown cells in controlled-environment soil microcosms. The stabilized cells degraded 4-CP equally efficient as freshly grown cells in two different set-ups using both hygienized and non-treated soils. The desiccated microbial product was successfully employed in an outdoor pot trial showing its effectiveness under more realistic environmental conditions. No significant phytoremediation effects on 4-CP degradation were observed in the outdoor pot experiment. The 4-CP degradation kinetics from both the microcosms and the outdoor pot trial were used to generate a predictive model of 4-CP biodegradation potentially useful for larger-scale operations, enabling better bioremediation set-ups and saving of resources. This study also opens up the possibility of formulating and stabilizing also other Arthrobacter strains possessing different desirable pollutant-degrading capabilities.
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Affiliation(s)
- Joakim Bjerketorp
- Department of Molecular Sciences, Swedish University of Agricultural Sciences-SLU, Uppsala, Sweden
| | - Wilfred F M Röling
- Department Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Xin-Mei Feng
- RISE Research Institutes of Sweden, Uppsala, Sweden
| | - Armando Hernández Garcia
- Department of Molecular Sciences, Swedish University of Agricultural Sciences-SLU, Uppsala, Sweden
| | - Hermann J Heipieper
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Sebastian Håkansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences-SLU, Uppsala, Sweden.
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18
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Wang M, Qian Y, Liu X, Wei P, Deng M, Wang L, Wu H, Zhu G. Multiple spectroscopic analyses reveal the fate and metabolism of sulfamide herbicide triafamone in agricultural environments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 230:107-115. [PMID: 28649038 DOI: 10.1016/j.envpol.2017.06.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/20/2017] [Accepted: 06/08/2017] [Indexed: 05/22/2023]
Abstract
Triafamone, a sulfamide herbicide, has been extensively utilized for weed control in rice paddies in Asia. However, its fate and transformation in the environment have not been established. Through a rice paddy microcosm-based simulation trial combined with multiple spectroscopic analyses, we isolated and identified three novel metabolites of triafamone, including hydroxyl triafamone (HTA), hydroxyl triafamone glycoside (HTAG), and oxazolidinedione triafamone (OTA). When triafamone was applied to rice paddies at a concentration of 34.2 g active ingredient/ha, this was predominantly distributed in the paddy soil and water, and then rapidly dissipated in accordance with the first-order rate model, with half-lives of 4.3-11.0 days. As the main transformation pathway, triafamone was assimilated by the rice plants and was detoxified into HTAG, whereas the rest was reduced into HTA with subsequent formation of OTA. At the senescence stage, brown rice had incurred triafamone at a concentration of 0.0016 mg/kg, but the hazard quotient was <1, suggesting that long-term consumption of the triafamone-containing brown rice is relatively safe. The findings of the present study indicate that triafamone is actively metabolized in the agricultural environment, and elucidation of the link between environmental exposure to these triazine or oxazolidinedione moieties that contain metabolites and their potential impacts is warranted.
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Affiliation(s)
- Mengcen Wang
- Institute of Pesticide & Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Yuan Qian
- Institute of Pesticide & Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Xiaoyu Liu
- Institute of Pesticide & Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Peng Wei
- Institute of Pesticide & Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Man Deng
- Institute of Pesticide & Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Lei Wang
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, USA
| | - Huiming Wu
- School of Agricultural and Food Science, Zhejiang A&F University, Hangzhou, China
| | - Guonian Zhu
- Institute of Pesticide & Environmental Toxicology, Zhejiang University, Hangzhou, China.
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Wei X, Lyu S, Yu Y, Wang Z, Liu H, Pan D, Chen J. Phylloremediation of Air Pollutants: Exploiting the Potential of Plant Leaves and Leaf-Associated Microbes. FRONTIERS IN PLANT SCIENCE 2017; 8:1318. [PMID: 28804491 PMCID: PMC5532450 DOI: 10.3389/fpls.2017.01318] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/12/2017] [Indexed: 05/22/2023]
Abstract
Air pollution is air contaminated by anthropogenic or naturally occurring substances in high concentrations for a prolonged time, resulting in adverse effects on human comfort and health as well as on ecosystems. Major air pollutants include particulate matters (PMs), ground-level ozone (O3), sulfur dioxide (SO2), nitrogen dioxides (NO2), and volatile organic compounds (VOCs). During the last three decades, air has become increasingly polluted in countries like China and India due to rapid economic growth accompanied by increased energy consumption. Various policies, regulations, and technologies have been brought together for remediation of air pollution, but the air still remains polluted. In this review, we direct attention to bioremediation of air pollutants by exploiting the potentials of plant leaves and leaf-associated microbes. The aerial surfaces of plants, particularly leaves, are estimated to sum up to 4 × 108 km2 on the earth and are also home for up to 1026 bacterial cells. Plant leaves are able to adsorb or absorb air pollutants, and habituated microbes on leaf surface and in leaves (endophytes) are reported to be able to biodegrade or transform pollutants into less or nontoxic molecules, but their potentials for air remediation has been largely unexplored. With advances in omics technologies, molecular mechanisms underlying plant leaves and leaf associated microbes in reduction of air pollutants will be deeply examined, which will provide theoretical bases for developing leaf-based remediation technologies or phylloremediation for mitigating pollutants in the air.
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Affiliation(s)
- Xiangying Wei
- Fujian Univeristy Key Laboratory of Plant-Microbe Interaction, College of Life Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Environmental Horticulture and Mid-Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of FloridaApopka, FL, United States
| | - Shiheng Lyu
- Department of Environmental Horticulture and Mid-Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of FloridaApopka, FL, United States
- College of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Ying Yu
- College of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Zonghua Wang
- Fujian Univeristy Key Laboratory of Plant-Microbe Interaction, College of Life Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Hong Liu
- Fujian Univeristy Key Laboratory of Plant-Microbe Interaction, College of Life Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Resource and Environmental Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Dongming Pan
- College of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Jianjun Chen
- Fujian Univeristy Key Laboratory of Plant-Microbe Interaction, College of Life Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Environmental Horticulture and Mid-Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of FloridaApopka, FL, United States
- College of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
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20
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Kaliniene L, Šimoliūnas E, Truncaitė L, Zajančkauskaitė A, Nainys J, Kaupinis A, Valius M, Meškys R. Molecular Analysis of Arthrobacter Myovirus vB_ArtM-ArV1: We Blame It on the Tail. J Virol 2017; 91:e00023-17. [PMID: 28122988 PMCID: PMC5375659 DOI: 10.1128/jvi.00023-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/23/2017] [Indexed: 11/20/2022] Open
Abstract
This is the first report on a myophage that infects Arthrobacter A novel virus, vB_ArtM-ArV1 (ArV1), was isolated from soil using Arthrobacter sp. strain 68b for phage propagation. Transmission electron microscopy showed its resemblance to members of the family Myoviridae: ArV1 has an isometric head (∼74 nm in diameter) and a contractile, nonflexible tail (∼192 nm). Phylogenetic and comparative sequence analyses, however, revealed that ArV1 has more genes in common with phages from the family Siphoviridae than it does with any myovirus characterized to date. The genome of ArV1 is a linear, circularly permuted, double-stranded DNA molecule (71,200 bp) with a GC content of 61.6%. The genome includes 101 open reading frames (ORFs) yet contains no tRNA genes. More than 50% of ArV1 genes encode unique proteins that either have no reliable identity to database entries or have homologues only in Arthrobacter phages, both sipho- and myoviruses. Using bioinformatics approaches, 13 ArV1 structural genes were identified, including those coding for head, tail, tail fiber, and baseplate proteins. A further 6 ArV1 ORFs were annotated as encoding putative structural proteins based on the results of proteomic analysis. Phylogenetic analysis based on the alignment of four conserved virion proteins revealed that Arthrobacter myophages form a discrete clade that seems to occupy a position somewhat intermediate between myo- and siphoviruses. Thus, the data presented here will help to advance our understanding of genetic diversity and evolution of phages that constitute the order CaudoviralesIMPORTANCE Bacteriophages, which likely originated in the early Precambrian Era, represent the most numerous population on the planet. Approximately 95% of known phages are tailed viruses that comprise three families: Podoviridae (with short tails), Siphoviridae (with long noncontractile tails), and Myoviridae (with contractile tails). Based on the current hypothesis, myophages, which may have evolved from siphophages, are thought to have first emerged among Gram-negative bacteria, whereas they emerged only later among Gram-positive bacteria. The results of the molecular characterization of myophage vB_ArtM-ArV1 presented here conform to the aforementioned hypothesis, since, at a glance, bacteriophage vB_ArtM-ArV1 appears to be a siphovirus that possesses a seemingly functional contractile tail. Our work demonstrates that such "chimeric" myophages are of cosmopolitan nature and are likely characteristic of the ecologically important soil bacterial genus Arthrobacter.
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Affiliation(s)
- Laura Kaliniene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Aurelija Zajančkauskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Juozas Nainys
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
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Dobrovol’skaya TG, Khusnetdinova KA, Manucharova NA, Golovchenko AV. Structure of epiphytic bacterial communities of weeds. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717020072] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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22
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Remus-Emsermann MN, Schmid M, Gekenidis MT, Pelludat C, Frey JE, Ahrens CH, Drissner D. Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites. Stand Genomic Sci 2016; 11:75. [PMID: 28300228 PMCID: PMC5037603 DOI: 10.1186/s40793-016-0190-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 08/31/2016] [Indexed: 12/04/2022] Open
Abstract
Pseudomonas citronellolis is a Gram negative, motile gammaproteobacterium belonging to the order Pseudomonadales and the family Pseudomonadaceae. We isolated strain P3B5 from the phyllosphere of basil plants (Ocimum basilicum L.). Here we describe the physiology of this microorganism, its full genome sequence, and detailed annotation. The 6.95 Mbp genome contains 6071 predicted protein coding sequences and 96 RNA coding sequences. P. citronellolis has been the subject of many studies including the investigation of long-chain aliphatic compounds and terpene degradation. Plant leaves are covered by long-chain aliphates making up a waxy layer that is associated with the leaf cuticle. In addition, basil leaves are known to contain high amounts of terpenoid substances, hinting to a potential nutrient niche that might be exploited by P. citronellolis. Furthermore, the isolated strain exhibited resistance to several antibiotics. To evaluate the potential of this strain as source of transferable antibiotic resistance genes on raw consumed herbs we therefore investigated if those resistances are encoded on mobile genetic elements. The availability of the genome will be helpful for comparative genomics of the phylogenetically broad pseudomonads, in particular with the sequence of the P. citronellolis type strain PRJDB205 not yet publicly available. The genome is discussed with respect to a phyllosphere related lifestyle, aliphate and terpenoid degradation, and antibiotic resistance.
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Affiliation(s)
| | - Michael Schmid
- Agroscope, Institute for Plant Production Sciences IPS, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Maria-Theresia Gekenidis
- Agroscope, Institute for Food Sciences IFS, Wädenswil, Switzerland
- ETH Zurich, Institute of Food, Nutrition and Health, Zurich, Switzerland
| | - Cosima Pelludat
- Agroscope, Institute for Plant Production Sciences IPS, Wädenswil, Switzerland
| | - Jürg E. Frey
- Agroscope, Institute for Plant Production Sciences IPS, Wädenswil, Switzerland
| | - Christian H. Ahrens
- Agroscope, Institute for Plant Production Sciences IPS, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - David Drissner
- Agroscope, Institute for Food Sciences IFS, Wädenswil, Switzerland
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Wang L, Nie Y, Tang YQ, Song XM, Cao K, Sun LZ, Wang ZJ, Wu XL. Diverse Bacteria with Lignin Degrading Potentials Isolated from Two Ranks of Coal. Front Microbiol 2016; 7:1428. [PMID: 27667989 PMCID: PMC5016517 DOI: 10.3389/fmicb.2016.01428] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/29/2016] [Indexed: 11/13/2022] Open
Abstract
Taking natural coal as a “seed bank” of bacterial strains able to degrade lignin that is with molecular structure similar to coal components, we isolated 393 and 483 bacterial strains from a meager lean coal sample from Hancheng coalbed and a brown coal sample from Bayannaoer coalbed, respectively, by using different media. Statistical analysis showed that isolates were significantly more site-specific than medium-specific. Of the 876 strains belonging to 27 genera in Actinobacteria, Firmicutes, and Proteobacteria, 612 were positive for lignin degradation function, including 218 strains belonging to 35 species in Hancheng and 394 strains belonging to 19 species in Zhongqi. Among them, the dominant lignin-degrading strains were Thauera (Hancheng), Arthrobacter (Zhongqi) and Rhizobium (both). The genes encoding the laccases- or laccase-like multicopper oxidases, key enzymes in lignin production and degradation, were detected in three genera including Massila for the first time, which was in high expression by real time PCR (qRT-PCR) detection, confirming coal as a good seed bank.
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Affiliation(s)
- Lu Wang
- School of Earth and Space Sciences, Peking UniversityBeijing, China; College of Engineering, Peking UniversityBeijing, China
| | - Yong Nie
- College of Engineering, Peking University Beijing, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University Chengdu, China
| | - Xin-Min Song
- State Key Laboratory of Enhanced Oil Recovery, Research Institute of Petroleum Exploration and Development Beijing, China
| | - Kun Cao
- Xinchun Production Plant, Sinopec Shengli Oilfield, Karamay China
| | - Li-Zhu Sun
- Xinchun Production Plant, Sinopec Shengli Oilfield, Karamay China
| | - Zhi-Jian Wang
- Xinchun Production Plant, Sinopec Shengli Oilfield, Karamay China
| | - Xiao-Lei Wu
- College of Engineering, Peking University Beijing, China
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Weyens N, Thijs S, Popek R, Witters N, Przybysz A, Espenshade J, Gawronska H, Vangronsveld J, Gawronski SW. The Role of Plant-Microbe Interactions and Their Exploitation for Phytoremediation of Air Pollutants. Int J Mol Sci 2015; 16:25576-604. [PMID: 26516837 PMCID: PMC4632817 DOI: 10.3390/ijms161025576] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/13/2015] [Accepted: 10/19/2015] [Indexed: 01/06/2023] Open
Abstract
Since air pollution has been linked to a plethora of human health problems, strategies to improve air quality are indispensable. Despite the complexity in composition of air pollution, phytoremediation was shown to be effective in cleaning air. Plants are known to scavenge significant amounts of air pollutants on their aboveground plant parts. Leaf fall and runoff lead to transfer of (part of) the adsorbed pollutants to the soil and rhizosphere below. After uptake in the roots and leaves, plants can metabolize, sequestrate and/or excrete air pollutants. In addition, plant-associated microorganisms play an important role by degrading, detoxifying or sequestrating the pollutants and by promoting plant growth. In this review, an overview of the available knowledge about the role and potential of plant-microbe interactions to improve indoor and outdoor air quality is provided. Most importantly, common air pollutants (particulate matter, volatile organic compounds and inorganic air pollutants) and their toxicity are described. For each of these pollutant types, a concise overview of the specific contributions of the plant and its microbiome is presented. To conclude, the state of the art and its related future challenges are presented.
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Affiliation(s)
- Nele Weyens
- Centre for Environmental Sciences, Hasselt University, Agoralaan building D, Diepenbeek 3590, Belgium.
| | - Sofie Thijs
- Centre for Environmental Sciences, Hasselt University, Agoralaan building D, Diepenbeek 3590, Belgium.
| | - Robert Popek
- Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw 02-766, Poland.
| | - Nele Witters
- Centre for Environmental Sciences, Hasselt University, Agoralaan building D, Diepenbeek 3590, Belgium.
| | - Arkadiusz Przybysz
- Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw 02-766, Poland.
| | - Jordan Espenshade
- Centre for Environmental Sciences, Hasselt University, Agoralaan building D, Diepenbeek 3590, Belgium.
| | - Helena Gawronska
- Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw 02-766, Poland.
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University, Agoralaan building D, Diepenbeek 3590, Belgium.
| | - Stanislaw W Gawronski
- Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw 02-766, Poland.
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Bringel F, Couée I. Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics. Front Microbiol 2015; 6:486. [PMID: 26052316 PMCID: PMC4440916 DOI: 10.3389/fmicb.2015.00486] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/03/2015] [Indexed: 11/13/2022] Open
Abstract
The phyllosphere, which lato sensu consists of the aerial parts of plants, and therefore primarily, of the set of photosynthetic leaves, is one of the most prevalent microbial habitats on earth. Phyllosphere microbiota are related to original and specific processes at the interface between plants, microorganisms and the atmosphere. Recent -omics studies have opened fascinating opportunities for characterizing the spatio-temporal structure of phyllosphere microbial communities in relation with structural, functional, and ecological properties of host plants, and with physico-chemical properties of the environment, such as climate dynamics and trace gas composition of the surrounding atmosphere. This review will analyze recent advances, especially those resulting from environmental genomics, and how this novel knowledge has revealed the extent of the ecosystemic impact of the phyllosphere at the interface between plants and atmosphere. Highlights • The phyllosphere is one of the most prevalent microbial habitats on earth. • Phyllosphere microbiota colonize extreme, stressful, and changing environments. • Plants, phyllosphere microbiota and the atmosphere present a dynamic continuum. • Phyllosphere microbiota interact with the dynamics of volatile organic compounds and atmospheric trace gasses.
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Affiliation(s)
- Françoise Bringel
- Laboratory of Molecular Genetics, Genomics, and Microbiology, Université de Strasbourg/CNRS, UNISTRA UMR 7156 Strasbourg, France
| | - Ivan Couée
- Ecosystems-Biodiversity-Evolution, Université de Rennes 1/CNRS, UMR 6553 Rennes, France
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Medina-Martínez MS, Allende A, Barberá GG, Gil MI. Climatic variations influence the dynamic of epiphyte bacteria of baby lettuce. Food Res Int 2015. [DOI: 10.1016/j.foodres.2014.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Šimoliūnas E, Kaliniene L, Stasilo M, Truncaitė L, Zajančkauskaitė A, Staniulis J, Nainys J, Kaupinis A, Valius M, Meškys R. Isolation and characterization of vB_ArS-ArV2 - first Arthrobacter sp. infecting bacteriophage with completely sequenced genome. PLoS One 2014; 9:e111230. [PMID: 25333962 PMCID: PMC4205034 DOI: 10.1371/journal.pone.0111230] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/26/2014] [Indexed: 02/05/2023] Open
Abstract
This is the first report on a complete genome sequence and biological characterization of the phage that infects Arthrobacter. A novel virus vB_ArS-ArV2 (ArV2) was isolated from soil using Arthrobacter sp. 68b strain for phage propagation. Based on transmission electron microscopy, ArV2 belongs to the family Siphoviridae and has an isometric head (∼63 nm in diameter) with a non-contractile flexible tail (∼194×10 nm) and six short tail fibers. ArV2 possesses a linear, double-stranded DNA genome (37,372 bp) with a G+C content of 62.73%. The genome contains 68 ORFs yet encodes no tRNA genes. A total of 28 ArV2 ORFs have no known functions and lack any reliable database matches. Proteomic analysis led to the experimental identification of 14 virion proteins, including 9 that were predicted by bioinformatics approaches. Comparative phylogenetic analysis, based on the amino acid sequence alignment of conserved proteins, set ArV2 apart from other siphoviruses. The data presented here will help to advance our understanding of Arthrobacter phage population and will extend our knowledge about the interaction between this particular host and its phages.
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Affiliation(s)
- Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Laura Kaliniene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Miroslav Stasilo
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Aurelija Zajančkauskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Juozas Staniulis
- Laboratory of Plant Viruses, Institute of Botany, Nature Research Centre, Vilnius, Lithuania
| | - Juozas Nainys
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
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Scheublin TR, Deusch S, Moreno-Forero SK, Müller JA, van der Meer JR, Leveau JHJ. Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds. Environ Microbiol 2014; 16:2212-25. [PMID: 24373130 DOI: 10.1111/1462-2920.12375] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 12/12/2013] [Indexed: 11/28/2022]
Abstract
Arthrobacter chlorophenolicus A6 is a Gram-positive, 4-chlorophenol-degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome-wide expression profile of A.chlorophenolicus on leaves of common bean (Phaseolus vulgaris) compared with growth on agar surfaces. In phyllosphere-grown cells, we found elevated expression of several genes known to contribute to epiphytic fitness, for example those involved in nutrient acquisition, attachment, stress response and horizontal gene transfer. A surprising result was the leaf-induced expression of a subset of the so-called cph genes for the degradation of 4-chlorophenol. This subset encodes the conversion of the phenolic compound hydroquinone to 3-oxoadipate, and was shown to be induced not only by 4-chlorophenol but also hydroquinone, its glycosylated derivative arbutin, and phenol. Small amounts of hydroquinone, but not arbutin or phenol, were detected in leaf surface washes of P.vulgaris by gas chromatography-mass spectrometry. Our findings illustrate the utility of genomics approaches for exploration and improved understanding of a microbial habitat. Also, they highlight the potential for phyllosphere-based priming of bacteria to stimulate pollutant degradation, which holds promise for the application of phylloremediation.
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Affiliation(s)
- Tanja R Scheublin
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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