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Li J, Liu K, Dong Y, Chen L, Wang Z, Chen J, Zhang X. Potential effects of soil petroleum contamination on decomposition of Artemisia annua plant litter. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2024; 26:1022-1030. [PMID: 38747329 DOI: 10.1039/d4em00096j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
The accumulation of petroleum contaminants in phytoremediating plants can significantly impact the decomposition of their litter. However, the mechanisms underlying these effects and the potential influence of the contaminant concentration remain unclear. In this study, litter from Artemisia annua plants grown in soil with varying concentrations of petroleum (0, 15, 30, and 45 g kg-1) was collected. The litter samples were then inoculated with soil microorganisms and subjected to an indoor simulation of decomposition under controlled temperature and humidity conditions. Changes in the chemical properties, activities of decomposition-related enzymes in the litter, and decomposition rates were measured. Additionally, structural equation modeling was employed to analyze the mechanism through which soil petroleum contamination affects litter decomposition. The findings revealed several key points: (1) increasing soil petroleum contamination tended to reduce the concentration of carbon and nitrogen in litter while increasing those of lignin and total petroleum hydrocarbons (TPH). (2) Soil petroleum contamination tended to increase the activities of both total lignocellulases and total nutrient cycling-related enzymes in litter. (3) Soil petroleum contamination might indirectly inhibit the activity of lignocellulases by increasing the concentration of lignin and TPH in litter. However, it might also directly accelerate the activity of these enzymes, resulting in contradictory effects on litter decomposition. (4) Finally, A. annua litter produced in soil contaminated with 15 and 30 g kg-1 of petroleum exhibited significantly lower decomposition rates than that from uncontaminated soil.
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Affiliation(s)
- Jiahao Li
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China.
| | - Kaixuan Liu
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China.
| | - Yuxin Dong
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China.
| | - Lingsu Chen
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China.
| | - Ziquan Wang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China.
| | - Jinqiang Chen
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China.
| | - Xiaoxi Zhang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China.
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Kończak B, Wiesner-Sękala M, Ziembińska-Buczyńska A. The European trees phyllosphere characteristics and its potential in air bioremediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123977. [PMID: 38621454 DOI: 10.1016/j.envpol.2024.123977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/08/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The air pollution remediation is naturally carried out by plants. Their overground parts called phyllosphere are a type of a natural filter on which pollutants can be adsorb. Moreover, microbial communities living in phyllosphere perform a variety of biochemical processes removing also chemical pollutants. As their pollution is nowadays a burning issue especially for highly developed countries, the development of effective and ecological technologies for air treatment are of the utmost importance. The use of phyllosphere bacteria in the process of air bioremediation is a promising technology. This article reviews the role of phyllospheric bacteria in air bioremediation processes especially linked with the moderate climate plants. Research results published so far indicate that phyllosphere bacteria are able to metabolize the air pollutants but their potential is strictly determined by plant-phyllospheric bacteria interaction. The European tree species most commonly used for this purpose are also presented. The collected information filled the gap in the practical use of tree species in air bioremediation in the moderate climate zone.
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Affiliation(s)
- B Kończak
- Department of Water Protection, Central Mining Institute - National Research Institute, Plac Gwarków 1, 40-166, Katowice, Poland.
| | - M Wiesner-Sękala
- Department of Water Protection, Central Mining Institute - National Research Institute, Plac Gwarków 1, 40-166, Katowice, Poland.
| | - A Ziembińska-Buczyńska
- Department of Environmental Biotechnology, Faculty of Power and Environmental Engineering, Silesian University of Technology, str. Akademicka 2, 44-100, Gliwice, Poland.
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Banerjee S, Gupta N, Pramanik K, Gope M, GhoshThakur R, Karmakar A, Gogoi N, Hoque RR, Mandal NC, Balachandran S. Microbes and microbial strategies in carcinogenic polycyclic aromatic hydrocarbons remediation: a systematic review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:1811-1840. [PMID: 38063960 DOI: 10.1007/s11356-023-31140-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/16/2023] [Indexed: 01/18/2024]
Abstract
Degradation, detoxification, or removal of the omnipresent polycyclic aromatic hydrocarbons (PAHs) from the ecosphere as well as their prevention from entering into food chain has never appeared simple. In this context, cost-effective, eco-friendly, and sustainable solutions like microbe-mediated strategies have been adopted worldwide. With this connection, measures have been taken by multifarious modes of microbial remedial strategies, i.e., enzymatic degradation, biofilm and biosurfactant production, application of biochar-immobilized microbes, lactic acid bacteria, rhizospheric-phyllospheric-endophytic microorganisms, genetically engineered microorganisms, and bioelectrochemical techniques like microbial fuel cell. In this review, a nine-way directional approach which is based on the microbial resources reported over the last couple of decades has been described. Fungi were found to be the most dominant taxa among the CPAH-degrading microbial community constituting 52.2%, while bacteria, algae, and yeasts occupied 37.4%, 9.1%, and 1.3%, respectively. In addition to these, category-wise CPAH degrading efficiencies of each microbial taxon, consortium-based applications, CPAH degradation-related molecular tools, and factors affecting CPAH degradation are the other important aspects of this review in light of their appropriate selection and application in the PAH-contaminated environment for better human-health management in order to achieve a sustainable ecosystem.
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Affiliation(s)
- Sandipan Banerjee
- Mycology and Plant Pathology Laboratory, Department of Botany, Visva-Bharati, Santiniketan, 731235, West Bengal, India
| | - Nitu Gupta
- Department of Environmental Science, Tezpur University, Napaam, Tezpur, Assam, 784028, India
| | - Krishnendu Pramanik
- Microbiology and Microbial Bioinformatics Laboratory, Department of Botany, Cooch Behar Panchanan Barma University, Panchanan Nagar, Vivekananda Street, Cooch Behar, 736101, West Bengal, India
| | - Manash Gope
- Department of Environmental Science, The University of Burdwan, Golapbag, 713104, West Bengal, India
| | - Richik GhoshThakur
- Department of Environmental Studies, Visva-Bharati, Santiniketan, 731235, West Bengal, India
| | - Animesh Karmakar
- Department of Chemistry, Visva-Bharati, Santiniketan, 731235, West Bengal, India
| | - Nayanmoni Gogoi
- Department of Environmental Science, Tezpur University, Napaam, Tezpur, Assam, 784028, India
| | - Raza Rafiqul Hoque
- Department of Environmental Science, Tezpur University, Napaam, Tezpur, Assam, 784028, India
| | - Narayan Chandra Mandal
- Mycology and Plant Pathology Laboratory, Department of Botany, Visva-Bharati, Santiniketan, 731235, West Bengal, India
| | - Srinivasan Balachandran
- Department of Environmental Studies, Visva-Bharati, Santiniketan, 731235, West Bengal, India.
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Wang Z, Peng D, Fu C, Luo X, Guo S, Li L, Yin H. Pan-metagenome reveals the abiotic stress resistome of cigar tobacco phyllosphere microbiome. FRONTIERS IN PLANT SCIENCE 2023; 14:1248476. [PMID: 38179476 PMCID: PMC10765411 DOI: 10.3389/fpls.2023.1248476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/03/2023] [Indexed: 01/06/2024]
Abstract
The important role of microbial associations in mediating plant protection and responses to abiotic stresses has been widely recognized. However, there have been limited studies on the functional profile of the phyllosphere microbiota from tobacco (Nicotiana tabacum), hindering our understanding of the mechanisms underlying stress resilience in this representative and easy-to-cultivate model species from the solanaceous family. To address this knowledge gap, our study employed shotgun metagenomic sequencing for the first time to analyze the genetic catalog and identify putative plant growth promoting bacteria (PGPB) candidates that confer abiotic stress resilience throughout the growth period of cigar tobacco in the phyllosphere. We identified abundant genes from specific bacterial lineages, particularly Pseudomonas, within the cigar tobacco phyllospheric microbiome. These genes were found to confer resilience against a wide range of stressors, including osmotic and drought stress, heavy metal toxicity, temperature perturbation, organic pollutants, oxidative stress, and UV light damage. In addition, we conducted a virome mining analysis on the metagenome to explore the potential roles of viruses in driving microbial adaptation to environmental stresses. Our results identified a total of 3,320 scaffolds predicted to be viral from the cigar tobacco phyllosphere metagenome, with various phages infecting Pseudomonas, Burkholderia, Enterobacteria, Ralstonia, and related viruses. Within the virome, we also annotated genes associated with abiotic stress resilience, such as alkaline phosphatase D (phoD) for nutrient solubilization and glutamate-5-semialdehyde dehydrogenase (proA) for osmolyte synthesis. These findings shed light on the unexplored roles of viruses in facilitating and transferring abiotic stress resilience in the phyllospheric microbiome through beneficial interactions with their hosts. The findings from this study have important implications for agricultural practices, as they offer potential strategies for harnessing the capabilities of the phyllosphere microbiome to enhance stress tolerance in crop plants.
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Affiliation(s)
- Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Deyuan Peng
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Changwu Fu
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Xianxue Luo
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Shijie Guo
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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Jin MK, Yang YT, Zhao CX, Huang XR, Chen HM, Zhao WL, Yang XR, Zhu YG, Liu HJ. ROS as a key player in quinolone antibiotic stress on Arabidopsis thaliana: From the perspective of photosystem function, oxidative stress and phyllosphere microbiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157821. [PMID: 35931174 DOI: 10.1016/j.scitotenv.2022.157821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/31/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
With the increasing use of antibiotics, their ecological impacts have received widespread attention. However, research on the toxicity of quinolone antibiotics is still limited, especially regarding the oxidative stress and phyllosphere of plants. In this study, the toxic effects of enrofloxacin, norfloxacin, and levofloxacin on Arabidopsis thaliana and their underlying mechanisms were investigated. The toxicity of the three quinolone antibiotics decreased in the following order: enrofloxacin > norfloxacin > levofloxacin. Physiological cellular changes, such as plasmolysis and chloroplast swelling, were observed using electron microscopy. Photosynthetic efficiency was inhibited with a decline in the effective photochemical quantum yield of photosystem II (Y(II)) and non-photochemical quenching (NPQ), indicating that quinolone antibiotics might reduce light energy conversion efficiency and excess light energy dissipation. Oxidative stress occurred in A. thaliana after quinolone antibiotic treatment, with an increase in reactive oxygen species (ROS) levels and malondialdehyde (MDA) content. High ROS levels stimulated the over-expression of superoxide-responsive genes for self-protection. Structural equation modeling (SEM) analysis showed that photosynthesis inhibition and cellular damage caused by oxidative stress were critical factors for growth inhibition, suggesting that the antioxidant response activated by ROS might be a potential mechanism. Furthermore, the diversity of the phyllospheric microbial communities decreased after enrofloxacin exposure. Additionally, specific microbes were preferentially recruited to the phyllosphere because of the higher ROS levels.
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Affiliation(s)
- Ming-Kang Jin
- School of Environmental Science and Engineering, Instrumental Analysis Center, Zhejiang Gongshang University, Hangzhou 310018, PR China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Yu-Tian Yang
- Centre for Environmental Policy, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Cai-Xia Zhao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Xin-Rong Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Han-Mei Chen
- School of Environmental Science and Engineering, Instrumental Analysis Center, Zhejiang Gongshang University, Hangzhou 310018, PR China
| | - Wen-Lu Zhao
- School of Environmental Science and Engineering, Instrumental Analysis Center, Zhejiang Gongshang University, Hangzhou 310018, PR China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Hui-Jun Liu
- School of Environmental Science and Engineering, Instrumental Analysis Center, Zhejiang Gongshang University, Hangzhou 310018, PR China; International Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, Zhejiang Gongshang University, Hangzhou, Zhejiang 310012, PR China.
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Li Y, Ma J, Li Y, Xiao C, Shen X, Chen J, Xia X. Nitrogen addition facilitates phytoremediation of PAH-Cd cocontaminated dumpsite soil by altering alfalfa growth and rhizosphere communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150610. [PMID: 34597578 DOI: 10.1016/j.scitotenv.2021.150610] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Thousands of unlined landfills and open dumpsites seriously threatened the safety of soil and groundwater due to leachate leakage with a mass of pollutants, particularly heavy metals, organic contaminants and ammonia. Phytoremediation is widely used in the treatment of cocontaminated soils because it is cost-effective and environmentally friendly. However, the extent to which phytoremediation efficiency and plant physiological responses are affected by the high nitrogen (N) content in such cocontaminated soil is still uncertain. Here, pot experiments were conducted to investigate the effects of N addition on the applicability of legume alfalfa remediation for polycyclic aromatic hydrocarbon‑cadmium (PAHCd) co-/contaminated soil and the corresponding microbial regulation mechanism. The results showed that the PAH dissipation rates and Cd removal rates in the high-contamination groups increased with the external N supply, among which the pyrene dissipation rates in the cocontaminated soil was elevated most significantly, from 78.10% to 87.25%. However, the phytoremediation efficiency weakened in low cocontaminated soil, possibly because the excessive N content had inhibitory effects on the rhizobium Ensifer and restrained alfalfa growth. Furthermore, the relative abundance of PAH-degrading bacteria in the rhizosphere dominated PAH dissipation. As reflected by principal coordinate analysis (PCoA) analysis and hierarchical dendrograms, the microbial community composition changed with N addition, and a more pronounced shift was found in the rhizosphere relative to the endosphere or shoots of alfalfa. This study will provide a theoretical basis for legume plant remediation of dumpsites as well as soil contaminated with multiple pollutants.
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Affiliation(s)
- Yijia Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No. 19, Xinjiekouwai Street, HaiDian District, Beijing 100875, PR China.
| | - Junwei Ma
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No. 19, Xinjiekouwai Street, HaiDian District, Beijing 100875, PR China.
| | - Yuqian Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No. 19, Xinjiekouwai Street, HaiDian District, Beijing 100875, PR China.
| | - Chen Xiao
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No. 19, Xinjiekouwai Street, HaiDian District, Beijing 100875, PR China.
| | - Xinyi Shen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No. 19, Xinjiekouwai Street, HaiDian District, Beijing 100875, PR China.
| | - Jiajun Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No. 19, Xinjiekouwai Street, HaiDian District, Beijing 100875, PR China.
| | - Xinghui Xia
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No. 19, Xinjiekouwai Street, HaiDian District, Beijing 100875, PR China.
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Alves-Júnior M, de Sousa FO, Silva TF, Albino UB, Garcia MG, Moreira SMCDO, Vieira MRDS. Functional and morphological analysis of isolates of phylloplane and rhizoplane endophytic bacteria interacting in different cocoa production systems in the Amazon. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100039. [PMID: 34841330 PMCID: PMC8610332 DOI: 10.1016/j.crmicr.2021.100039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 11/25/2022] Open
Abstract
Endophytic bacteria colonize different internal tissues of plants without damaging their cells. They can establish themselves in the same niche as other microorganisms and develop antagonistic activities against phytopathogens. There is little research on the functional and morphological characterization of these bacteria in production systems in the Amazon. Thus, the objective of this work was to functionally and morphologically characterize endophytic bacteria isolated from cocoa trees (Theobroma cacao L.) and evaluate their antagonistic potential against phytopathogens. A total of 197 endophytic bacteria isolates were obtained from leaves and roots of cocoa plants with different production systems and at different times of the year. The characterization of functional groups consisted of proteolytic, amylolytic and cellulolytic activity and ability to fix nitrogen and solubilize phosphate. Morphological diversity was evaluated mainly according to the following parameters: shape, color, size and elevation of the colony. Thirteen isolates of endophytic bacteria, selected by cluster analysis, were used to evaluate the antagonistic potential in paired trials against four species of phytopathogenic fungi. The largest amount of endophytic bacteria was isolated from the root (95.9%), in the dry season. The most expressive activities with regards to the enzyme index were amylolytic (71.9%), proteolytic (70.2%) and nitrogen fixing (38.6%), respectively. The similarity analysis formed two clusters with isolates CS R 2.4 and CS R 2.25 exhibiting 100% similarity. Five isolates displayed inhibitory activity against phytopathogenic fungi, most notably isolate TS R 2.19, which exhibited antagonistic activity against all fungi and mycelial growth inhibition rates between 25.7% and 50.7%. Understanding the interaction between endophytes in cocoa plants is important as a possible additional tool in biological control. Our studies are incipient and the first to be carried out in different cocoa production systems in the state of Pará, Brazil.
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Affiliation(s)
- Miguel Alves-Júnior
- Faculty of Agronomic Engineering, Laboratory of Agricultural and Forestry Phytopathology, Federal University of Pará, Altamira, PA, 68372-040, Brazil
| | - Fabiana Oliveira de Sousa
- Faculty of Agronomic Engineering, Laboratory of Agricultural and Forestry Phytopathology, Federal University of Pará, Altamira, PA, 68372-040, Brazil
| | - Thays Ferreira Silva
- Faculty of Agronomic Engineering, Laboratory of Agricultural and Forestry Phytopathology, Federal University of Pará, Altamira, PA, 68372-040, Brazil
| | - Ulisses Brigatto Albino
- Faculty of Chemistry, Institute of Exact Sciences, Federal University of the South and Southeast of Pará, Marabá, PA 68507-590, Brazil
| | - Magali Gonçalves Garcia
- Faculty of Biological Sciences, Laboratory of Microbiology, Federal University of Pará, Altamira, PA 68372-040, Brazil
| | | | - Marcos Ribeiro da Silva Vieira
- Faculty of Agronomic Engineering, Laboratory of Physiology and Post-Harvest, Technology, Federal University of Pará, Altamira, PA 68372-040, Brazil
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Yan K, Han W, Zhu Q, Li C, Dong Z, Wang Y. Leaf surface microtopography shaping the bacterial community in the phyllosphere: evidence from 11 tree species. Microbiol Res 2021; 254:126897. [PMID: 34710835 DOI: 10.1016/j.micres.2021.126897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/27/2021] [Accepted: 10/13/2021] [Indexed: 10/20/2022]
Abstract
Phyllosphere bacteria are an important component of environmental microbial communities and are closely related to plant health and ecosystem stability. However, the relationships between the inhabitation and assembly of phyllosphere bacteria and leaf microtopography are still obscure. In this study, the phyllosphere bacterial communities and leaf microtopographic features (vein density, stomatal length, and density) of eleven tree species were fully examined. Both the absolute abundance and diversity of phyllosphere bacterial communities were significantly different among the tree species, and leaf vein density dominated the variation. TITAN analysis showed that leaf vein density also played more important roles in regulating the relative abundance of bacteria than stomatal features, and 6 phyla and 62 genera of phyllosphere bacteria showed significant positive responses to leaf vein density. Moreover, LEfSe analysis showed that the leaves with higher vein density had more bacterial biomarkers. Leaf vein density also changed the co-occurrence pattern of phyllosphere bacteria, and the co-occurrence network demonstrated more negative correlations and more nodes on the leaves with larger leaf vein density, indicating that higher densities of leaf veins improved the stability of the phyllosphere bacterial community. Phylogenetic analysis showed that deterministic processes (especially homogeneous selection) dominated the assembly process of phyllosphere bacterial communities. The leaf vein density increased the degree of bacterial clustering at the phylogenetic level. Therefore, the inhabitation and assembly of the phyllosphere bacterial community are related to leaf microtopography, which provides deeper insight into the interaction between plants and bacteria.
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Affiliation(s)
- Kun Yan
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Wenhao Han
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Qiliang Zhu
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Chuanrong Li
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Zhi Dong
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Yanping Wang
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an, 271018, PR China.
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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: 61] [Impact Index Per Article: 20.3] [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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Terzaghi E, Posada-Baquero R, Di Guardo A, Ortega-Calvo JJ. Microbial degradation of pyrene in holm oak (Quercus ilex) phyllosphere: Role of particulate matter in regulating bioaccessibility. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147431. [PMID: 33964783 DOI: 10.1016/j.scitotenv.2021.147431] [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: 02/23/2021] [Revised: 04/09/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
In this study we first measured the mineralization of pyrene on leaves of urban holm oak (Quercus ilex) by autochthonous microorganisms and an inoculated PAH degrading bacterium (i.e., Mycobacterium gilvum), selected as a model phyllosphere species, as well as the leaf-water (KLW) and leaf-air (KLA) partition coefficients for this chemical. Mineralization was investigated in two different experimental systems in terms of leaf and microorganism environment. Additionally, the influence on pyrene partitioning and mineralization when particulate matter (PM) was present on the leaf surface or removed was studied. Mineralization of 14C-labeled pyrene by autochthonous microorganisms was lower than 1% after approximately two weeks, while M. gilvum mineralized 5% to 17% of pyrene. These extents corresponded to mineralization half-lives that ranged between ~30 to ~200 days. We proposed that PM present at the leaf surface reduced the accumulation of pyrene by inner compartments (cuticle) distantly located from microbial cells and enhanced the bioaccessibility of pyrene, speeding up microbial activity and therefore mineralization. These results highlight that plant-phyllosphere microorganism interaction is more complex than currently established and deserves additional studies to further comprehend the air purification ecosystem service of phyllosphere microorganisms.
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Affiliation(s)
- Elisa Terzaghi
- Department of Science and High Technology, University of Insubria, Via Valleggio 11, 22100 Como, Italy.
| | - Rosa Posada-Baquero
- Instituto de Recursos Naturales y Agrobiologıá de Sevilla (IRNAS-CSIC), E-41080 Seville, Spain
| | - Antonio Di Guardo
- Department of Science and High Technology, University of Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Josè-J Ortega-Calvo
- Instituto de Recursos Naturales y Agrobiologıá de Sevilla (IRNAS-CSIC), E-41080 Seville, Spain
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11
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Haider FU, Ejaz M, Cheema SA, Khan MI, Zhao B, Liqun C, Salim MA, Naveed M, Khan N, Núñez-Delgado A, Mustafa A. Phytotoxicity of petroleum hydrocarbons: Sources, impacts and remediation strategies. ENVIRONMENTAL RESEARCH 2021; 197:111031. [PMID: 33744268 DOI: 10.1016/j.envres.2021.111031] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Extraction and exploration of petroleum hydrocarbons (PHs) to satisfy the rising world population's fossil fuel demand is playing havoc with human beings and other life forms by contaminating the ecosystem, particularly the soil. In the current review, we highlighted the sources of PHs contamination, factors affecting the PHs accumulation in soil, mechanisms of uptake, translocation and potential toxic effects of PHs on plants. In plants, PHs reduce the seed germination andnutrients translocation, and induce oxidative stress, disturb the plant metabolic activity and inhibit the plant physiology and morphology that ultimately reduce plant yield. Moreover, the defense strategy in plants to mitigate the PHs toxicity and other potential remediation techniques, including the use of organic manure, compost, plant hormones, and biochar, and application of microbe-assisted remediation, and phytoremediation are also discussed in the current review. These remediation strategies not only help to remediate PHs pollutionin the soil rhizosphere but also enhance the morphological and physiological attributes of plant and results to improve crop yield under PHs contaminated soils. This review aims to provide significant information on ecological importance of PHs stress in various interdisciplinary investigations and critical remediation techniques to mitigate the contamination of PHs in agricultural soils.
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Affiliation(s)
- Fasih Ullah Haider
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Key Lab of Arid-land Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Mukkaram Ejaz
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, PR China
| | - Sardar Alam Cheema
- Department of Agronomy, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Muhammad Imran Khan
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Baowei Zhao
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, PR China
| | - Cai Liqun
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Key Lab of Arid-land Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
| | | | - Muhammad Naveed
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, 12 FL 32611, USA
| | - Avelino Núñez-Delgado
- Depart. Soil Sci. and Agric. Chem., Engineering Polytech. School, Lugo, Univ. Santiago de Compostela, Spain
| | - Adnan Mustafa
- National Engineering Laboratory for Improving Quality of Arable Land, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
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12
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Khoiri AN, Cheevadhanarak S, Jirakkakul J, Dulsawat S, Prommeenate P, Tachaleat A, Kusonmano K, Wattanachaisaereekul S, Sutheeworapong S. Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management. Front Microbiol 2021; 12:623799. [PMID: 33828538 PMCID: PMC8019924 DOI: 10.3389/fmicb.2021.623799] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.
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Affiliation(s)
- Ahmad Nuruddin Khoiri
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Supapon Cheevadhanarak
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Jiraporn Jirakkakul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Sudarat Dulsawat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Peerada Prommeenate
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Anuwat Tachaleat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Kanthida Kusonmano
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Songsak Wattanachaisaereekul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Faculty of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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13
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Terzaghi E, De Nicola F, Cerabolini BEL, Posada-Baquero R, Ortega-Calvo JJ, Di Guardo A. Role of photo- and biodegradation of two PAHs on leaves: Modelling the impact on air quality ecosystem services provided by urban trees. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 739:139893. [PMID: 32535463 DOI: 10.1016/j.scitotenv.2020.139893] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 06/11/2023]
Abstract
Urban trees provide important ecosystem services, including air quality improvement. Polycyclic aromatic hydrocarbons (PAHs) are among the most important pollutants in air, due to their elevated concentrations and toxicity. Plants can act as filters of PAHs and as "chemical reactors" for pollutant removal, therefore reducing air concentrations. Here, the first assessment of photo- vs. biodegradation of PAHs on leaves of urban trees is presented. A dynamic air-vegetation-soil model (SoilPlusVeg) was improved to simulate the fate of two representative PAHs with contrasting physico-chemical properties (phenanthrene and benzo[a]pyrene). Simulations were performed for two different environmental scenarios from Italy (Como and Naples), selected for their dissimilar meteorological parameters, plant species and emission levels. The effect of photo- and biodegradation on leaf concentrations and fluxes towards air and soil was investigated comparing deciduous (maple, cornel and hazelnut) and evergreen (holm oak) broadleaf woods. The results showed that biodegradation in the phyllosphere could not be neglected when evaluating the ecosystem services provided by urban trees, as this process contributed significantly to the reductions (up to 25% on average) in PAH leaf concentrations and fluxes to air and soil; however, the reductions revealed ample variations with time (up to more than two orders of magnitude) showing the dependence on meteorological parameters, air compartment structure, as well as type of woods. These findings permitted to improve the ecological realism of the simulations and obtain more accurate results when predicting organic contaminant uptake and release by plant leaves, including potential for food chain transfer and long-range transport.
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Affiliation(s)
- Elisa Terzaghi
- Department of Science and High Technology, University of Insubria, Via Valleggio 11, 22100 Como, Italy.
| | - Flavia De Nicola
- Department of Sciences and Technologies, University of Sannio, Via F. De Sanctis SNC, 82100 Benevento, Italy
| | - Bruno E L Cerabolini
- Department of Biotechnologies and Life Sciences, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy
| | - Rosa Posada-Baquero
- Instituto de Recursos Naturales y Agrobiologıá de Sevilla (IRNAS-CSIC), Avda. Reina Mercedes, 10, E-41080 Seville, Spain
| | - Josè-J Ortega-Calvo
- Instituto de Recursos Naturales y Agrobiologıá de Sevilla (IRNAS-CSIC), Avda. Reina Mercedes, 10, E-41080 Seville, Spain
| | - Antonio Di Guardo
- Department of Science and High Technology, University of Insubria, Via Valleggio 11, 22100 Como, Italy
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14
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Allamin IA, Halmi MIE, Yasid NA, Ahmad SA, Abdullah SRS, Shukor Y. Rhizodegradation of Petroleum Oily Sludge-contaminated Soil Using Cajanus cajan Increases the Diversity of Soil Microbial Community. Sci Rep 2020; 10:4094. [PMID: 32139706 PMCID: PMC7057954 DOI: 10.1038/s41598-020-60668-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 02/12/2020] [Indexed: 11/08/2022] Open
Abstract
Most components of petroleum oily sludge (POS) are toxic, mutagenic and cancer-causing. Often bioremediation using microorganisms is hindered by the toxicity of POS. Under this circumstance, phytoremediation is the main option as it can overcome the toxicity of POS. Cajanus cajan a legume plant, was evaluated as a phyto-remediating agent for petroleum oily sludge-spiked soil. Culture dependent and independent methods were used to determine the rhizosphere microorganisms' composition. Degradation rates were estimated gravimetrically. The population of total heterotrophic bacteria (THRB) was significantly higher in the uncontaminated soil compared to the contaminated rhizosphere soil with C. cajan, but the population of hydrocarbon-utilizing bacteria (HUB) was higher in the contaminated rhizosphere soil. The results show that for 1 to 3% oily sludge concentrations, an increase in microbial counts for all treatments from day 0 to 90 d was observed with the contaminated rhizosphere CR showing the highest significant increase (p < 0.05) in microbial counts compared to other treatments. The metagenomic study focused on the POS of 3% (w/w) and based on the calculated bacterial community abundance indices showed an increase in the values for Ace, Cho, Shannon (Shannon-Weaver) and the Simpson's (measured as InvSimpson) indices in CR3 compared to CN3. Both the Simpson's and the Shannon values for CR3 were higher than CN3 indicating an increase in diversity upon the introduction of C. cajan into the contaminated soil. The PCoA plot revealed community-level differences between the contaminated non-rhizosphere control and contaminated rhizosphere microbiota. The PCoA differentiated the two treatments based on the presence or absence of plant. The composition and taxonomic analysis of microbiota-amplified sequences were categorized into eight phyla for the contaminated non-rhizosphere and ten phyla for the contaminated rhizosphere. The overall bacterial composition of the two treatments varied, as the distribution shows a similar variation between the two treatments in the phylum distribution. The percentage removal of total petroleum hydrocarbon (TPH) after 90 days of treatments with 1, 2, 3, 4, and 5% (w/w) of POS were 92, 90, 89, 68.3 and 47.3%, respectively, indicating removal inhibition at higher POS concentrations. As the search for more eco-friendly and sustainable remediating green plant continues, C. cajan shows great potential in reclaiming POS contaminated soil. Our findings will provide solutions to POS polluted soils and subsequent re-vegetation.
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Affiliation(s)
- Ibrahim Alkali Allamin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State, Nigeria
| | - Mohd Izuan Effendi Halmi
- Department of Land Management, Faculty of Agriculture, University Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Nur Adeela Yasid
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Rozaimah Sheikh Abdullah
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Selangor, Malaysia
| | - Yunus Shukor
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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15
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Waigi MG, Wang J, Yang B, Gudda FO, Ling W, Liu J, Gao Y. Endophytic Bacteria in in planta Organopollutant Detoxification in Crops. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 252:1-50. [PMID: 31451946 DOI: 10.1007/398_2019_33] [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] [Indexed: 06/10/2023]
Abstract
Microbe-assisted organopollutant removal, or in planta crop decontamination, is based on an interactive system between organopollutant-degrading endophytic bacteria (DEBOP) and crops in alleviating organic toxins in plants. This script focuses on the fast-growing body of literature that has recently bloomed in organopollutant control in agricultural plants. The various facets of DEBOP under study include their colonization, distribution, plant growth-promoting mechanisms, and modes of action in the detoxification process in plants. Also, an assessment of the biotechnological advances, advantages, and bottlenecks in accelerating the implementation of this decontamination strategy will be undertaken. The highlighted key research directions from this review will shape the future of agro-environmental sustainability and preservation of human health.
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Affiliation(s)
- Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jian Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fredrick Owino Gudda
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Juan Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.
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16
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Lumactud R, Fulthorpe RR. Endophytic Bacterial Community Structure and Function of Herbaceous Plants From Petroleum Hydrocarbon Contaminated and Non-contaminated Sites. Front Microbiol 2018; 9:1926. [PMID: 30190710 PMCID: PMC6115521 DOI: 10.3389/fmicb.2018.01926] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/30/2018] [Indexed: 02/01/2023] Open
Abstract
Bacterial endophytes (BEs) are non-pathogenic residents of healthy plant tissues that can confer benefits to plants. Many Bacterial endophytes have been shown to contribute to plant growth and health, alleviation of plant stress and to in-planta contaminant-degradation. This study examined the endophytic bacterial communities of plants growing abundantly in a heavily hydrocarbon contaminated site, and compared them to those found in the same species at a non-contaminated. We used culture- dependent and independent methods to characterize the community structure, hydrocarbon degrading capabilities, and plant growth promoting traits of cultivable endophytes isolated from Achillea millefolium, Solidago Canadensis, and Daucus carota plants from these two sites. Culture- dependent and independent analyses revealed class Gammaproteobacteria predominated in all the plants regardless of the presence of petroleum hydrocarbon, with Pantoea spp. as largely dominant. It was interesting to note a >50% taxonomic overlap (genus level) of 16s rRNA high throughput amplicon sequences with cultivable endophytes. PERMANOVA analysis of TRFLP fragments revealed significant structural differences between endophytic bacterial communities from hydrocarbon-contaminated and non-contaminated soils-however, there was no marked difference in their functional capabilities. Pantoea spp. demonstrated plant beneficial characteristics, such as P solubilization, indole-3-acetic acid production and presence of 1-aminocyclopropane-1-carboxylate deaminase. Our findings reveal that functional capabilities of bacterial isolates being examined were not influenced by the presence of contamination; and that the stem endosphere supports ubiquitous BEs that were consistent throughout plant hosts and sites.
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Affiliation(s)
- Rhea Lumactud
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Roberta R Fulthorpe
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada
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17
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Montanari-Coelho KK, Costa AT, Polonio JC, Azevedo JL, Marin SRR, Fuganti-Pagliarini R, Fujita Y, Yamaguchi-Shinozaki K, Nakashima K, Pamphile JA, Nepomuceno AL. Endophytic bacterial microbiome associated with leaves of genetically modified (AtAREB1) and conventional (BR 16) soybean plants. World J Microbiol Biotechnol 2018; 34:56. [PMID: 29594576 DOI: 10.1007/s11274-018-2439-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
Abstract
Plant leaves (phyllosphere) have a great potential for colonization and microbial growth, consisting of a dynamic environment in which several factors can interfere with the microbial population structure. The use of genetically modified (GM) plants has introduced several traits in agriculture, such as the improvement of plant drought tolerance, as observed in the AtAREB1 transcription factor overexpression in soybean (Glycine max L. Merrill). The present study aimed at investigating the taxonomic and functional profile of the leaf microbial community of bacteria found in GM (drought-tolerant event 1Ea2939) and conventional (BR 16) soybean plants. Bacterial DNA was extracted from leaf samples collected from each genotype and used for microbial diversity and richness analysis through the MiSeq Illumina platform. Functional prediction was performed using the PICRUSt tool and the STAMP v 2.1.3 software. The obtainment of the GM event 1Ea2939 showed minimum effects on the microbial community and in the potential for chemical-genetic communication, i.e. in the potential for symbiotic and/or mutualistic interaction between plants and their natural microbiota.
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Affiliation(s)
| | - Alessandra Tenório Costa
- Departamento de Biotecnologia, Genética e Biologia Celular (DBC), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Julio Cesar Polonio
- Departamento de Biotecnologia, Genética e Biologia Celular (DBC), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - João Lúcio Azevedo
- Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Renata Fuganti-Pagliarini
- Empresa Brasileira de Pesquisa Agropecuária, Centro Nacional de Pesquisa de Soja (EMBRAPA/Soja), Londrina, Brazil
| | - Yasunari Fujita
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | | | - Kazuo Nakashima
- Laboratory of Plant Molecular Physiology, Tokyo University, Tokyo, Japan
| | - João Alencar Pamphile
- Departamento de Biotecnologia, Genética e Biologia Celular (DBC), Universidade Estadual de Maringá, Maringá, Paraná, Brazil.
| | - Alexandre Lima Nepomuceno
- Empresa Brasileira de Pesquisa Agropecuária, Centro Nacional de Pesquisa de Soja (EMBRAPA/Soja), Londrina, Brazil
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18
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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: 58] [Impact Index Per Article: 8.3] [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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19
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Treesubsuntorn C, Boraphech P, Thiravetyan P. Trimethylamine removal by plant capsule of Sansevieria kirkii in combination with Bacillus cereus EN1. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:10139-10149. [PMID: 28258430 DOI: 10.1007/s11356-017-8679-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 02/20/2017] [Indexed: 06/06/2023]
Abstract
Trimethylamine (TMA) contamination produces a strong "fishy" odor and can cause pathological changes in humans. By screening native microorganisms from Sansevieria kirkii exposed to 100 ppm TMA, it was shown that endophytic bacteria number 1 (EN1) and number 2 (EN2) have a higher TMA tolerance and removal capacity than other bacteria species in a closed system. In addition, EN1 and EN2 demonstrated the ability to produce high quantities of indole-3-acetic acid (IAA) and use 1-aminocyclopropane-1-carboxylic acid (ACC), which is found normally in plant growth-promoting bacteria (PGPB). Moreover, 16S ribosomal DNA (rDNA) sequences of EN1 and EN2 identification showed that EN1 and EN2 was the same bacteria species, Bacillus cereus. B. cereus EN1 was chosen to apply with S. kirkii to remove TMA in a plant capsule, which was compared to control conditions. It was found that 500 g of soil with S. kirkii inoculated with B. cereus EN1 had a higher TMA removal efficiency than other conditions. Moreover, the flow rate of TMA-contaminated gas was varied (0.03-1 L min-1) to calculate the loading rate and elimination capacity. The maximum loading rate of 500 g soil with B. cereus EN1-inoculated S. kirkii was 2500 mg m-3 h-1, while other conditions showed only around 250-750 mg m-3 h-1. Therefore, a plant capsule with B. cereus EN1-inoculated S. kirkii had the potential to be applied in TMA-contaminated air.
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Affiliation(s)
- Chairat Treesubsuntorn
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Phattara Boraphech
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Paitip Thiravetyan
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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20
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Tan Y, Cui Y, Li H, Kuang A, Li X, Wei Y, JI X. Diversity and composition of rhizospheric soil and root endogenous bacteria inPanax notoginsengduring continuous cropping practices. J Basic Microbiol 2017; 57:337-344. [DOI: 10.1002/jobm.201600464] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/10/2016] [Accepted: 12/16/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Yong Tan
- Faculty of Life Science and Technology; Kunming University of Science and Technology; Kunming China
| | - Yinshan Cui
- Faculty of Life Science and Technology; Kunming University of Science and Technology; Kunming China
| | - Haoyu Li
- Faculty of Life Science and Technology; Kunming University of Science and Technology; Kunming China
| | - Anxiu Kuang
- Department of Biology; University of Texas Rio Grande Valley; Edinburg Texas
| | - Xiaoran Li
- Faculty of Life Science and Technology; Kunming University of Science and Technology; Kunming China
| | - Yunlin Wei
- Faculty of Life Science and Technology; Kunming University of Science and Technology; Kunming China
| | - Xiuling JI
- Faculty of Life Science and Technology; Kunming University of Science and Technology; Kunming China
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Gkorezis P, Daghio M, Franzetti A, Van Hamme JD, Sillen W, Vangronsveld J. The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective. Front Microbiol 2016; 7:1836. [PMID: 27917161 PMCID: PMC5116465 DOI: 10.3389/fmicb.2016.01836] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/01/2016] [Indexed: 11/24/2022] Open
Abstract
Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.
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Affiliation(s)
- Panagiotis Gkorezis
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | - Matteo Daghio
- Department of Environmental Sciences, University of Milano-BicoccaMilano, Italy
- Department of Biological Sciences, Thompson Rivers University, KamloopsBC, Canada
| | - Andrea Franzetti
- Department of Environmental Sciences, University of Milano-BicoccaMilano, Italy
| | | | - Wouter Sillen
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
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Lumactud R, Shen SY, Lau M, Fulthorpe R. Bacterial Endophytes Isolated from Plants in Natural Oil Seep Soils with Chronic Hydrocarbon Contamination. Front Microbiol 2016; 7:755. [PMID: 27252685 PMCID: PMC4878295 DOI: 10.3389/fmicb.2016.00755] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 05/04/2016] [Indexed: 11/13/2022] Open
Abstract
The bacterial endophytic communities of four plants growing abundantly in soils highly contaminated by hydrocarbons were analyzed through culturable and culture-independent means. Given their tolerance to the high levels of petroleum contamination at our study site, we sought evidence that Achillea millefolium, Solidago canadensis, Trifolium aureum, and Dactylis glomerata support high levels of hydrocarbon degrading endophytes. A total of 190 isolates were isolated from four plant species. The isolates were identified by partial 16S rDNA sequence analysis, with class Actinobacteria as the dominant group in all species except S. canadensis, which was dominated by Gammaproteobacteria. Microbacterium foliorum and Plantibacter flavus were present in all the plants, with M. foliorum showing predominance in D. glomerata and both endophytic bacterial species dominated T. aureum. More than 50% of the isolates demonstrated degradative capabilities for octanol, toluene, naphthalene, kerosene, or motor oil based on sole carbon source growth screens involving the reduction of tetrazolium dye. P. flavus isolates from all the sampled plants showed growth on all the petroleum hydrocarbons (PHCs) substrates tested. Mineralization of toluene and naphthalene was confirmed using gas-chromatography. 16S based terminal restriction fragment length polymorphism analysis revealed significant differences between the endophytic bacterial communities showing them to be plant host specific at this site. To our knowledge, this is the first account of the degradation potential of bacterial endophytes in these commonly occurring pioneer plants that were not previously known as phytoremediating plants.
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Affiliation(s)
- Rhea Lumactud
- Department of Physical and Environmental Sciences, University of Toronto-Scarborough Toronto, ON, Canada
| | - Shu Yi Shen
- Department of Physical and Environmental Sciences, University of Toronto-Scarborough Toronto, ON, Canada
| | - Mimas Lau
- Department of Physical and Environmental Sciences, University of Toronto-Scarborough Toronto, ON, Canada
| | - Roberta Fulthorpe
- Department of Physical and Environmental Sciences, University of Toronto-Scarborough Toronto, ON, Canada
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Zhang M, Wang J, Zhang Z, Song Z, Zhang Z, Zhang B, Zhang G, Wu WM. A field pilot-scale study of biological treatment of heavy oil-produced water by biological filter with airlift aeration and hydrolytic acidification system. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:4919-4930. [PMID: 26549708 DOI: 10.1007/s11356-015-5721-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/30/2015] [Indexed: 06/05/2023]
Abstract
Heavy oil-produced water (HOPW) is a by-product during heavy oil exploitation and can cause serious environmental pollution if discharged without adequate treatment. Commercial biochemical treatment units are important parts of HOPW treatment processes, but many are not in stable operation because of the toxic and refractory substances, salt, present. Therefore, pilot-scale experiments were conducted to evaluate the performance of hydrolytic acidification-biological filter with airlift aeration (HA-BFAA), a novel HOPW treatment system. Four strains isolated from oily sludge were used for bioaugmentation to enhance the biodegradation of organic pollutants. The isolated bacteria were evaluated using 3-day biochemical oxygen demand, oil, dodecyl benzene sulfonic acid, and chemical oxygen demand (COD) removals as evaluation indices. Bioaugmentation enhanced the COD removal by 43.5 mg/L under a volume load of 0.249 kg COD/m(3) day and hydraulic retention time of 33.6 h. The effluent COD was 70.9 mg/L and the corresponding COD removal was 75.0 %. The optimum volumetric air-to-water ratio was below 10. The removal ratios of the total extractable organic pollutants, alkanes, and poly-aromatic hydrocarbons were 71.1, 94.4, and 94.0 %, respectively. Results demonstrated that HA-BFAA was an excellent HOPW treatment system.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum, Beijing, 102249, People's Republic of China
| | - Junming Wang
- Dalian Design Branch, China Petroleum Engineering & Construction Corporation, Dalian, 116011, China
| | - Zhongzhi Zhang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum, Beijing, 102249, People's Republic of China.
| | - Zhaozheng Song
- State Key Laboratory of Heavy Oil Processing, Faculty of Sciences, China University of Petroleum, Beijing, 102249, People's Republic of China
| | - Zhenjia Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Beiyu Zhang
- Dalian Design Branch, China Petroleum Engineering & Construction Corporation, Dalian, 116011, China
| | - Guangqing Zhang
- School of Mechanical, Materials & Mechatronic Engineering, University of Wollongong, Wollongong, NSW2522, Australia
| | - Wei-Min Wu
- Department of Civil & Environmental Engineering, Center for Sustainable Development & Global Competitiveness, Stanford University, Stanford, CA, 94305-4020, USA
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24
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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: 54] [Impact Index Per Article: 6.0] [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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25
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Ali N, Al-Awadhi H, Dashti N, Khanafer M, El-Nemr I, Sorkhoh N, Radwan SS. Bioremediation of Atmospheric Hydrocarbons via Bacteria Naturally Associated with Leaves of Higher Plants. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2015; 17:1160-1170. [PMID: 25946637 DOI: 10.1080/15226514.2015.1045125] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Bacteria associated with leaves of sixteen cultivated and wild plant species from all over Kuwait were analyzed by a culture-independent approach. This technique depended on partial sequencing of 16S rDNA regions in total genomic DNA from the bacterial consortia and comparing the resulting sequences with those in the GenBank database. To release bacterial cells from leaves, tough methods such as sonication co-released too much leaf chloroplasts whose DNA interfered with the bacterial DNA. A more satisfactory bacterial release with a minimum of chloroplast co-release was done by gently rubbing the leaf surfaces with soft tooth brushes in phosphate buffer. The leaves of all plant species harbored on their surfaces bacterial communities predominated by hydrocarbonoclastic (hydrocarbon-utilizing) bacterial genera. Leaves of 6 representative plants brought about in the laboratory effective removal of volatile hydrocarbons in sealed microcosms. Each individual plant species had a unique bacterial community structure. Collectively, the phyllospheric microflora on the studied plants comprised the genera Flavobacterium, Halomonas, Arthrobacter, Marinobacter, Neisseria, Ralstonia, Ochrobactrum. Exiguobacterium, Planomicrobium, Propionibacterium, Kocuria, Rhodococcus and Stenotrophomonas. This community structure was dramatically different from the structure we determined earlier for the same plants using the culture-dependent approach, although in both cases, hydrocarbonoclastic bacteria were frequent.
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Affiliation(s)
- N Ali
- a Department of Biological Sciences , Faculty of Science, Kuwait University , Safat , Kuwait
| | - H Al-Awadhi
- a Department of Biological Sciences , Faculty of Science, Kuwait University , Safat , Kuwait
| | - N Dashti
- a Department of Biological Sciences , Faculty of Science, Kuwait University , Safat , Kuwait
| | - M Khanafer
- a Department of Biological Sciences , Faculty of Science, Kuwait University , Safat , Kuwait
| | - I El-Nemr
- a Department of Biological Sciences , Faculty of Science, Kuwait University , Safat , Kuwait
| | - N Sorkhoh
- a Department of Biological Sciences , Faculty of Science, Kuwait University , Safat , Kuwait
| | - S S Radwan
- a Department of Biological Sciences , Faculty of Science, Kuwait University , Safat , Kuwait
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26
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Afzal M, Khan QM, Sessitsch A. Endophytic bacteria: prospects and applications for the phytoremediation of organic pollutants. CHEMOSPHERE 2014; 117:232-42. [PMID: 25078615 DOI: 10.1016/j.chemosphere.2014.06.078] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 05/18/2023]
Abstract
Recently, there has been an increased effort to enhance the efficacy of phytoremediation of contaminated environments by exploiting plant-microbe interactions. The combined use of plants and endophytic bacteria is an emerging approach for the clean-up of soil and water polluted with organic compounds. In plant-endophyte partnerships, plants provide the habitat as well as nutrients to their associated endophytic bacteria. In response, endophytic bacteria with appropriate degradation pathways and metabolic activities enhance degradation of organic pollutants, and diminish phytotoxicity and evapotranspiration of organic pollutants. Moreover, endophytic bacteria possessing plant growth-promoting activities enhance the plant's adaptation and growth in soil and water contaminated with organic pollutants. Overall, the application of endophytic bacteria gives new insights into novel protocols to improve phytoremediation efficiency. However, successful application of plant-endophyte partnerships for the clean-up of an environment contaminated with organic compounds depends on the abundance and activity of the degrading endophyte in different plant compartments. Although many endophytic bacteria have the potential to degrade organic pollutants and improve plant growth, their contribution to enhance phytoremediation efficiency is still underestimated. A better knowledge of plant-endophyte interactions could be utilized to increase the remediation of polluted soil environments and to protect the foodstuff by decreasing agrochemical residues in food crops.
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Affiliation(s)
- Muhammad Afzal
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan.
| | - Qaiser M Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, 3430 Tulln, Austria
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27
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Al-Mailem D, Eliyas M, Khanafer M, Radwan S. Culture-dependent and culture-independent analysis of hydrocarbonoclastic microorganisms indigenous to hypersaline environments in Kuwait. MICROBIAL ECOLOGY 2014; 67:857-65. [PMID: 24682340 DOI: 10.1007/s00248-014-0386-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 01/20/2014] [Indexed: 05/15/2023]
Abstract
The halophilic, hydrocarbonoclastic bacteria and archaea inhabiting two hypersaline coastal areas in Kuwait, one in the north and the other in the south, were counted and characterized. Environmental parameters in both areas were similar, with the exception of the soil organic carbon content, which was in the north higher than in the south. The hydrocarbonoclastic bacterial and haloarchaeal numbers and identities as analyzed using nutrient media of various salinities were similar in soil and pond water samples from both areas. The bacterial species recorded by this culture-dependent method belonged to the genera Halomonas, Chromohalobacter, Marinobacter, Exiguobacterium, Stenotrophomonas, Pseudomonas, Salinivibrio, and Bacillus. The haloarchaeal species belonged to the genera Haloferax and Halobacterium. When analyzed by fingerprinting of their amplified genomic DNA followed by sequencing of the electrophoresis-resolved bands, the same environmental samples revealed a different microbial composition. Bacterial phylotypes recorded by this culture-independent method were affiliated with the genera Ochrobactrum, Stenotrophomonas, Rhodococcus, and "Halomicrobium," whereas the archaeal phylotypes were affiliated with Halorussus, Halomicrobium, and Halorientalis. The observed diversity and composition similarity of the hydrocarbonocalastic microflora in both hypersaline areas suggest an effective potential for oil mineralization therein. This potential has been confirmed experimentally.
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Affiliation(s)
- Dina Al-Mailem
- Microbiology Program, Department of Biological Sciences, Faculty of Science, Kuwait University, PO Box 5969, Safat, 13060, Kuwait
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28
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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: 92] [Impact Index Per Article: 8.4] [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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29
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Rastogi G, Coaker GL, Leveau JH. New insights into the structure and function of phyllosphere microbiota through high-throughput molecular approaches. FEMS Microbiol Lett 2013; 348:1-10. [DOI: 10.1111/1574-6968.12225] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/21/2013] [Accepted: 07/24/2013] [Indexed: 10/26/2022] Open
Affiliation(s)
- Gurdeep Rastogi
- Department of Plant Pathology; University of California; Davis; CA; USA
| | - Gitta L. Coaker
- 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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30
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Nowicka D, Ginter-Kramarczyk D, Holderna-Odachowska A, Budnik I, Kaczorek E, Lukaszewski Z. Biodegradation of oxyethylated fatty alcohols by bacteria Microbacterium strain E19. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2013; 91:32-38. [PMID: 23395454 DOI: 10.1016/j.ecoenv.2013.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 01/06/2013] [Accepted: 01/07/2013] [Indexed: 06/01/2023]
Abstract
The Microbacterium sp. E19 (E19) has been isolated from soil contaminated with crude oil and is a candidate for surfactant enhanced remediation of hydrocarbon polluted soil. Oxyethylated alcohols (OA) are candidates for this process enhancement. The aim of this work was the investigation of biodegradation of a representative oxyethylated fatty alcohol (polydispersal surfactant C12E10(C12E10)) by E19 under static model conditions with the surfactant as a sole source of organic carbon. LC-MS was used for the identification of metabolites and determination of surfactant and metabolite concentrations. Apart from [M+NH4](+) ethoxylate 'fingerprints', [M+2NH4](++) 'fingerprints' (m/z=22) were used for the identification of particular species. Primary biodegradation of C12E10 by E19 is almost complete over 30 days of the test (97 percent). The major metabolites during the initial period of the test are homologs of oxyethylated alcohols ω-carboxylated in the oxyethylene chain and poly(ethylene glycols). 1/3 of the total C12Ex is metabolized along this pathway. Concentration of these metabolites is stable over the subsequent days of the test. Further biodegradation of C12Ex causes an enrichment of the residue with C12Ex homologs having a longer oxyethylene chain. However, intermediates of this process were not identified.
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Affiliation(s)
- Dorota Nowicka
- Institute of Chemistry, Poznan University of Technology, pl.Skłodowskiej-Curie 5, 60-965 Poznan, Poland
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31
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Ding T, Palmer MW, Melcher U. Community terminal restriction fragment length polymorphisms reveal insights into the diversity and dynamics of leaf endophytic bacteria. BMC Microbiol 2013; 13:1. [PMID: 23286760 PMCID: PMC3546043 DOI: 10.1186/1471-2180-13-1] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 12/20/2012] [Indexed: 12/02/2022] Open
Abstract
Background Plant endophytic bacteria play an important role benefiting plant growth or being pathogenic to plants or organisms that consume those plants. Multiple species of bacteria have been found co-inhabiting plants, both cultivated and wild, with viruses and fungi. For these reasons, a general understanding of plant endophytic microbial communities and their diversity is necessary. A key issue is how the distributions of these bacteria vary with location, with plant species, with individual plants and with plant growing season. Results Five common plant species were collected monthly for four months in the summer of 2010, with replicates from four different sampling sites in the Tallgrass Prairie Preserve in Osage County, Oklahoma, USA. Metagenomic DNA was extracted from ground, washed plant leaf samples, and fragments of the bacterial 16S rDNA genes were amplified for analysis of terminal restriction fragment length polymorphism (T-RFLP). We performed mono-digestion T-RFLP with restriction endonuclease DdeI, to reveal the structures of leaf endophytic bacterial communities, to identify the differences between plant-associated bacterial communities in different plant species or environments, and to explore factors affecting the bacterial distribution. We tested the impacts of three major factors on the leaf endophytic bacterial communities, including host plant species, sampling dates and sampling locations. Conclusions Results indicated that all of the three factors were significantly related (α = 0.05) to the distribution of leaf endophytic bacteria, with host species being the most important, followed by sampling dates and sampling locations.
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Affiliation(s)
- Tao Ding
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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32
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Khan S, Afzal M, Iqbal S, Khan QM. Plant-bacteria partnerships for the remediation of hydrocarbon contaminated soils. CHEMOSPHERE 2013; 90:1317-32. [PMID: 23058201 DOI: 10.1016/j.chemosphere.2012.09.045] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 09/08/2012] [Accepted: 09/10/2012] [Indexed: 05/06/2023]
Abstract
Plant-bacteria partnerships have been extensively studied and applied to improve crop yield. In addition to their application in agriculture, a promising field to exploit plant-bacteria partnerships is the remediation of soil and water polluted with hydrocarbons. Application of effective plant-bacteria partnerships for the remediation of hydrocarbons depend mainly on the presence and metabolic activities of plant associated rhizo- and endophytic bacteria possessing specific genes required for the degradation of hydrocarbon pollutants. Plants and their associated bacteria interact with each other whereby plant supplies the bacteria with a special carbon source that stimulates the bacteria to degrade organic contaminants in the soil. In return, plant associated-bacteria can support their host plant to overcome contaminated-induced stress responses, and improve plant growth and development. In addition, plants further get benefits from their associated-bacteria possessing hydrocarbon-degradation potential, leading to enhanced hydrocarbon mineralization and lowering of both phytotoxicity and evapotranspiration of volatile hydrocarbons. A better understanding of plant-bacteria partnerships could be exploited to enhance the remediation of hydrocarbon contaminated soils in conjunction with sustainable production of non-food crops for biomass and biofuel production.
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Affiliation(s)
- Sumia Khan
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
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33
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Al-Bader D, Eliyas M, Rayan R, Radwan S. Air-dust-borne associations of phototrophic and hydrocarbon-utilizing microorganisms: promising consortia in volatile hydrocarbon bioremediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2012; 19:3997-4005. [PMID: 22529000 DOI: 10.1007/s11356-012-0897-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/27/2012] [Indexed: 05/31/2023]
Abstract
Aquatic and terrestrial associations of phototrophic and heterotrophic microorganisms active in hydrocarbon bioremediation have been described earlier. The question arises: do similar consortia also occur in the atmosphere? Dust samples at the height of 15 m were collected from Kuwait City air, and analyzed microbiologically for phototrophic and heterotrophic hydrocarbon-utilizing microorganisms, which were subsequently characterized according to their 16S rRNA gene sequences. The hydrocarbon utilization potential of the heterotrophs alone, and in association with the phototrophic partners, was measured quantitatively. The chlorophyte Gloeotila sp. and the two cyanobacteria Nostoc commune and Leptolyngbya thermalis were found associated with dust, and (for comparison) the cynobacteria Leptolyngbya sp. and Acaryochloris sp. were isolated from coastal water. All phototrophic cultures harbored oil vapor-utilizing bacteria in the magnitude of 10(5) g(-1). Each phototrophic culture had its unique oil-utilizing bacteria; however, the bacterial composition in Leptolyngbya cultures from air and water was similar. The hydrocarbon-utilizing bacteria were affiliated with Acinetobacter sp., Aeromonas caviae, Alcanivorax jadensis, Bacillus asahii, Bacillus pumilus, Marinobacter aquaeolei, Paenibacillus sp., and Stenotrophomonas maltophilia. The nonaxenic cultures, when used as inocula in batch cultures, attenuated crude oil in light and dark, and in the presence of antibiotics and absence of nitrogenous compounds. Aqueous and diethyl ether extracts from the phototrophic cultures enhanced the growth of the pertinent oil-utilizing bacteria in batch cultures, with oil vapor as a sole carbon source. It was concluded that the airborne microbial associations may be effective in bioremediating atmospheric hydrocarbon pollutants in situ. Like the aquatic and terrestrial habitats, the atmosphere contains dust-borne associations of phototrophic and heterotrophic hydrocarbon-utilizing bacteria that are active in hydrocarbon attenuation.
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Affiliation(s)
- Dhia Al-Bader
- Department of Biological Sciences, Faculty of Science, Kuwait University, PO Box 5969, Safat, Kuwait, 13060, Kuwait
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