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Kolařík M, Vrublevskaya M, Kajzrová S, Kulišová M, Kolouchová IJ. Taxonomic analysis reveals host preference of rare fungi in endophytes of Vitis vinifera from the Czech Republic. Folia Microbiol (Praha) 2023; 68:961-975. [PMID: 37289415 DOI: 10.1007/s12223-023-01066-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/20/2023] [Indexed: 06/09/2023]
Abstract
This paper represents the results of screening a diversity of fungal endophytes associated with Vitis vinifera leaves and canes in the Czech Republic. The characterization of strains is based on morphological and phylogenetic analyses of ITS, EF1α and TUB2 sequence data. Our strain selection covers 16 species and seven orders belonging to Ascomycota and Basidiomycota. Together with ubiquitous fungi, we report on several poorly known plant-associated fungi, Angustimassarina quercicola (= A. coryli, a synonym proposed in this study) and Pleurophoma pleurospora. Other species, such as Didymella negriana, D. variabilis, Neosetophoma sp. (species identical or sister to N. rosae), Phragmocamarosporium qujingensis and Sporocadus rosigena, have so far been little known and rarely found, but are frequent on V. vinifera in different parts of the world and obviously belong to a microbiota with a strong preference for this plant. Detailed taxonomical identification allowed us to identify species with apparent stable associations with V. vinifera, for which further interactions with V. vinifera can be expected. Our study is the first to focus on V. vinifera endophytes in Central Europe and expands the knowledge about their taxonomy, ecology and geography.
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Affiliation(s)
- Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic.
| | - Maria Vrublevskaya
- Department of Biotechnology, University of Chemistry and Technology, Technická 5, 166 28, Prague, Czech Republic
| | - Soňa Kajzrová
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Markéta Kulišová
- Department of Biotechnology, University of Chemistry and Technology, Technická 5, 166 28, Prague, Czech Republic
| | - Irena Jarošová Kolouchová
- Department of Biotechnology, University of Chemistry and Technology, Technická 5, 166 28, Prague, Czech Republic
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2
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Anand U, Pal T, Yadav N, Singh VK, Tripathi V, Choudhary KK, Shukla AK, Sunita K, Kumar A, Bontempi E, Ma Y, Kolton M, Singh AK. Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability. MICROBIAL ECOLOGY 2023; 86:1455-1486. [PMID: 36917283 PMCID: PMC10497456 DOI: 10.1007/s00248-023-02190-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.
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Affiliation(s)
- Uttpal Anand
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Midreshet Ben-Gurion, Israel.
| | - Tarun Pal
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Midreshet Ben-Gurion, Israel
| | - Niraj Yadav
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker Campus, 8499000, Midreshet Ben-Gurion, Israel
| | - Vipin Kumar Singh
- Department of Botany, K.S. Saket P.G. College, Ayodhya affiliated to Dr. Rammanohar Lohia Avadh University, Ayodhya, 224123, Uttar Pradesh, India
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, 211007, Uttar Pradesh, India
| | - Krishna Kumar Choudhary
- Department of Botany, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Awadhesh Kumar Shukla
- Department of Botany, K.S. Saket P.G. College, Ayodhya affiliated to Dr. Rammanohar Lohia Avadh University, Ayodhya, 224123, Uttar Pradesh, India
| | - Kumari Sunita
- Department of Botany, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | - Ajay Kumar
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Center, P.O. Box 15159, 7505101, Rishon, Lezion, Israel
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, University of Brescia, Via Branze 38, 25123, Brescia, Italy.
| | - Ying Ma
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Max Kolton
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker Campus, 8499000, Midreshet Ben-Gurion, Israel
| | - Amit Kishore Singh
- Department of Botany, Bhagalpur National College (A constituent unit of Tilka Manjhi Bhagalpur University), Bhagalpur, 812007, Bihar, India.
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3
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Doty SL, Joubert PM, Firrincieli A, Sher AW, Tournay R, Kill C, Parikh SS, Okubara P. Potential Biocontrol Activities of Populus Endophytes against Several Plant Pathogens Using Different Inhibitory Mechanisms. Pathogens 2022; 12:pathogens12010013. [PMID: 36678361 PMCID: PMC9862643 DOI: 10.3390/pathogens12010013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The plant microbiome can be used to bolster plant defense against abiotic and biotic stresses. Some strains of endophytes, the microorganisms within plants, can directly inhibit the growth of plant fungal pathogens. A previously isolated endophyte from wild Populus (poplar), WPB of the species Burkholderia vietnamiensis, had robust in vitro antifungal activity against pathogen strains that are highly virulent and of concern to Pacific Northwest agriculture: Rhizoctonia solani AG-8, Fusarium culmorum 70110023, and Gaemannomyces graminis var. tritici (Ggt) ARS-A1, as well as activity against the oomycete, Pythium ultimum 217. A direct screening method was developed for isolation of additional anti-fungal endophytes from wild poplar extracts. By challenging pathogens directly with dilute extracts, eleven isolates were found to be inhibitory to at least two plant pathogen strains and were therefore chosen for further characterization. Genomic analysis was conducted to determine if these endophyte strains harbored genes known to be involved in antimicrobial activities. The newly isolated Bacillus strains had gene clusters for production of bacillomycin, fengicyn, and bacillibactin, while the gene cluster for the synthesis of sessilin, viscosin and tolaasin were found in the Pseudomonas strains. The biosynthesis gene cluster for occidiofungin (ocf) was present in the Burkholderia vietnamiensis WPB genome, and an ocf deletion mutant lost inhibitory activity against 3 of the 4 pathogens. The new isolates lacked the gene cluster for occidiofungin implying they employ different modes of action. Other symbiotic traits including nitrogen fixation, phosphate solubilization, and the production of auxins and siderophores were investigated. Although it will be necessary to conduct in vivo tests of the candidates with pathogen-infected agricultural crops, the wild poplar tree microbiome may be a rich source of beneficial endophyte strains with potential for biocontrol applications against a variety of pathogens and utilizing varying modes of action.
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Affiliation(s)
- Sharon L. Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Correspondence:
| | - Pierre M. Joubert
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Andrea Firrincieli
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy
| | - Andrew W. Sher
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
| | - Robert Tournay
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
| | - Carina Kill
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Native Roots School, Taos, NM 87571, USA
| | - Shruti S. Parikh
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Department of Food Science and Technology, University of California, Davis, CA 95616, USA
| | - Patricia Okubara
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
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4
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Xiang L, Harindintwali JD, Wang F, Redmile-Gordon M, Chang SX, Fu Y, He C, Muhoza B, Brahushi F, Bolan N, Jiang X, Ok YS, Rinklebe J, Schaeffer A, Zhu YG, Tiedje JM, Xing B. Integrating Biochar, Bacteria, and Plants for Sustainable Remediation of Soils Contaminated with Organic Pollutants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16546-16566. [PMID: 36301703 PMCID: PMC9730858 DOI: 10.1021/acs.est.2c02976] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 05/06/2023]
Abstract
The contamination of soil with organic pollutants has been accelerated by agricultural and industrial development and poses a major threat to global ecosystems and human health. Various chemical and physical techniques have been developed to remediate soils contaminated with organic pollutants, but challenges related to cost, efficacy, and toxic byproducts often limit their sustainability. Fortunately, phytoremediation, achieved through the use of plants and associated microbiomes, has shown great promise for tackling environmental pollution; this technology has been tested both in the laboratory and in the field. Plant-microbe interactions further promote the efficacy of phytoremediation, with plant growth-promoting bacteria (PGPB) often used to assist the remediation of organic pollutants. However, the efficiency of microbe-assisted phytoremediation can be impeded by (i) high concentrations of secondary toxins, (ii) the absence of a suitable sink for these toxins, (iii) nutrient limitations, (iv) the lack of continued release of microbial inocula, and (v) the lack of shelter or porous habitats for planktonic organisms. In this regard, biochar affords unparalleled positive attributes that make it a suitable bacterial carrier and soil health enhancer. We propose that several barriers can be overcome by integrating plants, PGPB, and biochar for the remediation of organic pollutants in soil. Here, we explore the mechanisms by which biochar and PGPB can assist plants in the remediation of organic pollutants in soils, and thereby improve soil health. We analyze the cost-effectiveness, feasibility, life cycle, and practicality of this integration for sustainable restoration and management of soil.
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Affiliation(s)
- Leilei Xiang
- CAS
Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Jean Damascene Harindintwali
- CAS
Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS
Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- Institute
for Environmental Research, RWTH Aachen
University, 52074 Aachen, Germany
| | - Marc Redmile-Gordon
- Department
of Environmental Horticulture, Royal Horticultural
Society, Wisley, Surrey GU23 6QB, U.K.
| | - Scott X. Chang
- Department
of Renewable Resources, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Yuhao Fu
- CAS
Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao He
- CAS
Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Zhejiang University, Hangzhou 310058, China
| | - Bertrand Muhoza
- College
of Food Science, Northeast Agricultural
University, Harbin, Heilongjiang 150030, China
| | - Ferdi Brahushi
- Department
of Agroenvironment and Ecology, Agricultural
University of Tirana, Tirana 1029, Albania
| | - Nanthi Bolan
- School of
Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia 6001, Australia
| | - Xin Jiang
- CAS
Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Sik Ok
- Korea
Biochar Research Center, APRU Sustainable Waste Management Program
& Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic
of Korea
| | - Jörg Rinklebe
- Department
of Soil and Groundwater Management, Bergische
Universität, 42285 Wuppertal, Germany
| | - Andreas Schaeffer
- Institute
for Environmental Research, RWTH Aachen
University, 52074 Aachen, Germany
- School
of the Environment, State Key Laboratory of Pollution Control and
Resource Reuse, Nanjing University, 210023 Nanjing, China
- Key
Laboratory of the Three Gorges Reservoir Region’s Eco-Environment, Chongqing University, 400045 Chongqing, China
| | - Yong-guan Zhu
- University
of Chinese Academy of Sciences, Beijing 100049, China
- Key
Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State
Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of
Sciences, Beijing 100085, China
| | - James M. Tiedje
- Center
for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, United States
| | - Baoshan Xing
- Stockbridge
School of Agriculture, University of Massachusetts, Amherst, Massachusetts 01003, United States
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5
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Pal G, Saxena S, Kumar K, Verma A, Sahu PK, Pandey A, White JF, Verma SK. Endophytic Burkholderia: Multifunctional roles in plant growth promotion and stress tolerance. Microbiol Res 2022; 265:127201. [PMID: 36167006 DOI: 10.1016/j.micres.2022.127201] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/21/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022]
Abstract
The genus Burkholderia has proven potential in improving plant performance. In recent decades, a huge diversity of Burkholderia spp. have been reported with diverse capabilities of plant symbiosis which could be harnessed to enhance plant growth and development. Colonization of endophytic Burkholderia spp. have been extensively studied through techniques like advanced microscopy, fluorescent labelling, PCR based assays, etc., and found to be systemically distributed in plants. Thus, use of these biostimulant microbes holds the promise of improving quality and quantity of crops. The endophytic Burkholderia spp. have been found to support plant functions along with boosting nutrient availability, especially under stress. Endophytic Burkholderia spp. improve plant survival against deadly pathogens via mechanisms like competition, induced systemic resistance, and antibiosis. At the same time, they are reported to extend plant tolerance towards multiple abiotic stresses especially drought, salinity, and cold. Several attempts have been made to decipher the potential of Burkholderia spp. by genome mining, and these bacteria have been found to harbour genes for plant symbiosis and for providing multiple benefits to host plants. Characteristics specific for host recognition and nutrient acquisition were confirmed in endophytic Burkholderia by genomics and proteomics-based studies. This could pave the way for harnessing Burkholderia spp. for biotechnological applications like biotransformation, phytoremediation, insecticidal activity, antimicrobials, etc. All these make Burkholderia spp. a promising microbial agent in improving plant performance under multiple adversities. Thus, the present review highlights critical roles of endophytic Burkholderia spp., their colonization, alleviation of biotic and abiotic stresses, biotechnological applications and genomic insights.
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Affiliation(s)
- Gaurav Pal
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, UP, India
| | - Samiksha Saxena
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Kanchan Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, UP, India
| | - Anand Verma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, UP, India
| | - Pramod K Sahu
- National Bureau of Agriculturally Important Microorganisms, Mau, UP, India
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - James F White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA.
| | - Satish K Verma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, UP, India.
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Su A, Xu Y, Xu M, Ding S, Li M, Zhang Y. Resilience of the wheat root-associated microbiome to the disturbance of phenanthrene. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156487. [PMID: 35667431 DOI: 10.1016/j.scitotenv.2022.156487] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/25/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
The microbial communities are of high importance to the restoration of ecological function and plant health, while little information about the influence of exogenous pollutants on the resilience and temporal dynamics of root microbial communities is available. In this study, a greenhouse experiment was conducted to investigate the effects of exogenous phenanthrene in terms of time and pollution disturbance on the wheat root-associated microbial communities. It was found that a high phenanthrene degradation rate of 86 % was achieved in the rhizosphere of wheat after the first-week planting. Compared to phenanthrene pollution, temporal changes had more significant impacts on the wheat root microbial communities. Obvious change of microbes influenced by PHE had been revealed at the initial three-week planting even most of PHE has been degraded, and the enriched microbes in the rhizosphere were affiliated to Altererythrobacter, Massilia, Mycobacterium, Ramlibacter, Sphingobium, Novosphingobium and Romboutsia. However, at the later stage after four-week incubation, the wheat root-associated microbial communities gradually recovered to the state without pollution. The results of this study were helpful to deepen the understanding of the response of root-associated microbial resilience to the exogenous phenanthrene pollution, and would benefit the stability and balance of agricultural ecology facing exogenous organic pollutants.
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Affiliation(s)
- Aoxue Su
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
| | - Yan Xu
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058 Hangzhou, China.
| | - Minmin Xu
- Shandong Academy of Environmental Sciences Co., LTD., Jinan 250100, China
| | - Shuang Ding
- China National Institute of Standardization, Beijing, China
| | - Mingyue Li
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
| | - Ying Zhang
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
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7
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Wang X, Sun J, Liu R, Zheng T, Tang Y. Plant contribution to the remediation of PAH-contaminated soil of Dagang Oilfield by Fire Phoenix. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:43126-43137. [PMID: 35091936 DOI: 10.1007/s11356-021-18230-7] [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: 08/31/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Pot experiments were conducted to evaluate plant contribution during remediation of the polycyclic aromatic hydrocarbons (PAH)-contaminated soil of Dagang Oilfield by Fire Phoenix (a mixture of Festuca L.). The results showed that Fire Phoenix could grow in soil contaminated by high and low concentrations of PAHs. After being planted for 150 days, the total removal rate of six PAHs in the high and low PAH concentrations was 80.36% and 79.79%, significantly higher than the 58.79% and 53.29% of the unplanted control group, respectively. Thus, Fire Phoenix can effectively repair the soil contaminated by different concentrations of PAHs. In high concentrations of PAHs, the results indicated a positive linear relationship between PAH absorption in tissues of Fire Phoenix and the growth time in the early stage. In contrast, the contents of PAHs were just slightly increased in the late period of plant growth. The main factor for the dissipation of PAHs was plant-promoted biodegradation (99.04%-99.93%), suggesting a low contribution of PAH uptake and transformation (0.07%-0.96%). The results revealed that Fire Phoenix did not remove the PAHs in the soil by accumulation but promoted PAH dissipation in the soil by stimulating the microbial metabolism in the rhizosphere.
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Affiliation(s)
- Xiaomei Wang
- School of Municipal and Environmental Engineering, Shenyang Jianzhu University, Shenyang, 110179, China
| | - Jianping Sun
- School of Municipal and Environmental Engineering, Shenyang Jianzhu University, Shenyang, 110179, China
| | - Rui Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China.
| | - Tingyu Zheng
- Zhongke Dingshi Environmental Engineering Co., Ltd, Beijing, 100028, China
| | - Yingnan Tang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
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8
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Selection of Endophytic Strains for Enhanced Bacteria-Assisted Phytoremediation of Organic Pollutants Posing a Public Health Hazard. Int J Mol Sci 2021; 22:ijms22179557. [PMID: 34502466 PMCID: PMC8431480 DOI: 10.3390/ijms22179557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 08/31/2021] [Accepted: 08/31/2021] [Indexed: 01/01/2023] Open
Abstract
Anthropogenic activities generate a high quantity of organic pollutants, which have an impact on human health and cause adverse environmental effects. Monitoring of many hazardous contaminations is subject to legal regulations, but some substances such as therapeutic agents, personal care products, hormones, and derivatives of common organic compounds are currently not included in these regulations. Classical methods of removal of organic pollutants involve economically challenging processes. In this regard, remediation with biological agents can be an alternative. For in situ decontamination, the plant-based approach called phytoremediation can be used. However, the main disadvantages of this method are the limited accumulation capacity of plants, sensitivity to the action of high concentrations of hazardous pollutants, and no possibility of using pollutants for growth. To overcome these drawbacks and additionally increase the efficiency of the process, an integrated technology of bacteria-assisted phytoremediation is being used recently. For the system to work, it is necessary to properly select partners, especially endophytes for specific plants, based on the knowledge of their metabolic abilities and plant colonization capacity. The best approach that allows broad recognition of all relationships occurring in a complex community of endophytic bacteria and its variability under the influence of various factors can be obtained using culture-independent techniques. However, for practical application, culture-based techniques have priority.
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9
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Yang Y, Zhang ZW, Liu RX, Ju HY, Bian XK, Zhang WZ, Zhang CB, Yang T, Guo B, Xiao CL, Bai H, Lu WY. Research progress in bioremediation of petroleum pollution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:46877-46893. [PMID: 34254241 DOI: 10.1007/s11356-021-15310-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
With the enhancement of environmental protection awareness, research on the bioremediation of petroleum hydrocarbon environmental pollution has intensified. Bioremediation has received more attention due to its high efficiency, environmentally friendly by-products, and low cost compared with the commonly used physical and chemical restoration methods. In recent years, bacterium engineered by systems biology strategies have achieved biodegrading of many types of petroleum pollutants. Those successful cases show that systems biology has great potential in strengthening petroleum pollutant degradation bacterium and accelerating bioremediation. Systems biology represented by metabolic engineering, enzyme engineering, omics technology, etc., developed rapidly in the twentieth century. Optimizing the metabolic network of petroleum hydrocarbon degrading bacterium could achieve more concise and precise bioremediation by metabolic engineering strategies; biocatalysts with more stable and excellent catalytic activity could accelerate the process of biodegradation by enzyme engineering; omics technology not only could provide more optional components for constructions of engineered bacterium, but also could obtain the structure and composition of the microbial community in polluted environments. Comprehensive microbial community information lays a certain theoretical foundation for the construction of artificial mixed microbial communities for bioremediation of petroleum pollution. This article reviews the application of systems biology in the enforce of petroleum hydrocarbon degradation bacteria and the construction of a hybrid-microbial degradation system. Then the challenges encountered in the process and the application prospects of bioremediation are discussed. Finally, we provide certain guidance for the bioremediation of petroleum hydrocarbon-polluted environment.
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Affiliation(s)
- Yong Yang
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
- CNOOC EnerTech-Safety & Environmental Protection Co., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China
| | - Zhan-Wei Zhang
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Rui-Xia Liu
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Hai-Yan Ju
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Xue-Ke Bian
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Wan-Ze Zhang
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Chuan-Bo Zhang
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Ting Yang
- CNOOC EnerTech-Safety & Environmental Protection Co., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China
| | - Bing Guo
- CNOOC EnerTech-Safety & Environmental Protection Co., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China
| | - Chen-Lei Xiao
- CNOOC EnerTech-Safety & Environmental Protection Co., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China
| | - He Bai
- China Offshore Environmental Service Ltd., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China.
- Tianjin Huakan Environmental Protection Technology Co. Ltd., No. 67 Guangrui West Rd, Hedong District, Tianjin, 300170, China.
| | - Wen-Yu Lu
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China.
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10
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Moqsud MA. Bioremediation of polluted soil due to tsunami by using recycled waste glass. Sci Rep 2021; 11:14272. [PMID: 34253815 PMCID: PMC8275791 DOI: 10.1038/s41598-021-93806-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 06/30/2021] [Indexed: 11/08/2022] Open
Abstract
In this research, bioremediation of tsunami-affected polluted soil has been conducted by using collective microorganisms and recycled waste glass. The Tohoku earthquake, which was a mega earthquake in Japan triggered a huge tsunami on March 11th, 2011 that caused immeasurable damage to the geo-environmental conditions by polluting the soil with heavy metals and excessive salt content. Traditional methods to clean this polluted soil was not possible due to the excess cost and efforts. Laboratory experiments were conducted to examine the capability of bioremediation of saline soil by using recycled waste glass. Different collective microorganisms which were incubated inside the laboratory were used. The electrical conductivity (EC) was measured at different specified depths. It was noticed that the electrical conductivity decreased with the assist of the microbial metabolisms significantly. Collective microorganisms (CM2) were the highly capable to reduce salinity (up to 75%) while using recycled waste glass as their habitat.
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Affiliation(s)
- M Azizul Moqsud
- Department of Civil and Environmental Engineering, Yamaguchi University, Ube City, 755-8611, Japan.
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11
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Wilhelm RC, DeRito CM, Shapleigh JP, Madsen EL, Buckley DH. Phenolic acid-degrading Paraburkholderia prime decomposition in forest soil. ISME COMMUNICATIONS 2021; 1:4. [PMID: 36717596 PMCID: PMC9723775 DOI: 10.1038/s43705-021-00009-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/21/2021] [Accepted: 03/01/2021] [Indexed: 02/03/2023]
Abstract
Plant-derived phenolic acids are catabolized by soil microorganisms whose activity may enhance the decomposition of soil organic carbon (SOC). We characterized whether phenolic acid-degrading bacteria enhance SOC mineralization in forest soils when primed with 13C-labeled p-hydroxybenzoic acid (pHB). We further tested whether pHB-induced priming could explain differences in SOC content among mono-specific tree plantations in a 70-year-old common garden experiment. pHB addition primed significant losses of SOC (3-13 µmols C g-1 dry wt soil over 7 days) compared to glucose, which reduced mineralization (-3 to -8 µmols C g-1 dry wt soil over 7 days). The principal degraders of pHB were Paraburkholderia and Caballeronia in all plantations regardless of tree species or soil type, with one predominant phylotype (RP11ASV) enriched 23-fold following peak pHB respiration. We isolated and confirmed the phenolic degrading activity of a strain matching this phylotype (RP11T), which encoded numerous oxidative enzymes, including secretion signal-bearing laccase, Dyp-type peroxidase and aryl-alcohol oxidase. Increased relative abundance of RP11ASV corresponded with higher pHB respiration and expression of pHB monooxygenase (pobA), which was inversely proportional to SOC content among plantations. pobA expression proved a responsive measure of priming activity. We found that stimulating phenolic-acid degrading bacteria can prime decomposition and that this activity, corresponding with differences in tree species, is a potential mechanism in SOC cycling in forests. Overall, this study highlights the ecology and function of Paraburkholderia whose associations with plant roots and capacity to degrade phenolics suggest a role for specialized bacteria in the priming effect.
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Affiliation(s)
- Roland C Wilhelm
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, NY, USA.
| | | | - James P Shapleigh
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY, USA
| | - Eugene L Madsen
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, NY, USA
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12
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Paniagua Voirol LR, Valsamakis G, Yu M, Johnston PR, Hilker M. How the 'kitome' influences the characterization of bacterial communities in lepidopteran samples with low bacterial biomass. J Appl Microbiol 2020; 130:1780-1793. [PMID: 33128818 DOI: 10.1111/jam.14919] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/02/2020] [Accepted: 10/23/2020] [Indexed: 12/26/2022]
Abstract
AIMS We aimed to elucidate whether the DNA extraction kit and bacteria therein affect the characterization of bacterial communities associated with butterfly samples harbouring different bacterial abundancies. METHODS AND RESULTS We analysed bacteria associated with eggs of Pieris brassicae and with adults of this butterfly, which were either untreated or treated with antibiotics (ABs). Three DNA extraction kits were used. Regardless of the extraction kit used, PCR amplification of the bacterial 16S rRNA gene detected very low bacterial presence in eggs and AB-treated butterflies. In untreated butterflies, bacterial signal intensity varied according to the kit and primers used. Sequencing (MiSeq) of the bacterial communities in untreated and AB-treated butterflies revealed a low alpha diversity in untreated butterflies because of the dominance of few bacteria genera, which were detectable regardless of the kit. However, a significantly greater alpha diversity was found in AB-treated butterflies, evidencing a true bias of the results due to bacterial contaminants in the kit. CONCLUSIONS The so-called 'kitome' can impact the profiling of Lepidoptera-associated bacteria in samples with low bacterial biomass. SIGNIFICANCE AND IMPACT OF THE STUDY Our study highlights the necessity of method testing and analysis of negative controls when investigating Lepidoptera-associated bacterial communities.
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Affiliation(s)
- L R Paniagua Voirol
- Applied Zoology/Animal Ecology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany
| | - G Valsamakis
- Applied Zoology/Animal Ecology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany
| | - M Yu
- Applied Zoology/Animal Ecology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany
| | - P R Johnston
- Evolutionary Biology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany.,Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - M Hilker
- Applied Zoology/Animal Ecology, Institute of Biology, Freie Universitaet Berlin, Berlin, Germany
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13
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Verâne J, Dos Santos NCP, da Silva VL, de Almeida M, de Oliveira OMC, Moreira ÍTA. Phytoremediation of polycyclic aromatic hydrocarbons (PAHs) in mangrove sediments using Rhizophora mangle. MARINE POLLUTION BULLETIN 2020; 160:111687. [PMID: 33181957 DOI: 10.1016/j.marpolbul.2020.111687] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 09/12/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
A phytoremediation experiment was carried out in mesocosms to investigate the performance of Rhizophora mangle in the remediation of polycyclic aromatic hydrocarbons (PAHs) in mangrove sediment contaminated with crude oil. The water pH of the experiments (phytoremediation and natural attenuation) ranged from 4.9 to 8.4 at 0 and 90 days, respectively. The oxy-reduction potential (Eh) ranged from oxidising (108.0 mV, time 0) to reducing (approximately -110.0 mV, time 90) environments. Dissolved oxygen (DO) ranged from 5.7 mg L-1 (time 0) to 4.5 mg L-1 and 3.6 mg L-1 (time 90) in phytoremediation and natural attenuation, respectively. The sediments had silty texture and an average concentration of 5% organic matter (OM). Phytoremediation (60.76%) showed better efficiency in the remediation of the 16 PAHs compared to natural attenuation (49.57%). Principal component analyses showed a correlation between the concentrations of PAHs with pH, Eh, OM and DO in both experiments.
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Affiliation(s)
- Jéssica Verâne
- Geoscience Institute, Federal University of Bahia (UFBA), Street Barão de Jeremoabo, s/n, 40170-290 Salvador, BA, Brazil.
| | - Naiara C P Dos Santos
- Department of Environmental Engineering, Polytechnic School, Federal University of Bahia (UFBA), Street Prof. Aristídes Novis, 2, Federação, 40170290 Salvador, BA, Brazil
| | - Verônica L da Silva
- Department of Environmental Engineering, Polytechnic School, Federal University of Bahia (UFBA), Street Prof. Aristídes Novis, 2, Federação, 40170290 Salvador, BA, Brazil
| | - Marcos de Almeida
- Geoscience Institute, Federal University of Bahia (UFBA), Street Barão de Jeremoabo, s/n, 40170-290 Salvador, BA, Brazil
| | - Olívia M C de Oliveira
- Geoscience Institute, Federal University of Bahia (UFBA), Street Barão de Jeremoabo, s/n, 40170-290 Salvador, BA, Brazil
| | - Ícaro T A Moreira
- Department of Environmental Engineering, Polytechnic School, Federal University of Bahia (UFBA), Street Prof. Aristídes Novis, 2, Federação, 40170290 Salvador, BA, Brazil.
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14
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Comparison of Two Inoculation Methods of Endophytic Bacteria to Enhance Phytodegradation Efficacy of an Aged Petroleum Hydrocarbons Polluted Soil. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10081196] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Endophyte-enhanced phytodegradation is a promising technology to clean up polluted soils. To improve the success rate of this nature-based remediation approach, it is important to advance the inoculation method as this has been shown to strongly affect the final outcome. However, studies evaluating inoculation strategies and their effect on hydrocarbon degradation are limited. This study aims to investigate two different manners of endophyte inoculation in Lolium perenne growing in an aged petroleum hydrocarbon polluted soil: (1) direct soil inoculation (SI), and (2) pre-inoculation of the caryopses followed by soil inoculation (PI). Different endophytic bacterial strains, Rhodococcus erythropolis 5WK and Rhizobium sp. 10WK, were applied individually as well as in combination. Depending on the method of inoculation, the petroleum hydrocarbon (PHC) degradation potential was significantly different. The highest PHC removal was achieved after pre-inoculation of ryegrass caryopses with a consortium of both bacterial strains. Moreover, both strains established in the aged-polluted soil and could also colonize the roots and shoots of L. perenne. Importantly, used endophytes showed the selective colonization of the environment compartments. Our findings show that the method of inoculation determines the efficiency of the phytodegradation process, especially the rate of PHC degradation. This study provides valuable information for choosing the most cost-effective and beneficial means to optimize phytodegradation.
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15
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Cullings K, Stott MB, Marinkovich N, DeSimone J, Bhardwaj S. Phylum-level diversity of the microbiome of the extremophilic basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert: An island of biodiversity in a thermal soil desert. Microbiologyopen 2020; 9:e1062. [PMID: 32478485 PMCID: PMC7424252 DOI: 10.1002/mbo3.1062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022] Open
Abstract
We used high‐throughput DNA sequencing methods combined with bio‐geochemical profiles to characterize the internal environment and community structure of the microbiome of the basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert from soils within a geothermal feature of Yellowstone National Park. Pisolithus arhizus is unique in that it forms closed fruiting bodies that sequester visible sulfur within. Fourier transform infrared spectroscopy (FTIR) analysis demonstrates that the P. arhizus fruiting body also concentrates copper, manganese, nickel, and zinc and contains pure granular silica. Gas chromatography‐mass spectrometry (GC‐MS) analysis indicates an environment rich in hydrocarbons. Oxygen probe analysis reveals that zones of up to 4× atmospheric oxygen exist within nanometers of zones of near anoxia. Analysis of microbial community structure using high‐throughput DNA sequencing methods shows that the fruiting body supports a microbiome that reflects the physiochemical environment of the fruiting body. Diversity and richness measures indicate a microbiome that is significantly richer and more diverse than that of the soils in which P. arhizus grows. Further, P. arhizus sporocarps are enriched significantly in Proteobacteria (primarily Burkholderia) Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Nitrospirae, Elusimicrobia, and Latescibacteria (WS3) while soils are enriched in Actinobacteria (primarily Mycobacterium), Dormibacteraeota (AD3), and Eremiobacteraeota (WPS‐2). Finally, pairwise % similarity comparisons indicate that P. arhizus harbors two lineages that may represent new groups in the candidate phylum radiation (CPR). Together, these results demonstrate that P. arhizus provides a novel environment for microbiome studies and provides for interesting hypotheses regarding the evolution, origins, and functions of symbioses and novel microbes.
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Affiliation(s)
- Ken Cullings
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Julia DeSimone
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Shilpa Bhardwaj
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
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16
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Removal Efficiencies of Constructed Wetland Planted with Phragmites and Vetiver in Treating Synthetic Wastewater Contaminated with High Concentration of PAHs. SUSTAINABILITY 2020. [DOI: 10.3390/su12083357] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This study aimed to evaluate the capability of horizontal subsurface flow constructed wetlands (HSFCWs) in treating contaminated wastewater with a high concentration of polycyclic aromatic hydrocarbons (PAHs) (Phenanthrene, Pyrene, and Benzo[a]Pyrene), using two plants, namely Phragmites and Vetiver. The investigated parameters were (1) PAHs uptake by the plants, (2) PAHs removal efficiencies, (3) accumulated PAHs in the soil of CWs, (4) shoot/root concentration factor, (5) translocation factor, and (6) PAHs correlation to lipid contains in the plants. During the treatment period, the results showed that the highest concentration of Phenanthrene in the shoot and the root systems of Phragmites, was 229.3 and 192 μg/g; Pyrene was 69.1 and 59.2 µg/g; and Benzo[a]Pyrene 25.1 and 20.2 µg/g, respectively. Meanwhile, in the Vetiver shoot and root systems were Phenanthrene 87.5 and 64.1 µg/g; Pyrene 63.2 and 42.1 µg/g; and Benzo[a]Pyrene 21.3 and 27.3 µg/g, respectively. The removal rates of Phenanthrene, Pyrene, and Benzo[a]Pyrene (PAHs compounds) by the CW planted with Phragmites were found to be 83%, 71%, and 81%, respectively, while the removal rates by CW planted with Vetiver were found to be 67%, 66%, and 73%, respectively. Moreover, the removal rates by unplanted CW were found to be 62%, 58%, and 55%, respectively. The results indicated that the HSFCW planted with Phragmites has an effective pathway to remove high concentrations of PAHs.
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17
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Lopez-Echartea E, Strejcek M, Mukherjee S, Uhlik O, Yrjälä K. Bacterial succession in oil-contaminated soil under phytoremediation with poplars. CHEMOSPHERE 2020; 243:125242. [PMID: 31995861 DOI: 10.1016/j.chemosphere.2019.125242] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/13/2019] [Accepted: 10/26/2019] [Indexed: 05/18/2023]
Abstract
Petroleum hydrocarbons (PHCs) continue to be among the most common pollutants in soil worldwide. Phytoremediation has become a sustainable way of dealing with PHC contamination. We conducted the off-site phytoremediation of PHC-polluted soil from an oil tanker truck accident, where poplars were used for the phytoremediation of the oil-polluted soil in a boreal climate during a seven-year treatment. The succession of bacterial communities over the entire phytoremediation process was monitored using microbial ecological tools relying on high-throughput 16S rRNA gene sequencing. Upon the successful depletion of PHCs from soil, endophytic communities were analyzed in order to assess the complete plant-associated microbiome after the ecological recovery. The rhizosphere-associated soil exhibited different bacterial dynamics than unplanted soil, but both soils experienced succession of bacteria over time, with diversity being negatively correlated with PHC concentration. In the relatively short growing season in North Europe, seasonal variations in environmental conditions were identified that contributed to the dynamics of bacterial communities. Overall, our study proved that phytoremediation using poplar trees can be used to assist in the removal of PHCs from soils in boreal climate conditions and provides new insight into the succession patterns of bacterial communities associated with these plants.
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Affiliation(s)
- Eglantina Lopez-Echartea
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Michal Strejcek
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Shinjini Mukherjee
- KU Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Leuven, Belgium
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Kim Yrjälä
- University of Helsinki, Department of Forest Sciences, Helsinki, Finland; Zhejiang A&F University, State Key Laboratory of Subtropical Silviculture, Zhejiang, China.
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18
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Abstract
The ability of endophytes to colonize every plant tissue has led to the opportunity of using the microorganism in a lot of biological applications. Endophytes are beneficial to their host cells as such its application is observed in every aspects of life. This study therefore endeavored to give an analysis of endophytes, what they were and what they had been used for till the present time. Sampling of several literature studies in endophytes was done in this study to enable a complete understanding of the mechanism of application of the actions of endophytes, so as to be able to do a thorough assessment of the current state in the knowledge of the microbes. From the complete analysis of the literature on the application and use of endophytes, in nutrient asquition and increase the stress tolerance in plants. This study provided a platform for further research gaps through the presentation of what endophytes were, what they had been used for till date, the mechanism of operation of the micro-organism and the type of interaction between them and their hosts. There are still ways to improve on the methods of application of endophytes as a type of biological organism. This will be done by adjusting to the current trends in biological studies using molecular mechanization, following an intensive further study on endophyte mechanisms.
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19
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Khoshkholgh Sima NA, Ebadi A, Reiahisamani N, Rasekh B. Bio-based remediation of petroleum-contaminated saline soils: Challenges, the current state-of-the-art and future prospects. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 250:109476. [PMID: 31476519 DOI: 10.1016/j.jenvman.2019.109476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/17/2019] [Accepted: 08/25/2019] [Indexed: 06/10/2023]
Abstract
Exploiting synergism between plants and microbes offers a potential means of remediating soils contaminated with petroleum hydrocarbons (PHCs). Salinity alters the physicochemical characteristics of soils and suppresses the growth of both plants and soil microbes, so the bioremediation of saline soils requires the use of plants and in microbes which can tolerate salinity. This review focuses on the management of PHC-contaminated saline soils, surveying what is currently known with respect to the potential of halophytes (plants adapted to saline environments) acting in concert with synergistic microbes to degrade PHCs. The priority is to identify optimal combinations of halophyte(s) and the bacteria present as endophytes and/or associated with the rhizosphere, and to determine what are the factors which most strongly affect their viability.
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Affiliation(s)
- Nayer Azam Khoshkholgh Sima
- Agricultural Biotechnology Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Ali Ebadi
- Agricultural Biotechnology Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Narges Reiahisamani
- Agricultural Biotechnology Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Behnam Rasekh
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry, Tehran, Iran.
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20
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Chen S, Ma Z, Li S, Waigi MG, Jiang J, Liu J, Ling W. Colonization of polycyclic aromatic hydrocarbon-degrading bacteria on roots reduces the risk of PAH contamination in vegetables. ENVIRONMENT INTERNATIONAL 2019; 132:105081. [PMID: 31404844 DOI: 10.1016/j.envint.2019.105081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
This is a primary investigation on the mitigation of polycyclic aromatic hydrocarbon (phenanthrene as a model PAH) contamination in vegetables including water spinach (Ipomoea aquatica Forsk), pakchoi (Brassica campestris) and Chinese cabbage (Brassica chinensis) using a gfp-labeled PAH-degrading bacterium (RS1-gfp). Effective root colonization led to dense RS1-gfp populations inhabiting the rhizosphere and endosphere of the vegetables, which subsequently led to a reduction in phenanthrene accumulation and risk in vegetables. When compared with the controls without RS1-gfp, the amount of phenanthrene accumulation due to strain RS1-gfp colonization reduced by up to ~93.7% in roots and ~75.2% in shoots of vegetables, respectively. The estimated incremental lifetime cancer risk (ILCR) for adults due to phenanthrene in vegetables was reduced by 24.6%-48% through RS1-gfp inoculation. The proposed method was developed to circumvent the risk of phenanthrene contamination in vegetables by inoculating PAH-degrading bacteria. The findings provide an in-depth understanding of PAH detoxification in agricultural plants grown on contaminated sites by exploiting bacteria like RS1-gfp, which portray both rhizo- and endophytic lifestyles.
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Affiliation(s)
- Shuang Chen
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhao Ma
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shunyao Li
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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21
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He W, Megharaj M, Wu CY, Subashchandrabose SR, Dai CC. Endophyte-assisted phytoremediation: mechanisms and current application strategies for soil mixed pollutants. Crit Rev Biotechnol 2019; 40:31-45. [PMID: 31656090 DOI: 10.1080/07388551.2019.1675582] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phytoremediation uses plants and associated microbes to remove pollutants from the environment and is considered a promising bioremediation method. Compared with well-described single contaminant treatments, the number of studies reporting phytoremediation of soil mixed pollutants has increased recently. Endophytes, including bacteria and fungi, exhibit beneficial traits for the promotion of plant growth, stress alleviation, and biodegradation. Moreover, endophytes either directly or indirectly assist host plants to survive high concentrations of organic and inorganic pollutants in the soil. Endophytic microorganisms can also regulate the plant metabolism in different ways, exhibiting a variety of physiological characteristics. This review summarizes the taxa and physiological properties of endophytic microorganisms that may participate in the detoxification of contaminant mixtures. Furthermore, potential biomolecules that may enhance endophyte mediated phytoremediation are discussed. The practical applications of pollutant-degrading endophytes and current strategies for applying this valuable bio-resource to soil phytoremediation are summarized.
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Affiliation(s)
- Wei He
- College of Life Sciences, Nanjing Normal University, Nanjing, China.,Global Centre for Environmental Remediation (GCER), The University of Newcastle (UoN), Callaghan, Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), The University of Newcastle (UoN), Callaghan, Australia
| | - Chun-Ya Wu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), The University of Newcastle (UoN), Callaghan, Australia
| | - Chuan-Chao Dai
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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22
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Hou L, Liu R, Li N, Dai Y, Yan J. Study on the efficiency of phytoremediation of soils heavily polluted with PAHs in petroleum-contaminated sites by microorganism. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:31401-31413. [PMID: 31485937 DOI: 10.1007/s11356-019-05828-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 06/24/2019] [Indexed: 06/10/2023]
Abstract
The effects of Fire Phoenix (a mixture of Festuca L.) and Purple coneflower (Echinacea purpurea (L.) Moench) on the remediation of two different high concentrations of PAH-contaminated soils were studied under the effect of strain N12 (Mycobacterium sp.), and the changes in rhizosphere enzymatic activity were preliminarily studied. The results of three culture stages (60 d, 120 d, and 150 d) showed that N12 has a promotional effect on the biomass of Fire Phoenix and E. purpurea, and the effect of N12 on the biomass of Fire Phoenix is better. Under the strengthening of N12, the maximum removal rates of Fire Phoenix reached 86.77% and 67.82% at two high PAH concentrations (A and B, respectively). The activity of dehydrogenase (DHO) is positively correlated with the degradation rate of PAHs at the A concentration (P < 0.05). The activity of DHO in soil will continue to increase at a higher level of the B concentration, but the positive correlation between the activity of DHO and the degradation rate of PAH is weakened. In the rhizosphere soil of the two plants, the change in polyphenol oxidase (PPO) activity with time has a significant negative correlation with the degradation rate of PAHs (P < 0.05). The experiment proved that Fire Phoenix is more suitable for the remediation of heavy PAH-contaminated soil under the condition of microorganism-strengthening, and it can achieve a better degradation effect when the concentrations of PAHs are < 150 mg·kg-1. Results provide a further scientific basis for the remediation of contaminated sites.
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Affiliation(s)
- Liqun Hou
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, Liaoning, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui Liu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, Liaoning, China.
| | - Na Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, Liaoning, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyuan Dai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, Liaoning, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Yan
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, Liaoning, China
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Mitter EK, Kataoka R, de Freitas JR, Germida JJ. Potential use of endophytic root bacteria and host plants to degrade hydrocarbons. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2019; 21:928-938. [PMID: 30907105 DOI: 10.1080/15226514.2019.1583637] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Microbe-assisted phytoremediation depends on competent root-associated microorganisms that enhance remediation efficiency of organic compounds. Endophytic bacteria are a key element of the root microbiome and may assist plant degradation of contaminants. The aim of this study was to investigate the application of four hydrocarbon-degrading endophytic strains previously isolated from an oil sands reclamation area. Strains EA1-17 (Stenotrophomonas sp.), EA2-30 (Flavobacterium sp.), EA4-40 (Pantoea sp.), and EA6-5 (Pseudomonas sp.) were inoculated in white sweet clover growing on soils amended with diesel at 5,000, 10,000, and 20,000 mg·kg-1. Our results indicate that plant growth inhibition caused by diesel fuel toxicity was overcome in inoculated plants, which showed significantly higher plant biomass. Analysis of soil F2 and F3 hydrocarbon fractions also revealed that these soils were remediated by inoculated plants when diesel was applied at 10,000 mg·kg-1 and 20,000 mg·kg-1. In addition, quantification of hydrocarbon-degrading genes suggests that all bacterial strains successfully colonized sweet clover plants. Overall, the endophytic strain EA6-5 (Pseudomonas sp.), which harbored hydrocarbon-degrading genes, was the most effective candidate in phytoremediation experiments and could be a strategy to increase plant tolerance and hydrocarbon degradation in contaminated (e.g., diesel fuel) soils.
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Affiliation(s)
- Eduardo K Mitter
- a Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ryota Kataoka
- b Department of Environmental Sciences , University of Yamanashi, Takeda , Kofu , Yamanashi , Japan
| | - J Renato de Freitas
- c Department of Soil Science , University of Saskatchewan , Saskatoon , Canada
| | - James J Germida
- c Department of Soil Science , University of Saskatchewan , Saskatoon , Canada
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Pseudomonas protegens MP12: A plant growth-promoting endophytic bacterium with broad-spectrum antifungal activity against grapevine phytopathogens. Microbiol Res 2019; 219:123-131. [DOI: 10.1016/j.micres.2018.11.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 10/16/2018] [Accepted: 11/22/2018] [Indexed: 11/22/2022]
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Anyasi RO, Atagana HI, Sutherland R. Comparative Study of the Colonization of Chromolaena and Tobacco Plants by Bacteria safensis CS4 using Different Methods of Inoculation. Pak J Biol Sci 2019; 22:309-317. [PMID: 31930841 DOI: 10.3923/pjbs.2019.309.317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVES This study entails the effectiveness of colonization of bacterial endophytes following inoculation of the cells in plants. METHODOLOGY Different methods of inoculation including seed immersion, root immersion and foliar spray were studied on Chromolaena odorata and Nicotiana tabacum for 10, 20 and 30 days. This was to ascertain the colonization ability of the endophytic strain amongst the two set of plants. The foliar parts of the plants were assessed post inoculation for the presence of the bacteria strain, followed by the growth parameters in the plant. Significant differences at p<0.05 of colonization were established by the different inoculation methods. RESULTS Foliar spray demonstrated the highest colonization in both Chromolaena and tobacco plants followed by root immersion. Leaf inoculation in tobacco plant demonstrated a positive colonization which is not significant. However, seed inoculation provided colonization in Chromolaena plant at 10, 20 and 30 days post inoculation at a frequency lower than that of tobacco. With root immersion in Chromolaena, there was colonization at 10 days post inoculation, no colonization at 20 days post inoculation, but colonization re-appeared at 30 days (PI). Growth index measured demonstrated a positive relationship between the inoculation of the endophyte and the growth parameters which included stem length and germination rate. CONCLUSION This study, therefore, showed that the bacteria strain B. safensis CS4 can effectively be horizontally transferred into tobacco and Chromolaena plants using different methods. Foliar spraying demonstrated the optimal colonization of the strain in the plant leaves.
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Xu HY, Ge JL, Zhang LL, Zhang C, Jin R, Wang XH. A Dibenz[a,h]Anthracene-Degrading Strain Amycolatopsis sp. Y1-2 from Soils in the Coal Mining Areas. Polycycl Aromat Compd 2018. [DOI: 10.1080/10406638.2018.1539019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Hong-Ying Xu
- School of Environment and Safety, Taiyuan University of Science and Technology, Taiyuan, China
| | - Jing-Li Ge
- School of Environment and Safety, Taiyuan University of Science and Technology, Taiyuan, China
| | - Ling-Li Zhang
- School of Environment and Safety, Taiyuan University of Science and Technology, Taiyuan, China
| | - Chan Zhang
- School of Environment and Safety, Taiyuan University of Science and Technology, Taiyuan, China
| | - Ru Jin
- School of Environment and Safety, Taiyuan University of Science and Technology, Taiyuan, China
| | - Xiao-Hui Wang
- School of Environment and Safety, Taiyuan University of Science and Technology, Taiyuan, China
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Ebadi A, Khoshkholgh Sima NA, Olamaee M, Hashemi M, Ghorbani Nasrabadi R. Remediation of saline soils contaminated with crude oil using the halophyte Salicornia persica in conjunction with hydrocarbon-degrading bacteria. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 219:260-268. [PMID: 29751257 DOI: 10.1016/j.jenvman.2018.04.115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 03/27/2018] [Accepted: 04/29/2018] [Indexed: 06/08/2023]
Abstract
The negative impact of salinity on plant growth and the survival of rhizosphere biota complicates the application of bioremediation to crude oil-contaminated saline soils. Here, a comparison was made between the remedial effect of treating the soil with Pseudomonas aeruginosa, a salinity tolerant hydrocarbon-degrading consortium in conjunction with either the halophyte Salicornia persica or the non-halophyte Festuca arundinacea. The effect of the various treatments on salinized soils was measured by assessing the extent of total petroleum hydrocarbon (TPH) degradation, the soil's dehydrogenase activity, the abundance of the bacteria and the level of phytotoxicity as measured by a bioassay. When a non-salinized soil was assessed after a treatment period of 120 days, the ranking for effectiveness with respect to TPH removal was F. arundinacea > P. aeruginosa > S. persica > no treatment control, while in the presence of salinity, the ranking changed to S. persica > P. aeruginosa > F. arundinacea > no treatment control. Combining the planting of S. persica or F. arundinacea with P. aeruginosa inoculation ("bioaugmentation") boosted the degradation of TPH up to 5-17%. Analyses of the residual oil contamination revealed that long chain alkanes (above C20) were particularly strongly degraded following the bioaugmentation treatments. The induced increase in dehydrogenase activity and the abundance of the bacteria (3.5 and 10 fold respectively) achieved in the bioaugmentation/S. persica treatment resulted in 46-76% reduction in soil phytotoxicity in a saline soil. The indication was that bioaugmentation of halophyte can help to mitigate the adverse effects on the effectiveness of bioremediation in a crude oil-contaminated saline soil.
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Affiliation(s)
- Ali Ebadi
- Agricultural Biotechnology Research Institute of Iran (ABRII), AREEO, P. O. Box: 31535-1897, Karaj, Iran.
| | | | - Mohsen Olamaee
- Department of Soil Science, Gorgan University of Agricultural Sciences & Natural Resources, Gorgan, Iran.
| | - Maryam Hashemi
- Agricultural Biotechnology Research Institute of Iran (ABRII), AREEO, P. O. Box: 31535-1897, Karaj, Iran.
| | - Reza Ghorbani Nasrabadi
- Department of Soil Science, Gorgan University of Agricultural Sciences & Natural Resources, Gorgan, Iran.
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Hussain I, Aleti G, Naidu R, Puschenreiter M, Mahmood Q, Rahman MM, Wang F, Shaheen S, Syed JH, Reichenauer TG. Microbe and plant assisted-remediation of organic xenobiotics and its enhancement by genetically modified organisms and recombinant technology: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 628-629:1582-1599. [PMID: 30045575 DOI: 10.1016/j.scitotenv.2018.02.037] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/31/2018] [Accepted: 02/03/2018] [Indexed: 05/18/2023]
Abstract
Environmental problems such as the deterioration of groundwater quality, soil degradation and various threats to human, animal and ecosystem health are closely related to the presence of high concentrations of organic xenobiotics in the environment. Employing appropriate technologies to remediate contaminated soils is crucial due to the site-specificity of most remediation methods. The limitations of conventional remediation technologies include poor environmental compatibility, high cost of implementation and poor public acceptability. This raises the call to employ biological methods for remediation. Bioremediation and microbe-assisted bioremediation (phytoremediation) offer many ecological and cost-associated benefits. The overall efficiency and performance of bio- and phytoremediation approaches can be enhanced by genetically modified microbes and plants. Moreover, phytoremediation can also be stimulated by suitable plant-microbe partnerships, i.e. plant-endophytic or plant-rhizospheric associations. Synergistic interactions between recombinant bacteria and genetically modified plants can further enhance the restoration of environments impacted by organic pollutants. Nevertheless, releasing genetically modified microbes and plants into the environment does pose potential risks. These can be minimized by adopting environmental biotechnological techniques and guidelines provided by environmental protection agencies and other regulatory frameworks. The current contribution provides a comprehensive overview on enhanced bioremediation and phytoremediation approaches using transgenic plants and microbes. It also sheds light on the mitigation of associated environmental risks.
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Affiliation(s)
- Imran Hussain
- AIT Austrian Institute of Technology, Centre for Energy, Environmental Resources and Technologies, Tulln, Austria; Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Austria
| | - Gajender Aleti
- AIT Austrian Institute of Technology, Centre for Energy, Environmental Resources and Technologies, Tulln, Austria
| | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, New South Wales, Australia
| | - Markus Puschenreiter
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Qaisar Mahmood
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Mohammad Mahmudur Rahman
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, New South Wales, Australia
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shahida Shaheen
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Jabir Hussain Syed
- Department of Meteorology, COMSATS Institute of Information Technology, Park Road Tarlai Kalan 45550, Islamabad, Pakistan; Department of Civil and Environmental Engineering, Hong Kong Polytechnic University, Hong Kong.
| | - Thomas G Reichenauer
- AIT Austrian Institute of Technology, Centre for Energy, Environmental Resources and Technologies, Tulln, Austria.
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Brzeszcz J, Kaszycki P. Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility. Biodegradation 2018; 29:359-407. [PMID: 29948519 DOI: 10.1007/s10532-018-9837-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
Environmental pollution with petroleum toxic products has afflicted various ecosystems, causing devastating damage to natural habitats with serious economic implications. Some crude oil components may serve as growth substrates for microorganisms. A number of bacterial strains reveal metabolic capacities to biotransform various organic compounds. Some of the hydrocarbon degraders are highly biochemically specialized, while the others display a versatile metabolism and can utilize both saturated aliphatic and aromatic hydrocarbons. The extended catabolic profiles of the latter group have been subjected to systematic and complex studies relatively rarely thus far. Growing evidence shows that numerous bacteria produce broad biochemical activities towards different hydrocarbon types and such an enhanced metabolic potential can be found in many more species than the already well-known oil-degraders. These strains may play an important role in the removal of heterogeneous contamination. They are thus considered to be a promising solution in bioremediation applications. The main purpose of this article is to provide an overview of the current knowledge on aerobic bacteria involved in the mineralization or transformation of both n-alkanes and aromatic hydrocarbons. Variant scientific approaches enabling to evaluate these features on biochemical as well as genetic levels are presented. The distribution of multidegradative capabilities between bacterial taxa is systematically shown and the possibility of simultaneous transformation of complex hydrocarbon mixtures is discussed. Bioinformatic analysis of the currently available genetic data is employed to enable generation of phylogenetic relationships between environmental strain isolates belonging to the phyla Actinobacteria, Proteobacteria, and Firmicutes. The study proves that the co-occurrence of genes responsible for concomitant metabolic bioconversion reactions of structurally-diverse hydrocarbons is not unique among various systematic groups.
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Affiliation(s)
- Joanna Brzeszcz
- Department of Microbiology, Oil and Gas Institute-National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland.
| | - Paweł Kaszycki
- Unit of Biochemistry, Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Kraków, al. 29 Listopada 54, 31-425, Kraków, Poland
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Wu T, Xu J, Xie W, Yao Z, Yang H, Sun C, Li X. Pseudomonas aeruginosa L10: A Hydrocarbon-Degrading, Biosurfactant-Producing, and Plant-Growth-Promoting Endophytic Bacterium Isolated From a Reed ( Phragmites australis). Front Microbiol 2018; 9:1087. [PMID: 29887849 PMCID: PMC5980988 DOI: 10.3389/fmicb.2018.01087] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/07/2018] [Indexed: 12/19/2022] Open
Abstract
Bacterial endophytes with the capacity to degrade petroleum hydrocarbons and promote plant growth may facilitate phytoremediation for the removal of petroleum hydrocarbons from contaminated soils. A hydrocarbon-degrading, biosurfactant-producing, and plant-growth-promoting endophytic bacterium, Pseudomonas aeruginosa L10, was isolated from the roots of a reed, Phragmites australis, in the Yellow River Delta, Shandong, China. P. aeruginosa L10 efficiently degraded C10-C26n-alkanes from diesel oil, as well as common polycyclic aromatic hydrocarbons (PAHs) such as naphthalene, phenanthrene, and pyrene. In addition, P. aeruginosa L10 could produce biosurfactant, which was confirmed by the oil spreading method, and surface tension determination of inocula. Moreover, P. aeruginosa L10 had plant growth-stimulating attributes, including siderophore and indole-3-acetic acid (IAA) release, along with 1-aminocyclopropane-1-carboxylic (ACC) deaminase activity. To explore the mechanisms underlying the phenotypic traits of endophytic P. aeruginosa L10, we sequenced its complete genome. From the genome, we identified genes related to petroleum hydrocarbon degradation, such as putative genes encoding monooxygenase, dioxygenase, alcohol dehydrogenase, and aldehyde dehydrogenase. Genome annotation revealed that P. aeruginosa L10 contained a gene cluster involved in the biosynthesis of rhamnolipids, rhlABRI, which should be responsible for the observed biosurfactant activity. We also identified two clusters of genes involved in the biosynthesis of siderophore (pvcABCD and pchABCDREFG). The genome also harbored tryptophan biosynthetic genes (trpAB, trpDC, trpE, trpF, and trpG) that are responsible for IAA synthesis. Moreover, the genome contained the ACC deaminase gene essential for ACC deaminase activity. This study will facilitate applications of endophytic P. aeruginosa L10 to phytoremediation by advancing the understanding of hydrocarbon degradation, biosurfactant synthesis, and mutualistic interactions between endophytes and host plants.
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Affiliation(s)
- Tao Wu
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China.,Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, China
| | - Jie Xu
- Department of Bioengineering, Binzhou Vocational College, Binzhou, China
| | - Wenjun Xie
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China.,Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, China
| | - Zhigang Yao
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China.,Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, China
| | - Hongjun Yang
- Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, China
| | - Chunlong Sun
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China.,Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, China
| | - Xiaobin Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Kong FX, Sun GD, Liu ZP. Degradation of polycyclic aromatic hydrocarbons in soil mesocosms by microbial/plant bioaugmentation: Performance and mechanism. CHEMOSPHERE 2018; 198:83-91. [PMID: 29421764 DOI: 10.1016/j.chemosphere.2018.01.097] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 06/08/2023]
Abstract
In order to study the degradation of polycyclic aromatic hydrocarbons (PAHs) in an aged and highly contaminated soil, four bioremediation strategies (indigenous microorganisms, microbial bioaugmentation with a PAH-degrading and bioemulsifier-producing strain, Rhodococcus ruber Em1, plant bioaugmentation with Orychophragmus violaceus and their combination) were compared and the enhanced degradation mechanism was investigated in soil mesocosms. Degradation rates over a period of 175 days showed that Em1 combined with Orychophragmus violaceus promoted a significant enhancement of PAHs degradation. In inoculated microcosms with Rhodococcus ruberEm1, mineralization reached a lower level in the absence than in the presence of plants. Elimination of PAHs was significantly enhanced (increased by 54.45%) in the bioaugmented mesocosms. Quantitative PCR indicated that copy numbers of linA and RHD-like gene (encoding PAH-ring hydroxylating dioxygenase) in the mesocosm with plant were three and five times higher than those in the mesocosm without plant, respectively. Transcript copy numbers of RHD-like gene and 16S rRNA gene of strain Em1 in mesocosm with plant were two and four times higher than those in the mesocosm without plant, respectively. Taken together, the results of this study show that plants or Rhodococcus ruber Em1 enhance total PAHs removal, moreover their effects are necessarily cumulative by combined strains and plants.
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Affiliation(s)
- Fan-Xin Kong
- State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil & Gas Pollution Control, China University of Petroleum, Beijing, 102249, China
| | - Guang-Dong Sun
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research Beijing, 100038, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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Feng F, Li Y, Ge J, Chen J, Jiang W, He S, Liu X, Yu X. Degradation of chlorpyrifos by an endophytic bacterium of the Sphingomonas genus (strain HJY) isolated from Chinese chives (Allium tuberosum). JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2017; 52:736-744. [PMID: 28937878 DOI: 10.1080/03601234.2017.1356675] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The degradation of chlorpyrifos (CP) by an endophytic bacterial strain (HJY) isolated from Chinese chives (Allium tuberosum Rottl. ex Spreng) was investigated. Strain HJY was identified as Sphingomonas sp. based on morphological, physiological, and biochemical tests and a 16S rDNA sequence analysis. Approximately 96% of 20 mg L-1 CP was degraded by strain HJY over 15 days in liquid minimal salts medium (MSM). The CP degradation rate could also be increased by glucose supplementation. The optimal conditions for the removal of 20 mg L-1 CP by strain HJY in MSM were 2% inoculum density, pH 6.0, and 30-35°C. The CP degradation rate constant and half-life were 0.2136 ± 0.0063 d-1 and 3.2451 ± 0.0975 d, respectively, under these conditions, but were raised to 0.7961 ± 0.1925 d-1 and 0.8707 ± 0.3079 d with 1% glucose supplementation. The detection of metabolic products and screening for degrading genes indicated that O,O-diethyl O-3,5,6-trichloropyridinol was the major degradation product from CP, while it was likely that some functional genes were undetected and the mechanism responsible for CP degradation by strain HJY remained unknown. Strain HJY is potentially useful for the reduction of CP residues in Chinese chives and may be used for the in situ phytoremediation of CP.
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Affiliation(s)
- Fayun Feng
- a Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base , Nanjing , China
- b Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences , Nanjing , China
| | - Yisong Li
- c Department of Plant Protection, Agricultural College , Shihezi University , Xinjiang , China
| | - Jing Ge
- a Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base , Nanjing , China
- b Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences , Nanjing , China
| | - Jinjin Chen
- a Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base , Nanjing , China
| | - Wayne Jiang
- d Department of Entomology , Michigan State University , East Lansing , Michigan , USA
| | - Shuang He
- b Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences , Nanjing , China
- c Department of Plant Protection, Agricultural College , Shihezi University , Xinjiang , China
| | - Xianjing Liu
- b Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences , Nanjing , China
| | - Xiangyang Yu
- a Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base , Nanjing , China
- b Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences , Nanjing , China
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Feng F, Ge J, Li Y, He S, Zhong J, Liu X, Yu X. Enhanced degradation of chlorpyrifos in rice (Oryza sativa L.) by five strains of endophytic bacteria and their plant growth promotional ability. CHEMOSPHERE 2017. [PMID: 28622646 DOI: 10.1016/j.chemosphere.2017.05.178] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Endophytic bacteria reside in plant tissues, such as roots, stems, leaves and seeds. Most of them can stimulate plant growth or alleviate phytotoxicity of pollutants. There are handful species with dual functions stimulating plant growth and degrading pollutants have been reported. Five endophytic bacteria were isolated from chlorpyrifos (CP) treated rice plants and identified as Pseudomonas aeruginosa strain RRA, Bacillus megaterium strain RRB, Sphingobacterium siyangensis strain RSA, Stenotrophomonas pavanii strain RSB and Curtobacterium plantarum strain RSC according to morphological characteristics, physiological and biochemical tests, and 16S rDNA phylogeny. All of them possessed some plant growth promotional traits, including indole acetic acid and siderophore production, secretion of phosphate solubilization and 1-aminocyclopropane-1-carboxylate deaminase. The bacteria were marked with the green fluorescent protein (gfp) gene and successfully colonized into rice plants. All isolates were able to degrade CP in vitro and in vivo. The five isolates degraded more than 90% of CP in 24 h when the initial concentration was lower than 5 mg/L. CP degradation was significantly enhanced in the infested rice plants and rice grains. The final CP residual was reduced up to 80% in the infested rice grains compared to the controls. The results indicate that these isolates are promising bio-inoculants for the removal or detoxification of CP residues in rice plants and grains.
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Affiliation(s)
- Fayun Feng
- Key Laboratory of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base/Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Nanjing 210014, China
| | - Jing Ge
- Key Laboratory of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base/Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Nanjing 210014, China; Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Yisong Li
- Department of Plant Protection, Agricultural College, Shihezi University, Xinjiang, 832000, China
| | - Shuang He
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China; Department of Plant Protection, Agricultural College, Shihezi University, Xinjiang, 832000, China
| | - Jianfeng Zhong
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Xianjing Liu
- Key Laboratory of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base/Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Nanjing 210014, China
| | - Xiangyang Yu
- Key Laboratory of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base/Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Nanjing 210014, China; Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China.
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Lopes R, Cerdeira L, Tavares GS, Ruiz JC, Blom J, Horácio ECA, Mantovani HC, Queiroz MVD. Genome analysis reveals insights of the endophytic Bacillus toyonensis BAC3151 as a potentially novel agent for biocontrol of plant pathogens. World J Microbiol Biotechnol 2017; 33:185. [DOI: 10.1007/s11274-017-2347-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/19/2017] [Indexed: 02/02/2023]
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Doty SL, Freeman JL, Cohu CM, Burken JG, Firrincieli A, Simon A, Khan Z, Isebrands JG, Lukas J, Blaylock MJ. Enhanced Degradation of TCE on a Superfund Site Using Endophyte-Assisted Poplar Tree Phytoremediation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:10050-10058. [PMID: 28737929 DOI: 10.1021/acs.est.7b01504] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Trichloroethylene (TCE) is a widespread environmental pollutant common in groundwater plumes associated with industrial manufacturing areas. We had previously isolated and characterized a natural bacterial endophyte, Enterobacter sp. strain PDN3, of poplar trees, that rapidly metabolizes TCE, releasing chloride ion. We now report findings from a successful three-year field trial of endophyte-assisted phytoremediation on the Middlefield-Ellis-Whisman Superfund Study Area TCE plume in the Silicon Valley of California. The inoculated poplar trees exhibited increased growth and reduced TCE phytotoxic effects with a 32% increase in trunk diameter compared to mock-inoculated control poplar trees. The inoculated trees excreted 50% more chloride ion into the rhizosphere, indicative of increased TCE metabolism in planta. Data from tree core analysis of the tree tissues provided further supporting evidence of the enhanced rate of degradation of the chlorinated solvents in the inoculated trees. Test well groundwater analyses demonstrated a marked decrease in concentration of TCE and its derivatives from the tree-associated groundwater plume. The concentration of TCE decreased from 300 μg/L upstream of the planted area to less than 5 μg/L downstream of the planted area. TCE derivatives were similarly removed with cis-1,2-dichloroethene decreasing from 160 μg/L to less than 5 μg/L and trans-1,2-dichloroethene decreasing from 3.1 μg/L to less than 0.5 μg/L downstream of the planted trees. 1,1-dichloroethene and vinyl chloride both decreased from 6.8 and 0.77 μg/L, respectively, to below the reporting limit of 0.5 μg/L providing strong evidence of the ability of the endophytic inoculated trees to effectively remove TCE from affected groundwater. The combination of native pollutant-degrading endophytic bacteria and fast-growing poplar tree systems offers a readily deployable, cost-effective approach for the degradation of TCE, and may help mitigate potential transfer up the food chain, volatilization to the atmosphere, as well as direct phytotoxic impacts to plants used in this type of phytoremediation.
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Affiliation(s)
- Sharon L Doty
- University of Washington , Seattle, Washington 98195-2100, United States
| | - John L Freeman
- Intrinsyx Technologies Corporation, NASA Ames Research Park, Moffett Field, California 94035-1000, United States
| | - Christopher M Cohu
- Phytoremediation and Phytomining Consultants United, Grand Junction, Colorado 81507, United States
| | - Joel G Burken
- Department of Civil, Architectural, and Environmental Engineering, Missouri University of Science and Technology , Rolla, Missouri 65409, United States
| | - Andrea Firrincieli
- Dept. for Innovation in Biological, Agro-Food, and Forest Systems, University of Tuscia , Viterbo, Italy
| | - Andrew Simon
- Edenspace Systems Corporation , Purcellville, Virginia 20134, United States
| | - Zareen Khan
- University of Washington , Seattle, Washington 98195-2100, United States
| | - J G Isebrands
- Environmental Forestry Consultants LLC, New London, Wisconsin 54961, United States
| | - Joseph Lukas
- Earth Resources Technology, Inc., Moffett Field, California 94035, United States
| | - Michael J Blaylock
- Edenspace Systems Corporation , Purcellville, Virginia 20134, United States
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36
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Pawlik M, Cania B, Thijs S, Vangronsveld J, Piotrowska-Seget Z. Hydrocarbon degradation potential and plant growth-promoting activity of culturable endophytic bacteria of Lotus corniculatus and Oenothera biennis from a long-term polluted site. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:19640-19652. [PMID: 28681302 PMCID: PMC5570797 DOI: 10.1007/s11356-017-9496-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 06/08/2017] [Indexed: 05/15/2023]
Abstract
Many endophytic bacteria exert beneficial effects on their host, but still little is known about the bacteria associated with plants growing in areas heavily polluted by hydrocarbons. The aim of the study was characterization of culturable hydrocarbon-degrading endophytic bacteria associated with Lotus corniculatus L. and Oenothera biennis L. collected in long-term petroleum hydrocarbon-polluted site using culture-dependent and molecular approaches. A total of 26 hydrocarbon-degrading endophytes from these plants were isolated. Phylogenetic analyses classified the isolates into the phyla Proteobacteria and Actinobacteria. The majority of strains belonged to the genera Rhizobium, Pseudomonas, Stenotrophomonas, and Rhodococcus. More than 90% of the isolates could grow on medium with diesel oil, approximately 20% could use n-hexadecane as a sole carbon and energy source. PCR analysis revealed that 40% of the isolates possessed the P450 gene encoding for cytochrome P450-type alkane hydroxylase (CYP153). In in vitro tests, all endophytic strains demonstrated a wide range of plant growth-promoting traits such as production of indole-3-acetic acid, hydrogen cyanide, siderophores, and phosphate solubilization. More than 40% of the bacteria carried the gene encoding for the 1-aminocyclopropane-1-carboxylic acid deaminase (acdS). Our study shows that the diversity of endophytic bacterial communities in tested plants was different. The results revealed also that the investigated plants were colonized by endophytic bacteria possessing plant growth-promoting features and a clear potential to degrade hydrocarbons. The properties of isolated endophytes indicate that they have the high potential to improve phytoremediation of petroleum hydrocarbon-polluted soils.
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Affiliation(s)
- Małgorzata Pawlik
- Department of Microbiology, University of Silesia, Katowice, Poland.
| | - Barbara Cania
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Munich, Germany
| | - Sofie Thijs
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
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Ebadi A, Khoshkholgh Sima NA, Olamaee M, Hashemi M, Ghorbani Nasrabadi R. Effective bioremediation of a petroleum-polluted saline soil by a surfactant-producing Pseudomonas aeruginosa consortium. J Adv Res 2017; 8:627-633. [PMID: 28831308 PMCID: PMC5552007 DOI: 10.1016/j.jare.2017.06.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/15/2017] [Accepted: 06/28/2017] [Indexed: 01/13/2023] Open
Abstract
Bacteria able to produce biosurfactants can use petroleum-based hydrocarbons as a carbon source. Herein, four biosurfactant-producing Pseudomonas aeruginosa strains, isolated from oil-contaminated saline soil, were combined to form a bacterial consortium. The inoculation of the consortium to contaminated soil alleviated the adverse effects of salinity on biodegradation and increased the rate of degradation of petroleum hydrocarbon approximately 30% compared to the rate achieved in non-treated soil. In saline condition, treatment of polluted soil with the consortium led to a significant boost in the activity of dehydrogenase (approximately 2-fold). A lettuce seedling bioassay showed that, following the treatment, the soil's level of phytotoxicity was reduced up to 30% compared to non-treated soil. Treatment with an appropriate bacterial consortium can represent an effective means of reducing the adverse effects of salinity on the microbial degradation of petroleum and thus provides enhancement in the efficiency of microbial remediation of oil-contaminated saline soils.
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Affiliation(s)
- Ali Ebadi
- Department of Soil Science, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Nayer Azam Khoshkholgh Sima
- Agricultural Biotechnology Research Institute of Iran (ABRII), AREEO, P.O. Box: 31535-1897, Karaj, Iran
- Corresponding author.
| | - Mohsen Olamaee
- Department of Soil Science, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Maryam Hashemi
- Agricultural Biotechnology Research Institute of Iran (ABRII), AREEO, P.O. Box: 31535-1897, Karaj, Iran
| | - Reza Ghorbani Nasrabadi
- Department of Soil Science, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
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Feng NX, Yu J, Zhao HM, Cheng YT, Mo CH, Cai QY, Li YW, Li H, Wong MH. Efficient phytoremediation of organic contaminants in soils using plant-endophyte partnerships. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 583:352-368. [PMID: 28117167 DOI: 10.1016/j.scitotenv.2017.01.075] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 05/20/2023]
Abstract
Soil pollution with organic contaminants is one of the most intractable environmental problems today, posing serious threats to humans and the environment. Innovative strategies for remediating organic-contaminated soils are critically needed. Phytoremediation, based on the synergistic actions of plants and their associated microorganisms, has been recognized as a powerful in situ approach to soil remediation. Suitable combinations of plants and their associated endophytes can improve plant growth and enhance the biodegradation of organic contaminants in the rhizosphere and/or endosphere, dramatically expediting the removal of organic pollutants from soils. However, for phytoremediation to become a more widely accepted and predictable alternative, a thorough understanding of plant-endophyte interactions is needed. Many studies have recently been conducted on the mechanisms of endophyte-assisted phytoremediation of organic contaminants in soils. In this review, we highlight the superiority of organic pollutant-degrading endophytes for practical applications in phytoremediation, summarize alternative strategies for improving phytoremediation, discuss the fundamental mechanisms of endophyte-assisted phytoremediation, and present updated information regarding the advances, challenges, and new directions in the field of endophyte-assisted phytoremediation technology.
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Affiliation(s)
- Nai-Xian Feng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jiao Yu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yu-Ting Cheng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China.
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ming-Hung Wong
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China; Consortium on Health, Environment, Education and Research (CHEER), Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong, China
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Oliveira V, Gomes NCM, Santos M, Almeida A, Lillebø AI, Ezequiel J, Serôdio J, Silva AMS, Simões MMQ, Rocha SM, Cunha Â. Effects of the Inoculant Strain Pseudomonas sp. SPN31 nah + and of 2-Methylnaphthalene Contamination on the Rhizosphere and Endosphere Bacterial Communities of Halimione portulacoides. Curr Microbiol 2017; 74:575-583. [DOI: 10.1007/s00284-017-1197-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/08/2017] [Indexed: 01/19/2023]
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Deng S, Zeng D. Removal of phenanthrene in contaminated soil by combination of alfalfa, white-rot fungus, and earthworms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:7565-7571. [PMID: 28116628 DOI: 10.1007/s11356-017-8466-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/16/2017] [Indexed: 06/06/2023]
Abstract
The aim of this study was to investigate the removal of phenanthrene by combination of alfalfa, white-rot fungus, and earthworms in soil. A 60-day experiment was conducted. Inoculation with earthworms and/or white-rot fungus increased alfalfa biomass and phenanthrene accumulation in alfalfa. However, inoculations of alfalfa and white-rot fungus can significantly decrease the accumulation of phenanthrene in earthworms. The removal rates for phenanthrene in soil were 33, 48, 66, 74, 85, and 93% under treatments control, only earthworms, only alfalfa, earthworms + alfalfa, alfalfa + white-rot fungus, and alfalfa + earthworms + white-rot fungus, respectively. The present study demonstrated that the combination of alfalfa, earthworms, and white-rot fungus is an effective way to remove phenanthrene in the soil. The removal is mainly via stimulating both microbial development and soil enzyme activity.
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Affiliation(s)
- Shuguang Deng
- School of Resource and Environmental Engineering, Wuhan University of Technology, Wuhan, 430070, China
| | - Defang Zeng
- School of Resource and Environmental Engineering, Wuhan University of Technology, Wuhan, 430070, China.
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Feng F, Ge J, Li Y, Cheng J, Zhong J, Yu X. Isolation, Colonization, and Chlorpyrifos Degradation Mediation of the Endophytic Bacterium Sphingomonas Strain HJY in Chinese Chives (Allium tuberosum). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:1131-1138. [PMID: 28103027 DOI: 10.1021/acs.jafc.6b05283] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The endophyte-plant interaction can benefit the host in many different ways. An endophytic bacterium strain (HJY) capable of degrading chlorpyrifos (CP) was isolated from Chinese chives (Allium tuberosum Rottl. ex Spreng). The isolated bacterium HJY classified as Sphingomonas sp. strain HJY could use CP as the sole carbon source. After being marked with the gfp gene, the colonization and distribution of strain HJY-gfp were directly observed in different tissues of Chinese chives with a confocal laser scanning microscope. The inoculation of strain HJY-gfp in Chinese chives resulted in a higher degradation of CP inside the plants than in uninoculated plants. With drench application, up to 70 and 66% of CP were removed from shoots and roots of inoculated Chinese chives, respectively. Moreover, up to 75% of CP was removed from the soil containing plants inoculated with HJY-gfp. With foliage application, the applied concentration of chlorpyrifos affected the degradation performance of strain HJY in Chinese chives. Significant differences were observed only between inoculated and uninoculated Chinese chives with the low applied concentration of CP. Together, other than natural endophyte-assisted plant protection for food safety, the interaction of HJY and plant may be also a promising strategy for in situ bioremediation of soil contaminated with CP.
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Affiliation(s)
- Fayun Feng
- Key Laboratory of Food Quality and Safety of Jiangsu Province- State Key Laboratory Breeding Base , 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences , 50 Zhongling Street, Nanjing 210014, China
| | - Jing Ge
- Key Laboratory of Food Quality and Safety of Jiangsu Province- State Key Laboratory Breeding Base , 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences , 50 Zhongling Street, Nanjing 210014, China
| | - Yisong Li
- Department of Plant Protection, Agricultural College, Shihezi University , Xinjiang 832000, China
| | - Jinjin Cheng
- Key Laboratory of Food Quality and Safety of Jiangsu Province- State Key Laboratory Breeding Base , 50 Zhongling Street, Nanjing 210014, China
| | - Jianfeng Zhong
- Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences , 50 Zhongling Street, Nanjing 210014, China
| | - Xiangyang Yu
- Key Laboratory of Food Quality and Safety of Jiangsu Province- State Key Laboratory Breeding Base , 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences , 50 Zhongling Street, Nanjing 210014, China
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42
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Patra JK, Vishnuprasad CN, Das G. Bioprospecting of Endophytes for Agricultural and Environmental Sustainability. Microb Biotechnol 2017. [PMCID: PMC7120099 DOI: 10.1007/978-981-10-6847-8_19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The term endophytes refers to a group of endosymbionts usually bacterium, fungus or interactive bacterium-fungal species residing asymptomatically and grows within plants for at least a part of their life cycle intra- and intercelullarly in the tissues of higher plants without causing any visible manifestation of disease. The endophytes represent a potential source of novel natural and ecofriendly products for medicinal, agricultural and industrial uses with least adverse effect on the environment. The enormous biological diversity coupled with their capability to biosynthesize bioactive secondary metabolites has provided the momentum for the researchers working on endophytes. The present review was undertaken to highlight the biotechnological processes and bioprospection of endophytes as potential antimicrobial agents, secondary metabolites, antibiotics, antagonists against disease causing phytopathogens, cytotoxic, anticancer, insecticidal, antioxidant antiviral compounds andisolation and production of bioactive compounds with potent enzymatic activities. Endophyte enhances biodegradation and hydrolysis processes significantly important against pathogenic infection, biotransformation studies and production of compounds with immense industrial applications. The interaction of the endophytic microbiota with the plants are more protected and can withstand the adverse environmental conditions and contribute to plant growth, productivity, carbon sequestration, enhanced phytoremediation efficiencies and amelioration of metal induced toxicity. The strategies governed by the endophytes for efficient production of novel bioactive phytocompounds was comprehensively discussed. The review envisaged the biodiversity, transmission of endophytes, plant endophyte interactions for the production of bioactive compounds for therapeutic, environmental and agricultural sustainability.
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Affiliation(s)
| | | | - Gitishree Das
- Dongguk University, Goyang-si, Gyeonggi-do, Korea (Republic of)
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Weir E, Doty S. Social acceptability of phytoremediation: The role of risk and values. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2016; 18:1029-36. [PMID: 27167719 DOI: 10.1080/15226514.2016.1183571] [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] [Indexed: 05/22/2023]
Abstract
A former gas production site that was converted to a public park was chosen as the research location for the present study. Some of the contaminants at the site have been remediated; however, much of the soil is still contaminated with polycyclic aromatic hydrocarbons (PAHs). PAHs are toxic pollutants that have been shown to have numerous negative health effects. The primary form of remediation at the site has been capping, which is usually considered a temporary remediation strategy since it does not remove contaminants from the site but simply covers them, and this requires repeated re-capping efforts. Endophyte-assisted phytoremediation using willow shrubs is an alternative remediation strategy that could improve soil quality and permanently reduce contaminant levels in the soil. The goal of the present study was to explore the social acceptability of utilizing phytoremediation strategies. Surveys were used to explore public perceptions of the park and of using phytoremediation to clean up existing contamination. Results indicated a high level of social acceptability of phytoremediation at the park. Additionally, ecocentrism was shown to be a significant predictor of phytoremediation acceptability. Risk and anthropocentrism were not significant predictors of acceptability. Results suggest that messages intended to encourage the use and acceptability of phytoremediation should focus on the environmental benefits of phytoremediation.
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Affiliation(s)
- Ellen Weir
- a School of Environmental and Forest Sciences, University of Washington , Seattle , WA , USA
| | - Sharon Doty
- a School of Environmental and Forest Sciences, University of Washington , Seattle , WA , USA
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44
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De Felice A, Di Lorenzo F, Scherlach K, Ross C, Silipo A, Hertweck C, Molinaro A. Structural investigation of the lipopolysaccharide O-chain isolated from Burkholderia fungorum strain DSM 17061. Carbohydr Res 2016; 433:31-5. [DOI: 10.1016/j.carres.2016.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/04/2016] [Accepted: 07/06/2016] [Indexed: 01/18/2023]
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45
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Gong X, Liu Y, Huang D, Zeng G, Liu S, Tang H, Zhou L, Hu X, Zhou Y, Tan X. Effects of exogenous calcium and spermidine on cadmium stress moderation and metal accumulation in Boehmeria nivea (L.) Gaudich. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:8699-8708. [PMID: 26801927 DOI: 10.1007/s11356-016-6122-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/14/2016] [Indexed: 05/29/2023]
Abstract
Cadmium (Cd) is a detrimental metal in the environment and it is easily taken up by plants, thus entering the food chain and posing a severe threat to human health. Phytoremediation being low cost, highly stable, and environmentally friendly has been considered as a promising green technology for Cd remediation. The addition of exogenous substances to the culture media has been recognized as an efficient strategy to improve plant phytoremediation capability. Pot trials were conducted to investigate the combined effects of exogenous calcium (Ca) and spermidine (Spd) on Cd-induced toxicity in Boehmeria nivea (L.) Gaudich. (ramie). Results showed that the application of 5-mM exogenous Ca significantly alleviated Cd toxicity in ramie by reducing Cd accumulation, depressing H2O2 and malondialdehyde contents, increasing plants dry weights and chlorophyll concentrations, as well as altering the activities of total superoxide dismutase and guaiacol peroxidase. Furthermore, as a non-Cd hyperaccumulator plant, ramie hyperaccumulated Cd and suffered more severe toxic effects of Cd by the treatment of 1 mM Ca/Cd. The aggravated Cd toxicity could be compensated by the addition of exogenous Spd via the promotion of plant growth and the reduction of the oxidative stress. Overall, the combination effects of 1 mM Ca and Spd appeared to be more superior compared to other treatments in the plants under Cd stress with a higher Cd accumulation ability and the evaluated Cd stress tolerance.
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Affiliation(s)
- Xiaomin Gong
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, People's Republic of China
| | - Yunguo Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China.
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, People's Republic of China.
| | - Danlian Huang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, People's Republic of China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, People's Republic of China
| | - Shaobo Liu
- College of Metallurgy and Environmental Research, Central South University, Changsha, 410004, People's Republic of China
| | - Hui Tang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, People's Republic of China
| | - Lu Zhou
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, People's Republic of China
| | - Xi Hu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, People's Republic of China
| | - Yaoyu Zhou
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, People's Republic of China
| | - Xiaofei Tan
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, People's Republic of China
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46
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Patil SM, Chandanshive VV, Rane NR, Khandare RV, Watharkar AD, Govindwar SP. Bioreactor with Ipomoea hederifolia adventitious roots and its endophyte Cladosporium cladosporioides for textile dye degradation. ENVIRONMENTAL RESEARCH 2016; 146:340-349. [PMID: 26803212 DOI: 10.1016/j.envres.2016.01.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/08/2016] [Accepted: 01/13/2016] [Indexed: 06/05/2023]
Abstract
In vitro grown untransformed adventitious roots (AR) culture of Ipomoea hederifolia and its endophytic fungus (EF) Cladosporium cladosporioides decolorized Navy Blue HE2R (NB-HE2R) at a concentration of 20 ppm up to 83.3 and 65%, respectively within 96h. Whereas the AR-EF consortium decolorized the dye more efficiently and gave 97% removal within 36h. Significant inductions in the enzyme activities of lignin peroxidase, tyrosinase and laccase were observed in roots, while enzymes like tyrosinase, laccase and riboflavin reductase activities were induced in EF. Metabolites of dye were analyzed using UV-vis spectroscopy, FTIR and gas chromatography-mass spectrometry. Possible metabolic pathways of NB-HE2R were proposed with AR, EF and AR-EF systems independently. Looking at the superior efficacy of AR-EF system, a rhizoreactor was developed for the treatment of NB-HE2R at a concentration of 1000 ppm. Control reactor systems with independently grown AR and EF gave 94 and 85% NB-HE2R removal, respectively within 36h. The AR-EF rhizoreactor, however, gave 97% decolorization. The endophyte colonization additionally increased root and shoot lengths of candidate plants through mutualism. Combined bioreactor strategies can be effectively used for future eco-friendly remediation purposes.
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Affiliation(s)
- Swapnil M Patil
- Department of Biotechnology, Shivaji University, Kolhapur-416004, India
| | | | - Niraj R Rane
- Department of Biotechnology, Shivaji University, Kolhapur-416004, India
| | - Rahul V Khandare
- Department of Biotechnology, Shivaji University, Kolhapur-416004, India
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Andreolli M, Lampis S, Zapparoli G, Angelini E, Vallini G. Diversity of bacterial endophytes in 3 and 15 year-old grapevines of Vitis vinifera cv. Corvina and their potential for plant growth promotion and phytopathogen control. Microbiol Res 2016; 183:42-52. [DOI: 10.1016/j.micres.2015.11.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/22/2015] [Indexed: 11/28/2022]
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Shen SY, Fulthorpe R. Seasonal variation of bacterial endophytes in urban trees. Front Microbiol 2015; 6:427. [PMID: 26042095 PMCID: PMC4437045 DOI: 10.3389/fmicb.2015.00427] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/22/2015] [Indexed: 02/01/2023] Open
Abstract
Bacterial endophytes, non-pathogenic bacteria residing within plants, contribute to the growth and development of plants and their ability to adapt to adverse conditions. In order to fully exploit the capabilities of these bacteria, it is necessary to understand the extent to which endophytic communities vary between species and over time. The endophytes of Acer negundo, Ulmus pumila, and Ulmus parvifolia were sampled over three seasons and analyzed using culture dependent and independent methods (culture on two media, terminal restriction fragment length polymorphism, and tagged pyrosequencing of 16S ribosomal amplicons). The majority of culturable endophytes isolated were Actinobacteria, and all the samples harbored Bacillus, Curtobacterium, Frigoribacterium, Methylobacterium, Paenibacilllus, and Sphingomonas species. Regardless of culture medium used, only the culturable communities obtained in the winter for A. negundo could be distinguished from those of Ulmus spp. In contrast, the nonculturable communities were dominated by Proteobacteria and Actinobacteria, particularly Erwinia, Ralstonia, and Sanguibacter spp. The presence and abundance of various bacterial classes and phyla changed with the changing seasons. Multivariate analysis on the culture independent data revealed significant community differences between the endophytic communities of A. negundo and Ulmus spp., but overall season was the main determinant of endophytic community structure. This study suggests studies on endophytic populations of urban trees should expect to find significant seasonal and species-specific community differences and sampling should proceed accordingly.
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Affiliation(s)
- Shu Yi Shen
- 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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Stopnisek N, Zühlke D, Carlier A, Barberán A, Fierer N, Becher D, Riedel K, Eberl L, Weisskopf L. Molecular mechanisms underlying the close association between soil Burkholderia and fungi. ISME JOURNAL 2015; 10:253-64. [PMID: 25989372 DOI: 10.1038/ismej.2015.73] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 03/24/2015] [Accepted: 03/26/2015] [Indexed: 01/27/2023]
Abstract
Bacterial species belonging to the genus Burkholderia have been repeatedly reported to be associated with fungi but the extent and specificity of these associations in soils remain undetermined. To assess whether associations between Burkholderia and fungi are widespread in soils, we performed a co-occurrence analysis in an intercontinental soil sample collection. This revealed that Burkholderia significantly co-occurred with a wide range of fungi. To analyse the molecular basis of the interaction, we selected two model fungi frequently co-occurring with Burkholderia, Alternaria alternata and Fusarium solani, and analysed the proteome changes caused by cultivation with either fungus in the widespread soil inhabitant B. glathei, whose genome we sequenced. Co-cultivation with both fungi led to very similar changes in the B. glathei proteome. Our results indicate that B. glathei significantly benefits from the interaction, which is exemplified by a lower abundance of several starvation factors that were highly expressed in pure culture. However, co-cultivation also gave rise to stress factors, as indicated by the increased expression of multidrug efflux pumps and proteins involved in oxidative stress response. Our data suggest that the ability of Burkholderia to establish a close association with fungi mainly lies in the capacities to utilize fungal-secreted metabolites and to overcome fungal defense mechanisms. This work indicates that beneficial interactions with fungi might contribute to the survival strategy of Burkholderia species in environments with sub-optimal conditions, including acidic soils.
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Affiliation(s)
- Nejc Stopnisek
- Institute of Plant Biology, University of Zurich, Zürich, Switzerland.,Institute for Sustainability Sciences, Agroscope, Zürich, Switzerland
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Aurélien Carlier
- Institute of Plant Biology, University of Zurich, Zürich, Switzerland
| | - Albert Barberán
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Leo Eberl
- Institute of Plant Biology, University of Zurich, Zürich, Switzerland
| | - Laure Weisskopf
- Institute of Plant Biology, University of Zurich, Zürich, Switzerland.,Institute for Sustainability Sciences, Agroscope, Zürich, Switzerland
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Hong Y, Liao D, Chen J, Khan S, Su J, Li H. A comprehensive study of the impact of polycyclic aromatic hydrocarbons (PAHs) contamination on salt marsh plants Spartina alterniflora: implication for plant-microbe interactions in phytoremediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:7071-7081. [PMID: 25501539 DOI: 10.1007/s11356-014-3912-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/24/2014] [Indexed: 06/04/2023]
Abstract
These pot experiments aimed to investigate the effects of polycyclic aromatic hydrocarbons (PAHs) on plant uptake, rhizophere, endophytic bacteria, and phytoremediation potentials of contaminated sediments. Salt marsh plant Spartina alterniflora was selected and cultivated in phenanthrene (PHE)- and pyrene (PYR)-contaminated sediments (for 70 days). The results indicated that the amount of PHE removed from the sediments ranged from 13 to 36 %, while PYR ranged from 11 to 30 %. In rhizophere sediment, dehydrogenase activities were significantly (P < 0.05) enhanced by higher concentration of PHE treatments, while polyphenol oxidase activities were prohibited more than 10 % in non-rhizophere sediment. Compared with the control, PHE treatments had also significantly (P < 0.05) lower total microbial biomass; especially for gram-negative bacteria, this decrease was more than 24 %. However, the PYR treatments had little effect on the dehydrogenase, polyphenol oxidase, and total phospholipid fatty acid analysis (PLFA) biomass. The greatest abundance of PAH-ring hydroxylating dioxygenases isolated from gram-negative bacteria (PAH-RHDα-GN) of rhizoplane and endophyte in roots were found at high concentration of PHE treatments and increased by more than 100- and 3-fold, respectively. These results suggested that PAH pollution would result in the comprehensive effect on S. alterniflora, whose endophytic bacteria might play important roles in the phytoremediation potential of PAH-contaminated sediments.
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Affiliation(s)
- Youwei Hong
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China,
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