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Brereton NJB, Gonzalez E, Desjardins D, Labrecque M, Pitre FE. Co-cropping with three phytoremediation crops influences rhizosphere microbiome community in contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:135067. [PMID: 31818595 DOI: 10.1016/j.scitotenv.2019.135067] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Human industrial activities have left millions of hectares of land polluted with trace element metals and persistent organic pollutants (POPs) around the world. Although contaminated sites are environmentally damaging, high economic costs often discourage soil remediation efforts. Phytoremediation is a potential green technology solution but can be challenging due to the diversity of anthropogenic contaminants. Co-cropping could provide improved tolerance to diverse soil challenges by taking advantage of distinct crop capabilities. Co-cropping of three species with potentially complementary functions, Festuca arundinacea, Salix miyabeana and Medicago sativa, perform well on diversely contaminated soils. Here, rhizosphere microbiomes of each crop in monoculture and in all co-cropping combinations were compared using 16S rRNA gene amplification, sequencing and differential abundance analysis. The hyperaccumulating F. arundinacea rhizosphere microbiome included putative plant growth promoting bacteria (PGPB) and metal tolerance species, such as Rhizorhapis suberifaciens, Cellvibrio fibrivorans and Pseudomonas lini. The rhizosphere microbiome of the fast-growing tree S. miyabeana included diverse taxa involved in POP degradation, including the species Phenylobacterium panacis. The well-characterised nitrogen-fixing M. sativa microbiome species, Sinorhizobium meliloti, was identified alongside others involved in nutrient acquisition and putative yet-to-be-cultured Candidatus saccharibacteria (TM7-1 group). The majority of differentially abundant rhizosphere-associated bacterial species were maintained in co-cropping pairs, with pairs having higher numbers of differentially abundant taxa than monocultures in all cases. This was not the case when all three crops were co-cropped, where most host-specific bacterial species were not detected as differentially abundant, indicating the potential for reduced rhizosphere functionality. The crops cultivated in pairs here retained rhizosphere microbiome bacteria involved in these monoculture ecosystem services of plant growth promotion, POP tolerance and degradation, and improved nutrient acquisition. These findings provide a promising outlook of the potential for complementary co-cropping strategies for phytoremediation of the multifaceted anthropogenic pollution which can disastrously affect soils around the world.
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Affiliation(s)
- N J B Brereton
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada.
| | - E Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC H3A 0G1, Canada; Department of Human Genetics, McGill University, Montreal H3A 1B1, Canada
| | - D Desjardins
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada
| | - M Labrecque
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada; Montreal Botanical Garden, Montreal, QC H1X 2B2, Canada
| | - F E Pitre
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada; Montreal Botanical Garden, Montreal, QC H1X 2B2, Canada
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Ganuza M, Pastor N, Boccolini M, Erazo J, Palacios S, Oddino C, Reynoso MM, Rovera M, Torres AM. Evaluating the impact of the biocontrol agent Trichoderma harzianum ITEM 3636 on indigenous microbial communities from field soils. J Appl Microbiol 2018; 126:608-623. [PMID: 30382616 DOI: 10.1111/jam.14147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/09/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
AIM To investigate the impact of inoculating peanut seeds with the biocontrol agent Trichoderma harzianum ITEM 3636 on the structure of bacterial and fungal communities from agricultural soils. METHODS AND RESULTS Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing (NGS) of amplicons (or marker gene amplification metagenomics) were performed to investigate potential changes in the structure of microbial communities from fields located in a peanut-producing area in the province of Córdoba, Argentina. Fields had history of peanut smut (caused by Thecaphora frezii) incidence. The Shannon indexes (H'), which estimate diversity, obtained from the PCR-DGGE assays did not show significant differences neither for bacterial nor for fungal communities between control and inoculation treatments. On the other hand, the number of operational taxonomic units obtained after NGS was similar between all the analysed samples. Moreover, results of alpha and beta diversity showed that there were no significant variations between the relative abundances of the most representative bacterial and fungal phyla and genera, in both fields. CONCLUSIONS Trichoderma harzianum ITEM 3636 decreases the incidence and severity of agriculturally relevant diseases without causing significant changes in the microbial communities of agricultural soils. SIGNIFICANCE AND IMPACT OF THE STUDY Our investigations provide information on the structure of bacterial and fungal communities in peanut-producing fields after inoculation of seeds with a biocontrol agent.
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Affiliation(s)
- M Ganuza
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.,UNRC-CONICET, Río Cuarto, Argentina
| | - N Pastor
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.,UNRC-CONICET, Río Cuarto, Argentina
| | - M Boccolini
- INTA EEA - Instituto Nacional de Tecnología Agropecuaria Estación Experimental Marcos Juárez, Marcos Juárez, Córdoba, Argentina
| | - J Erazo
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.,UNRC-CONICET, Río Cuarto, Argentina
| | - S Palacios
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.,UNRC-CONICET, Río Cuarto, Argentina
| | - C Oddino
- Facultad de Agronomía y Veterinaria, UNRC, Río Cuarto, Córdoba, Argentina
| | - M M Reynoso
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.,UNRC-CONICET, Río Cuarto, Argentina
| | - M Rovera
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - A M Torres
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.,UNRC-CONICET, Río Cuarto, Argentina
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Huang Y, Kuang Z, Deng Z, Zhang R, Cao L. Endophytic bacterial and fungal communities transmitted from cotyledons and germs in peanut (Arachis hypogaea L.) sprouts. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:16458-16464. [PMID: 28551744 DOI: 10.1007/s11356-017-9254-4] [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] [Received: 10/10/2016] [Accepted: 05/10/2017] [Indexed: 06/07/2023]
Abstract
Seed-borne endophytes could be transmitted into sprouts. Whether this happened in peanuts and the difference between microbial taxa in peanut germs and cotyledons remain unknown. In this research, Illumina-based sequencing was employed to investigate the microbial taxa in peanut germs, cotyledons, and sprouts. Sulfur-oxidizing bacteria was isolated and inoculated into peanut sprouts, and then, the growth of peanut seedlings was measured. The results illustrated that diverse bacteria and fungi were detected in peanut germs, cotyledons, and sprouts. The number of bacterial OTUs declined with the germination from germs and cotyledons to sprouts. However, the number of fungal OTUs increased during the seedling procedure. Seed-borne dominant bacterial genera Halothiobacillus and Synechococcus and fungal genera Humicola, Emericella, and Penicillium were detected in sprouts. Based on the endophytic community information, the Halothiobacillus strains were isolated from sprouts. Pot experiments that illustrated the growth of peanut seedlings inoculated with the strain were promoted. These results provide new understanding into plant-microbe interactions in peanut and suggest that the selection for biocontrol agents based on mycobiome and bacteriome analysis is reliable and feasible compared with the present greenhouse selection.
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Affiliation(s)
- Yali Huang
- College of Fundamental Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zaoyuan Kuang
- College of Fundamental Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zujun Deng
- School of Basic Courses, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ren Zhang
- College of Fundamental Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Lixiang Cao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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Haldar S, Sengupta S. Impact of plant development on the rhizobacterial population ofArachis hypogaea: a multifactorial analysis. J Basic Microbiol 2015; 55:922-8. [DOI: 10.1002/jobm.201400683] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 11/26/2014] [Indexed: 12/24/2022]
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Paulucci NS, Gallarato LA, Reguera YB, Vicario JC, Cesari AB, García de Lema MB, Dardanelli MS. Arachis hypogaea PGPR isolated from Argentine soil modifies its lipids components in response to temperature and salinity. Microbiol Res 2015; 173:1-9. [PMID: 25801965 DOI: 10.1016/j.micres.2014.12.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/23/2014] [Accepted: 12/26/2014] [Indexed: 11/17/2022]
Abstract
The aim of this work was to clarify the mechanism related to plant growth promoting of a bacterial strain (L115) isolated from Arachis hypogaea rhizospheres and the effects of high growth temperature and salinity on phospholipids and fatty acids composition. L115 was isolated from peanut rhizospheres and identified according to the sequence analysis of the 16S rRNA gene. Phenotypic, metabolic and plant growth promoting rhizobacteria (PGPR) characteristics of L115 were tested. Inoculation test in plant growth chamber was performed. In addition, L115 was exposed to a 37 °C and 300 mM NaCl and phospholipids and fatty acid composition were evaluated. L115 strain was identified as Ochrobactrum intermedium and was able to increase the peanut shoot and root length as well as dry weight, indicating a PGPR role by being able to produce indole acetic acid and siderophores and present ACC deaminase activity. In addition, L115 showed tolerance to both high growth temperature and 300 mM NaCl. The most striking change was a decreased percentage of 18:1 fatty acid and an increase in 16:0 and 18:0 fatty acids, under high growth temperature or a combination of increased temperature and salinity. The most important change in phospholipid levels was an increase in phosphatidylcholine biosynthesis in all growth conditions. L115 can promote the growth of peanut and can tolerate high growth temperature and salinity modifying the fatty acid unsaturation degree and increasing phosphatidylcholine levels. This work is the first to report the importance of the genus Ochrobactrum as PGPR on peanut growth as well as on the metabolic behaviour against abiotic stresses that occur in soil. This knowledge will be useful for developing strategies to improve the growth of this bacterium under stress and to enhance its bioprocess for the production of inoculants.
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Affiliation(s)
- Natalia S Paulucci
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, CPX5804BYA Río Cuarto, Córdoba, Argentina.
| | - Lucas A Gallarato
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, CPX5804BYA Río Cuarto, Córdoba, Argentina
| | - Yanina B Reguera
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, CPX5804BYA Río Cuarto, Córdoba, Argentina
| | - Julio C Vicario
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, CPX5804BYA Río Cuarto, Córdoba, Argentina
| | - Adriana B Cesari
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, CPX5804BYA Río Cuarto, Córdoba, Argentina
| | - Mirta B García de Lema
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, CPX5804BYA Río Cuarto, Córdoba, Argentina
| | - Marta S Dardanelli
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, CPX5804BYA Río Cuarto, Córdoba, Argentina
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Gonzalez-Martinez A, Rodriguez-Sanchez A, Muñoz-Palazon B, Garcia-Ruiz MJ, Osorio F, van Loosdrecht MCM, Gonzalez-Lopez J. Microbial community analysis of a full-scale DEMON bioreactor. Bioprocess Biosyst Eng 2014; 38:499-508. [PMID: 25245398 DOI: 10.1007/s00449-014-1289-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 09/16/2014] [Indexed: 12/28/2022]
Abstract
Full-scale applications of autotrophic nitrogen removal technologies for the treatment of digested sludge liquor have proliferated during the last decade. Among these technologies, the aerobic/anoxic deammonification process (DEMON) is one of the major applied processes. This technology achieves nitrogen removal from wastewater through anammox metabolism inside a single bioreactor due to alternating cycles of aeration. To date, microbial community composition of full-scale DEMON bioreactors have never been reported. In this study, bacterial community structure of a full-scale DEMON bioreactor located at the Apeldoorn wastewater treatment plant was analyzed using pyrosequencing. This technique provided a higher-resolution study of the bacterial assemblage of the system compared to other techniques used in lab-scale DEMON bioreactors. Results showed that the DEMON bioreactor was a complex ecosystem where ammonium oxidizing bacteria, anammox bacteria and many other bacterial phylotypes coexist. The potential ecological role of all phylotypes found was discussed. Thus, metagenomic analysis through pyrosequencing offered new perspectives over the functioning of the DEMON bioreactor by exhaustive identification of microorganisms, which play a key role in the performance of bioreactors. In this way, pyrosequencing has been proven as a helpful tool for the in-depth investigation of the functioning of bioreactors at microbiological scale.
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Bafana A. Diversity and metabolic potential of culturable root-associated bacteria from Origanum vulgare in sub-Himalayan region. World J Microbiol Biotechnol 2012; 29:63-74. [PMID: 22927014 DOI: 10.1007/s11274-012-1158-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 08/17/2012] [Indexed: 11/28/2022]
Abstract
Study of rhizospheric bacteria from important plants is very essential, as they are known to influence plant growth and productivity, and also produce industrially important metabolites. Origanum vulgare is a perennial medicinal aromatic plant rich in phenolic antioxidants. Present study investigates the diversity of culturable root-associated bacteria from this plant in Palampur, India, which constitutes a unique ecosystem due to high rain fall, wide temperature fluctuations and acidic soil. Both root endophytes and rhizospheric soil bacteria were isolated, which resulted in a total of 120 morphologically different isolates. They were found to group into 21 phylotypes based on restriction fragment length polymorphism analysis. Growth medium composition had significant effect on the diversity of the isolated bacterial populations. The isolates were characterized for various metabolic, plant growth promoting (PGP) and other biotechnologically useful activities, based on which they were clustered into groups by principal component analysis. Majority of the isolates belonged to γ-Proteobacteria and Firmicutes. Pseudomonas and Stenotrophomonas were the most dominant species and together constituted 27.5 % of the total isolates. Many isolates, especially γ-Proteobacteria, showed very high PGP activities. Few isolates exhibited very high antioxidant activity, which may find potential applications in food and health industries. Firmicutes were catabolically the most versatile group and produced several hydrolytic enzymes. To the best of our knowledge, it is the first study describing rhizospheric microbial community of O. vulgare.
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Affiliation(s)
- Amit Bafana
- Biotechnology Division, Institute of Himalayan Bioresource Technology (IHBT), Council of Scientific and Industrial Research (CSIR), Palampur 176061, India.
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Application of targeted metagenomics to explore abundance and diversity of CO₂-fixing bacterial community using cbbL gene from the rhizosphere of Arachis hypogaea. Gene 2012; 506:18-24. [PMID: 22766402 DOI: 10.1016/j.gene.2012.06.083] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 06/25/2012] [Indexed: 11/23/2022]
Abstract
Sequestration of CO(2) by autotrophic bacteria is a key process of biogeochemical carbon cycling in soil ecosystem. Rhizosphere is a rich niche of microbial activity and diversity, influenced by change in atmospheric CO(2). Structural changes in rhizosphere composition influence microbial communities and the nutrient cycling. In the present study, the bacterial diversity and population dynamics were established using cbbL and 16S rRNA gene targeted metagenomics approach from the rhizosphere of Arachis hypogaea. A total of 108 cbbL clones were obtained from the rhizospheric soil which revealed predominance of cbbL sequences affiliated to Rhizobium leguminosarum, Bradyrhizobium sp., Sinorhizobium meliloti, Ochrobactrum anthropi and a variety of uncultured cbbL harboring bacteria. The 16S rRNA gene clone library exhibited the dominance of Firmicutes (34.4%), Proteobacteria (18.3%), Actinobacteria (17.2%) and Bacteroidetes (16.1%). About 43% nucleotide sequences of 16S rRNA gene clone library were novel genera which showed <95% homology with published sequences. Gene copy number of cbbL and 16S rRNA genes, determined by quantitative real-time PCR (qRT PCR), was 9.38 ± 0.75 × 10(7) and 5.43 ± 0.79 × 10(8) (per g dry soil), respectively. The results exhibited bacterial community structure with high bacterial diversity and abundance of CO(2)-fixing bacteria, which can be explored further for their role in carbon cycling, sustainable agriculture and environment management.
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