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Ahmed A, He P, He Y, Singh BK, Wu Y, Munir S, He P. Biocontrol of plant pathogens in omics era-with special focus on endophytic bacilli. Crit Rev Biotechnol 2024; 44:562-580. [PMID: 37055183 DOI: 10.1080/07388551.2023.2183379] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 08/24/2022] [Accepted: 02/06/2023] [Indexed: 04/15/2023]
Abstract
Nearly all plants and their organs are inhabited by endophytic microbes which play a crucial role in plant fitness and stress resilience. Harnessing endophytic services can provide effective solutions for a sustainable increase in agriculture productivity and can be used as a complement or alternative to agrochemicals. Shifting agriculture practices toward the use of nature-based solutions can contribute directly to the global challenges of food security and environmental sustainability. However, microbial inoculants have been used in agriculture for several decades with inconsistent efficacy. Key reasons of this inconsistent efficacy are linked to competition with indigenous soil microflora and inability to colonize plants. Endophytic microbes provide solutions to both of these issues which potentially make them better candidates for microbial inoculants. This article outlines the current advancements in endophytic research with special focus on endophytic bacilli. A better understanding of diverse mechanisms of disease control by bacilli is essential to achieve maximum biocontrol efficacy against multiple phytopathogens. Furthermore, we argue that integration of emerging technologies with strong theoretical frameworks have the potential to revolutionize biocontrol approaches based on endophytic microbes.
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Affiliation(s)
- Ayesha Ahmed
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Pengfei He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yueqiu He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
- Global Centre for Land Based Innovation, Western Sydney University, Penrith South, New South Wales, Australia
| | - Yixin Wu
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shahzad Munir
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Pengbo He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
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Tian Y, Liu Y, Uwaremwe C, Zhao X, Yue L, Zhou Q, Wang Y, Tran LSP, Li W, Chen G, Sha Y, Wang R. Characterization of three new plant growth-promoting microbes and effects of the interkingdom interactions on plant growth and disease prevention. Plant Cell Rep 2023; 42:1757-1776. [PMID: 37674059 DOI: 10.1007/s00299-023-03060-3] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/12/2023] [Indexed: 09/08/2023]
Abstract
KEY MESSAGE The novel interkingdom PGPM consortia enhanced the ability of plant growth promotion and disease resistance, which would be beneficial to improve plant growth in sustainable agriculture through engineering microbiome. Plant growth-promoting microbes (PGPMs) play important roles in promoting plant growth and bio-controlling of pathogens. Much information reveals that the plant growth-promoting ability of individual PGPM affects plant growth. However, the effects of the PGPM consortia properties on plant growth remain largely unexplored. Here, we characterized three new PGPM strains including Rhodotorula graminis JJ10.1 (termed as J), Pseudomonas psychrotolerans YY7 (termed as Y) and P. chlororaphis T8 (termed as T), and assessed their effects in combination with Bacillus amyloliquefaciens FZB42 (termed as F) on plant growth promotion and disease prevention in Arabidopsis thaliana and tomato (Solanum lycopersicum) plants by investigating morphological changes, whole-genome sequencing and plant growth promoting (PGP) characterization. Results revealed that the three new strains R. graminis JJ10.1, P. psychrotolerans YY7 and P. chlororaphis T8 had the potential for being combined with B. amyloliquefaciens FZB42 to form interkingdom PGPM consortia. The combinations of R. graminis JJ10.1, B. amyloliquefaciens FZB42, and P. psychrotolerans YY7, i. e. JF and JYF, exhibited the strongest ability of synergetic biofilm production. Furthermore, the growth-promotion abilities of the consortia were significantly enhanced compared with those of individual strains under both inoculation and volatile organic compounds (VOCs) treatment. Importantly, the consortia showed stronger abilities of in planta disease prevention than individual strains. Findings of our study may provide future guidance for engineering the minimal microbiome communities to improve plant growth and/or disease resistance in sustainable agriculture.
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Affiliation(s)
- Yuan Tian
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yang Liu
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Constantine Uwaremwe
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xia Zhao
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Liang Yue
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qin Zhou
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yun Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Weiqiang Li
- Jilin Da'an Agro-Ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun, 130102, People's Republic of China
| | - Gaofeng Chen
- Gansu Shangnong Biotechnology Co. Ltd, Baiyin, 730900, People's Republic of China
| | - Yuexia Sha
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, People's Republic of China
| | - Ruoyu Wang
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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Martínez-Martínez JG, Rosales-Loredo S, Hernández-Morales A, Arvizu-Gómez JL, Carranza-Álvarez C, Macías-Pérez JR, Rolón-Cárdenas GA, Pacheco-Aguilar JR. Bacterial Communities Associated with the Roots of Typha spp. and Its Relationship in Phytoremediation Processes. Microorganisms 2023; 11:1587. [PMID: 37375088 DOI: 10.3390/microorganisms11061587] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/11/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Heavy metal pollution is a severe concern worldwide, owing to its harmful effects on ecosystems. Phytoremediation has been applied to remove heavy metals from water, soils, and sediments by using plants and associated microorganisms to restore contaminated sites. The Typha genus is one of the most important genera used in phytoremediation strategies because of its rapid growth rate, high biomass production, and the accumulation of heavy metals in its roots. Plant growth-promoting rhizobacteria have attracted much attention because they exert biochemical activities that improve plant growth, tolerance, and the accumulation of heavy metals in plant tissues. Because of their beneficial effects on plants, some studies have identified bacterial communities associated with the roots of Typha species growing in the presence of heavy metals. This review describes in detail the phytoremediation process and highlights the application of Typha species. Then, it describes bacterial communities associated with roots of Typha growing in natural ecosystems and wetlands contaminated with heavy metals. Data indicated that bacteria from the phylum Proteobacteria are the primary colonizers of the rhizosphere and root-endosphere of Typha species growing in contaminated and non-contaminated environments. Proteobacteria include bacteria that can grow in different environments due to their ability to use various carbon sources. Some bacterial species exert biochemical activities that contribute to plant growth and tolerance to heavy metals and enhance phytoremediation.
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Affiliation(s)
| | - Stephanie Rosales-Loredo
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosí 79060, Mexico
| | - Alejandro Hernández-Morales
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosí 79060, Mexico
| | - Jackeline Lizzeta Arvizu-Gómez
- Secretaría de Investigación y Posgrado, Centro Nayarita de Innovación y Transferencia de Tecnología (CENITT), Universidad Autónoma de Nayarit, Tepic 63173, Mexico
| | - Candy Carranza-Álvarez
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosí 79060, Mexico
| | - José Roberto Macías-Pérez
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosí 79060, Mexico
| | - Gisela Adelina Rolón-Cárdenas
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosí 79060, Mexico
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Ge J, Li D, Ding J, Xiao X, Liang Y. Microbial coexistence in the rhizosphere and the promotion of plant stress resistance: A review. Environ Res 2023; 222:115298. [PMID: 36642122 DOI: 10.1016/j.envres.2023.115298] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 10/15/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Plants can recruit soil microorganisms into the rhizosphere when experiencing various environmental stresses, including biotic (e.g., insect pests) and abiotic (e.g., heavy metal pollution, droughts, floods, and salinity) stresses. However, species coexistence in plant resistance has not received sufficient attention. Current research on microbial coexistence is only at the community scale, and there is a limited understanding of the interaction patterns between species, especially microbe‒microbe interactions. The relevant interaction patterns are limited to a few model strains. The coexisting microbial communities form a stable system involving complex nutritional competition, metabolic exchange, and even interdependent interactions. This pattern of coexistence can ultimately enhance plant stress tolerance. Hence, a systematic understanding of the coexistence pattern of rhizosphere microorganisms under stress is essential for the precise development and utilization of synthetic microbial communities and the achievement of efficient ecological control. Here, we integrated current analytical methods and introduced several new experimental methods to elucidate rhizosphere microbial coexistence patterns. Some advancements (e.g., network analysis, coculture experiments, and synthetic communities) that can be applied to plant stress resistance are also updated. This review aims to summarize the key role and potential application prospects of microbial coexistence in the resistance of plants to environmental stresses. Our suggestions, enhancing plant resistance with coexisting microbes, would allow us to gain further knowledge on plant-microbial and microbial-microbial functions, and facilitate translation to more effective measures.
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Affiliation(s)
- Jiaqi Ge
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Dong Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jixian Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xian Xiao
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, China.
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
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Rubio-Santiago J, Hernández-Morales A, Rolón-Cárdenas GA, Arvizu-Gómez JL, Soria-Guerra RE, Carranza-Álvarez C, Rubio-Salazar JE, Rosales-Loredo S, Pacheco-Aguilar JR, Macías-Pérez JR, Aldaba-Muruato LR, Vázquez-Martínez J. Characterization of Endophytic Bacteria Isolated from Typha latifolia and Their Effect in Plants Exposed to Either Pb or Cd. Plants (Basel) 2023; 12:498. [PMID: 36771585 PMCID: PMC9920544 DOI: 10.3390/plants12030498] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Plant-associated bacteria in heavy-metal-contaminated environments could be a biotechnological tool to improve plant growth. The present work aimed to isolate lead- and cadmium-tolerant endophytic bacteria from the roots of Typha latifolia growing in a site contaminated with these heavy metals. Endophytic bacteria were characterized according to Pb and Cd tolerance, plant-growth-promoting rhizobacteria activities, and their effect on T. latifolia seedlings exposed and non-exposed to Pb and Cd. Pb-tolerant isolates were identified as Pseudomonas azotoformans JEP3, P. fluorescens JEP8, and P. gessardii JEP33, while Cd-tolerant bacteria were identified as P. veronii JEC8, JEC9, and JEC11. They all exert biochemical activities, including indole acetic acid synthesis, siderophore production, and phosphate solubilization. Plant-bacteria interaction assays showed that P. azotoformans JEP3, P. fluorescens JEP8, P. gessardii JEP33, and P. veronii JEC8, JEC9, JEC11 promote the growth of T. latifolia seedlings by increasing the root and shoot length, while in plants exposed to either 5 mg/L of Pb or 10 mg/L of Cd, all bacterial isolates increased the shoot length and the number of roots per plant, suggesting that they are plant-growth-promoting rhizobacteria that could contribute to T. latifolia adaptation to the heavy metal polluted site.
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Affiliation(s)
- Jesús Rubio-Santiago
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Alejandro Hernández-Morales
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosi 79060, Mexico
| | - Gisela Adelina Rolón-Cárdenas
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosi 79060, Mexico
| | - Jackeline Lizzeta Arvizu-Gómez
- Secretaría de Investigación y Posgrado, Centro Nayarita de Innovación y Transferencia de Tecnología (CENITT), Universidad Autónoma de Nayarit, Tepic 63173, Mexico
| | - Ruth Elena Soria-Guerra
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Candy Carranza-Álvarez
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosi 79060, Mexico
| | | | - Stephanie Rosales-Loredo
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosi 79060, Mexico
| | | | - José Roberto Macías-Pérez
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosi 79060, Mexico
| | - Liseth Rubí Aldaba-Muruato
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, San Luis Potosi 79060, Mexico
| | - Juan Vázquez-Martínez
- Departamento de Ingeniería Química y Bioquímica; Tecnológico Nacional de México Campus Irapuato, Guanajuato 36821, Mexico
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Ali S, Tyagi A, Mushtaq M, Al-Mahmoudi H, Bae H. Harnessing plant microbiome for mitigating arsenic toxicity in sustainable agriculture. Environ Pollut 2022; 300:118940. [PMID: 35122918 DOI: 10.1016/j.envpol.2022.118940] [Citation(s) in RCA: 2] [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: 09/08/2021] [Revised: 01/08/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Heavy metal toxicity has become an impediment to agricultural productivity, which presents major human health concerns in terms of food safety. Among them, arsenic (As) a non-essential heavy metal has gained worldwide attention because of its noxious effects on agriculture and public health. The increasing rate of global warming and anthropogenic activities have promptly exacerbated As levels in the agricultural soil, thereby causing adverse effects to crop genetic and phenotypic traits and rendering them vulnerable to other stresses. Conventional breeding and transgenic approaches have been widely adapted for producing heavy metal resilient crops; however, they are time-consuming and labor-intensive. Hence, finding new mitigation strategies for As toxicity would be a game-changer for sustainable agriculture. One such promising approach is harnessing plant microbiome in the era of 'omics' which is gaining prominence in recent years. The use of plant microbiome and their cocktails to combat As metal toxicity has gained widespread attention, because of their ability to metabolize toxic elements and offer an array of perquisites to host plants such as increased nutrient availability, stress resilience, soil fertility, and yield. A comprehensive understanding of below-ground plant-microbiome interactions and their underlying molecular mechanisms in exhibiting resilience towards As toxicity will help in identifying elite microbial communities for As mitigation. In this review, we have discussed the effect of As, their accumulation, transportation, signaling, and detoxification in plants. We have also discussed the role of the plant microbiome in mitigating As toxicity which has become an intriguing research frontier in phytoremediation. This review also provides insights on the advancements in constructing the beneficial synthetic microbial communities (SynComs) using microbiome engineering that will facilitate the development of the most advanced As remedial tool kit in sustainable agriculture.
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Affiliation(s)
- Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea
| | - Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea
| | | | - Henda Al-Mahmoudi
- Directorate of Programs, International Center for Biosaline Agriculture, Dubai, United Arab Emirates
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
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Roychoudhury T, Ray B, Seal A. Metabolically dependent consortia in biofilm: A new horizon for green agriculture. Biocatalysis and Agricultural Biotechnology 2022. [DOI: 10.1016/j.bcab.2021.102256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Yang J, Li EH, Yang C, Xia Y, Zhou R. Effects of South-to-North Water Diversion Project Cascade Dams on Riparian Vegetation Along the Middle and Lower Reaches of the Hanjiang River, China. Front Plant Sci 2022; 13:849010. [PMID: 35273631 PMCID: PMC8901726 DOI: 10.3389/fpls.2022.849010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 01/31/2022] [Indexed: 05/20/2023]
Abstract
The influence of the construction of dams for water diversion on the ecological environment has attracted recent widespread attention. Over time, dams have emerged as one of the most important factors affecting the vegetation along the riparian zones of rivers. To elucidate the effects of cascade dams on riparian vegetation along the middle and lower reaches of the Hanjiang River, we examined riparian vegetation types upstream and downstream from dams. A total of 14 sample sites and 131 quadrats perpendicular to the river were investigated in June 2019, and 14 sample sites and 134 quadrats were investigated in October 2019. The riparian vegetation was divided into 15 (in June) and 11 (in October) vegetation types by two-way indicator species analysis (TWINSPAN). Significant differences were found between the vegetation types upstream and downstream of dams. Redundancy analysis (RDA) showed that soil moisture content, distance from the water, altitude and soil total nitrogen (TN) were the main environmental factors affecting plants distributions, and soil moisture content was the main factor affecting the zonal distribution of vegetation. By analyzing the impact of cascade dams on the hydrological regime, we found that the construction of cascade dams led to the differentiation of vegetation types upstream and downstream of the dam, and the riparian habitats were fragmented by these dams. This study provides both an important reference for the protection of riparian vegetation and riparian ecosystems and a basis for the management and restoration of river ecosystems after the construction of cascade dams.
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Affiliation(s)
- Jiao Yang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei Province, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - En-Hua Li
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei Province, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: En-Hua Li,
| | - Chao Yang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei Province, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Ying Xia
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei Province, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Rui Zhou
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei Province, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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9
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Beltran-Garcia MJ, Martinez-Rodriguez A, Olmos-Arriaga I, Valdez-Salas B, Chavez-Castrillon YY, Di Mascio P, White JF. Probiotic Endophytes for More Sustainable Banana Production. Microorganisms 2021; 9:1805. [PMID: 34576701 DOI: 10.3390/microorganisms9091805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/14/2022] Open
Abstract
Climatic factors and pathogenic fungi threaten global banana production. Moreover, bananas are being cultivated using excessive amendments of nitrogen and pesticides, which shift the microbial diversity in plants and soil. Advances in high-throughput sequencing (HTS) technologies and culture-dependent methods have provided valuable information about microbial diversity and functionality of plant-associated endophytic communities. Under stressful (biotic or abiotic) conditions, plants can recruit sets of microorganisms to alleviate specific potentially detrimental effects, a phenomenon known as “cry for help”. This mechanism is likely initiated in banana plants infected by Fusarium wilt pathogen. Recently, reports demonstrated the synergistic and cumulative effects of synthetic microbial communities (SynComs) on naturally occurring plant microbiomes. Indeed, probiotic SynComs have been shown to increase plant resilience against biotic and abiotic stresses and promote growth. This review focuses on endophytic bacterial diversity and keystone taxa of banana plants. We also discuss the prospects of creating SynComs composed of endophytic bacteria that could enhance the production and sustainability of Cavendish bananas (Musa acuminata AAA), the fourth most important crop for maintaining global food security.
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Rolón-Cárdenas GA, Arvizu-Gómez JL, Pacheco-Aguilar JR, Vázquez-Martínez J, Hernández-Morales A. Cadmium-tolerant endophytic Pseudomonas rhodesiae strains isolated from Typha latifolia modify the root architecture of Arabidopsis thaliana Col-0 in presence and absence of Cd. Braz J Microbiol 2021; 52:349-361. [PMID: 33236245 PMCID: PMC7966613 DOI: 10.1007/s42770-020-00408-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/19/2020] [Indexed: 10/22/2022] Open
Abstract
In this work, we isolated four Cd-tolerant endophytic bacteria from Typha latifolia roots that grow at a Cd-contaminated site. Bacterial isolates GRC065, GRC066, GRC093, and GRC140 were identified as Pseudomonas rhodesiae. These bacterial isolates tolerate cadmium and have abilities for phosphate solubilization, siderophore production, indole acetic acid (IAA) synthesis, and ACC deaminase activity, suggesting that they are plant growth-promoting rhizobacteria. Bacterial inoculation in Arabidopsis thaliana seedlings showed that P. rhodesiae strains increase total fresh weight and number of lateral roots concerning non-inoculated plants. These results indicated that P. rhodesiae strains promote A. thaliana seedlings growth by modifying the root system. On the other hand, in A. thaliana seedlings exposed to 2.5 mg/l of Cd, P. rhodesiae strains increased the number and density of lateral roots concerning non-inoculated plants, indicating that they modify the root architecture of A. thaliana seedlings exposed to cadmium. The results showed that P. rhodesiae strains promote the development of lateral roots in A. thaliana seedlings cultivated in both conditions, with and without cadmium. These results suggest that P. rhodesiae strains could exert a similar role inside the roots of T. latifolia that grow in the Cd-contaminated environment.
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Affiliation(s)
- Gisela Adelina Rolón-Cárdenas
- Posgrado en Ciencias Químicas, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, San Luis Potosí, Mexico
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, Romualdo del Campo 501, Fraccionamiento Rafael Curiel, CP 79060, Ciudad Valles, San Luis Potosí, Mexico
| | - Jackeline Lizzeta Arvizu-Gómez
- Secretaría de Investigación y Posgrado, Centro Nayarita de Innovación y Transferencia de Tecnología (CENITT), Universidad Autónoma de Nayarit, Tepic, Nayarit, Mexico
| | | | - Juan Vázquez-Martínez
- Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México (TecNM), Instituto Tecnológico Superior de Irapuato, Irapuato, Guanajuato, Mexico
| | - Alejandro Hernández-Morales
- Posgrado en Ciencias Químicas, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, San Luis Potosí, Mexico.
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, Romualdo del Campo 501, Fraccionamiento Rafael Curiel, CP 79060, Ciudad Valles, San Luis Potosí, Mexico.
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11
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Liu X, Yang C, Yu X, Yu H, Zhuang W, Gu H, Xu K, Zheng X, Wang C, Xiao F, Wu B, He Z, Yan Q. Revealing structure and assembly for rhizophyte-endophyte diazotrophic community in mangrove ecosystem after introduced Sonneratia apetala and Laguncularia racemosa. Sci Total Environ 2020; 721:137807. [PMID: 32179356 DOI: 10.1016/j.scitotenv.2020.137807] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 01/31/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 06/10/2023]
Abstract
Biological nitrogen fixation (BNF) mediated by diazotrophic communities is a major source of bioavailable nitrogen in mangrove wetlands, which plays important roles in maintaining the health and stability of mangrove ecosystems. Recent large-scale mangrove afforestation activities have drawn great attention due to introduced mangrove species and their potential impacts on bio-functionalities of local ecosystems. However, the effects of introduced mangrove species on diazotrophic communities remain unclear. Here, we analyzed rhizosphere and endosphere diazotrophic communities between native mangrove species (Avicennia marina) and introduced mangrove species (Sonneratia apetala and Laguncularia racemose) by sequencing nifH gene amplicons. Our results showed that S. apetala and L. racemose introduction significantly (P < 0.05) increased nutrition components (e.g., total carbon and total nitrogen) in rhizosphere, as well as the diazotrophs richness in rhizosphere and endosphere. The relative abundance of clusters III diazotrophs in the rhizosphere and Rhizobium in the endosphere were significantly increased with L. racemosa or S. apetala introduction. Fe and pH were the main environmental factors driving the divergence of endophyte-rhizophyte diazotrophs between native and introduced mangroves. The correlation-based network analyses indicated that the interaction among rhizophyte-endophyte diazotrophs is more harmonious in native mangrove, while there exist more competition in introduced mangroves. These findings expand our current understanding of BNF in mangrove afforestation, and providing new perspectives to sustainable management of mangrove ecosystem.
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Affiliation(s)
- Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Chao Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Wei Zhuang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Wang
- South China Sea Institution, Sun Yat-sen University, Zhuhai 519082, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; South China Sea Institution, Sun Yat-sen University, Zhuhai 519082, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
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12
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Giongo A, Medina-silva R, Astarita LV, Borges LGDA, Oliveira RR, Simão TLL, Gano KA, Davis-richardson AG, Brown CT, Fagen JR, Arzivenco PM, Neto CP, Abichequer AD, Lindholz CG, Baptista-silva A, Mondin CA, Utz LRP, Triplett EW, Eizirik E. Seasonal Physiological Parameters and Phytotelmata Bacterial Diversity of Two Bromeliad Species (Aechmea gamosepala and Vriesea platynema) from the Atlantic Forest of Southern Brazil. Diversity 2019; 11:111. [DOI: 10.3390/d11070111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ecology of complex microhabitats remains poorly characterized in most tropical and subtropical biomes, and holds potential to help understand the structure and dynamics of different biodiversity components in these ecosystems. We assessed nutritional and metabolic parameters of two bromeliad species (Aechmea gamosepala and Vriesea platynema) at an Atlantic Forest site and used 16S rDNA metabarcoding to survey the microbial communities inhabiting their tanks. We observed that levels of some nutrients (e.g., nitrogen) varied across seasons consistently in both species, while others (e.g., phenolic compounds) presented considerable differences between the two bromeliads. In contrast, patterns of tank microbial diversity did not follow a similar temporal trend. There was extensive variation in microbial composition among samples, which included intra-specific differences but also some consistent differences between the two bromeliads. For example, Citrobacter, Klebsiella and Pantoea presented significantly different abundances in the two species. Interestingly, the dominant bacterial genera in both species included Pseudomonas and Enterobacter, which have been reported to include plant-beneficial species. Overall, our data contribute to the characterization of the nutritional status of Atlantic Forest bromeliads and the composition of their prokaryotic communities, laying the foundation for detailed investigations targeting the ecological interactions between these plants and their associated microbes.
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13
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Trifi H, Najjari A, Achouak W, Barakat M, Ghedira K, Mrad F, Saidi M, Sghaier H. Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation. Genomics 2020; 112:981-9. [PMID: 31220587 DOI: 10.1016/j.ygeno.2019.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/15/2019] [Indexed: 11/23/2022]
Abstract
Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria valorizable into (1) removal of radioactive elements and toxic heavy metals, (2) promotion of plant growth, (3) oxidation and (4) reduction of sulfate. These bacteria can be explored further for applications in the bioremediation of by-products, like PG, by different processes.
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Hu LY, Li D, Sun K, Cao W, Fu WQ, Zhang W, Dai CC. Mutualistic fungus Phomopsis liquidambari increases root aerenchyma formation through auxin-mediated ethylene accumulation in rice (Oryza sativa L.). Plant Physiol Biochem 2018; 130:367-376. [PMID: 30055345 DOI: 10.1016/j.plaphy.2018.07.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 05/21/2018] [Accepted: 07/17/2018] [Indexed: 06/08/2023]
Abstract
The fungal endophyte Phomopsis liquidambari can improve nitrification rates and alter the abundance and composition of ammonia-oxidizers in the soil rhizosphere of rice. Aerenchyma is related to oxygen transport efficiency and contributes to the enhanced rhizospheric nitrification under flooding conditions. However, whether and how P. liquidambari affects aerenchyma formation is largely unknown. We therefore conducted pot and hydroponic experiments to investigate the changes of aerenchyma area, ethylene and indole-3-acetic acid (IAA) levels in rice with or without P. liquidambari infection. Our results showed that the larger aerenchyma area in rice roots with P. liquidambari inoculation was associated with markedly up-regulated expression of genes related to aerenchyma formation. Meanwhile, P. liquidambari inoculation substantially elevated root porosity (POR) and radial oxygen loss (ROL), leading to the enhancement of oxidation-reduction potential (ORP) under pot condition. Besides, P. liquidambari significantly increased IAA and ethylene levels in rice by stimulating the expression of genes involved in auxin and ethylene biosyntheses. Furthermore, auxin that partly acting upstream of ethylene signalling played an essential role in P. liquidambari-promoted aerenchyma formation. These results verified the direct contribution of P. liquidambari in promoting aerenchyma formation via the accumulation of IAA and ethylene in rice roots, which provides a constructive suggestion for improving hypoxia tolerance through plant-endophyte interactions.
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Affiliation(s)
- Li-Yan Hu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China
| | - Dan Li
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China
| | - Wei Cao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China
| | - Wan-Qiu Fu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China.
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15
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Mukherjee G, Saha C, Naskar N, Mukherjee A, Mukherjee A, Lahiri S, Majumder AL, Seal A. An Endophytic Bacterial Consortium modulates multiple strategies to improve Arsenic Phytoremediation Efficacy in Solanum nigrum. Sci Rep 2018; 8:6979. [PMID: 29725058 PMCID: PMC5934359 DOI: 10.1038/s41598-018-25306-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 04/16/2018] [Indexed: 12/31/2022] Open
Abstract
Endophytic microbes isolated from plants growing in contaminated habitats possess specialized properties that help their host detoxify the contaminant/s. The possibility of using microbe-assisted phytoremediation for the clean-up of Arsenic (As) contaminated soils of the Ganga-Brahmaputra delta of India, was explored using As-tolerant endophytic microbes from an As-tolerant plant Lantana camara collected from the contaminated site and an intermediate As-accumulator plant Solanum nigrum. Endophytes from L. camara established within S. nigrum as a surrogate host. The microbes most effectively improved plant growth besides increasing bioaccumulation and root-to-shoot transport of As when applied as a consortium. Better phosphate nutrition, photosynthetic performance, and elevated glutathione levels were observed in consortium-treated plants particularly under As-stress. The consortium maintained heightened ROS levels in the plant without any deleterious effect and concomitantly boosted distinct antioxidant defense mechanisms in the shoot and root of As-treated plants. Increased consortium-mediated As(V) to As(III) conversion appeared to be a crucial step in As-detoxification/translocation. Four aquaporins were differentially regulated by the endophytes and/or As. The most interesting finding was the strong upregulation of an MRP transporter in the root by the As + endophytes, which suggested a major alteration of As-detoxification/accumulation pattern upon endophyte treatment that improved As-phytoremediation.
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Affiliation(s)
- Gairik Mukherjee
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Chinmay Saha
- Department of Endocrinology & Metabolism, Institute Of Post Graduate Medical Education & Research and SSKM Hospital, Room No. 9A, 4th Floor, Ronald Ross Building, 244, AJC Bose Road, Kolkata, 700020, India
| | - Nabanita Naskar
- Department of Environmental Science, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
- Saha Institute of Nuclear Physics, Sector - 1, Block - AF Bidhannagar, Kolkata, 700064, India
| | - Abhishek Mukherjee
- Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Arghya Mukherjee
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Susanta Lahiri
- Saha Institute of Nuclear Physics, Sector - 1, Block - AF Bidhannagar, Kolkata, 700064, India
- Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Arun Lahiri Majumder
- Division of Plant Biology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Anindita Seal
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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16
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Chen L, Liao H. Engineering crop nutrient efficiency for sustainable agriculture. J Integr Plant Biol 2017; 59:710-735. [PMID: 28600834 DOI: 10.1111/jipb.12559] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/06/2017] [Indexed: 05/21/2023]
Abstract
Increasing crop yields can provide food, animal feed, bioenergy feedstocks and biomaterials to meet increasing global demand; however, the methods used to increase yield can negatively affect sustainability. For example, application of excess fertilizer can generate and maintain high yields but also increases input costs and contributes to environmental damage through eutrophication, soil acidification and air pollution. Improving crop nutrient efficiency can improve agricultural sustainability by increasing yield while decreasing input costs and harmful environmental effects. Here, we review the mechanisms of nutrient efficiency (primarily for nitrogen, phosphorus, potassium and iron) and breeding strategies for improving this trait, along with the role of regulation of gene expression in enhancing crop nutrient efficiency to increase yields. We focus on the importance of root system architecture to improve nutrient acquisition efficiency, as well as the contributions of mineral translocation, remobilization and metabolic efficiency to nutrient utilization efficiency.
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Affiliation(s)
- Liyu Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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17
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Tao L, Wang B, Zhong Y, Pow SH, Zeng X, Qin C, Zhang P, Chen S, He W, Tan Y, Liu H, Jiang Y, Chen W, Chen YZ. Database and Bioinformatics Studies of Probiotics. J Agric Food Chem 2017; 65:7599-7606. [PMID: 28727425 DOI: 10.1021/acs.jafc.7b01815] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Probiotics have been widely explored for health benefits, animal cares, and agricultural applications. Recent advances in microbiome, microbiota, and microbial dark matter research have fueled greater interests in and paved ways for the study of the mechanisms of probiotics and the discovery of new probiotics from uncharacterized microbial sources. A probiotics database named PROBIO was developed to facilitate these efforts and the need for the information on the known probiotics, which provides the comprehensive information about the probiotic functions of 448 marketed, 167 clinical trial/field trial, and 382 research probiotics for use or being studied for use in humans, animals, and plants. The potential applications of the probiotics data are illustrated by several literature-reported investigations, which have used the relevant information for probing the function and mechanism of the probiotics and for discovering new probiotics. PROBIO can be accessed free of charge at http://bidd2.nus.edu.sg/probio/homepage.htm .
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Affiliation(s)
- Lin Tao
- School of Medicine, Hangzhou Normal University , Hangzhou, P. R. China 310012
| | - Bohua Wang
- College of Life and Environmental Sciences, Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Hunan University of Arts and Science , Changde, Hunan, P. R. China 415000
- Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University , Nanchang, P. R. China 330045
| | - Yafen Zhong
- Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University , Nanchang, P. R. China 330045
| | - Siok Hoon Pow
- Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore , Singapore 117543
| | - Xian Zeng
- Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore , Singapore 117543
| | - Chu Qin
- Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore , Singapore 117543
| | - Peng Zhang
- Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore , Singapore 117543
| | - Shangying Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore , Singapore 117543
| | - Weidong He
- Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore , Singapore 117543
| | - Ying Tan
- The Key Laboratory of Chemical Biology, Guangdong Province, Graduate School at Shenzhen, Tsinghua University , Shenzhen, Guangdong, P. R. China 518055
| | - Hongxia Liu
- The Key Laboratory of Chemical Biology, Guangdong Province, Graduate School at Shenzhen, Tsinghua University , Shenzhen, Guangdong, P. R. China 518055
| | - Yuyang Jiang
- The Key Laboratory of Chemical Biology, Guangdong Province, Graduate School at Shenzhen, Tsinghua University , Shenzhen, Guangdong, P. R. China 518055
| | - Weiping Chen
- Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University , Nanchang, P. R. China 330045
| | - Yu Zong Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore , Singapore 117543
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18
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Li Q, Zhao J, Xiong C, Li X, Chen Z, Li P, Huang W. Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii). PLoS One 2017; 12:e0175720. [PMID: 28410376 PMCID: PMC5391931 DOI: 10.1371/journal.pone.0175720] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 03/30/2017] [Indexed: 01/06/2023] Open
Abstract
The aim of this study was to investigate the effect of an ectomycorrhizal fungus (Tuber indicum) on the diversity of microbial communities associated with an indigenous tree, Pinus armandii, and the microbial communities in the surrounding ectomycorhizosphere soil. High-throughput sequencing was used to analyze the richness of microbial communities in the roots or rhizosphere of treatments with or without ectomycorrhizae. The results indicated that the bacterial diversity of ectomycorhizosphere soil was significantly lower compared with the control soil. Presumably, the dominance of truffle mycelia in ectomycorhizosphere soil (80.91%) and ectomycorrhizae (97.64%) was the main factor that resulted in lower diversity and abundance of endophytic pathogenic fungi, including Fusarium, Monographella, Ustilago and Rhizopus and other competitive mycorrhizal fungi, such as Amanita, Lactarius and Boletus. Bacterial genera Reyranena, Rhizomicrobium, Nordella, Pseudomonas and fungal genera, Cuphophyllus, Leucangium, Histoplasma were significantly more abundant in ectomycorrhizosphere soil and ectomycorrhizae. Hierarchical cluster analysis of the similarities between rhizosphere and ectomycorrhizosphere soil based on the soil properties differed significantly, indicating the mycorrhizal synthesis may have a feedback effect on soil properties. Meanwhile, some soil properties were significantly correlated with bacterial and fungal diversity in the rhizosphere or root tips. Overall, this work illustrates the interactive network that exists among ectomycorrhizal fungi, soil properties and microbial communities associated with the host plant and furthers our understanding of the ecology and cultivation of T. indicum.
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Affiliation(s)
- Qiang Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
- College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Jian Zhao
- College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Xiaolin Li
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Zuqin Chen
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Ping Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
- * E-mail:
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