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Qu X, Pan Y, Wang P, Ran L, Qin G, Li Q, Kang P. Response of Phyllosphere and Rhizosphere Microbial Communities to Salt Stress of Tamarix chinensis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1091. [PMID: 38674498 PMCID: PMC11054833 DOI: 10.3390/plants13081091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024]
Abstract
As carriers of direct contact between plants and the atmospheric environment, the microbiomes of phyllosphere microorganisms are increasingly recognized as an important area of study. Salt secretion triggered by salt-secreting halophytes elicits changes in the community structure and functions of phyllosphere microorganisms, and often provides positive feedback to the individual plant/community environment. In this study, the contents of Na+ and K+ in the rhizosphere, plant and phyllosphere of Tamarix chinensis were increased under 200 mmol/L NaCl stress. The increase in electrical conductivity, Na+ and K+ in the phyllosphere not only decreased the diversity of bacterial and fungal communities, but also decreased the relative abundance of Actinobacteriota and Basidiomycota. Influenced by electrical conductivity and Na+, the bacteria-fungus co-occurrence network under salt stress has higher complexity. Changes in the structure of the phyllosphere microbial community further resulted in a significant increase in the relative abundance of the bacterial energy source and fungal pathotrophic groups. The relative abundance of Actinobacteriota and Acidobacteriota in rhizosphere showed a decreasing trend under salt stress, while the complexity of the rhizosphere co-occurrence network was higher than that of the control. In addition, the relative abundances of functional groups of rhizosphere bacteria in the carbon cycle and phosphorus cycle increased significantly under stress, and were significantly correlated with electrical conductivity and Na+. This study investigated the effects of salinity on the structure and physicochemical properties of phyllosphere and rhizosphere microbial communities of halophytes, and highlights the role of phyllosphere microbes as ecological indicators in plant responses to stressful environments.
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Affiliation(s)
- Xuan Qu
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Yaqing Pan
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Peiqin Wang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Lele Ran
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Guifei Qin
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Qunfang Li
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Peng Kang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
- Innovation Team for Genetic Improvement of Economic Forests, North Minzu University, Yinchuan 750021, China
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Hakobyan A, Velte S, Sickel W, Quandt D, Stoll A, Knief C. Tillandsia landbeckii phyllosphere and laimosphere as refugia for bacterial life in a hyperarid desert environment. MICROBIOME 2023; 11:246. [PMID: 37936139 PMCID: PMC10631034 DOI: 10.1186/s40168-023-01684-x] [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: 06/15/2023] [Accepted: 09/28/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND The lack of water is a major constraint for microbial life in hyperarid deserts. Consequently, the abundance and diversity of microorganisms in common habitats such as soil are strongly reduced, and colonization occurs primarily by specifically adapted microorganisms that thrive in particular refugia to escape the harsh conditions that prevail in these deserts. We suggest that plants provide another refugium for microbial life in hyperarid deserts. We studied the bacterial colonization of Tillandsia landbeckii (Bromeliaceae) plants, which occur in the hyperarid regions of the Atacama Desert in Chile, one of the driest and oldest deserts on Earth. RESULTS We detected clear differences between the bacterial communities being plant associated to those of the bare soil surface (PERMANOVA, R2 = 0.187, p = 0.001), indicating that Tillandsia plants host a specific bacterial community, not only dust-deposited cells. Moreover, the bacterial communities in the phyllosphere were distinct from those in the laimosphere, i.e., on buried shoots (R2 = 0.108, p = 0.001), indicating further habitat differentiation within plant individuals. The bacterial taxa detected in the phyllosphere are partly well-known phyllosphere colonizers, but in addition, some rather unusual taxa (subgroup2 Acidobacteriae, Acidiphilum) and insect endosymbionts (Wolbachia, "Candidatus Uzinura") were found. The laimosphere hosted phyllosphere-associated as well as soil-derived taxa. The phyllosphere bacterial communities showed biogeographic patterns across the desert (R2 = 0.331, p = 0.001). These patterns were different and even more pronounced in the laimosphere (R2 = 0.467, p = 0.001), indicating that different factors determine community assembly in the two plant compartments. Furthermore, the phyllosphere microbiota underwent temporal changes (R2 = 0.064, p = 0.001). CONCLUSIONS Our data demonstrate that T. landbeckii plants host specific bacterial communities in the phyllosphere as well as in the laimosphere. Therewith, these plants provide compartment-specific refugia for microbial life in hyperarid desert environments. The bacterial communities show biogeographic patterns and temporal variation, as known from other plant microbiomes, demonstrating environmental responsiveness and suggesting that bacteria inhabit these plants as viable microorganisms. Video Abstract.
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Affiliation(s)
- Anna Hakobyan
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Stefanie Velte
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Wiebke Sickel
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
- Institute of Biodiversity, Johann Heinrich Von Thünen Institute, Brunswick, Germany
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas Ceaza, La Serena, Chile
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | - Claudia Knief
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany.
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Muyshondt B, Wuyts K, Van Mensel A, Smets W, Lebeer S, Aleixo C, Alós Ortí M, Casanelles-Abella J, Chiron F, Giacomo P, Laanisto L, Moretti M, Niinemets Ü, Pinho P, Tryjanowski P, Woszczyło P, Samson R. Phyllosphere bacterial communities in urban green areas throughout Europe relate to urban intensity. FEMS Microbiol Ecol 2022; 98:6695091. [PMID: 36085374 DOI: 10.1093/femsec/fiac106] [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: 04/25/2022] [Revised: 08/25/2022] [Accepted: 09/07/2022] [Indexed: 12/14/2022] Open
Abstract
The phyllosphere harbours a diverse and specific bacterial community, which influences plant health and ecosystem functioning. In this study, we investigated the impact of urban green areas connectivity and size on the composition and diversity of phyllosphere bacterial communities. Hereto, we evaluated the diversity and composition of phyllosphere bacterial communities of 233 Platanus x acerifolia and Acer pseudoplatanus trees in 77 urban green areas throughout 6 European cities. The community composition and diversity significantly differed between cities but only to a limited extent between tree species. We could show that urban intensity correlated significantly with the community composition of phyllosphere bacteria. In particular, a significant correlation was found between the relative abundances for 29 out of the 50 most abundant families and the urban intensity: the abundances of classic phyllosphere families, such as Acetobacteraceae, Planctomycetes, and Beijerinkiaceae, decreased with urban intensity (i.e. more abundant in areas with more green, lower air pollution, and lower temperature), while those related to human activities, such as Enterobacteriaceae and Bacillaceae, increased with urban intensity. The results of this study suggest that phyllosphere bacterial communities in European cities are associated with urban intensity and that effect is mediated by several combined stress factors.
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Affiliation(s)
- Babette Muyshondt
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Karen Wuyts
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Anskje Van Mensel
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Wenke Smets
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Sarah Lebeer
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Cristiana Aleixo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, 3810-135, Lisbon, Portugal
| | - Marta Alós Ortí
- Chair of Biodiversity and Nature Tourism, Estonian University of Life Sciences, 51005, Tartu, Estonia
| | - Joan Casanelles-Abella
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland.,Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zurich, CH-8092, Zurich, Switzerland
| | - François Chiron
- CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, 91405 Orsay, France
| | - Puglielli Giacomo
- Chair of Biodiversity and Nature Tourism, Estonian University of Life Sciences, 51005, Tartu, Estonia
| | - Lauri Laanisto
- Chair of Biodiversity and Nature Tourism, Estonian University of Life Sciences, 51005, Tartu, Estonia
| | - Marco Moretti
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, 51006, Tartu, Estonia
| | - Pedro Pinho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, 3810-135, Lisbon, Portugal
| | - Piotr Tryjanowski
- Department of Zoology, Poznan University of Life Sciences, 60-637, Poland
| | - Patrycja Woszczyło
- Department of Zoology, Poznan University of Life Sciences, 60-637, Poland
| | - Roeland Samson
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
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Zhang W, Bahadur A, Sajjad W, Wu X, Zhang G, Liu G, Chen T. Seasonal Variation in Fungal Community Composition Associated with Tamarix chinensis Roots in the Coastal Saline Soil of Bohai Bay, China. MICROBIAL ECOLOGY 2021; 82:652-665. [PMID: 33598747 DOI: 10.1007/s00248-021-01680-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Coastal salinity typically alters the soil microbial communities, which subsequently affect the biogeochemical cycle of nutrients in the soil. The seasonal variation of the soil fungal communities in the coastal area, closely associated with plant population, is poorly understood. This study provides an insight into the fungal community's variations from autumn to winter and spring to summer at a well-populated area of salt-tolerant Tamarix chinensis and beach. The richness and diversity of fungal community were higher in the spring season and lower in the winter season, as showed by high throughput sequencing of the 18S rRNA gene. Ascomycota was the predominant phylum reported in all samples across the region, and higher difference was reported at order level across the seasonal variations. The redundancy analysis suggested that the abundance and diversity of fungal communities in different seasons are mainly correlated to total organic carbon and total nitrogen. Additionally, the saprotrophic and pathotrophic fungi decreased while symbiotic fungi increased in the autumn season. This study provides a pattern of seasonal variation in fungal community composition that further broadens our limited understanding of how the density of the salt-tolerant T. chinensis population of the coastal saline soil could respond to their seasonal variations.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Ali Bahadur
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Xiukun Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China.
| | - Tuo Chen
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
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Gilbert KJ, Renner T. Acid or base? How do plants regulate the ecology of their phylloplane? AOB PLANTS 2021; 13:plab032. [PMID: 34285793 PMCID: PMC8286713 DOI: 10.1093/aobpla/plab032] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/25/2021] [Indexed: 05/29/2023]
Abstract
Plants interface with and modify the external environment across their surfaces, and in so doing, can control or mitigate the impacts of abiotic stresses and also mediate their interactions with other organisms. Botanically, it is known that plant roots have a multi-faceted ability to modify rhizosphere conditions like pH, a factor with a large effect on a plant's biotic interactions with microbes. But plants can also modify pH levels on the surfaces of their leaves. Plants can neutralize acid rain inputs in a period of hours, and either acidify or alkalinize the pH of neutral water droplets in minutes. The pH of the phylloplane-that is, the outermost surface of the leaf-varies across species, from incredibly acidic (carnivorous plants: as low as pH 1) to exceptionally alkaline (species in the plant family, Malvaceae, up to pH 11). However, most species mildly acidify droplets on the phylloplane by 1.5 orders of magnitude in pH. Just as rhizosphere pH helps shape the plant microbiome and is known to influence belowground interactions, so too can phylloplane pH influence aboveground interactions in plant canopies. In this review, we discuss phylloplane pH regulation from the physiological, molecular, evolutionary, and ecological perspectives and address knowledge gaps and identify future research directions.
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Affiliation(s)
- Kadeem J Gilbert
- Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, PA 16802, USA
| | - Tanya Renner
- Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, PA 16802, USA
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6
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Boraks A, Plunkett GM, Doro TM, Alo F, Sam C, Tuiwawa M, Ticktin T, Amend AS. Scale-Dependent Influences of Distance and Vegetation on the Composition of Aboveground and Belowground Tropical Fungal Communities. MICROBIAL ECOLOGY 2021; 81:874-883. [PMID: 33025061 DOI: 10.1007/s00248-020-01608-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
Fungi provide essential ecosystem services and engage in a variety of symbiotic relationships with trees. In this study, we investigate the spatial relationship of trees and fungi at a community level. We characterized the spatial dynamics for above- and belowground fungi using a series of forest monitoring plots, at nested spatial scales, located in the tropical South Pacific, in Vanuatu. Fungal communities from different habitats were sampled using metagenomic analysis of the nuclear ribosomal ITS1 region. Fungal communities exhibited strong distance-decay of similarity across our entire sampling range (3-110,000 m) and also at small spatial scales (< 50 m). Unexpectedly, this pattern was inverted at an intermediate scale (3.7-26 km). At large scales (80-110 km), belowground and aboveground fungal communities responded inversely to increasing geographic distance. Aboveground fungal community turnover (beta diversity) was best explained, at all scales, by geographic distance. In contrast, belowground fungal community turnover was best explained by geographic distance at small scales and tree community composition at large scales. Fungal communities from various habitats respond differently to the influences of habitat and geographic distance. At large geographic distances (80-110 km), community turnover for aboveground fungi is better explained by spatial distance, whereas community turnover for belowground fungi is better explained by plant community turnover. Future syntheses of spatial dynamics among fungal communities must explicitly consider geographic scale to appropriately contextualize community turnover.
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Affiliation(s)
- André Boraks
- Department of Botany, University of Hawai'i - Mānoa, 3190 Maile Way, Honolulu, HI, 96822, USA.
| | - Gregory M Plunkett
- New York Botanical Garden, 2900 Southern Blvd., Bronx, NY, 10458-5126, USA
| | - Thomas Morris Doro
- Vanuatu National Herbarium - Vanuatu Department of Forestry, PMB 9064, Port-Vila, Vanuatu
| | - Frazer Alo
- Vanuatu National Herbarium - Vanuatu Department of Forestry, PMB 9064, Port-Vila, Vanuatu
| | - Chanel Sam
- Vanuatu National Herbarium - Vanuatu Department of Forestry, PMB 9064, Port-Vila, Vanuatu
| | - Marika Tuiwawa
- South Pacific Regional Herbarium, University of the South Pacific, Private Mail Bag, Laucala Campus, Suva, Fiji Islands
| | - Tamara Ticktin
- Department of Botany, University of Hawai'i - Mānoa, 3190 Maile Way, Honolulu, HI, 96822, USA
| | - Anthony S Amend
- Department of Botany, University of Hawai'i - Mānoa, 3190 Maile Way, Honolulu, HI, 96822, USA
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7
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Gilbert KJ, Bittleston LS, Naive MAK, Kiszewski AE, Buenavente PAC, Lohman DJ, Pierce NE. Investigation of an Elevational Gradient Reveals Strong Differences Between Bacterial and Eukaryotic Communities Coinhabiting Nepenthes Phytotelmata. MICROBIAL ECOLOGY 2020; 80:334-349. [PMID: 32291478 PMCID: PMC7371667 DOI: 10.1007/s00248-020-01503-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/25/2020] [Indexed: 05/24/2023]
Abstract
Elevation is an important determinant of ecological community composition. It integrates several abiotic features and leads to strong, repeatable patterns of community structure, including changes in the abundance and richness of numerous taxa. However, the influence of elevational gradients on microbes is understudied relative to plants and animals. To compare the influence of elevation on multiple taxa simultaneously, we sampled phytotelm communities within a tropical pitcher plant (Nepenthes mindanaoensis) along a gradient from 400 to 1200 m a.s.l. We use a combination of metabarcoding and physical counts to assess diversity and richness of bacteria, micro-eukaryotes, and arthropods, and compare the effect of elevation on community structure to that of regulation by a number of plant factors. Patterns of community structure differed between bacteria and eukaryotes, despite their living together in the same aquatic microhabitats. Elevation influences community composition of eukaryotes to a significantly greater degree than it does bacteria. When examining pitcher characteristics, pitcher dimorphism has an effect on eukaryotes but not bacteria, while variation in pH levels strongly influences both taxa. Consistent with previous ecological studies, arthropod abundance in phytotelmata decreases with elevation, but some patterns of abundance differ between living inquilines and prey.
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Affiliation(s)
- Kadeem J Gilbert
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA.
- Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, PA, 16802, USA.
| | - Leonora S Bittleston
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 1-290, Cambridge, MA, 02139, USA
- Department of Biological Sciences, Boise State University, 1910 W University Dr, Boise, ID, 83725, USA
| | - Mark Arcebal K Naive
- Department of Biological Sciences, College of Science and Mathematics, Mindanao State University-Iligan Institute of Technology, Andres Bonifacio Ave, 9200, Iligan, Lanao del Norte, Philippines
| | - Anthony E Kiszewski
- Department of Natural and Applied Sciences, Bentley University, 175 Forest Street, Waltham, MA, 02452, USA
| | | | - David J Lohman
- Entomology Section, National Museum of Natural History, Manila, Philippines
- Biology Department, City College of New York, City University of New York, New York, NY, USA
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY, USA
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
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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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Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree. Appl Environ Microbiol 2016; 82:2854-2861. [PMID: 26944845 DOI: 10.1128/aem.00483-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 02/29/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The leaves of Tamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10 Tamarix aphylla trees along a 350-km longitudinal gradient. Shotgun metagenomic sequencing, contig assembly, and binning yielded 17 genome bins, six of which were >80% complete. These genomic bins, representing three phyla (Proteobacteria,Bacteroidetes, and Firmicutes), were closely related to halophilic and alkaliphilic taxa isolated from aquatic and soil environments. Comparison of these genomic bins to the genomes of their closest relatives revealed functional traits characteristic of bacterial populations inhabiting the Tamarix phyllosphere, independent of their taxonomic affiliation. These functions, most notably light-sensing genes, are postulated to represent important adaptations toward colonization of this habitat. IMPORTANCE Plant leaves are an extensive and diverse microbial habitat, forming the main interface between solar energy and the terrestrial biosphere. There are hundreds of thousands of plant species in the world, exhibiting a wide range of morphologies, leaf surface chemistries, and ecological ranges. In order to understand the core adaptations of microorganisms to this habitat, it is important to diversify the type of leaves that are studied. This study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the globally distributed, salt-secreting desert tree Tamarix aphylla Draft genomes of these bacteria were assembled, using the culture-independent technique of assembly and binning of metagenomic data. Analysis of the genomes reveals traits that are important for survival in this habitat, most notably, light-sensing and light utilization genes.
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Oliveira Alvarenga D, Rigonato J, Henrique Zanini Branco L, Soares Melo I, Fatima Fiore M. Phyllonema aviceniicola gen. nov., sp. nov. and Foliisarcina bertiogensis gen. nov., sp. nov., epiphyllic cyanobacteria associated with Avicennia schaueriana leaves. Int J Syst Evol Microbiol 2016; 66:689-700. [DOI: 10.1099/ijsem.0.000774] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Danillo Oliveira Alvarenga
- University of São Paulo, Center for Nuclear Energy in Agriculture, Avenida Centenário 303, 13400-970 Piracicaba, SP, Brazil
| | - Janaina Rigonato
- University of São Paulo, Center for Nuclear Energy in Agriculture, Avenida Centenário 303, 13400-970 Piracicaba, SP, Brazil
| | - Luis Henrique Zanini Branco
- São Paulo State University, Institute of Bioscience, Languages and Exact Sciences, 15054-000 São José do Rio Preto, SP, Brazil
| | - Itamar Soares Melo
- Embrapa Environment, Laboratory of Environmental Microbiology, 13820-000 Jaguariúna, SP, Brazil
| | - Marli Fatima Fiore
- University of São Paulo, Center for Nuclear Energy in Agriculture, Avenida Centenário 303, 13400-970 Piracicaba, SP, Brazil
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11
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Lambais MR, Lucheta AR, Crowley DE. Bacterial community assemblages associated with the phyllosphere, dermosphere, and rhizosphere of tree species of the Atlantic forest are host taxon dependent. MICROBIAL ECOLOGY 2014; 68:567-574. [PMID: 24889284 DOI: 10.1007/s00248-014-0433-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 05/08/2014] [Indexed: 06/03/2023]
Abstract
Bacterial communities associated with tree canopies have been shown to be specific to their plant hosts, suggesting that plant species-specific traits may drive the selection of microbial species that comprise their microbiomes. To further examine the degree to which the plant taxa drive the assemblage of bacterial communities in specific plant microenvironments, we evaluated bacterial community structures associated with the phyllosphere, dermosphere, and rhizosphere of seven tree species representing three orders, four families and four genera of plants from a pristine Dense Ombrophilous Atlantic forest in Brazil, using a combination of PCR-DGGE of 16S rRNA genes and clone library sequencing. Results indicated that each plant species selected for distinct bacterial communities in the phyllosphere, dermosphere, and rhizosphere, and that the bacterial community structures are significantly related to the plant taxa, at the species, family, and order levels. Further characterization of the bacterial communities of the phyllosphere and dermosphere of the tree species showed that they were inhabited predominantly by species of Gammaproteobacteria, mostly related to Pseudomonas. In contrast, the rhizosphere bacterial communities showed greater species richness and evenness, and higher frequencies of Alphaproteobacteria and Acidobacteria Gp1. With individual tree species each selecting for their specific microbiomes, these findings greatly increase our estimates of the bacterial species richness in tropical forests and provoke questions concerning the ecological functions of the microbial communities that exist on different plant parts.
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Affiliation(s)
- Marcio R Lambais
- Department of Soil Science, University of São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil,
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12
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Abu-Ghosh S, Droby S, Korine C. Seasonal and plant-dependent variations in diversity, abundance and stress tolerance of epiphytic yeasts in desert habitats. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:373-382. [PMID: 24992536 DOI: 10.1111/1758-2229.12161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 03/01/2014] [Indexed: 06/03/2023]
Abstract
We studied the epiphytic yeast species of the plants of the Negev Desert and the Dead Sea region, Israel, which are considered one of the most extreme hyper-arid lands in the world. For this purpose, we developed isolation protocols; we performed morphological, cultural and molecular identification tests and compared yeast diversity between the locations and the plants. The composition of the yeast populations present in the study's plants underwent seasonal fluctuations, whereas differences in community compositions were significant within sites. The maximum number of species of yeast occurred in autumn and Cryptococcus spp. were predominant year round. The isolated yeast strains showed an unusual tolerance to extreme growth conditions, such as high temperatures (up to 72% viability at 50°C), lethal hydrogen peroxide and NaCl concentrations. These results suggest that epiphytic yeasts inhabit the plants of the Dead Sea region and the Negev Desert have a community structure that is unique to the plant species and have a high tolerance to the harsh conditions that enables them to adapt to an arid ecosystem.
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Affiliation(s)
- Said Abu-Ghosh
- Department of Postharvest Science, The Volcani Center, Agricultural Research Organization (ARO), Bet Dagan, 50250, Israel
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13
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Müller T, Ruppel S. Progress in cultivation-independent phyllosphere microbiology. FEMS Microbiol Ecol 2013; 87:2-17. [PMID: 24003903 PMCID: PMC3906827 DOI: 10.1111/1574-6941.12198] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 11/28/2022] Open
Abstract
Most microorganisms of the phyllosphere are nonculturable in commonly used media and culture conditions, as are those in other natural environments. This review queries the reasons for their ‘noncultivability’ and assesses developments in phyllospere microbiology that have been achieved cultivation independently over the last 4 years. Analyses of total microbial communities have revealed a comprehensive microbial diversity. 16S rRNA gene amplicon sequencing and metagenomic sequencing were applied to investigate plant species, location and season as variables affecting the composition of these communities. In continuation to culture-based enzymatic and metabolic studies with individual isolates, metaproteogenomic approaches reveal a great potential to study the physiology of microbial communities in situ. Culture-independent microbiological technologies as well advances in plant genetics and biochemistry provide methodological preconditions for exploring the interactions between plants and their microbiome in the phyllosphere. Improving and combining cultivation and culture-independent techniques can contribute to a better understanding of the phyllosphere ecology. This is essential, for example, to avoid human–pathogenic bacteria in plant food.
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Affiliation(s)
- Thomas Müller
- Leibniz-Centre for Agricultural Landscape Research, Müncheberg, Institute of Landscape Biogeochemistry, Müncheberg, Germany
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14
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Finkel OM, Burch AY, Elad T, Huse SM, Lindow SE, Post AF, Belkin S. Distance-decay relationships partially determine diversity patterns of phyllosphere bacteria on Tamarix trees across the Sonoran Desert [corrected]. Appl Environ Microbiol 2012; 78:6187-93. [PMID: 22752165 PMCID: PMC3416633 DOI: 10.1128/aem.00888-12] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 06/20/2012] [Indexed: 11/20/2022] Open
Abstract
Dispersal limitation in phyllosphere communities was measured on the leaf surfaces of salt-excreting Tamarix trees, which offer unique, discrete habitats for microbial assemblages. We employed 16S rRNA gene pyrosequencing to measure bacterial community dissimilarity on leaves of spatially dispersed Tamarix specimens in sites with uniform climatic conditions across the Sonoran Desert in the Southwestern United States. Our analyses revealed diverse bacterial communities with four dominant phyla that exhibited differential effects of environmental and geographic variables. Geographical distance was the most important parameter that affected community composition, particularly that of betaproteobacteria, which displayed a statistically significant, distance-decay relationship.
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Affiliation(s)
- Omri M. Finkel
- Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adrien Y. Burch
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Tal Elad
- Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Susan M. Huse
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biology Laboratory, Woods Hole, Massachusetts, USA
| | - Steven E. Lindow
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Anton F. Post
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biology Laboratory, Woods Hole, Massachusetts, USA
| | - Shimshon Belkin
- Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
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