1
|
Zhang M, Zhou Y, Cui X, Zhu L. The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis. Microorganisms 2024; 12:713. [PMID: 38674657 PMCID: PMC11051890 DOI: 10.3390/microorganisms12040713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.
Collapse
Affiliation(s)
| | | | | | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210098, China; (M.Z.); (Y.Z.); (X.C.)
| |
Collapse
|
2
|
Liu W, Cui X, Wang X, Shen C, Ji L, Zhang M, Wong MH, Zhang J, Shan S. Sugarcane mosaic virus reduced bacterial diversity and network complexity in the maize root endosphere. mSystems 2023; 8:e0019823. [PMID: 37382454 PMCID: PMC10469604 DOI: 10.1128/msystems.00198-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/18/2023] [Indexed: 06/30/2023] Open
Abstract
Sugarcane mosaic virus (SCMV) causes mosaic disease in crops such as maize and sugarcane by its vector-an aphid-and is transmitted top-down into the root system. However, understanding of the effects of the aphid-borne virus on root-associated microbes after plant invasion remains limited. The current project investigated maize root-associated (rhizosphere and endosphere) bacterial communities, potential interspecies interaction, and assembly processes in response to SCMV invasion based on 16S rRNA gene amplicon sequencing. SCMV was detected in the roots 9 days after inoculation, and leaf mosaic and chlorosis appeared. The SCMV invasion markedly reduced the α-diversity of endosphere bacteria compared with uninoculated controls (Mock). The connectivity and complexity of the bacterial co-occurrence network in the root endosphere decreased after SCMV invasion, implying that the plant virus may alter root endophyte-microbial interactions. Moreover, a signature that deviates more from stochastic processes was observed in virus-infected plants. Unexpectedly, the rhizosphere bacterial communities were rarely affected by the viral invasion. This study lays the foundation for elucidating the fate of the microbial component of the plant holobiont following aphid-borne virus exposure. IMPORTANCE Biotic (e.g., soil-borne viruses) stress can alter root-associated bacterial communities, essential in maintaining host plant growth and health. However, the regulation of root-associated microorganisms by plant viruses from shoots is still largely unknown. Our results show that plant virus invasion leads to reduced and simpler inter-microbial communication in the maize endosphere. In addition, stochastic processes act on bacterial community assembly in both rhizosphere and endosphere, and bacterial communities in virus-invaded plant endosphere tend to shift toward deterministic processes. Our study highlights the negative effects of plant viruses on root endophytes from the microbial ecology perspective, which may be microbially mediated mechanisms of plant diseases.
Collapse
Affiliation(s)
- Wenbo Liu
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Xin Cui
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Xinhai Wang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing, China
| | - Cheng Shen
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Lingfei Ji
- Department of Biology, University of York, Wentworth Way, York, United Kingdom
| | - Min Zhang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Ming Hung Wong
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
- Consortium on Health, Environment, Education and Research (CHEER), Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong, China
| | - Jin Zhang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Shengdao Shan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| |
Collapse
|
3
|
Li T, Wang M, Cui R, Li B, Wu T, Liu Y, Geng G, Xu Y, Wang Y. Waterlogging stress alters the structure of sugar beet rhizosphere microbial community structure and recruiting potentially beneficial bacterial. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115172. [PMID: 37354564 DOI: 10.1016/j.ecoenv.2023.115172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/16/2023] [Accepted: 06/18/2023] [Indexed: 06/26/2023]
Abstract
Waterlogging has been shown to have a significant inhibitory effect on plant growth. However, the response mechanisms of the soil environment of sugar beet seedlings under waterlogging conditions still need to be fully understood. This study aimed to investigate the effects of waterlogging treatments on the content of effective nutrients and the microbial communities in the rhizosphere and non-rhizosphere using high-throughput sequencing. We set up waterlogging and non-waterlogging treatments, sampled sugar beet seedlings after 10 days of waterlogging, determined the effective soil nutrients in the rhizosphere and non-rhizosphere of the plants, and analyzed the differences in microbial diversity at ten days of waterlogging. The results showed that waterlogging significantly affected available potassium (AK) content. The Ak content of waterlogged soil was significantly higher than that of non-waterlogged soil. Waterlogging caused no significant difference in available nitrogen (AN) content and pH. Moreover, the plant growth-promoting bacteria Pseudomonas was significantly enriched in sugar beet waterlogged rhizospheres compared with the non-waterlogged ones. Similarly, the harmful fungi Gibellulopsis and Alternaria were enriched in sugar beet non-waterlogged rhizosphere. The network analysis revealed that waterlogging built a less complex root-microbial network than non-waterlogging. These findings implied that sugar beets subjected to waterlogging stress were enriched with beneficial microorganisms in the rhizosphere, potentially alleviating the stress.
Collapse
Affiliation(s)
- Tai Li
- Heilongjiang Sugar Beet Engineering Technology Research Center, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74Xuefu Road, Harbin 150080, China; Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, College of Life Sciences, Heilongjiang University, 74Xuefu Road, Harbin 150080, China
| | - Meihui Wang
- Heilongjiang Sugar Beet Engineering Technology Research Center, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74Xuefu Road, Harbin 150080, China; Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, College of Life Sciences, Heilongjiang University, 74Xuefu Road, Harbin 150080, China
| | - Rufei Cui
- Heilongjiang Sugar Beet Engineering Technology Research Center, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74Xuefu Road, Harbin 150080, China; Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, College of Life Sciences, Heilongjiang University, 74Xuefu Road, Harbin 150080, China
| | - Bingchen Li
- Heilongjiang Sugar Beet Engineering Technology Research Center, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74Xuefu Road, Harbin 150080, China; Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, College of Life Sciences, Heilongjiang University, 74Xuefu Road, Harbin 150080, China
| | - Tong Wu
- College of Earth and Environmental Sciences, the University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yonglong Liu
- Heilongjiang Sugar Beet Engineering Technology Research Center, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74Xuefu Road, Harbin 150080, China; Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, College of Life Sciences, Heilongjiang University, 74Xuefu Road, Harbin 150080, China
| | - Gui Geng
- Heilongjiang Sugar Beet Engineering Technology Research Center, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74Xuefu Road, Harbin 150080, China; Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, College of Life Sciences, Heilongjiang University, 74Xuefu Road, Harbin 150080, China; National Sugar Crop Improvement Centre, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74Xuefu Road, Harbin 150080, China.
| | - Yao Xu
- Heilongjiang Sugar Beet Engineering Technology Research Center, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74Xuefu Road, Harbin 150080, China; Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, College of Life Sciences, Heilongjiang University, 74Xuefu Road, Harbin 150080, China
| | - Yuguang Wang
- Heilongjiang Sugar Beet Engineering Technology Research Center, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74Xuefu Road, Harbin 150080, China; Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, College of Life Sciences, Heilongjiang University, 74Xuefu Road, Harbin 150080, China; National Sugar Crop Improvement Centre, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74Xuefu Road, Harbin 150080, China.
| |
Collapse
|
4
|
Kumar M, Ansari WA, Zeyad MT, Singh A, Chakdar H, Kumar A, Farooqi MS, Sharma A, Srivastava S, Srivastava AK. Core microbiota of wheat rhizosphere under Upper Indo-Gangetic plains and their response to soil physicochemical properties. FRONTIERS IN PLANT SCIENCE 2023; 14:1186162. [PMID: 37255554 PMCID: PMC10226189 DOI: 10.3389/fpls.2023.1186162] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023]
Abstract
Wheat is widely cultivated in the Indo-Gangetic plains of India and forms the major staple food in the region. Understanding microbial community structure in wheat rhizosphere along the Indo-Gangetic plain and their association with soil properties can be an important base for developing strategies for microbial formulations. In the present study, an attempt was made to identify the core microbiota of wheat rhizosphere through a culture-independent approach. Rhizospheric soil samples were collected from 20 different sites along the upper Indo-Gangetic plains and their bacterial community composition was analyzed based on sequencing of the V3-V4 region of the 16S rRNA gene. Diversity analysis has shown significant variation in bacterial diversity among the sites. The taxonomic profile identified Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Planctomycetes, Verrucomicrobia, Firmicutes, and Cyanobacteria as the most dominant phyla in the wheat rhizosphere in the region. Core microbiota analysis revealed 188 taxa as core microbiota of wheat rhizosphere with eight genera recording more than 0.5% relative abundance. The order of most abundant genera in the core microbiota is Roseiflexus> Flavobacterium> Gemmatimonas> Haliangium> Iamia> Flavisolibacter> Ohtaekwangia> Herpetosiphon. Flavobacterium, Thermomonas, Massilia, Unclassified Rhizobiaceae, and Unclassified Crenarchaeota were identified as keystone taxa of the wheat rhizosphere. Correlation studies revealed, pH, organic carbon content, and contents of available nitrogen, phosphorus, and iron as the major factors driving bacterial diversity in the wheat rhizosphere. Redundancy analysis has shown the impact of different soil properties on the relative abundance of different genera of the core microbiota. The results of the present study can be used as a prelude to be developing microbial formulations based on core microbiota.
Collapse
Affiliation(s)
- Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Waquar Akhter Ansari
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Mohammad Tarique Zeyad
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Arjun Singh
- ICAR-Central Soil Salinity Research Institute, Regional Research Station (RRS), Lucknow, Uttar Pradesh, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Adarsh Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | | | - Anu Sharma
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Alok Kumar Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| |
Collapse
|
5
|
Pereira LB, Thomazella DPT, Teixeira PJPL. Plant-microbiome crosstalk and disease development. CURRENT OPINION IN PLANT BIOLOGY 2023; 72:102351. [PMID: 36848753 DOI: 10.1016/j.pbi.2023.102351] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/27/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Plants harbor a complex immune system to fight off invaders and prevent diseases. For decades, the interactions between plants and pathogens have been investigated primarily through the lens of binary interactions, largely neglecting the diversity of microbes that naturally inhabit plant tissues. Recent research, however, demonstrates that resident microbes are more than mere spectators. Instead, the plant microbiome extends host immune function and influences the outcome of a pathogen infection. Both plants and the interacting microbes produce a large diversity of metabolites that form an intricate chemical network of nutrients, signals, and antimicrobial molecules. In this review, we discuss the involvement of the plant microbiome in disease development, focusing on the biochemical conversation that occurs between plants and their associated microbiota before, during and after infection. We also highlight outstanding questions and possible directions for future research.
Collapse
Affiliation(s)
- Letícia B Pereira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Daniela P T Thomazella
- Department of Genetics, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Paulo J P L Teixeira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil.
| |
Collapse
|
6
|
Ren Z, Chen AJ, Zong Q, Du Z, Guo Q, Liu T, Chen W, Gao L. Microbiome Signature of Endophytes in Wheat Seed Response to Wheat Dwarf Bunt Caused by Tilletia controversa Kühn. Microbiol Spectr 2023; 11:e0039022. [PMID: 36625645 PMCID: PMC9927297 DOI: 10.1128/spectrum.00390-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/20/2022] [Indexed: 01/11/2023] Open
Abstract
Wheat dwarf bunt leads to the replacement of seeds with fungal galls containing millions of teliospores of the pathogen Tilletia controversa Kühn. As one of the most devastating internationally quarantined wheat diseases, wheat dwarf bunt spreads to cause distant outbreaks by seeds containing teliospores. In this study, based on a combination of amplicon sequencing and isolation approaches, we analyzed the seed microbiome signatures of endophytes between resistant and susceptible cultivars after infection with T. controversa. Among 310 bacterial species obtained only by amplicon sequencing and 51 species obtained only by isolation, we found 14 overlapping species by both methods; we detected 128 fungal species only by amplicon sequencing, 56 only by isolation, and 5 species by both methods. The results indicated that resistant uninfected cultivars hosted endophytic communities that were much more stable and beneficial to plant health than those in susceptible infected cultivars. The susceptible group showed higher diversity than the resistant group, the infected group showed more diversity than the uninfected group, and the microbial communities in seeds were related to infection or resistance to the pathogen. Some antagonistic microbes significantly suppressed the germination rate of the pathogen's teliospores, providing clues for future studies aimed at developing strategies against wheat dwarf bunt. Collectively, this research advances the understanding of the microbial assembly of wheat seeds upon exposure to fungal pathogen (T. controversa) infection. IMPORTANCE This is the first study on the microbiome signature of endophytes in wheat seed response to wheat dwarf bunt caused by Tilletia controversa Kühn. Some antagonistic microbes suppressed the germination of teliospores of the pathogen significantly, which will provide clues for future studies against wheat dwarf bunt. Collectively, this research first advances the understanding of the microbial assembly of wheat seed upon exposure to the fungal pathogen (T. controversa) infection.
Collapse
Affiliation(s)
- Zhaoyu Ren
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Amanda Juan Chen
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, People’s Republic of China
| | - Qianqian Zong
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- Xinjiang Agricultural University, Urumqi, Xinjiang, People’s Republic of China
| | - Zhenzhen Du
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Qingyuan Guo
- Xinjiang Agricultural University, Urumqi, Xinjiang, People’s Republic of China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Li Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| |
Collapse
|
7
|
Lu Q, Hu C, Cai L, Wu C, Zhang H, Wei L, Zhang T, Hu H, Liu S, Lei J, Ge T, Dai L, Yang J, Chen J. Changes in soil fungal communities after onset of wheat yellow mosaic virus disease. Front Bioeng Biotechnol 2022; 10:1033991. [PMID: 36324899 PMCID: PMC9621598 DOI: 10.3389/fbioe.2022.1033991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/30/2022] [Indexed: 10/29/2023] Open
Abstract
Rhizosphere-associated microbes have important implications for plant health, but knowledge of the association between the pathological conditions of soil-borne virus-infected wheat and soil microbial communities, especially changes in fungal communities, remains limited. We investigated the succession of fungal communities from bulk soil to wheat rhizosphere soil in both infected and healthy plants using amplicon sequencing methods, and assessed their potential role in plant health. The results showed that the diversity of fungi in wheat rhizosphere and bulk soils significantly differed post wheat yellow mosaic virus disease onset. The structure differences in fungal community at the two wheat health states or two compartment niches were evident, soil physicochemical properties (i.e., NH4 +) contribute to differences in fungal community structure and alpha diversity. Comparison analysis showed Mortierellomycetes and Dothideomycetes as dominant communities in healthy wheat soils at class level. The genus Pyronemataceae and Solicoccozyma were significantly are significantly enriched in rhizosphere soil of diseased plant, the genus Cystofilobasidium, Cladosporium, Mortierella, and Stephanonectria are significantly enriched in bulk soil of healthy plant. Co-occurrence network analysis showed that the fungi in healthy wheat soil has higher mutual benefit and connectivity compared with diseased wheat. The results of this study demonstrated that the occurrence of wheat yellow mosaic virus diseases altered both fungal community diversity and composition, and that NH4 + is the most important soil physicochemical factor influencing fungal diversity and community composition.
Collapse
Affiliation(s)
- Qisen Lu
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Cailin Hu
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Linna Cai
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Chuanfa Wu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Haoqing Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Liang Wei
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tianye Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Haichao Hu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shuang Liu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jiajia Lei
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tida Ge
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Liangying Dai
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| |
Collapse
|
8
|
Liu Y, Xiao M, Shahbaz M, Hu Z, Zhu Z, Lu S, Yu Y, Yao H, Chen J, Ge T. Microplastics in soil can increase nutrient uptake by wheat. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129547. [PMID: 35999743 DOI: 10.1016/j.jhazmat.2022.129547] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Microplastics can perturb microbial nutrient-mining strategies. However, the mechanism by which microplastics affect the resource-acquisition strategies of crops in agricultural systems remains unknown. The nutrient-acquisition potential of crops and microbes was investigated under treatments with two common microplastics (polyethylene [PE] and polyvinyl chloride [PVC]) at 0%, 1%, and 5% (w/w). Different root resource-acquisition strategies disturbed microbial nutrient turnover in the rhizosphere in response to microplastic addition. Specifically, the β-1,4-glucosidase (BG) hotspot expanded, whereas the rhizosphere expansion of BG activity decreased. A decrease of less than PE1% (w/w) and an expansion of less than PE5% (w/w) in the 1,4-N-acetyl-glucosaminidase (NAG) hotspot with wider rhizosphere expansion of NAG activity indicated that higher doses of PE allow roots to uptake additional N. The phosphomonoesterase (PHOS) hotspot decreased in PE1% (w/w) and expanded in PE5% (w/w), but rhizosphere expansion did not change under PE treatments. However, both NAG and PHOS hotspots expanded with decreasing rhizosphere expansion under PVC treatments, indicating that PVC limits the utilization of available N and P, forcing the crop to obtain nutrients from the narrow root zone. These results indicate that adding PE microplastics increases the demand for and consumption of NH4+-N and NO3--N by wheat.
Collapse
Affiliation(s)
- Yuhuai Liu
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, PR China
| | - Mouliang Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China
| | - Muhammad Shahbaz
- Centre for Environmental and Climate Science, Lund University, 223 62 Lund, Sweden
| | - Zhi'e Hu
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, PR China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China
| | - Zhenke Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China
| | - Shunbao Lu
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, PR China.
| | - Yongxiang Yu
- Ningbo Key Lab of Urban Environment Process and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo 315830, PR China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Huaiying Yao
- Ningbo Key Lab of Urban Environment Process and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo 315830, PR China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China
| | - Tida Ge
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, PR China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China.
| |
Collapse
|
9
|
Wang H, Wu C, Zhang H, Xiao M, Ge T, Zhou Z, Liu Y, Peng S, Peng P, Chen J. Characterization of the belowground microbial community and co-occurrence networks of tobacco plants infected with bacterial wilt disease. World J Microbiol Biotechnol 2022; 38:155. [PMID: 35796795 DOI: 10.1007/s11274-022-03347-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/23/2022] [Indexed: 11/25/2022]
Abstract
Characterizing the microbial communities associated with soil-borne disease incidence is a key approach in understanding the potential role of microbes in protecting crops from pathogens. In this study, we compared the soil properties and microbial composition of the rhizosphere soil and roots of healthy and bacterial wilt-infected tobacco plants to assess their potential influence on plant health. Our results revealed that the relative abundance of pathogens was higher in diseased plants than in healthy plants. Moreover, compared with healthy plants, there was a significantly higher microbial alpha diversity in the roots and rhizosphere soil of diseased plants. In addition, we detected a lower abundance of certain plant microbiota, including species in the genera Penicillium, Trichoderma, and Burkholderia in the rhizosphere of diseased plants, which were found to be significantly negatively associated with the relative abundance of Ralstonia. Indeed, compared with healthy plants, the co-occurrence networks of diseased plants included a larger number of associations linked to plant health. Furthermore, structural equation modeling revealed that these specific microbes were correlated with disease suppression, thereby implying that they may play important roles in maintaining plant health. In conclusion, our findings provide important insights into the relationships between soil-borne disease incidence and changes in the belowground microbial community. These findings will serve as a basis for further research investigating the use of specific plant-associated genera to inhibit soil-borne diseases.
Collapse
Affiliation(s)
- Haiting Wang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha, 410004, Hunan, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Chuanfa Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Haoqing Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Mouliang Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Tida Ge
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha, 410004, Hunan, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Zhicheng Zhou
- Tobacco Research Institute of Hunan Province, Changsha, 410004, China
| | - Yongjun Liu
- Tobacco Research Institute of Hunan Province, Changsha, 410004, China
| | - Shuguang Peng
- Tobacco Research Institute of Hunan Province, Changsha, 410004, China
| | - Peiqin Peng
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha, 410004, Hunan, China.
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China.
| |
Collapse
|
10
|
Su D, Chen S, Zhou W, Yang J, Luo Z, Zhang Z, Tian Y, Dong Q, Shen X, Wei S, Tong J, Cui X. Comparative Analysis of the Microbial Community Structures Between Healthy and Anthracnose-Infected Strawberry Rhizosphere Soils Using Illumina Sequencing Technology in Yunnan Province, Southwest of China. Front Microbiol 2022; 13:881450. [PMID: 35651487 PMCID: PMC9149601 DOI: 10.3389/fmicb.2022.881450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Anthracnose caused by Colletotrichum spp. was widespread in recent years and resulted in great damage to strawberry production. Soil microbial communities were key contributors to host nutrition, development, and immunity; however, the difference between the microbial communities of healthy and anthracnose-infected strawberry rhizosphere soils remains unclear. In this study, the Illumina sequencing technique was used to comparatively study the prokaryotic and fungal community compositions and structures between healthy and anthracnose-infected strawberry rhizosphere soils in Yuxi, Yunnan Province. Both microbial community diversities and richness of anthracnose-infected strawberry rhizosphere soils were higher than those of healthy strawberry rhizosphere soils. A total of 2,518 prokaryotic and 556 fungal operational taxonomic units (OTUs) were obtained at the 97% similarity threshold. Proteobacteria, Thaumarchaeota, and Acidobacteria were the dominant prokaryotic phyla; Ascomycota, unclassified_k__Fungi, and Mortierellomycota were the dominant fungal phyla. The relative abundances of beneficial bacterial phyla Actinobacteria and Firmicutes, genera Streptomyces, Azospirillum, and Bacillus were significantly reduced in anthracnose-infected strawberry rhizosphere soils; the relative abundance of beneficial fungal species Trichoderma asperellum shows a similar tendency with bacterial abundance. Besides Colletotrichum, 15 other potential fungal pathogen genera and seven fungal pathogen species were identified; among the potential pathogen genera and species, eight pathogen genera and Fusarium oxysporum showed significant differences between healthy and anthracnose-infected strawberry rhizosphere soils. The results suggested that strawberry planted in this area may be infected by other fungal pathogens except for Colletotrichum spp. Our present research will provide theoretical basis and data reference for the isolation and identification of strawberry pathogens and potential probiotics in future works.
Collapse
Affiliation(s)
- Daifa Su
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Shanyan Chen
- Kunming Academy of Agricultural Science, Kunming, China
| | - Wenxing Zhou
- Kunming Academy of Agricultural Science, Kunming, China
| | - Junyu Yang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Zhiwei Luo
- Kunming Academy of Agricultural Science, Kunming, China
| | | | - Yunxia Tian
- Kunming Academy of Agricultural Science, Kunming, China
| | - Qionge Dong
- Kunming Academy of Agricultural Science, Kunming, China
| | - Xuemei Shen
- Kunming Academy of Agricultural Science, Kunming, China
| | - Shijie Wei
- Kunming Academy of Agricultural Science, Kunming, China
| | - Jiangyun Tong
- Kunming Academy of Agricultural Science, Kunming, China
| | - Xiaolong Cui
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| |
Collapse
|
11
|
Chen G, Wu C, Wang F, Lyu H, Lu Y, Yan C, Chen J, Deng Y, Ge T. Microbial community changes in different underground compartments of potato affected yield and quality. 3 Biotech 2022; 12:106. [PMID: 35462950 PMCID: PMC8991295 DOI: 10.1007/s13205-022-03167-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/19/2022] [Indexed: 01/04/2023] Open
Abstract
Soil microbial communities are critical to plant health and productivity. Crop-associated microbial diversity may exhibit spatial specificity across regions and soil compartments. However, we lack sound evidence for the impact of variation in soil microbial diversity on plant productivity caused by regional differences. The main aims of this study are to explore the structure and functionality of the belowground (potato tuber surface and rhizosphere) microbial communities in three compartments and assess whether these communities contribute to potato productivity. Significant differences in alpha and beta diversities of belowground microbiota were detected in different compartments and regions, mainly due to differences in available soil nutrients and pH. Changes to microbial diversity between bulk soil and rhizosphere or tuber surface soil were significantly negatively correlated with potato yield and nutrient content and positively correlated with starch content. We further found some bacterial (Mucilaginibacter, Dokdonella, and Salinispora) and fungal (Solicoccozyma, Scytalidium, and Humicola) genera closely associated with potato yield and quality. Aggregated boosted tree prediction revealed that soil physicochemical properties and microbial diversity of tuber surface soil contributed more to potato yield; tuber surface soil bacterial contributed more to potato starch and nutrient content. Our findings provide experimental evidence that the significant differences in soil microbial diversity and specific microbial taxa enrichment may potentially influence crop productivity under soil physicochemical property change scenarios in the agricultural ecosystem. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03167-6.
Collapse
|