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Cao H, Xu L, Song J, Xun M, Zhang W, Yang H. Bacterial community structure and co-occurrence networks in the rhizosphere and root endosphere of the grafted apple. BMC Microbiol 2024; 24:53. [PMID: 38341527 PMCID: PMC10858598 DOI: 10.1186/s12866-024-03210-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Compared with aerial plant tissues (such as leaf, stem, and flower), root-associated microbiomes play an indisputable role in promoting plant health and productivity. We thus explored the similarities and differences between rhizosphere and root endosphere bacterial community in the grafted apple system. RESULTS Using pot experiments, three microhabitats (bulk soil, rhizosphere and root endosphere) samples were obtained from two-year-old apple trees grafted on the four different rootstocks. We then investigated the bacterial community composition, diversity, and co-occurrence network in three microhabitats using the Illumina sequencing methods. Only 63 amplicon sequence variants (ASVs) out of a total of 24,485 were shared in the rhizosphere and root endosphere of apple grafted on the four different rootstocks (M9T337, Malus hupehensis Rehd., Malus robusta Rehd., and Malus baccata Borkh.). The core microbiome contained 8 phyla and 25 families. From the bulk soil to the rhizosphere to the root endosphere, the members of the phylum and class levels demonstrated a significant enrichment and depletion pattern. Co-occurrence network analysis showed the network complexity of the rhizosphere was higher than the root endosphere. Most of the keystone nodes in both networks were classified as Proteobacteria, Actinobacteriota and Bacteroidetes and were low abundance species. CONCLUSION The hierarchical filtration pattern existed not only in the assembly of root endosphere bacteria, but also in the core microbiome. Moreover, most of the core ASVs were high-abundance species, while the keystone ASVs of the network were low-abundance species.
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Affiliation(s)
- Hui Cao
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, Shandong Province, China.
- College of Horticulture Science and Engineering, Shandong Agricultural University, State Key Laboratory of Crop Biology, Tai'an, 271018, Shandong Province, China.
| | - Longxiao Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, State Key Laboratory of Crop Biology, Tai'an, 271018, Shandong Province, China
| | - Jianfei Song
- College of Horticulture Science and Engineering, Shandong Agricultural University, State Key Laboratory of Crop Biology, Tai'an, 271018, Shandong Province, China
| | - Mi Xun
- College of Horticulture Science and Engineering, Shandong Agricultural University, State Key Laboratory of Crop Biology, Tai'an, 271018, Shandong Province, China
| | - Weiwei Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, State Key Laboratory of Crop Biology, Tai'an, 271018, Shandong Province, China
| | - Hongqiang Yang
- College of Horticulture Science and Engineering, Shandong Agricultural University, State Key Laboratory of Crop Biology, Tai'an, 271018, Shandong Province, China.
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Wentzien NM, Fernández-González AJ, Villadas PJ, Valverde-Corredor A, Mercado-Blanco J, Fernández-López M. Thriving beneath olive trees: The influence of organic farming on microbial communities. Comput Struct Biotechnol J 2023; 21:3575-3589. [PMID: 37520283 PMCID: PMC10372477 DOI: 10.1016/j.csbj.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
Soil health and root-associated microbiome are interconnected factors involved in plant health. The use of manure amendment on agricultural fields exerts a direct benefit on soil nutrient content and water retention, among others. However, little is known about the impact of manure amendment on the root-associated microbiome, particularly in woody species. In this study, we aimed to evaluate the effects of ovine manure on the microbial communities of the olive rhizosphere and root endosphere. Two adjacent orchards subjected to conventional (CM) and organic (OM) management were selected. We used metabarcoding sequencing to assess the bacterial and fungal communities. Our results point out a clear effect of manure amendment on the microbial community. Fungal richness and diversity were increased in the rhizosphere. The fungal biomass in the rhizosphere was more than doubled, ranging from 1.72 × 106 ± 1.62 × 105 (CM) to 4.54 × 106 ± 8.07 × 105 (OM) copies of the 18 S rRNA gene g-1 soil. Soil nutrient content was also enhanced in the OM orchard. Specifically, oxidable organic matter, total nitrogen, nitrate, phosphorous, potassium and sulfate concentrations were significantly increased in the OM orchard. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. Lastly, microbial co-occurrence network showed more positive interactions, complexity and shorter geodesic distance in the OM orchard. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.
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Affiliation(s)
- Nuria M. Wentzien
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | - Antonio J. Fernández-González
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | - Pablo J. Villadas
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | | | - Jesús Mercado-Blanco
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- Crop Protection Department, Instituto de Agricultura Sostenible (CSIC), 14004 Córdoba, Spain
| | - Manuel Fernández-López
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
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Chen J, Deng Y, Yu X, Wu G, Gao Y, Ren A. Epichloë Endophyte Infection Changes the Root Endosphere Microbial Community Composition of Leymus Chinensis Under Both Potted and Field Growth Conditions. Microb Ecol 2023; 85:604-616. [PMID: 35194659 DOI: 10.1007/s00248-022-01983-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Epichloë endophytes can not only affect the growth and resistance of the host plant but also change the biotic and abiotic properties of the soil where the host is situated. Here, we used endophyte-infected (EI) and endophyte-free (EF) Leymus chinensis as plant materials, to study the microbial diversity and composition in the host root endosphere and rhizosphere soil under both pot and field conditions. The results showed that endophyte infection did not affect the diversity of either bacteria or fungi in the root zone. There were significant differences in both bacterial and fungal communities between the root endosphere and the rhizosphere, and between the field and the pot, while endophytes only affected root endosphere microbial communities. The bacterial families affected by endophyte infection changed from 29.07% under field conditions to 40% under pot conditions. In contrast, the fungal families affected by endophyte infection were maintained at nearly 50% under both field and pot conditions. That is to say, bacterial communities in the root endosphere were more strongly affected by environmental conditions, and in comparison, the fungal communities were more strongly affected by species specificity. Endophytes significantly affected the fungal community composition of the host root endosphere in both potted and field plants, only the effect was more obvious in potted plants. Endophyte infection increased the abundance of three fungal families (Thelebolaceae, Herpotrichiellaceae and Trimorphomycetaceae) under both field and potted conditions. In potted plants, endophytes also altered the dominant fungi from pathogenic Pleosporales to saprophytic Chaetomiaceae. Endophyte infection increased the relative abundance of arbuscular mycorrhizal fungi and saprophytic fungi, especially under potted conditions.Overall, endophytes significantly affected the fungal community composition of the host root endosphere in both potted and field plants. Endophytes had a greater impact on root endosphere microorganisms than the rhizosphere, a greater impact on fungal communities than bacteria, and a greater impact on root endosphere microorganisms under potted conditions than at field sites.
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Affiliation(s)
- Jing Chen
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yongkang Deng
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xinhe Yu
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Guanghong Wu
- Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin, 300387, China.
| | - Yubao Gao
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Anzhi Ren
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
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Wang L, Gong L, Gan D, Li X, Yao J, Wang L, Qu J, Cong J, Zhang Y. Diversity, function and assembly of the Trifolium repens L. root-associated microbiome under lead stress. J Hazard Mater 2022; 438:129510. [PMID: 35816797 DOI: 10.1016/j.jhazmat.2022.129510] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/19/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Root-associated microbial layers provide unique niches that drive specific microbe assemblies. While the rhizosphere microbiome has long received much attention, endophytic microbes remain largely elusive. Characterizing metal-tolerant plants' strategies for assembling different root-associated microbial layers is important for optimizing phytoremediation. Here, a pre-stratified rhizo-box assay was conducted with Trifolium repens L. under greenhouse conditions with artificial Pb-contaminated soil. Cultivation compensated for the pollution-driven loss of soil microbial biomass carbon, enzyme activities and abundance. The acid-soluble Pb proportion increased in the rhizosphere (from 6.5-13.7% to 7.1-18.0%) compared with bulk soil. Under stress, root-layer variants were a considerable source of variation in the microbiome, with the endosphere representing a unique and independent niche. A core set of root microbes were selected by T. repens, with Proteobacteria and Actinobacteria composed of diverse plant-growth-promoting bacteria (PGPBs) and metal-tolerant members. Cluster analysis revealed endosphere-enriched genera, with Rhizobium, Nocardioides, Novosphingobium, Phyllobacterium, and Sphingomonas being the most dominant. Finally, inferred microbial metabolic pathways suggested that these potential metal-tolerant PGPB species provide critical services to hosts, enabling them to tolerate and even flourish in contaminated soil. Our results provide novel insights for understanding how root-associated microbes help metal-tolerant plants cope with abiotic stress.
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Affiliation(s)
- Lei Wang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Li Gong
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Deping Gan
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Xinying Li
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Jiaxuan Yao
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Lei Wang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Jianhua Qu
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Jingmin Cong
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Ying Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China.
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Liao LB, Chen XX, Xiang J, Zhang NN, Wang ET, Shi FS. Zanthoxylum bungeanum root-rot associated shifts in microbiomes of root endosphere, rhizosphere, and soil. PeerJ 2022; 10:e13808. [PMID: 35945942 PMCID: PMC9357373 DOI: 10.7717/peerj.13808] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/07/2022] [Indexed: 01/18/2023] Open
Abstract
Root-rot disease has lead to serious reduction in yields and jeopardized the survival of the economically and ecologically important Zanthoxylum bungeanum trees cultured in Sichuan Province. In order to investigate the interaction between the microbiome and the root-rot disease, a metagenomic analysis was performed to characterize the microbial communities and functions in Z. bungeanum root endosphere, rhizosphere and bulk soil with/without root-rot disease. Soil physicochemical properties, microbial population size and enzyme activities were also analyzed for finding their interactions with the root-rot disease. As results, lower total nitrogen (TN) and available phosphorus (AP) contents but higher pH in rhizosphere and bulk soil, as well as lower substrate-induced respiration (SIR) and higher protease activity in bulk soil of diseased trees were found, in comparison with that of healthy trees. Microbial diversity and community composition were changed by root-rot disease in the endosphere, but not in rhizosphere and bulk soils. The endophytic microbiome of diseased trees presented higher Proteobacteria abundance and lower abundances of Bacteroidetes, Firmicutes and dominant fungal phyla. The relative abundances of nitrogen cycle- and carbon cycle-related genes in endophytic microbiomes were different between the diseased and healthy trees. Based on ANOSIM and PCoA, functional profiles (KEGG and CAZy) of microbiomes in rhizosphere and bulk soil shifted significantly between the diseased and healthy trees. In addition, soil pH, TN, AP, SIR, invertase and protease were estimated as the main factors influencing the shifts of taxonomic and functional groups in microbiomes of rhizosphere and bulk soil. Conclusively, the imbalance of root and soil microbial function groups might lead to shifts in the root endosphere-rhizosphere microenvironment, which in turn resulted in Z. bungeanum root-rot.
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Affiliation(s)
- Li Bin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,University of Chinese Academy of Sciences, Beijing, China,CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chendu, China
| | - Xiao Xia Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,University of Chinese Academy of Sciences, Beijing, China,CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chendu, China
| | - Jun Xiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Nan Nan Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chendu, China
| | - En Tao Wang
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Fu Sun Shi
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chendu, China
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Hernández-Álvarez C, García-Oliva F, Cruz-Ortega R, Romero MF, Barajas HR, Piñero D, Alcaraz LD. Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations. Sci Total Environ 2022; 805:150136. [PMID: 34818799 DOI: 10.1016/j.scitotenv.2021.150136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 05/10/2023]
Abstract
Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants were grown in soils from sites with different drought levels, using in situ collected soils as the microbial source. We described and analyzed bacterial diversity by 16S rRNA gene sequencing (N = 48) from the soil, rhizosphere, and endosphere. Proteobacteria were the most abundant phylum present in humid and arid samples, while Actinobacteriota abundance was higher in arid ones. The β-diversity analyses showed split microbiomes between arid and humid microbiomes, and aridity and soil pH levels could explain it. These differences between humid and arid microbiomes were maintained in the common garden experiment, showing that it is possible to transplant in situ diversity to the greenhouse. We detected a total of 1009 bacterial genera; 199 exclusively associated with roots under arid conditions. By 16S and shotgun metagenomics, we identified dry-associated taxa such as Cellvibrio, Ensifer adhaerens, and Streptomyces flavovariabilis. With shotgun metagenomic sequencing of rhizospheres (N = 6), we identified 2969 protein families in the squash core metagenome and found an increased number of exclusively protein families from arid (924) than humid samples (158). We found arid conditions enriched genes involved in protein degradation and folding, oxidative stress, compatible solute synthesis, and ion pumps associated with osmotic regulation. Plant phenotyping allowed us to correlate bacterial communities with plant growth. Our study revealed that it is possible to evaluate microbiome diversity ex-situ and identify critical species and genes involved in plant-microbe interactions in historically arid locations.
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Affiliation(s)
- Cristóbal Hernández-Álvarez
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Mexico
| | - Rocío Cruz-Ortega
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico
| | - Miguel F Romero
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico
| | - Hugo R Barajas
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico
| | - Luis D Alcaraz
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico.
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Gao P, Song B, Xu R, Sun X, Lin H, Xu F, Li B, Sun W. Structure and variation of root-associated bacterial communities of Cyperus rotundus L. in the contaminated soils around Pb/Zn mine sites. Environ Sci Pollut Res Int 2021; 28:58523-58535. [PMID: 34115291 DOI: 10.1007/s11356-021-14595-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
Soil contamination due to mining activities is a great concern in China. Although the effects of mining pollution resulting in changes of soil characteristics and the microbiome have been documented, studies on the responses of plant root-associated microbial assemblages remain scarce. In this work, we collected bulk soil, rhizosphere soil, and root endosphere samples of Cyperus rotundus L (Cyp) plants from two Pb/Zn mines, of which, one was abandoned (SL) and the other was active (GD), to investigate the bacterial community responses across different site contamination levels and Cyp plant compartments. For comparison, one unpolluted site (SD) was included. Results revealed that soils from the SL and GD sites were seriously contaminated by metal(loid)s, including Pb, Zn, As, and Sb. Bacterial richness and diversity depended on the sampling site and plant compartment. All sample types from the SL site had the lowest bacterial diversities and their bacterial communities also exhibited distinct patterns compared to GD and SD samples. As for the specific sampling site, bacterial communities from the root endosphere exhibited different patterns from those in bulk and rhizosphere soil. Compared to the GD and SD sites, the root endosphere and the rhizosphere soil from the SL site shared core microbes, including Halomonas, Pelagibacterium, and Chelativorans, suggesting that they play key roles in Cyp plant survival in such harsh environments.
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Affiliation(s)
- Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Benru Song
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Fuqing Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China.
- School of Environment, Henan Normal University, Xinxiang, Henan, China.
- Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan, China.
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Sun X, Song B, Xu R, Zhang M, Gao P, Lin H, Sun W. Root-associated (rhizosphere and endosphere) microbiomes of the Miscanthus sinensis and their response to the heavy metal contamination. J Environ Sci (China) 2021; 104:387-398. [PMID: 33985741 DOI: 10.1016/j.jes.2020.12.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
The plant root-associated microbiomes, including both the rhizosphere and the root endosphere microbial community, are considered as a critical extension of the plant genome. Comparing to the well-studied rhizosphere microbiome, the understanding of the root endophytic microbiome is still in its infancy. Miscanthus sinensis is a pioneering plant that could thrive on metal contaminated lands and holds the potential for phytoremediation applications. Characterizing its root-associated microbiome, especially the root endophytic microbiome, could provide pivotal knowledge for phytoremediation of mine tailings. In the current study, M. sinensis residing in two Pb/Zn tailings and one uncontaminated site were collected. The results demonstrated that the metal contaminant fractions exposed strong impacts on the microbial community structures. Their influences on the microbial community, however, gradually decreases from the bulk soil through the rhizosphere soil and finally to the endosphere, which resulting in distinct root endophytic microbial community structures compared to both the bulk and rhizosphere soil. Diverse members affiliated with the order Rhizobiales was identified as the core microbiome residing in the root of M. sinensis. In addition, enrichment of plant-growth promoting functions within the root endosphere were predicted, suggesting the root endophytes may provide critical services to the host plant. The current study provides new insights into taxonomy and potential functions of the root-associated microbiomes of the pioneer plant, M. sinensis, which may facilitate future phytoremediation practices.
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Affiliation(s)
- Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Benru Song
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
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Cerqueira F, Christou A, Fatta-Kassinos D, Vila-Costa M, Bayona JM, Piña B. Effects of prescription antibiotics on soil- and root-associated microbiomes and resistomes in an agricultural context. J Hazard Mater 2020; 400:123208. [PMID: 32593021 DOI: 10.1016/j.jhazmat.2020.123208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/22/2020] [Accepted: 06/11/2020] [Indexed: 05/23/2023]
Abstract
The use of treated wastewater for crop irrigation is rapidly increasing to respond to the ever-growing demands for water and food resources. However, this practice may contribute to the spread of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in agricultural settings. To evaluate this potential risk, we analyzed microbiomes and resistomes of soil and Lactuca sativa L. (lettuce) root samples from pots irrigated with tap water spiked with 0, 20, or 100 μg L-1 of a mixture of three antibiotics (Trimethoprim, Ofloxacin, Sulfamethoxazole). The presence of antibiotics induced changes in bacterial populations, particularly in soil, as revealed by 16S rDNA sequence analysis. Parallel shotgun sequencing identified a total of 56 different ARGs conferring resistance against 14 antibiotic families. Antibiotic -treated samples showed increased loads of ARGs implicated in mutidrug resistance or in both direct and indirect acquired resistance. These changes correlated with the prevalence of Xantomonadales species in the root microbiomes. We interpret these data as indicating different strategies of soil and root microbiomes to cope with the presence of antibiotics, and as a warning that their presence may increase the loads of ARBs and ARGs in edible plant parts, therefore constituting a potential risk for human consumers.
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Affiliation(s)
- Francisco Cerqueira
- Institute of Environmental Assessment and Water Research (IDAEA), Spanish National Research Council, Barcelona, Spain
| | - Anastasis Christou
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Environment, P.O. Box 22016, 1516, Nicosia, Cyprus
| | - Despo Fatta-Kassinos
- Civil and Environmental Engineering Department and Nireas, International Water Research Center, University of Cyprus, P.O. Box 20538, 1678, Nicosia, Cyprus
| | - Maria Vila-Costa
- Institute of Environmental Assessment and Water Research (IDAEA), Spanish National Research Council, Barcelona, Spain
| | - Josep Maria Bayona
- Institute of Environmental Assessment and Water Research (IDAEA), Spanish National Research Council, Barcelona, Spain
| | - Benjamin Piña
- Institute of Environmental Assessment and Water Research (IDAEA), Spanish National Research Council, Barcelona, Spain.
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10
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Beirinckx S, Viaene T, Haegeman A, Debode J, Amery F, Vandenabeele S, Nelissen H, Inzé D, Tito R, Raes J, De Tender C, Goormachtig S. Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions. Microbiome 2020; 8:54. [PMID: 32305066 PMCID: PMC7166315 DOI: 10.1186/s40168-020-00833-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/19/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND When maize (Zea mays L.) is grown in the Northern hemisphere, its development is heavily arrested by chilling temperatures, especially at the juvenile phase. As some endophytes are beneficial for plants under stress conditions, we analyzed the impact of chilling temperatures on the root microbiome and examined whether microbiome-based analysis might help to identify bacterial strains that could promote growth under these temperatures. RESULTS We investigated how the maize root microbiome composition changed by means of 16S rRNA gene amplicon sequencing when maize was grown at chilling temperatures in comparison to ambient temperatures by repeatedly cultivating maize in field soil. We identified 12 abundant and enriched bacterial families that colonize maize roots, consisting of bacteria recruited from the soil, whereas seed-derived endophytes were lowly represented. Chilling temperatures modified the root microbiome composition only slightly, but significantly. An enrichment of several chilling-responsive families was detected, of which the Comamonadaceae and the Pseudomonadaceae were the most abundant in the root endosphere of maize grown under chilling conditions, whereas only three were strongly depleted, among which the Streptomycetaceae. Additionally, a collection of bacterial strains isolated from maize roots was established and a selection was screened for growth-promoting effects on juvenile maize grown under chilling temperatures. Two promising strains that promoted maize growth under chilling conditions were identified that belonged to the root endophytic bacterial families, from which the relative abundance remained unchanged by variations in the growth temperature. CONCLUSIONS Our analyses indicate that chilling temperatures affect the bacterial community composition within the maize root endosphere. We further identified two bacterial strains that boost maize growth under chilling conditions. Their identity revealed that analyzing the chilling-responsive families did not help for their identification. As both strains belong to root endosphere enriched families, visualizing and comparing the bacterial diversity in these communities might still help to identify new PGPR strains. Additionally, a strain does not necessarely need to belong to a high abundant family in the root endosphere to provoke a growth-promoting effect in chilling conditions. Video abstract.
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Affiliation(s)
- Stien Beirinckx
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | | | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Fien Amery
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | | | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Raul Tito
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Center for Microbiology, VIB, 3000 Leuven, Belgium
| | - Caroline De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
- Department of Applied Mathematics, Computer Sciences and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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11
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Fernández-González AJ, Cardoni M, Gómez-Lama Cabanás C, Valverde-Corredor A, Villadas PJ, Fernández-López M, Mercado-Blanco J. Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive. Microbiome 2020; 8:11. [PMID: 32007096 PMCID: PMC6995654 DOI: 10.1186/s40168-020-0787-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/13/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Verticillium wilt of olive (VWO) is caused by the soilborne fungal pathogen Verticillium dahliae. One of the best VWO management measures is the use of tolerant/resistant olive cultivars. Knowledge on the olive-associated microbiome and its potential relationship with tolerance to biotic constraints is almost null. The aims of this work are (1) to describe the structure, functionality, and co-occurrence interactions of the belowground (root endosphere and rhizosphere) microbial communities of two olive cultivars qualified as tolerant (Frantoio) and susceptible (Picual) to VWO, and (2) to assess whether these communities contribute to their differential disease susceptibility level. RESULTS Minor differences in alpha and beta diversities of root-associated microbiota were detected between olive cultivars regardless of whether they were inoculated or not with the defoliating pathotype of V. dahliae. Nevertheless, significant differences were found in taxonomic composition of non-inoculated plants' communities, "Frantoio" showing a higher abundance of beneficial genera in contrast to "Picual" that exhibited major abundance of potential deleterious genera. Upon inoculation with V. dahliae, significant changes at taxonomic level were found mostly in Picual plants. Relevant topological alterations were observed in microbial communities' co-occurrence interactions after inoculation, both at structural and functional level, and in the positive/negative edges ratio. In the root endosphere, Frantoio communities switched to highly connected and low modularized networks, while Picual communities showed a sharply different behavior. In the rhizosphere, V. dahliae only irrupted in the microbial networks of Picual plants. CONCLUSIONS The belowground microbial communities of the two olive cultivars are very similar and pathogen introduction did not provoke significant alterations in their structure and functionality. However, notable differences were found in their networks in response to the inoculation. This phenomenon was more evident in the root endosphere communities. Thus, a correlation between modifications in the microbial networks of this microhabitat and susceptibility/tolerance to a soilborne pathogen was found. Moreover, V. dahliae irruption in the Picual microbial networks suggests a stronger impact on the belowground microbial communities of this cultivar upon inoculation. Our results suggest that changes in the co-occurrence interactions may explain, at least partially, the differential VWO susceptibility of the tested olive cultivars. Video abstract.
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Affiliation(s)
- Antonio J. Fernández-González
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Calle Profesor Albareda 1, 18008 Granada, Spain
| | - Martina Cardoni
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, CSIC, Campus ‘Alameda del Obispo’ s/n, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Carmen Gómez-Lama Cabanás
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, CSIC, Campus ‘Alameda del Obispo’ s/n, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Antonio Valverde-Corredor
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, CSIC, Campus ‘Alameda del Obispo’ s/n, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Pablo J. Villadas
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Calle Profesor Albareda 1, 18008 Granada, Spain
| | - Manuel Fernández-López
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Calle Profesor Albareda 1, 18008 Granada, Spain
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, CSIC, Campus ‘Alameda del Obispo’ s/n, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain
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12
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Chen L, Fang K, Zhou J, Yang ZP, Dong XF, Dai GH, Zhang HB. Enrichment of soil rare bacteria in root by an invasive plant Ageratina adenophora. Sci Total Environ 2019; 683:202-209. [PMID: 31132698 DOI: 10.1016/j.scitotenv.2019.05.220] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/15/2019] [Accepted: 05/15/2019] [Indexed: 05/24/2023]
Abstract
The assembly of the root-associated microbiome provides mutual benefits for the host plant and bacteria in soils. It is interesting how invasive plants interact with the local soil microbial community and establish the soil bacterial community in the endosphere of these plants in the short term. In this study, we compared the bacterial community in the rhizosphere with that in the root endosphere of an invasive plant, Ageratina adenophora, using high-throughput sequencing. The results showed that the roots of A. adenophora selectively accumulated the genera Clostridium and Enterobacter, which are rarely distributed in the rhizosphere. This selective accumulation caused a switch in the bacterial composition at the phylum level from Bacteroidetes predominant in the rhizosphere to Proteobacteria dominant in the root endosphere of A. adenophora. Our data indicated the potential existence of a highly conserved signal recognition in which hosts, either invasive or native, enrich the endosphere bacteria, such as Clostridium, Enterobacter, etc., from the rhizosphere. Moreover, the accumulated bacteria were physiologically and genetically different at the strain level and displayed distinct roles in growth between invasive and native plants. The assembly of the bacterial community in the roots may be an advantageous strategy for A. adenophora in competition with native plants.
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Affiliation(s)
- Lin Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; School of Life Sciences, Yunnan University, Kunming 650091, China; School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Kai Fang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; School of Life Sciences, Yunnan University, Kunming 650091, China; School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Jie Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Zhi-Ping Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Xing-Fan Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Guang-Hui Dai
- Institute of Ecology and Geobotany, School of Ecology and Environment Science, Yunnan University, Kunming 650091, China
| | - Han-Bo Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; School of Life Sciences, Yunnan University, Kunming 650091, China; School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China.
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