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Li F, Sun A, Jiao X, Yu DT, Ren P, Wu BX, He P, Bi L, He JZ, Hu HW. Nitrogenous fertilizer plays a more important role than cultivars in shaping sorghum-associated microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 943:173831. [PMID: 38866152 DOI: 10.1016/j.scitotenv.2024.173831] [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: 04/02/2024] [Revised: 05/25/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
The plant microbiome plays a crucial role in facilitating plant growth through enhancing nutrient cycling, acquisition and transport, as well as alleviating stresses induced by nutrient limitations. Despite its significance, the relative importance of common agronomic practices, such as nitrogenous fertilizer, in shaping the plant microbiome across different cultivars remains unclear. This study investigated the dynamics of bacterial and fungal communities in leaf, root, rhizosphere, and bulk soil in response to nitrogenous fertilizer across ten sorghum varieties, using 16S rRNA and ITS gene amplicon sequencing, respectively. Our results revealed that nitrogen addition had a greater impact on sorghum-associated microbial communities compared to cultivar. Nitrogen addition significantly reduced bacterial diversity in all compartments except for the root endophytes. However, N addition significantly increased fungal diversity in both rhizosphere and bulk soils, while significantly reducing fungal diversity in the root endophytes. Furthermore, N addition significantly altered the community composition of bacteria and fungi in all four compartments, while cultivars only affected the community composition of root endosphere bacteria and fungi. Network analysis revealed that fertilization significantly reduced microbial network complexity and increased fungal-related network complexity. Collectively, this study provides empirical evidence that sorghum-associated microbiomes are predominantly shaped by nitrogenous fertilizer rather than by cultivars, suggesting that consistent application of nitrogenous fertilizer will ultimately alter plant-associated microbiomes regardless of cultivar selection.
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Affiliation(s)
- Fangfang Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Anqi Sun
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiaoyan Jiao
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Dan-Ting Yu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China.
| | - Peixin Ren
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Bing-Xue Wu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Peng He
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Li Bi
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ji-Zheng He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Dumigan CR, Deyholos MK. Soil and seed both influence bacterial diversity in the microbiome of the Cannabis sativa seedling endosphere. FRONTIERS IN PLANT SCIENCE 2024; 15:1326294. [PMID: 38450399 PMCID: PMC10914941 DOI: 10.3389/fpls.2024.1326294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/02/2024] [Indexed: 03/08/2024]
Abstract
Introduction Phytobiomes have a significant impact on plant health. The microbiome of Cannabis sativa is particularly interesting both because of renewed interest in this crop and because it is commercially propagated in two different ways (i.e. clonally and by seed). Angiosperms obtain a founding population of seed-borne endophytes from their seed-bearing parent. This study examines the influence of both seed and soil-derived bacteria on the endospheres of cannabis seedlings of both hemp- and drug-types. Methods A multi-factorial metagenomic study was conducted with three cannabis genotypes and two soil sources, which were tested both before and after autoclave sterilization. Seedlings were grown on soil, then rinsed and surface-sterilized, and 16S rDNA amplicons from seedling endophytes were sequenced, taxonomically classified, and used to estimate alpha- and beta-diversity in Qiime2. The statistical significance of differences in seedling microbiomes across treatments was tested, and PiCRUST2 was used to infer the functional relevance of these differences. Results Soil was found to have a profound effect on the alpha-diversity, beta-diversity, relative abundance, and functional genes of endophytic bacteria in germinating cannabis seedlings. Additionally, there was a significant effect of cannabis genotype on beta diversity, especially when genotypes were grown in sterilized soil. Gammaproteobacteria and Bacilli were the two most abundant taxa and were found in all genotypes and soil types, including sterilized soil. Discussion The results indicated that a component of cannabis seedling endosphere microbiomes is seed-derived and conserved across the environments tested. Functional prediction of seedling endophytes using piCRUST suggested a number of important functions of seed-borne endophytes in cannabis including nutrient and amino acid cycling, hormone regulation, and as precursors to antibiotics. This study suggested both seed and soil play a critical role in shaping the microbiome of germinating cannabis seedlings.
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Affiliation(s)
| | - Michael K. Deyholos
- Department of Biology, Faculty of Science, University of British Columbia, Kelowna, BC, Canada
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Massuela DC, Munz S, Hartung J, Nkebiwe PM, Graeff-Hönninger S. Cannabis Hunger Games: nutrient stress induction in flowering stage - impact of organic and mineral fertilizer levels on biomass, cannabidiol (CBD) yield and nutrient use efficiency. FRONTIERS IN PLANT SCIENCE 2023; 14:1233232. [PMID: 37794933 PMCID: PMC10547009 DOI: 10.3389/fpls.2023.1233232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/11/2023] [Indexed: 10/06/2023]
Abstract
Indoor medicinal cannabis cultivation systems enable year-round cultivation and better control of growing factors, however, such systems are energy and resource intensive. Nutrient deprivation during flowering can trigger nutrient translocation and modulate the production of cannabinoids, which might increase agronomic nutrient use efficiency, and thus, a more sustainable use of fertilizers. This experiment compares two fertilizer types (mineral and organic) applied in three dilutions (80, 160 and 240 mg N L-1) to evaluate the effect of nutrient deprivation during flowering on biomass, Cannabidiol (CBD) yield and nutrient use efficiency of N, P and K. This is the first study showing the potential to reduce fertilizer input while maintaining CBD yield of medicinal cannabis. Under nutrient stress, inflorescence yield was significantly lower at the final harvest, however, this was compensated by a higher CBD concentration, resulting in 95% of CBD yield using one-third less fertilizer. The higher nutrient use efficiency of N, P, and K in nutrient-deprived plants was achieved by a larger mobilization and translocation of nutrients increasing the utilization efficiency of acquired nutrients. The agronomic nutrient use efficiency of CBD yield - for N and K - increased 34% for the organic fertilizers and 72% for the mineral fertilizers comparing the dilution with one-third less nutrients (160) with the highest nutrient concentration (240). Differences in CBD yield between fertilizer types occurred only at the final harvest indicating limitations in nutrient uptake due to nutrient forms in the organic fertilizer. Our results showed a lower acquisition and utilization efficiency for the organic fertilizer, proposing the necessity to improve either the timing of bio-availability of organic fertilizers or the use of soil amendments.
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Affiliation(s)
| | - Sebastian Munz
- Agronomy, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Jens Hartung
- Biostatistics, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Peteh Mehdi Nkebiwe
- Department of Fertilization and Soil Matter Dynamics, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
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Ahmed B, Beneš F, Hajšlová J, Fišarová L, Vosátka M, Hijri M. Enhanced production of select phytocannabinoids in medical Cannabis cultivars using microbial consortia. FRONTIERS IN PLANT SCIENCE 2023; 14:1219836. [PMID: 37719209 PMCID: PMC10502174 DOI: 10.3389/fpls.2023.1219836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/09/2023] [Indexed: 09/19/2023]
Abstract
The root microbiome of medical cannabis plants has been largely unexplored due to past legal restrictions in many countries. Microbes that live on and within the tissue of Cannabis sativa L. similar to other plants, provide advantages such as stimulating plant growth, helping it absorb minerals, providing protection against pathogen attacks, and influencing the production of secondary metabolites. To gain insight into the microbial communities of C. sativa cultivars with different tetrahydrocannabinol (THC) and cannabidiol (CBD) profiles, a greenhouse trial was carried out with and without inoculants added to the growth substrate. Illumina MiSeq metabarcoding was used to analyze the root and rhizosphere microbiomes of the five cultivars. Plant biomass production showed higher levels in three of five cultivars inoculated with the arbuscular mycorrhizal fungus Rhizophagus irregularis and microbial suspension. The blossom dry weight of the cultivar THE was greater when inoculated with R. irregularis and microbial suspension than with no inoculation. Increasing plant biomass and blossom dry weight are two important parameters for producing cannabis for medical applications. In mature Cannabis, 12 phytocannabinoid compounds varied among cultivars and were affected by inoculants. Significant differences (p ≤ 0.01) in concentrations of cannabidivarinic acid (CBDVA), cannabidivarin (CBDV), cannabigerol (CBG), cannabidiol (CBD), and cannabigerolic acid (CBGA) were observed in all Cannabis cultivars when amended with F, K1, and K2 inoculants. We found microbes that were shared among cultivars. For example, Terrimicrobium sp., Actinoplanes sp., and Trichoderma reesei were shared by the cultivars ECC-EUS-THE, CCL-ECC, and EUS-THE, respectively. Actinoplanes sp. is a known species that produces phosphatase enzymes, while Trichoderma reesei is a fungal train that produces cellulase and contributes to organic matter mineralization. However, the role of Terrimicrobium sp. as an anaerobic bacterium remains unknown. This study demonstrated that the use of inoculants had an impact on the production of phytocannabinoids in five Cannabis cultivars. These inoculants could have useful applications for optimizing cannabis cultivation practices and increasing the production of phytocannabinoids.
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Affiliation(s)
- Bulbul Ahmed
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, Canada
| | - František Beneš
- Department of Food Analysis and Nutrition, University of Chemistry and Technology, Prague, Czechia
| | - Jana Hajšlová
- Department of Food Analysis and Nutrition, University of Chemistry and Technology, Prague, Czechia
| | - Lenka Fišarová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Miroslav Vosátka
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Mohamed Hijri
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, Canada
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AL Ubeed HMS, Wills RBH, Chandrapala J. Post-Harvest Operations to Generate High-Quality Medicinal Cannabis Products: A Systemic Review. Molecules 2022; 27:1719. [PMID: 35268820 PMCID: PMC8911901 DOI: 10.3390/molecules27051719] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 01/30/2023] Open
Abstract
The traditional Cannabis plant as a medicinal crop has been explored for many thousands of years. The Cannabis industry is rapidly growing; therefore, optimising drying methods and producing high-quality medical products have been a hot topic in recent years. We systemically analysed the current literature and drew a critical summary of the drying methods implemented thus far to preserve the quality of bioactive compounds from medicinal Cannabis. Different drying techniques have been one of the focal points during the post-harvesting operations, as drying preserves these Cannabis products with increased shelf life. We followed or even highlighted the most popular methods used. Drying methods have advanced from traditional hot air and oven drying methods to microwave-assisted hot air drying or freeze-drying. In this review, traditional and modern drying technologies are reviewed. Each technology will have different pros and cons of its own. Moreover, this review outlines the quality of the Cannabis plant component harvested plays a major role in drying efficiency and preserving the chemical constituents. The emergence of medical Cannabis, and cannabinoid research requires optimal post-harvesting processes for different Cannabis strains. We proposed the most suitable method for drying medicinal Cannabis to produce consistent, reliable and potent medicinal Cannabis. In addition, drying temperature, rate of drying, mode and storage conditions after drying influenced the Cannabis component retention and quality.
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Affiliation(s)
- Hebah Muhsien Sabiah AL Ubeed
- School of Science, College of Sciences, Engineering, Computing Technologies and Health and Medical Sciences, RMIT University, Bundoora, Melbourne, VIC 3083, Australia;
| | - Ronald B. H. Wills
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW 2258, Australia;
| | - Jayani Chandrapala
- School of Science, College of Sciences, Engineering, Computing Technologies and Health and Medical Sciences, RMIT University, Bundoora, Melbourne, VIC 3083, Australia;
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Balthazar C, Joly DL, Filion M. Exploiting Beneficial Pseudomonas spp. for Cannabis Production. Front Microbiol 2022; 12:833172. [PMID: 35095829 PMCID: PMC8795690 DOI: 10.3389/fmicb.2021.833172] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022] Open
Abstract
Among the oldest domesticated crops, cannabis plants (Cannabis sativa L., marijuana and hemp) have been used to produce food, fiber, and drugs for thousands of years. With the ongoing legalization of cannabis in several jurisdictions worldwide, a new high-value market is emerging for the supply of marijuana and hemp products. This creates unprecedented challenges to achieve better yields and environmental sustainability, while lowering production costs. In this review, we discuss the opportunities and challenges pertaining to the use of beneficial Pseudomonas spp. bacteria as crop inoculants to improve productivity. The prevalence and diversity of naturally occurring Pseudomonas strains within the cannabis microbiome is overviewed, followed by their potential mechanisms involved in plant growth promotion and tolerance to abiotic and biotic stresses. Emphasis is placed on specific aspects relevant for hemp and marijuana crops in various production systems. Finally, factors likely to influence inoculant efficacy are provided, along with strategies to identify promising strains, overcome commercialization bottlenecks, and design adapted formulations. This work aims at supporting the development of the cannabis industry in a sustainable way, by exploiting the many beneficial attributes of Pseudomonas spp.
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Affiliation(s)
- Carole Balthazar
- Department of Biology, Faculty of Sciences, Université de Moncton, Moncton, NB, Canada
| | - David L. Joly
- Department of Biology, Faculty of Sciences, Université de Moncton, Moncton, NB, Canada
| | - Martin Filion
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
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7
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Park SH, Pauli CS, Gostin EL, Staples SK, Seifried D, Kinney C, Vanden Heuvel BD. Effects of short-term environmental stresses on the onset of cannabinoid production in young immature flowers of industrial hemp (Cannabis sativa L.). J Cannabis Res 2022; 4:1. [PMID: 34980266 PMCID: PMC8725245 DOI: 10.1186/s42238-021-00111-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUNDS Cannabis sativa L. produces at least 120 cannabinoids. Although genetic variation is the main factor in cannabinoid production, the effects of short-term environmental stresses in the early flowering stage remains largely unknown. METHODS To investigate the effects of short-term environmental stresses on the onset of cannabinoid production in young immature flowers, a hemp variety, Green-Thunder (5-8% CBD/mg of dry weight), was treated with mechanical damage, insect herbivory, extreme heat, or drought stress for 5-7 days during the first 2 weeks of flowering. Three hemp tissues, including flowers, leaves, and stems, were collected from hemp grown under these stress conditions at multiple time points during the first 2 weeks after transition to the short photoperiod and analyzed using high pressure liquid chromatography to quantify phytocannabinoids including cannabigerolic acid (CBGA), cannabigerol (CBG), cannabidiolic acid (CBDA), cannabidiol (CBD), Δ-tetrahydrocannabinolic acid (THCA), Δ-tetrahydrocannabinol (THC), and cannabinol (CBN). RESULTS The 5 days of mechanical wounding did not affect the production of any of the cannabinoids during the initial stage of flowering. However, after 5 days of herbivore treatment, there was a significant difference in concentration between day 1 and day 6 of CBGA (control: 308 μg/g; treatment - 24 μg/g), CBG (control: 69 μg/g; treatment: 52 μg/g), and CBD (control: 755 μg/g; treatment: 194 μg/g) between the control and treatment plants. The 7 days of heat treatment at 45-50 oC significantly reduced the production of CBGA during this observed window (control: 206 μg/g; treatment: 182 μg/g) and CBG (control: 21 μg/g; treatment: - 112 μg/g). Notably, the largest change was observed after 7 days of drought stress, when plants showed a 40% greater accumulation of CBG (control: 336 μg/g; treatment: 622 μg/g), and a significant decrease (70-80%) in CBD (control: 1182 μg/g; treatment: 297 μg/g) and THC amounts (control: 3927 μg/g; treatment: 580 μg/g). CONCLUSIONS Although this observation is limited in the early flowering stage, the common field stresses are adequate to induce changes in the cannabinoid profiles, particularly drought stress being the most impactful stress for hemp flower initiation with the altering the cannabinoid production by decreasing CBD and THC accumulation while increasing CBG by 40%.
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Affiliation(s)
- Sang-Hyuck Park
- Institute of Cannabis Research, Colorado State University-Pueblo, 2200 Bonforte Blvd., Pueblo, CO, 81001, USA.
- Department of Biology, Colorado State University-Pueblo, 2200 Bonforte Blvd., Pueblo, CO, 81001, USA.
| | - Christopher S Pauli
- Institute of Cannabis Research, Colorado State University-Pueblo, 2200 Bonforte Blvd., Pueblo, CO, 81001, USA
| | - Eric L Gostin
- Department of Biology, Colorado State University-Pueblo, 2200 Bonforte Blvd., Pueblo, CO, 81001, USA
| | - S Kyle Staples
- Department of Biology, Colorado State University-Pueblo, 2200 Bonforte Blvd., Pueblo, CO, 81001, USA
| | - Dustin Seifried
- Department of Chemistry, Colorado State University-Pueblo, 2200 Bonforte Blvd., Pueblo, CO, 81001, USA
| | - Chad Kinney
- Institute of Cannabis Research, Colorado State University-Pueblo, 2200 Bonforte Blvd., Pueblo, CO, 81001, USA
- Department of Chemistry, Colorado State University-Pueblo, 2200 Bonforte Blvd., Pueblo, CO, 81001, USA
| | - Brian D Vanden Heuvel
- Department of Biology, Colorado State University-Pueblo, 2200 Bonforte Blvd., Pueblo, CO, 81001, USA
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Ahmed B, Smart LB, Hijri M. Microbiome of Field Grown Hemp Reveals Potential Microbial Interactions With Root and Rhizosphere Soil. Front Microbiol 2021; 12:741597. [PMID: 34867858 PMCID: PMC8634612 DOI: 10.3389/fmicb.2021.741597] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022] Open
Abstract
Hemp (Cannabis sativa L.) is a crop bred and grown for the production of fiber, grain, and floral extracts that contribute to health and wellness. Hemp plants interact with a myriad of microbiota inhabiting the phyllosphere, endosphere, rhizoplane, and rhizosphere. These microbes offer many ecological services, particularly those of below ground biotopes which are involved in nutrient cycling, uptake, and alleviating biotic and abiotic stress. The microbiota communities of the hemp rhizosphere in the field are not well documented. To discover core microbiota associated with field grown hemp, we cultivated single C. sativa cultivar, “TJ’s CBD,” in six different fields in New York and sampled hemp roots and their rhizospheric soil. We used Illumina MiSeq amplicon sequencing targeting 16S ribosomal DNA of bacteria and ITS of fungi to study microbial community structure of hemp roots and rhizospheres. We found that Planctobacteria and Ascomycota dominated the taxonomic composition of hemp associated microbial community. We identified potential core microbiota in each community (bacteria: eight bacterial amplicon sequence variant – ASV, identified as Gimesia maris, Pirellula sp. Lacipirellula limnantheis, Gemmata sp. and unclassified Planctobacteria; fungi: three ASVs identified as Fusarium oxysporum, Gibellulopsis piscis, and Mortierella minutissima). We found 14 ASVs as hub taxa [eight bacterial ASVs (BASV) in the root, and four bacterial and two fungal ASVs in the rhizosphere soil], and 10 BASV connected the root and rhizosphere soil microbiota to form an extended microbial communication in hemp. The only hub taxa detected in both the root and rhizosphere soil microbiota was ASV37 (Caulifigura coniformis), a bacterial taxon. The core microbiota and Network hub taxa can be studied further for biocontrol activities and functional investigations in the formulation of hemp bioinoculants. This study documented the microbial diversity and community structure of hemp grown in six fields, which could contribute toward the development of bioinoculants for hemp that could be used in organic farming.
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Affiliation(s)
- Bulbul Ahmed
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, Canada.,Horticulture Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, United States
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, United States
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, Canada.,African Genome Center, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
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9
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Wei G, Ning K, Zhang G, Yu H, Yang S, Dai F, Dong L, Chen S. Compartment Niche Shapes the Assembly and Network of Cannabis sativa-Associated Microbiome. Front Microbiol 2021; 12:714993. [PMID: 34675893 PMCID: PMC8524047 DOI: 10.3389/fmicb.2021.714993] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Interactions between plants and microbes may promote the growth of plants and regulate the production of secondary metabolites. Hemp (Cannabis sativa) is an annual herb and an important commercial crop. However, the assembly and network of hemp-associated microbiomes inhabiting in soil and plant compartments have not been comprehensively understood. This work investigated the assembly and network of bacterial and fungal communities living in soils (bulk and rhizosphere) and plant compartments (root, stem, leaf, and flower) of four hemp ecotypes cultivated in the same habitat. Microbiome assembly was predominantly shaped by compartment niche. Microbial alpha diversity was the highest in soil, continually decreased from root to flower. Core bacterial genera Pseudomonas, Bacillus, Rhizobium, Planococcus, and Sphingomonas were mostly enriched in aerial endosphere niches; Clitopilus, Plectosphaerella, and Mortierella were enriched in belowground endosphere. Microbial network complexity and connectivity decreased from root to flower. According to source tracking analysis, hemp microbiota primarily originated from soil and were subsequently filtered in different plant compartments. This work provides details on hemp-associated microbiome along the soil-plant continuum and a comprehensive understanding of the origin and transmission mode of endophytes in hemp.
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Affiliation(s)
- Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Kang Ning
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Haibin Yu
- Yunnan Industrial Investment Group, Yunnan Hemp Seed Industry Co., Ltd., Kunming, China
| | - Shuming Yang
- Yunnan Industrial Investment Group, Yunnan Hemp Seed Industry Co., Ltd., Kunming, China
| | - Fei Dai
- Yunnan Industrial Investment Group, Yunnan Hemp Seed Industry Co., Ltd., Kunming, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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10
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Comeau D, Balthazar C, Novinscak A, Bouhamdani N, Joly DL, Filion M. Interactions Between Bacillus Spp., Pseudomonas Spp. and Cannabis sativa Promote Plant Growth. Front Microbiol 2021; 12:715758. [PMID: 34616381 PMCID: PMC8488376 DOI: 10.3389/fmicb.2021.715758] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) deploy several mechanisms to improve plant health, growth and yield. The aim of this study was to evaluate the efficacy of two Pseudomonas spp. strains and three Bacillus spp. strains used as single treatments and in consortia to improve the yield of Cannabis sativa and characterize the impact of these treatments on the diversity, structure and functions of the rhizosphere microbiome. Herein, we demonstrate a significant C. sativa yield increase up to 70% when inoculated with three different Pseudomonas spp./Bacillus spp. consortia but not with single inoculation treatments. This growth-promoting effect was observed in two different commercial soil substrates commonly used to grow cannabis: Promix and Canna coco. Marker-based genomic analysis highlighted Bacillus spp. as the main modulator of the rhizosphere microbiome diversity and Pseudomonas spp. as being strongly associated with plant growth promotion. We describe an increase abundance of predicted PGPR metabolic pathways linked with growth-promoting interactions in C. sativa.
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Affiliation(s)
- Dominique Comeau
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | - Carole Balthazar
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | - Amy Novinscak
- Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, BC, Canada
| | - Nadia Bouhamdani
- Department of Chemistry and Biochemistry, University of Moncton, Moncton, NB, Canada
| | - David L Joly
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | - Martin Filion
- Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
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11
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Ahmed B, Hijri M. Potential impacts of soil microbiota manipulation on secondary metabolites production in cannabis. J Cannabis Res 2021; 3:25. [PMID: 34217364 PMCID: PMC8254954 DOI: 10.1186/s42238-021-00082-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/22/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Cannabis growing practices and particularly indoor cultivation conditions have a great influence on the production of cannabinoids. Plant-associated microbes may affect nutrient acquisition by the plant. However, beneficial microbes influencing cannabinoid biosynthesis remain largely unexplored and unexploited in cannabis production. OBJECTIVE To summarize study outcomes on bacterial and fungal communities associated with cannabis using high-throughput sequencing technologies and to uncover microbial interactions, species diversity, and microbial network connections that potentially influence secondary metabolite production in cannabis. MATERIALS AND METHOD A mini review was conducted including recent publications on cannabis and their associated microbiota and secondary metabolite production. RESULTS In this review, we provide an overview of the potential role of the soil microbiome in production of cannabinoids, and discussed that manipulation of cannabis-associated microbiome obtained through soil amendment interventions of diversified microbial communities sourced from natural forest soil could potentially help producers of cannabis to improve yields of cannabinoids and enhance the balance of cannabidiol (CBD) and tetrahydrocannabinol (THC) proportions. CONCLUSION Cannabis is one of the oldest cultivated crops in history, grown for food, fiber, and drugs for thousands of years. Extension of genetic variation in cannabis has developed into wide-ranging varieties with various complementary phenotypes and secondary metabolites. For medical or pharmaceutical purposes, the ratio of CBD to THC is key. Therefore, studying soil microbiota associated with cannabis and its potential impact on secondary metabolites production could be useful when selecting microorganisms as bioinoculant agents for enhanced organic cannabinoid production.
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Affiliation(s)
- Bulbul Ahmed
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada.
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Ben Guerir, Morocco.
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12
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Lei F, Liu X, Huang H, Fu S, Zou K, Zhang S, Zhou L, Zeng J, Liu H, Jiang L, Miao B, Liang Y. The Macleaya cordata Symbiont: Revealing the Effects of Plant Niches and Alkaloids on the Bacterial Community. Front Microbiol 2021; 12:681210. [PMID: 34177865 PMCID: PMC8219869 DOI: 10.3389/fmicb.2021.681210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
Endophytes are highly associated with plant growth and health. Exploring the variation of bacterial communities in different plant niches is essential for understanding microbe-plant interactions. In this study, high-throughput gene sequencing was used to analyze the composition and abundance of bacteria from the rhizospheric soil and different parts of the Macleaya cordata. The results indicated that the bacterial community structure varied widely among compartments. Bacterial diversity was observed to be the highest in the rhizospheric soil and the lowest in fruits. Proteobacteria, Actinobacteria, and Bacteroidetes were found as the dominant phyla. The genera Sphingomonas (∼47.77%) and Methylobacterium (∼45.25%) dominated in fruits and leaves, respectively. High-performance liquid chromatography (HPLC) was employed to measure the alkaloid content of different plant parts. Significant correlations were observed between endophytic bacteria and alkaloids. Especially, Sphingomonas showed a significant positive correlation with sanguinarine and chelerythrine. All four alkaloids were negatively correlated with the microbiota of stems. The predicted result of PICRUST2 revealed that the synthesis of plant alkaloids might lead to a higher abundance of endophytic microorganisms with genes related to alkaloid synthesis, further demonstrated the correlation between bacterial communities and alkaloids. This study provided the first insight into the bacterial community composition in different parts of Macleaya cordata and the correlation between the endophytic bacteria and alkaloids.
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Affiliation(s)
- Fangying Lei
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Haonan Huang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shaodong Fu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Kai Zou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Li Zhou
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Jianguo Zeng
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Luhua Jiang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
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13
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Profiling, isolation and characterisation of beneficial microbes from the seed microbiomes of drought tolerant wheat. Sci Rep 2021; 11:11916. [PMID: 34099781 PMCID: PMC8184954 DOI: 10.1038/s41598-021-91351-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 05/18/2021] [Indexed: 11/09/2022] Open
Abstract
Climate change is predicted to increase the incidence and severity of drought conditions, posing a significant challenge for agriculture globally. Plant microbiomes have been demonstrated to aid crop species in the mitigation of drought stress. The study investigated the differences between the seed microbiomes of drought tolerant and drought susceptible wheat lines. Furthermore, it highlighted and quantified the degree of drought tolerance conferred by specific microbes isolated from drought tolerant wheat seed microbiomes. Metagenomic and culture-based methods were used to profile and characterise the seed microbiome composition of drought tolerant and drought susceptible wheat lines under rainfed and drought conditions. Isolates from certain genera were enriched by drought tolerant wheat lines when placed under drought stress. Wheat inoculated with isolates from these targeted genera, such as Curtobacterium flaccumfaciens (Cf D3-25) and Arthrobacter sp. (Ar sp. D4-14) demonstrated the ability to promote growth under drought conditions. This study indicates seed microbiomes from genetically distinct wheat lines enrich for beneficial bacteria in ways that are both line-specific and responsive to environmental stress. As such, seed from stress-phenotyped lines represent an invaluable resource for the identification of beneficial microbes with plant growth promoting activity that could improve commercial crop production.
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14
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Peng H, Shahidi F. Cannabis and Cannabis Edibles: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1751-1774. [PMID: 33555188 DOI: 10.1021/acs.jafc.0c07472] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cannabis is an excellent natural source of fiber and various bioactive cannabinoids. So far, at least 120 cannabinoids have been identified, and more novel cannabinoids are gradually being unveiled by detailed cannabis studies. However, cannabinoids in both natural and isolated forms are especially vulnerable to oxygen, heat, and light. Therefore, a diversity of cannabinoids is associated with their chemical instability to a large extent. The research status of structural conversion of cannabinoids is introduced. On the other hand, the use of drug-type cannabis and the phytocannabinoids thereof has been rapidly popularized and plays an indispensable role in both medical therapy and daily recreation. The recent legalization of edible cannabis further extends its application into the food industry. The varieties of legal edible cannabis products in the current commercial market are relatively monotonous due to rigorous restrictions under the framework of Cannabis Regulations and infancy of novel developments. Meanwhile, patents/studies related to the safety and quality assurance systems of cannabis edibles are still rare and need to be developed. Furthermore, along with cannabinoids, many phytochemicals such as flavonoids, lignans, terpenoids, and polysaccharides exist in the cannabis matrix, and these may exhibit prebiotic/probiotic properties and improve the composition of the gut microbiome. During metabolism and excretion, the bioactive phytochemicals of cannabis, mostly the cannabinoids, may be structurally modified during enterohepatic detoxification and gut fermentation. However, the potential adverse effects of both acute and chronic exposure to cannabinoids and their vulnerable groups have been clearly recognized. Therefore, a comprehensive understanding of the chemistry, metabolism, toxicity, commercialization, and regulations regarding cannabinoid edibles is reviewed and updated in this contribution.
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Affiliation(s)
- Han Peng
- Department of Biochemistry Memorial University of Newfoundland, St. John's, Newfoundland, Canada A1B 3X9
| | - Fereidoon Shahidi
- Department of Biochemistry Memorial University of Newfoundland, St. John's, Newfoundland, Canada A1B 3X9
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15
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Montoya Z, Conroy M, Vanden Heuvel BD, Pauli CS, Park SH. Cannabis Contaminants Limit Pharmacological Use of Cannabidiol. Front Pharmacol 2020; 11:571832. [PMID: 33013414 PMCID: PMC7516211 DOI: 10.3389/fphar.2020.571832] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/25/2020] [Indexed: 01/15/2023] Open
Abstract
For nearly a century, Cannabis has been stigmatized and criminalized across the globe, but in recent years, there has been a growing interest in Cannabis due to the therapeutic potential of phytocannabinoids. With this emerging interest in Cannabis, concerns have arisen about the possible contaminations of hemp with pesticides, heavy metals, microbial pathogens, and carcinogenic compounds during the cultivation, manufacturing, and packaging processes. This is of particular concern for those turning to Cannabis for medicinal purposes, especially those with compromised immune systems. This review aims to provide types of contaminants and examples of Cannabis contamination using case studies that elucidate the medical consequences consumers risk when using adulterated Cannabis products. Thus, it is imperative to develop universal standards for cultivation and testing of products to protect those who consume Cannabis.
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Affiliation(s)
- Zackary Montoya
- Institute of Cannabis Research, Colorado State University-Pueblo, Pueblo, CO, United States
| | - Matthieu Conroy
- Institute of Cannabis Research, Colorado State University-Pueblo, Pueblo, CO, United States
| | | | - Christopher S Pauli
- Institute of Cannabis Research, Colorado State University-Pueblo, Pueblo, CO, United States
| | - Sang-Hyuck Park
- Institute of Cannabis Research, Colorado State University-Pueblo, Pueblo, CO, United States
- Department of Biology, Colorado State University-Pueblo, Pueblo, CO, United States
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16
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Zverev AO, Pershina EV, Shapkin VM, Kichko AK, Mitrofanova OP, Kobylyanskii VD, Yuzikhin OS, Belimov AA, Andronov EE. Molecular Analysis of the Rhizosphere Microbial Communities from Gramineous Plants Grown on Contrasting Soils. Microbiology (Reading) 2020. [DOI: 10.1134/s002626172001018x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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17
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Comeau D, Novinscak A, Joly DL, Filion M. Spatio-Temporal and Cultivar-Dependent Variations in the Cannabis Microbiome. Front Microbiol 2020; 11:491. [PMID: 32265895 PMCID: PMC7105690 DOI: 10.3389/fmicb.2020.00491] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/06/2020] [Indexed: 11/13/2022] Open
Abstract
The incipient legalization and commercialization of Cannabis sativa in Canada have promulgated research into characterizing the plant’s microbiome as it promotes many facets of plant growth and health. The emblematic production of commercially important secondary metabolites, namely tetrahydrocannabinol (THC), cannabidiol (CBD) and terpenes, has warranted investigating the modulating capacity of these molecules on the plant microbiome. C. sativa cultivars can be classified into chemotypes depending on the relative levels of THC and CBD they produce; their biosynthesis also varies spatially and temporally during the life cycle of the plant. To study the differential microbiome structure and diversity between cultivars in a spatio-temporal manner, we extracted microbial DNA from the rhizosphere, endorhizosphere, and phyllosphere during the entire life cycle of three different chemotypes; CBD Yummy (<1% THC/13% CBD), CBD shark (6% THC/10% CBD) and Hash (14% THC/ < 1% CBD). Illumina marker gene sequencing of bacterial (16S) and fungal (ITS) communities were coupled to the QIIME2, PICRUSt, and LEfSe pipelines for analysis. Our study describes spatio-temporal and cultivar-dependent variations in the fungal and bacterial microbiome of C. sativa, and details strong cultivar-dependent variance in the belowground microbiome. Furthermore, the predicted pathway abundance of the bacterial microbiome is concomitantly subject to spatio-temporal variations; pathways related to lipid, amino acid, glucose and pentose metabolism were noteworthy. These results describe, for the first time, spatio-temporal and cultivar-dependent variations in the microbiome of C. sativa produced under strict commercial settings. Describing the microbiome is the first step in discoveries that could help in engineering a plant growth and health promoting microbiome in future works.
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Affiliation(s)
- Dominique Comeau
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | - Amy Novinscak
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | - David L Joly
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | - Martin Filion
- Department of Biology, University of Moncton, Moncton, NB, Canada
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18
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Taghinasab M, Jabaji S. Cannabis Microbiome and the Role of Endophytes in Modulating the Production of Secondary Metabolites: An Overview. Microorganisms 2020; 8:E355. [PMID: 32131457 PMCID: PMC7143057 DOI: 10.3390/microorganisms8030355] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/19/2022] Open
Abstract
Plants, including cannabis (Cannabis sativa subsp. sativa), host distinct beneficial microbial communities on and inside their tissues and organs, including seeds. They contribute to plant growth, facilitating mineral nutrient uptake, inducing defence resistance against pathogens, and modulating the production of plant secondary metabolites. Understanding the microbial partnerships with cannabis has the potential to affect the agricultural practices by improving plant fitness and the yield of cannabinoids. Little is known about this beneficial cannabis-microbe partnership, and the complex relationship between the endogenous microbes associated with various tissues of the plant, and the role that cannabis may play in supporting or enhancing them. This review will consider cannabis microbiota studies and the effects of endophytes on the elicitation of secondary metabolite production in cannabis plants. The review aims to shed light on the importance of the cannabis microbiome and how cannabinoid compound concentrations can be stimulated through symbiotic and/or mutualistic relationships with endophytes.
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Affiliation(s)
| | - Suha Jabaji
- Plant Science Department, Faculty of Agricultural and Environmental Sciences, MacDonald Campus of McGill University, QC H9X 3V9, Canada;
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19
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Vujanovic V, Korber DR, Vujanovic S, Vujanovic J, Jabaji S. Scientific Prospects for Cannabis-Microbiome Research to Ensure Quality and Safety of Products. Microorganisms 2020; 8:E290. [PMID: 32093340 PMCID: PMC7074860 DOI: 10.3390/microorganisms8020290] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 01/06/2023] Open
Abstract
Cannabis legalization has occurred in several countries worldwide. Along with steadily growing research in Cannabis healthcare science, there is an increasing interest for scientific-based knowledge in plant microbiology and food science, with work connecting the plant microbiome and plant health to product quality across the value chain of cannabis. This review paper provides an overview of the state of knowledge and challenges in Cannabis science, and thereby identifies critical risk management and safety issues in order to capitalize on innovations while ensuring product quality control. It highlights scientific gap areas to steer future research, with an emphasis on plant-microbiome sciences committed to using cutting-edge technologies for more efficient Cannabis production and high-quality products intended for recreational, pharmaceutical, and medicinal use.
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Affiliation(s)
- Vladimir Vujanovic
- Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada;
| | - Darren R. Korber
- Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada;
| | - Silva Vujanovic
- Hospital Pharmacy, CISSS des Laurentides and Université de Montréal-Montreal, QC J8H 4C7, Canada;
| | - Josko Vujanovic
- Medical Imaging, CISSS-Laurentides, Lachute, QC J8H 4C7, Canada;
| | - Suha Jabaji
- Plant Science, McGill University, Ste-Anne-de-Bellevue, QC H9X 3V9, Canada;
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20
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The Xylella fastidiosa-Resistant Olive Cultivar "Leccino" Has Stable Endophytic Microbiota during the Olive Quick Decline Syndrome (OQDS). Pathogens 2019; 9:pathogens9010035. [PMID: 31906093 PMCID: PMC7168594 DOI: 10.3390/pathogens9010035] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/26/2022] Open
Abstract
Xylella fastidiosa is a highly virulent pathogen that causes Olive Quick Decline Syndrome (OQDS), which is currently devastating olive plantations in the Salento region (Apulia, Southern Italy). We explored the microbiome associated with X. fastidiosa-infected (Xf-infected) and -uninfected (Xf-uninfected) olive trees in Salento, to assess the level of dysbiosis and to get first insights into the potential role of microbial endophytes in protecting the host from the disease. The resistant cultivar “Leccino” was compared to the susceptible cultivar “Cellina di Nardò”, in order to identify microbial taxa and parameters potentially involved in resistance mechanisms. Metabarcoding of 16S rRNA genes and fungal ITS2 was used to characterize both total and endophytic microbiota in olive branches and leaves. “Cellina di Nardò” showed a drastic dysbiosis after X. fastidiosa infection, while “Leccino” (both infected and uninfected) maintained a similar microbiota. The genus Pseudomonas dominated all “Leccino” and Xf-uninfected “Cellina di Nardò” trees, whereas Ammoniphilus prevailed in Xf-infected “Cellina di Nardò”. Diversity of microbiota in Xf-uninfected “Leccino” was higher than in Xf-uninfected “Cellina di Nardò”. Several bacterial taxa specifically associated with “Leccino” showed potential interactions with X. fastidiosa. The maintenance of a healthy microbiota with higher diversity and the presence of cultivar-specific microbes might support the resistance of “Leccino” to X. fastidiosa. Such beneficial bacteria might be isolated in the future for biological treatment of the OQDS.
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21
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Kavamura VN, Robinson RJ, Hayat R, Clark IM, Hughes D, Rossmann M, Hirsch PR, Mendes R, Mauchline TH. Land Management and Microbial Seed Load Effect on Rhizosphere and Endosphere Bacterial Community Assembly in Wheat. Front Microbiol 2019; 10:2625. [PMID: 31803160 PMCID: PMC6873152 DOI: 10.3389/fmicb.2019.02625] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/29/2019] [Indexed: 11/13/2022] Open
Abstract
Microbial community ecology studies have traditionally utilized culture-based methodologies, though the advent of next-generation amplicon sequencing has facilitated superior resolution analyses of complex microbial communities. Here, we used culture-dependent and -independent approaches to explore the influence of land use as well as microbial seed load on bacterial community structure of the wheat rhizosphere and root endosphere. It was found that niche was an important factor in shaping the microbiome when using both methodological approaches, and that land use was also a discriminatory factor for the culture-independent-based method. Although culture-independent methods provide a higher resolution of analysis, it was found that in the rhizosphere, particular operational taxonomic units (OTUs) in the culture-dependent fraction were absent from the culture-independent fraction, indicating that deeper sequence analysis is required for this approach to be exhaustive. We also found that the microbial seed load defined the endosphere, but not rhizosphere, community structure for plants grown in soil which was not wheat adapted. Together, these findings increase our understanding of the importance of land management and microbial seed load in shaping the root microbiome of wheat and this knowledge will facilitate the exploitation of plant-microbe interactions for the development of novel microbial inoculants.
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Affiliation(s)
| | | | - Rifat Hayat
- Department of Soil Science and Soil and Water Conservation, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Ian M. Clark
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - David Hughes
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Maike Rossmann
- Laboratory of Environmental Microbiology, Embrapa Meio Ambiente, Jaguariúna, Brazil
| | - Penny R. Hirsch
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Meio Ambiente, Jaguariúna, Brazil
| | - Tim H. Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
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22
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Mighell K, Saltonstall K, Turner BL, Espinosa‐Tasón J, Van Bael SA. Abiotic and biotic drivers of endosymbiont community assembly in
Jatropha curcas. Ecosphere 2019. [DOI: 10.1002/ecs2.2941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Kimberly Mighell
- Ecology and Evolutionary Biology Tulane University 6823 Street Charles Avenue New Orleans Louisiana 70118 USA
| | - Kristin Saltonstall
- Smithsonian Tropical Research Institute Apartado 0843‐03092 Balboa Ancon Republic of Panama
| | - Benjamin L. Turner
- Smithsonian Tropical Research Institute Apartado 0843‐03092 Balboa Ancon Republic of Panama
| | - Jaime Espinosa‐Tasón
- Instituto de Investigación Agropecuaria de Panamá Calle Carlos Lara 157 Panama Republic of Panama
| | - Sunshine A. Van Bael
- Ecology and Evolutionary Biology Tulane University 6823 Street Charles Avenue New Orleans Louisiana 70118 USA
- Smithsonian Tropical Research Institute Apartado 0843‐03092 Balboa Ancon Republic of Panama
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23
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Saleh D, Jarry J, Rani M, Aliferis K, Seguin P, Jabaji S. Diversity, distribution and multi‐functional attributes of bacterial communities associated with the rhizosphere and endosphere of timothy (Phleum pratenseL.). J Appl Microbiol 2019; 127:794-811. [DOI: 10.1111/jam.14334] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 05/09/2019] [Accepted: 05/15/2019] [Indexed: 11/29/2022]
Affiliation(s)
- D. Saleh
- Department of Plant Science Department, Faculty of Agricultural and Environmental Sciences Macdonald Campus of McGill University Ste‐Anne‐De Bellevue QC Canada
| | - J. Jarry
- Department of Plant Science Department, Faculty of Agricultural and Environmental Sciences Macdonald Campus of McGill University Ste‐Anne‐De Bellevue QC Canada
| | - M. Rani
- Department of Plant Science Department, Faculty of Agricultural and Environmental Sciences Macdonald Campus of McGill University Ste‐Anne‐De Bellevue QC Canada
| | - K.A. Aliferis
- Laboratory of Pesticide Science Agricultural University of Athens Athens Greece
| | - P. Seguin
- Department of Plant Science Department, Faculty of Agricultural and Environmental Sciences Macdonald Campus of McGill University Ste‐Anne‐De Bellevue QC Canada
| | - S.H. Jabaji
- Department of Plant Science Department, Faculty of Agricultural and Environmental Sciences Macdonald Campus of McGill University Ste‐Anne‐De Bellevue QC Canada
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24
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McDonald D, Kaehler B, Gonzalez A, DeReus J, Ackermann G, Marotz C, Huttley G, Knight R. redbiom: a Rapid Sample Discovery and Feature Characterization System. mSystems 2019; 4:e00215-19. [PMID: 31239397 PMCID: PMC6593222 DOI: 10.1128/msystems.00215-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/07/2019] [Indexed: 01/11/2023] Open
Abstract
Meta-analyses at the whole-community level have been important in microbiome studies, revealing profound features that structure Earth's microbial communities, such as the unique differentiation of microbes from the mammalian gut relative to free-living microbial communities, the separation of microbiomes in saline and nonsaline environments, and the role of pH in driving soil microbial compositions. However, our ability to identify the specific features of a microbiome that differentiate these community-level patterns have lagged behind, especially as ever-cheaper DNA sequencing has yielded increasingly large data sets. One critical gap is the ability to search for samples that contain specific features (for example, sub-operational taxonomic units [sOTUs] identified by high-resolution statistical methods for removing amplicon sequencing errors). Here we introduce redbiom, a microbiome caching layer, which allows users to rapidly query samples that contain a given feature, retrieve sample data and metadata, and search for samples that match specified metadata values or ranges (e.g., all samples with a pH of >7), implemented using an in-memory NoSQL database called Redis. By default, redbiom allows public anonymous sample access for over 100,000 publicly available samples in the Qiita database. At over 100,000 samples, the caching server requires only 35 GB of resident memory. We highlight how redbiom enables a new type of characterization of microbiome samples and provide tutorials for using redbiom with QIIME 2. redbiom is open source under the BSD license, hosted on GitHub, and can be deployed independently of Qiita to enable search of proprietary or clinically restricted microbiome databases.IMPORTANCE Although analyses that combine many microbiomes at the whole-community level have become routine, searching rapidly for microbiomes that contain a particular sequence has remained difficult. The software we present here, redbiom, dramatically accelerates this process, allowing samples that contain microbiome features to be rapidly identified. This is especially useful when taxonomic annotation is limited, allowing users to identify environments in which unannotated microbes of interest were previously observed. This approach also allows environmental or clinical factors that correlate with specific features, or vice versa, to be identified rapidly, even at a scale of billions of sequences in hundreds of thousands of samples. The software is integrated with existing analysis tools to enable fast, large-scale microbiome searches and discovery of new microbiome relationships.
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Affiliation(s)
- Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Benjamin Kaehler
- School of Science, University of New South Wales, Canberra, Australia
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jeff DeReus
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Clarisse Marotz
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Gavin Huttley
- Research School of Biology, Australian National University, Canberra, Australia
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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Backer R, Schwinghamer T, Rosenbaum P, McCarty V, Eichhorn Bilodeau S, Lyu D, Ahmed MB, Robinson G, Lefsrud M, Wilkins O, Smith DL. Closing the Yield Gap for Cannabis: A Meta-Analysis of Factors Determining Cannabis Yield. FRONTIERS IN PLANT SCIENCE 2019; 10:495. [PMID: 31068957 PMCID: PMC6491815 DOI: 10.3389/fpls.2019.00495] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 04/01/2019] [Indexed: 05/20/2023]
Abstract
Until recently, the commercial production of Cannabis sativa was restricted to varieties that yielded high-quality fiber while producing low levels of the psychoactive cannabinoid tetrahydrocannabinol (THC). In the last few years, a number of jurisdictions have legalized the production of medical and/or recreational cannabis with higher levels of THC, and other jurisdictions seem poised to follow suit. Consequently, demand for industrial-scale production of high yield cannabis with consistent cannabinoid profiles is expected to increase. In this paper we highlight that currently, projected annual production of cannabis is based largely on facility size, not yield per square meter. This meta-analysis of cannabis yields reported in scientific literature aimed to identify the main factors contributing to cannabis yield per plant, per square meter, and per W of lighting electricity. In line with previous research we found that variety, plant density, light intensity and fertilization influence cannabis yield and cannabinoid content; we also identified pot size, light type and duration of the flowering period as predictors of yield and THC accumulation. We provide insight into the critical role of light intensity, quality, and photoperiod in determining cannabis yields, with particular focus on the potential for light-emitting diodes (LEDs) to improve growth and reduce energy requirements. We propose that the vast amount of genomics data currently available for cannabis can be used to better understand the effect of genotype on yield. Finally, we describe diversification that is likely to emerge in cannabis growing systems and examine the potential role of plant-growth promoting rhizobacteria (PGPR) for growth promotion, regulation of cannabinoid biosynthesis, and biocontrol.
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Affiliation(s)
- Rachel Backer
- Crop Physiology Laboratory, Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
- *Correspondence: Rachel Backer
| | - Timothy Schwinghamer
- Crop Physiology Laboratory, Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Phillip Rosenbaum
- Plant Systems Biology Laboratory, Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Vincent McCarty
- Plant Systems Biology Laboratory, Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Samuel Eichhorn Bilodeau
- Biomass Production Laboratory, Department of Bioresource Engineering, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Dongmei Lyu
- Crop Physiology Laboratory, Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Md Bulbul Ahmed
- Plant Systems Biology Laboratory, Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | | | - Mark Lefsrud
- Biomass Production Laboratory, Department of Bioresource Engineering, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Olivia Wilkins
- Plant Systems Biology Laboratory, Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Donald L. Smith
- Crop Physiology Laboratory, Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
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Cultivar and phosphorus effects on switchgrass yield and rhizosphere microbial diversity. Appl Microbiol Biotechnol 2018; 103:1973-1987. [PMID: 30535577 DOI: 10.1007/s00253-018-9535-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/10/2018] [Accepted: 11/18/2018] [Indexed: 01/16/2023]
Abstract
Switchgrass (Panicum virgatum L.) is a native perennial grass identified as a promising biofuel crop for production on marginal agricultural lands. As such, research into switchgrass fertility and the switchgrass rhizosphere microbiome has been ongoing in an effort to increase production sustainability. We examined the effects of cultivar and phosphorus (P) fertilization on biomass yield, P removal, and rhizosphere bacterial and fungal community structure in three switchgrass cultivars: Sunburst, Shawnee, and Liberty. The Liberty cv. is the first lowland-type bioenergy switchgrass adapted to USDA hardiness zones 4, 5, and 6. On a medium soil test P clay loam soil, biomass yield response to applied P was linear, increasing 135 kg ha-1 for every kilogram of P applied prior to establishment. Average post-frost biomass yield was 9.6 Mg ha-1 year-1 when unfertilized, and maximum biomass yield was 10.3 Mg ha-1 year-1 when fertilized at 58.6 kg ha-1 P, suggesting that P application on medium soil test P soils is beneficial for switchgrass establishment and early growth. Switchgrass cv. Shawnee was more productive than cvs. Liberty or Sunburst (11.3, 10.2, and 8.6 Mg ha-1 year-1, respectively). Both bacterial and fungal communities were significantly shaped by cultivar. These shifts, while inconsistent between year and cultivar, may reflect a selection of the microbial community from that present in soil to maximize total nutrient uptake, regardless of additional P amendments. Phosphorus fertilization did not affect microbial community structure. Results of this study suggest that the cultivar-associated selection of particular microbial taxa may have implications for increased productivity.
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Backer R, Rokem JS, Ilangumaran G, Lamont J, Praslickova D, Ricci E, Subramanian S, Smith DL. Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture. FRONTIERS IN PLANT SCIENCE 2018; 9:1473. [PMID: 30405652 PMCID: PMC6206271 DOI: 10.3389/fpls.2018.01473] [Citation(s) in RCA: 581] [Impact Index Per Article: 96.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/20/2018] [Indexed: 05/02/2023]
Abstract
Microbes of the phytomicrobiome are associated with every plant tissue and, in combination with the plant form the holobiont. Plants regulate the composition and activity of their associated bacterial community carefully. These microbes provide a wide range of services and benefits to the plant; in return, the plant provides the microbial community with reduced carbon and other metabolites. Soils are generally a moist environment, rich in reduced carbon which supports extensive soil microbial communities. The rhizomicrobiome is of great importance to agriculture owing to the rich diversity of root exudates and plant cell debris that attract diverse and unique patterns of microbial colonization. Microbes of the rhizomicrobiome play key roles in nutrient acquisition and assimilation, improved soil texture, secreting, and modulating extracellular molecules such as hormones, secondary metabolites, antibiotics, and various signal compounds, all leading to enhancement of plant growth. The microbes and compounds they secrete constitute valuable biostimulants and play pivotal roles in modulating plant stress responses. Research has demonstrated that inoculating plants with plant-growth promoting rhizobacteria (PGPR) or treating plants with microbe-to-plant signal compounds can be an effective strategy to stimulate crop growth. Furthermore, these strategies can improve crop tolerance for the abiotic stresses (e.g., drought, heat, and salinity) likely to become more frequent as climate change conditions continue to develop. This discovery has resulted in multifunctional PGPR-based formulations for commercial agriculture, to minimize the use of synthetic fertilizers and agrochemicals. This review is an update about the role of PGPR in agriculture, from their collection to commercialization as low-cost commercial agricultural inputs. First, we introduce the concept and role of the phytomicrobiome and the agricultural context underlying food security in the 21st century. Next, mechanisms of plant growth promotion by PGPR are discussed, including signal exchange between plant roots and PGPR and how these relationships modulate plant abiotic stress responses via induced systemic resistance. On the application side, strategies are discussed to improve rhizosphere colonization by PGPR inoculants. The final sections of the paper describe the applications of PGPR in 21st century agriculture and the roadmap to commercialization of a PGPR-based technology.
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Affiliation(s)
- Rachel Backer
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | - J. Stefan Rokem
- School of Medicine, Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - John Lamont
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | - Dana Praslickova
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | - Emily Ricci
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | | | - Donald L. Smith
- Department of Plant Science, McGill University, Montreal, QC, Canada
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Scott M, Rani M, Samsatly J, Charron JB, Jabaji S. Endophytes of industrial hemp (Cannabis sativa L.) cultivars: identification of culturable bacteria and fungi in leaves, petioles, and seeds. Can J Microbiol 2018; 64:664-680. [PMID: 29911410 DOI: 10.1139/cjm-2018-0108] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Plant endophytes are a group of microorganisms that reside asymptomatically within the healthy living tissue. The diversity and molecular and biochemical characterization of industrial hemp-associated endophytes have not been previously studied. This study explored the abundance and diversity of culturable endophytes residing in petioles, leaves, and seeds of three industrial hemp cultivars, and examined their biochemical attributes and antifungal potential. A total of 134 bacterial and 53 fungal strains were isolated from cultivars Anka, CRS-1, and Yvonne. The number of bacterial isolates was similarly distributed among the cultivars, with the majority recovered from petiole tissue. Most fungal strains originated from leaf tissue of cultivar Anka. Molecular and phylogenetic analyses grouped the endophytes into 18 bacterial and 13 fungal taxa, respectively. The most abundant bacterial genera were Pseudomonas, Pantoea, and Bacillus, and the fungal genera were Aureobasidium, Alternaria, and Cochliobolus. The presence of siderophores, cellulase production, and phosphorus solubilization were the main biochemical traits. In proof-of-concept experiments, re-inoculation of tomato roots with some endophytes confirmed their migration to aerial tissues of the plant. Taken together, this study demonstrates that industrial hemp harbours a diversity of microbial endophytes, some of which could be used in growth promotion and (or) in biological control designed experiments.
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Affiliation(s)
- Maryanne Scott
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Mamta Rani
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Jamil Samsatly
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Jean-Benoit Charron
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Suha Jabaji
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
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Grewe F, Huang JP, Leavitt SD, Lumbsch HT. Reference-based RADseq resolves robust relationships among closely related species of lichen-forming fungi using metagenomic DNA. Sci Rep 2017; 7:9884. [PMID: 28852019 PMCID: PMC5575168 DOI: 10.1038/s41598-017-09906-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/31/2017] [Indexed: 01/13/2023] Open
Abstract
Despite increasing availability of phylogenomic datasets, strategies to generate genome-scale data from organisms involved in symbiotic relationships remains challenging. Restriction site-associated DNA sequencing (RADseq) can effectively generated reduced representation genomic loci. However, when using metagenomic DNA from inseparable symbiotic organisms, RADseq loci may belong to any number of the organisms involved in these intimate associations. In this study, we explored the potential for a reference-based RADseq approach to generate data for lichen-forming fungi from metagenomic DNA extracted from intact lichens. We simulated RAD data from draft genomes of closely related lichenized fungi to test if RADseq can reconstruct robust evolutionary relationships. Subsequently, we generated empirical RADseq data from metagenomic lichen DNA, with RADseq loci mapped back to a reference genome to exclude loci from other lichen symbionts that are represented in metagenomic libraries. In all cases, phylogenetic reconstructions using RADseq loci recovered diversification histories consistent with a previous study based on more comprehensive genome sampling. Furthermore, RADseq loci were found to resolve relationships among closely related species, which were otherwise indistinguishable using a phylogenetic species recognition criterion. Our studies revealed that a modified, reference-based RADseq approach can successfully be implemented to generate symbiont-specific phylogenomic data from metagenomic reads.
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Affiliation(s)
- Felix Grewe
- Integrative Research Center, Science and Education, Field Museum of Natural History, 1400S Lake Shore Drive, Chicago, IL, 60605, USA.
| | - Jen-Pen Huang
- Integrative Research Center, Science and Education, Field Museum of Natural History, 1400S Lake Shore Drive, Chicago, IL, 60605, USA
| | - Steven D Leavitt
- Integrative Research Center, Science and Education, Field Museum of Natural History, 1400S Lake Shore Drive, Chicago, IL, 60605, USA.,Department of Biology & M. L. Bean Life Science Museum, Brigham Young University, Provo, UT, 84602, USA
| | - H Thorsten Lumbsch
- Integrative Research Center, Science and Education, Field Museum of Natural History, 1400S Lake Shore Drive, Chicago, IL, 60605, USA
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Ramalho MO, Bueno OC, Moreau CS. Microbial composition of spiny ants (Hymenoptera: Formicidae: Polyrhachis) across their geographic range. BMC Evol Biol 2017; 17:96. [PMID: 28381207 PMCID: PMC5382451 DOI: 10.1186/s12862-017-0945-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/23/2017] [Indexed: 11/10/2022] Open
Abstract
Background Symbiotic relationships between insects and bacteria are found across almost all insect orders, including Hymenoptera. However there are still many remaining questions about these associations including what factors drive host-associated bacterial composition. To better understand the evolutionary significance of this association in nature, further studies addressing a diversity of hosts across locations and evolutionary history are necessary. Ants of the genus Polyrhachis (spiny ants) are distributed across the Old World and exhibit generalist diets and habits. Using Next Generation Sequencing (NGS) and bioinformatics tools, this study explores the microbial community of >80 species of Polyrhachis distributed across the Old World and compares the microbiota of samples and related hosts across different biogeographic locations and in the context of their phylogenetic history. Results The predominant bacteria across samples were Enterobacteriaceae (Blochmannia - with likely many new strains), followed by Wolbachia (with multiple strains), Lactobacillus, Thiotrichaceae, Acinetobacter, Nocardia, Sodalis, and others. We recovered some exclusive strains of Enterobacteriaceae as specific to some subgenera of Polyrhachis, corroborating the idea of coevolution between host and bacteria for this bacterial group. Our correlation results (partial mantel and mantel tests) found that host phylogeny can influence the overall bacterial community, but that geographic location had no effect. Conclusions Our work is revealing important aspects of the biology of hosts in structuring the diversity and abundance of these host-associated bacterial communities including the role of host phylogeny and shared evolutionary history. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0945-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manuela Oliveira Ramalho
- Universidade Estadual Paulista "Júlio de Mesquita Filho" UNESP - Campus Rio Claro, Biologia, CEIS. Av. 24A, 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil. .,Field Museum of Natural History, Department of Science and Education, Integrative Research Center, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA.
| | - Odair Correa Bueno
- Universidade Estadual Paulista "Júlio de Mesquita Filho" UNESP - Campus Rio Claro, Biologia, CEIS. Av. 24A, 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Corrie Saux Moreau
- Field Museum of Natural History, Department of Science and Education, Integrative Research Center, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA
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31
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Samad A, Trognitz F, Compant S, Antonielli L, Sessitsch A. Shared and host-specific microbiome diversity and functioning of grapevine and accompanying weed plants. Environ Microbiol 2017; 19:1407-1424. [PMID: 27871147 DOI: 10.1111/1462-2920.13618] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/11/2016] [Accepted: 11/16/2016] [Indexed: 11/30/2022]
Abstract
Weeds and crop plants select their microbiota from the same pool of soil microorganisms, however, the ecology of weed microbiomes is poorly understood. We analysed the microbiomes associated with roots and rhizospheres of grapevine and four weed species (Lamium amplexicaule L., Veronica arvensis L., Lepidium draba L. and Stellaria media L.) growing in proximity in the same vineyard using 16S rRNA gene sequencing. We also isolated and characterized 500 rhizobacteria and root endophytes from L. draba and grapevine. Microbiome data analysis revealed that all plants hosted significantly different microbiomes in the rhizosphere as well as in root compartment, however, differences were more pronounced in the root compartment. The shared microbiome of grapevine and the four weed species contained 145 OTUs (54.2%) in the rhizosphere, but only nine OTUs (13.2%) in the root compartment. Seven OTUs (12.3%) were shared in all plants and compartments. Approximately 56% of the major OTUs (>1%) showed more than 98% identity to bacteria isolated in this study. Moreover, weed-associated bacteria generally showed a higher species richness in the rhizosphere, whereas the root-associated bacteria were more diverse in the perennial plants grapevine and L. draba. Overall, weed isolates showed more plant growth-promoting characteristics compared with grapevine isolates.
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Affiliation(s)
- Abdul Samad
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad-Lorenz-Straße 24, Tulln, 3430, Austria
| | - Friederike Trognitz
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad-Lorenz-Straße 24, Tulln, 3430, Austria
| | - Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad-Lorenz-Straße 24, Tulln, 3430, Austria
| | - Livio Antonielli
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad-Lorenz-Straße 24, Tulln, 3430, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad-Lorenz-Straße 24, Tulln, 3430, Austria
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32
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Gopal M, Gupta A. Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies. Front Microbiol 2016; 7:1971. [PMID: 28003808 PMCID: PMC5141590 DOI: 10.3389/fmicb.2016.01971] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 11/24/2016] [Indexed: 12/16/2022] Open
Abstract
“No plant is an island too…” Plants, though sessile, have developed a unique strategy to counter biotic and abiotic stresses by symbiotically co-evolving with microorganisms and tapping into their genome for this purpose. Soil is the bank of microbial diversity from which a plant selectively sources its microbiome to suit its needs. Besides soil, seeds, which carry the genetic blueprint of plants during trans-generational propagation, are home to diverse microbiota that acts as the principal source of microbial inoculum in crop cultivation. Overall, a plant is ensconced both on the outside and inside with a diverse assemblage of microbiota. Together, the plant genome and the genes of the microbiota that the plant harbors in different plant tissues, i.e., the ‘plant microbiome,’ form the holobiome which is now considered as unit of selection: ‘the holobiont.’ The ‘plant microbiome’ not only helps plants to remain fit but also offers critical genetic variability, hitherto, not employed in the breeding strategy by plant breeders, who traditionally have exploited the genetic variability of the host for developing high yielding or disease tolerant or drought resistant varieties. This fresh knowledge of the microbiome, particularly of the rhizosphere, offering genetic variability to plants, opens up new horizons for breeding that could usher in cultivation of next-generation crops depending less on inorganic inputs, resistant to insect pest and diseases and resilient to climatic perturbations. We surmise, from ever increasing evidences, that plants and their microbial symbionts need to be co-propagated as life-long partners in future strategies for plant breeding. In this perspective, we propose bottom–up approach to co-propagate the co-evolved, the plant along with the target microbiome, through – (i) reciprocal soil transplantation method, or (ii) artificial ecosystem selection method of synthetic microbiome inocula, or (iii) by exploration of microRNA transfer method – for realizing this next-generation plant breeding approach. Our aim, thus, is to bring closer the information accrued through the advanced nucleotide sequencing and bioinformatics in conjunction with conventional culture-dependent isolation method for practical application in plant breeding and overall agriculture.
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Affiliation(s)
- Murali Gopal
- Microbiology Section, ICAR-Central Plantation Crops Research Institute Kasaragod, India
| | - Alka Gupta
- Microbiology Section, ICAR-Central Plantation Crops Research Institute Kasaragod, India
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McKernan K, Spangler J, Helbert Y, Lynch RC, Devitt-Lee A, Zhang L, Orphe W, Warner J, Foss T, Hudalla CJ, Silva M, Smith DR. Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests. F1000Res 2016; 5:2471. [PMID: 27853518 PMCID: PMC5089129 DOI: 10.12688/f1000research.9662.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/03/2016] [Indexed: 12/26/2022] Open
Abstract
Background: The presence of bacteria and fungi in medicinal or recreational
Cannabis poses a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quantitative PCR (qPCR) approach marketed by Medicinal Genomics Corporation. Methods: A set of 15 medicinal
Cannabis samples were analyzed using 3M and Biomérieux culture-based platforms and by qPCR to quantify microbial DNA. All samples were then subjected to next-generation sequencing and metagenomics analysis to enumerate the bacteria and fungi present before and after growth on culture-based media. Results: Several pathogenic or toxigenic bacterial and fungal species were identified in proportions of >5% of classified reads on the samples, including
Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, Ralstonia pickettii, Salmonella enterica, Stenotrophomonas maltophilia, Aspergillus ostianus, Aspergillus sydowii, Penicillium citrinum and
Penicillium steckii. Samples subjected to culture showed substantial shifts in the number and diversity of species present, including the failure of
Aspergillus species to grow well on either platform. Substantial growth of
Clostridium botulinum and other bacteria were frequently observed on one or both of the culture-based TYM platforms. The presence of plant growth promoting (beneficial) fungal species further influenced the differential growth of species in the microbiome of each sample. Conclusions: These findings have important implications for the
Cannabis and food safety testing industries.
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Affiliation(s)
| | | | | | - Ryan C Lynch
- Medicinal Genomics Corporation, Woburn, MA, 01801, USA
| | | | - Lei Zhang
- Medicinal Genomics Corporation, Woburn, MA, 01801, USA
| | - Wendell Orphe
- Medicinal Genomics Corporation, Woburn, MA, 01801, USA
| | - Jason Warner
- Medicinal Genomics Corporation, Woburn, MA, 01801, USA
| | - Theodore Foss
- Medicinal Genomics Corporation, Woburn, MA, 01801, USA
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Warschefsky EJ, Klein LL, Frank MH, Chitwood DH, Londo JP, von Wettberg EJB, Miller AJ. Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes. TRENDS IN PLANT SCIENCE 2016; 21:418-437. [PMID: 26698413 DOI: 10.1016/j.tplants.2015.11.008] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/16/2015] [Accepted: 11/11/2015] [Indexed: 05/18/2023]
Abstract
Grafting is an ancient agricultural practice that joins the root system (rootstock) of one plant to the shoot (scion) of another. It is most commonly employed in woody perennial crops to indirectly manipulate scion phenotype. While recent research has focused on scions, here we investigate rootstocks, the lesser-known half of the perennial crop equation. We review natural grafting, grafting in agriculture, rootstock diversity and domestication, and developing areas of rootstock research, including molecular interactions and rootstock microbiomes. With growing interest in perennial crops as valuable components of sustainable agriculture, rootstocks provide one mechanism by which to improve and expand woody perennial cultivation in a range of environmental conditions.
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Affiliation(s)
- Emily J Warschefsky
- Florida International University, Department of Biological Sciences, 11200 Southwest 8th Street, Miami, FL 33199-2156, USA; Fairchild Tropical Botanic Garden, Kushlan Tropical Science Institute, 10901 Old Cutler Road, Coral Gables, FL 33156-4233, USA
| | - Laura L Klein
- Saint Louis University, Department of Biology, 3507 Laclede Avenue, St. Louis, MO 63103-2010, USA; Missouri Botanical Garden, 4344 Shaw Boulevard, St. Louis, MO 63110-2226, USA
| | - Margaret H Frank
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132-2918, USA
| | - Daniel H Chitwood
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132-2918, USA
| | - Jason P Londo
- United States Department of Agriculture, Agriculture Research Service: Grape Genetics Research Unit, 630 West North Street, Geneva, NY 14456-1371, USA
| | - Eric J B von Wettberg
- Florida International University, Department of Biological Sciences, 11200 Southwest 8th Street, Miami, FL 33199-2156, USA; Fairchild Tropical Botanic Garden, Kushlan Tropical Science Institute, 10901 Old Cutler Road, Coral Gables, FL 33156-4233, USA; Florida International University, International Center for Tropical Botany, 11200 Southwest 8th Street, Miami, FL 33199-2156, USA
| | - Allison J Miller
- Saint Louis University, Department of Biology, 3507 Laclede Avenue, St. Louis, MO 63103-2010, USA; Missouri Botanical Garden, 4344 Shaw Boulevard, St. Louis, MO 63110-2226, USA.
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35
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Pascual J, Blanco S, García-López M, García-Salamanca A, Bursakov SA, Genilloud O, Bills GF, Ramos JL, van Dillewijn P. Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches. PLoS One 2016; 11:e0146558. [PMID: 26741495 PMCID: PMC4711807 DOI: 10.1371/journal.pone.0146558] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/19/2015] [Indexed: 11/19/2022] Open
Abstract
Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone library and 454 amplicon pyrosequencing. The bacterial community was dominated by Proteobacteria (mostly Alphaproteobacteria and Betaproteobacteria), Actinobacteria, Acidobacteria, and Gemmatimonadetes. Although each approach gave a different perspective of the bacterial community, all classes/subclasses detected in the clone library and the cultured bacteria could be found in the pyrosequencing datasets. However, an exception caused by inconclusive taxonomic identification as a consequence of the short read length of pyrotags together with the detection of singleton sequences which corresponded to bacterial strains cultivated from the same sample highlight limitations and considerations which should be taken into account when analysing and interpreting amplicon datasets. Amplicon pyrosequencing of replicate rhizosphere soil samples taken a year later permit the definition of the core microbiome associated with Thymus zygis plants. Abundant bacterial families and predicted functional profiles of the core microbiome suggest that the main drivers of the bacterial community in the Thymus zygis rhizosphere are related to the nutrients originating from the plant root and to their participation in biogeochemical cycles thereby creating an intricate relationship with this aromatic plant to allow for a feedback ecological benefit.
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Affiliation(s)
- Javier Pascual
- Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
- MEDINA Foundation, Centre of Excellence for Innovative Medicines Research, Granada, Spain
| | - Silvia Blanco
- Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Marina García-López
- MEDINA Foundation, Centre of Excellence for Innovative Medicines Research, Granada, Spain
| | - Adela García-Salamanca
- Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Sergey A. Bursakov
- Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Olga Genilloud
- MEDINA Foundation, Centre of Excellence for Innovative Medicines Research, Granada, Spain
| | - Gerald F. Bills
- MEDINA Foundation, Centre of Excellence for Innovative Medicines Research, Granada, Spain
| | - Juan L. Ramos
- Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Pieter van Dillewijn
- Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
- * E-mail:
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McKernan K, Spangler J, Zhang L, Tadigotla V, Helbert Y, Foss T, Smith D. Cannabis microbiome sequencing reveals several mycotoxic fungi native to dispensary grade Cannabis flowers. F1000Res 2015; 4:1422. [PMID: 27303623 PMCID: PMC4897766 DOI: 10.12688/f1000research.7507.2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/04/2016] [Indexed: 11/21/2022] Open
Abstract
The Center for Disease Control estimates 128,000 people in the U.S. are hospitalized annually due to food borne illnesses. This has created a demand for food safety testing targeting the detection of pathogenic mold and bacteria on agricultural products. This risk extends to medical Cannabis and is of particular concern with inhaled, vaporized and even concentrated Cannabis products . As a result, third party microbial testing has become a regulatory requirement in the medical and recreational Cannabis markets, yet knowledge of the Cannabis microbiome is limited. Here we describe the first next generation sequencing survey of the fungal communities found in dispensary based Cannabis flowers by ITS2 sequencing, and demonstrate the sensitive detection of several toxigenic Penicillium and Aspergillus species, including P. citrinum and P. paxilli, that were not detected by one or more culture-based methods currently in use for safety testing.
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Affiliation(s)
| | | | - Lei Zhang
- Medicinal Genomics Corporation, Woburn, MA, USA
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Leavitt SD, Kraichak E, Nelsen MP, Altermann S, Divakar PK, Alors D, Esslinger TL, Crespo A, Lumbsch T. Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen‐forming family Parmeliaceae (Ascomycota). Mol Ecol 2015; 24:3779-97. [DOI: 10.1111/mec.13271] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 06/04/2015] [Accepted: 06/10/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Steven D. Leavitt
- Committee on Evolutionary Biology University of Chicago Chicago IL USA
- Science & Education The Field Museum Chicago IL USA
| | - Ekaphan Kraichak
- Science & Education The Field Museum Chicago IL USA
- Department of Botany Faculty of Science Kasetsart University Bangkok Thailand
| | - Matthew P. Nelsen
- Geological and Environmental Sciences Stanford University Stanford CA USA
| | | | - Pradeep K. Divakar
- Departamento de Biología Vegetal II Facultad de Farmacia Universidad Complutense de Madrid Madrid Spain
| | - David Alors
- Departamento de Biología Vegetal II Facultad de Farmacia Universidad Complutense de Madrid Madrid Spain
| | | | - Ana Crespo
- Departamento de Biología Vegetal II Facultad de Farmacia Universidad Complutense de Madrid Madrid Spain
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