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Chen M, Ding Z, Zhou M, Shang Y, Li C, Li Q, Bu T, Tang Z, Chen H. The diversity of endophytic fungi in Tartary buckwheat ( Fagopyrum tataricum) and its correlation with flavonoids and phenotypic traits. Front Microbiol 2024; 15:1360988. [PMID: 38559356 PMCID: PMC10979544 DOI: 10.3389/fmicb.2024.1360988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Tartary buckwheat (Fagopyrum tataricum) is a significant medicinal crop, with flavonoids serving as a crucial measure of its quality. Presently, the artificial cultivation of Tartary buckwheat yields low results, and the quality varies across different origins. Therefore, it is imperative to identify an effective method to enhance the yield and quality of buckwheat. Endophytic fungi reside within plants and form a mutually beneficial symbiotic relationship, aiding plants in nutrient absorption, promoting host growth, and improving secondary metabolites akin to the host. In this study, high-throughput sequencing technology was employed to assess the diversity of endophytic fungi in Tartary buckwheat. Subsequently, a correlation analysis was performed between fungi and metabolites, revealing potential increases in flavonoid content due to endophytic fungi such as Bipolaris, Hymenula, and Colletotrichum. Additionally, a correlation analysis between fungi and phenotypic traits unveiled the potential influence of endophytic fungi such as Bipolaris, Buckleyzyma, and Trichosporon on the phenotypic traits of Tartary buckwheat. Notably, the endophytic fungi of the Bipolaris genus exhibited the potential to elevate the content of Tartary buckwheat metabolites and enhance crop growth. Consequently, this study successfully identified the resources of endophytic fungi in Tartary buckwheat, explored potential functional endophytic fungi, and laid a scientific foundation for future implementation of biological fertilizers in improving the quality and growth of Tartary buckwheat.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hui Chen
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
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Ju M, Zhang Q, Wang R, Yan S, Zhang Q, Li P, Hao F, Gu P. Community ecological succession of endophytic fungi associates with medicinal compound accumulation in Sophora alopecuroides. Microbiol Spectr 2024; 12:e0307623. [PMID: 38236025 PMCID: PMC10845968 DOI: 10.1128/spectrum.03076-23] [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: 08/12/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
Endophytic fungi of medicinal plants are symbiotic with the host and play an important role in determining metabolites. To understand the relationship between the accumulation of Sophora alopecuroides' medicinal bioactive compounds and the ecological succession of endophytic fungi, here we collected samples from S. alopecuroides at four developmental stages (adult, flowering, podding, and mature) and different organs (roots, stems, leaves, and seeds) at the mature stage. We then used high-performance liquid chromatography-mass spectrometry and high-throughput sequencing on the internal transcribed spacer region to identify the medicinal compounds and endophytic fungal communities in each sample. The endophytic fungal community characteristics and accumulation of medicinally bioactive compounds of S. alopecuroides varied with the host's developmental stages and organs, with the highest total alkaloids content of 111.9 mg/g at the mature stage. Membership analysis and network connection analysis showed a total of 15 core endophytic fungi in different developmental stages and 16 core endophytic fungi in different organs at the mature stage. The unclassified Ascomycota, Aspergillus, and Alternaria were significantly and positively correlated with the medicinal compounds of S. alopecuroides at the mature stage (r > 0.6 or r < -0.6; P < 0.05). In this study, we identified key endophytic fungal resources that affect the content of medicinally bioactive compounds in S. alopecuroides. This discovery could lay the foundation for enhancing the yield of medicinally bioactive compounds in S. alopecuroides and the development and application of functional endophytic fungi.IMPORTANCESophora alopecuroides is a traditional Chinese herbal medicine. The major medicinal chemicals are considered to be quinolizidine alkaloids. Quinolizidine alkaloids have been widely used for the treatment of tumors, dysentery, and enteritis. Previous studies have found that endophytic fungi in S. alopecuroides can promote the accumulation of host quinolizidine alkaloids. However, the relationship between the accumulation of S. alopecuroides' medicinal bioactive compounds and the ecological succession of endophytic fungi remains unclear. In this study, we screened the key endophytic fungal resources affecting the content of medicinally bioactive compounds and laid the foundation for subsequent research on the mechanism by which endophytic fungi promote the accumulation of medicinally bioactive compounds in S. alopecuroides.
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Affiliation(s)
- Mingxiu Ju
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
| | - Qingchen Zhang
- Department of Pharmacotherapy and Translational Research, University of Florida, Gainesville, Florida, USA
| | - Ruotong Wang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Siyuan Yan
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
| | - Qiangqiang Zhang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
| | - Peng Li
- State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering, Ningxia University, Yinchuan, China
| | - Fengxia Hao
- State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering, Ningxia University, Yinchuan, China
| | - Peiwen Gu
- School of Agriculture, Ningxia University, Yinchuan, China
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Zhao Y, Ji X, Liu X, Qin L, Tan D, Wu D, Bai C, Yang J, Xie J, He Y. Age-dependent dendrobine biosynthesis in Dendrobium nobile: insights into endophytic fungal interactions. Front Microbiol 2023; 14:1294402. [PMID: 38149273 PMCID: PMC10749937 DOI: 10.3389/fmicb.2023.1294402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/13/2023] [Indexed: 12/28/2023] Open
Abstract
Introduction Dendrobium nobile (D. nobile), a valued Chinese herb known for its diverse pharmacological effects, owes much of its potency to the bioactive compound dendrobine. However, dendrobine content varies significantly with plant age, and the mechanisms governing this variation remain unclear. This study delves into the potential role of endophytic fungi in shaping host-microbe interactions and influencing plant metabolism. Methods Using RNA-seq, we examined the transcriptomes of 1-year-old, 2-year-old, and 3-year-old D. nobile samples and through a comprehensive analysis of endophytic fungal communities and host gene expression in D. nobile stems of varying ages, we aim to identify associations between specific fungal taxa and host genes. Results The results revealing 192 differentially expressed host genes. These genes exhibited a gradual decrease in expression levels as the plants aged, mirroring dendrobine content changes. They were enriched in 32 biological pathways, including phagosome, fatty acid degradation, alpha-linolenic acid metabolism, and plant hormone signal transduction. Furthermore, a significant shift in the composition of the fungal community within D. nobile stems was observed along the age gradient. Olipidium, Hannaella, and Plectospherella dominated in 1-year-old plants, while Strelitziana and Trichomerium prevailed in 2-year-old plants. Conversely, 3-year-old plants exhibited additional enrichment of endophytic fungi, including the genus Rhizopus. Two gene expression modules (mediumpurple3 and darkorange) correlated significantly with dominant endophytic fungi abundance and dendrobine accumulation. Key genes involved in dendrobine synthesis were found associated with plant hormone synthesis. Discussion This study suggests that the interplay between different endophytic fungi and the hormone signaling system in D. nobile likely regulates dendrobine biosynthesis, with specific endophytes potentially triggering hormone signaling cascades that ultimately influence dendrobine synthesis.
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Affiliation(s)
- Yongxia Zhao
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Xiaolong Ji
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Xiaoqi Liu
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Lin Qin
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Daopeng Tan
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Di Wu
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Chaojun Bai
- Guangxi Shenli Pharmaceutical Co., Ltd., Yulin, China
| | - Jiyong Yang
- Chishui Xintian Chinese Medicine Industry Development Co., Ltd., Zunyi, China
| | - Jian Xie
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
| | - Yuqi He
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium nobile, Engineering Research Center of Pharmaceutical Orchid Plant Breeding, High Efficiency Application in Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine, Zunyi Medical University, Zunyi, China
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Wang Y, Li P, Tian Y, Xiong Z, Zheng Z, Yi Z, Ao H, Wang Q, Li J. Bacterial seed endophyte and abiotic factors influence cadmium accumulation in rice (Oryza sativa) along the Yangtze River area. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 263:115352. [PMID: 37579590 DOI: 10.1016/j.ecoenv.2023.115352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/16/2023]
Abstract
Cadmium (Cd) contamination in rice (Oryza sativa) is particularly problematic due to its high risk to human health. Investigating the hidden roles of seed endophytes of rice in influencing Cd accumulation is essential to comprehensively understand the effects of biotic and abiotic factors to food security. Here, the content of Cd in soils and rice (Huanghuazhan) seeds from 19 sites along the Yangtze River exhibited considerable differences. From a biotic perspective, we observed the dominant endophytic bacteria, Stenotrophomonas (7.25 %), contribute to Cd control of rice (below 0.2 mg kg-1). Partial Least Squares (PLS) analysis further suggested that Enterobacteriaceae (15.48 %), altitude and pH were found to be the strong variables that might reduce the Cd uptake of rice. In contrast, Cytophagaceae (0.58 %), latitude and mean annual air pressure had the opposite effect. In pot experiments, after respectively inoculating the isolated endophytic bacteria Stenotrophomonas T4 and Enterobacter R1, N1 (f_Enterobacteriaceae), the Cd contents in shoot decreased by 47.6 %, 21.9 % and 33.0 % compared to controls. The distribution of Cd resistant genes (e.g., czcABC, nccAB, cznA) of Stenotrophomonas, Enterobacteriaceaea and Cytophagaceae further suggested their distinct manners in influencing the Cd uptake of rice. Overall, this study provides new insights into the food security threatened by globally widespread Cd pollution.
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Affiliation(s)
- Yujie Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Peng Li
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Yunhe Tian
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Ziqin Xiong
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhongyi Zheng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhenxie Yi
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Hejun Ao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qiming Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
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5
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Shen N, Chen Z, Cheng G, Lin W, Qin Y, Xiao Y, Chen H, Tang Z, Li Q, Yuan M, Bu T. Diversity, chemical constituents and biological activities of endophytic fungi from Alisma orientale (Sam.) Juzep. Front Microbiol 2023; 14:1190624. [PMID: 37415810 PMCID: PMC10320293 DOI: 10.3389/fmicb.2023.1190624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/01/2023] [Indexed: 07/08/2023] Open
Abstract
The dried tuber of Alisma orientale (Sam.) Juzep. (AOJ) is a traditional Chinese medicine with high medicinal value. The endophytic fungi of medicinal plants are a treasure house of natural compounds. However, there is a lack of research on the diversity and biological activity of endophytic fungi of AOJ. In this study, high-throughput sequencing technology was used to study the diversity of endophytic fungi in the roots and stems of AOJ, and endophytic fungi with a high output of phenols and flavonoids were screened by chromogenic reaction, and the antioxidant and antibacterial activities and chemical constituents of crude extracts of their fermentation broth were studied. A total of 3,426 amplicon sequence variants (ASVs) belonging to 9 phyla, 27 classes, 64 orders, 152 families, and 277 genera were identified from AOJ. There were significant differences in the endophytic fungal communities of AOJ roots and stems, as well as in the endophytic fungal communities of triangular AOJ and circular AOJ. In addition, 31 strains of endophytic fungi were isolated from AOJ, of which 6 strains had good antioxidant and antibacterial activities. The crude extract of YG-2 had the strongest free radical scavenging ability and bacteriostatic ability, and its IC50 DPPH, IC50 ABTS, and IC50⋅OH values were 0.009 ± 0.000 mg/mL, 0.023 ± 0.002 mg/mL, and 0.081 ± 0.006 mg/mL, respectively. The results of LC-MS showed that the main component of the crude extract of YG-2 was caffeic acid (10.12 μmol/g). Overall, the results of this study preliminarily elucidated the diversity and community composition of endophytic fungi of AOJ, indicating that AOJ endophytic fungi have abundant secondary metabolites and good antioxidant and antibacterial activities. This study provides an important reference for further research, development and utilization of AOJ endophytic fungi and a theoretical basis for the further development of the endophytic fungus YG-2 (Chaetomium globosum) as a source of antioxidants.
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Affiliation(s)
- Nayu Shen
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Zhao Chen
- Ya’an People’s Hospital, Ya’an, China
| | - GuiXin Cheng
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Wenjie Lin
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Yihan Qin
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Yirong Xiao
- Sichuan Agricultural University Hospital, Ya’an, China
| | - Hui Chen
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Zizhong Tang
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Qingfeng Li
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Ming Yuan
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Tongliang Bu
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
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Zheng Y, Wang J, Zhang X, Lei L, Yu R, Yao M, Han D, Zeng Q, Li X. Core root-associated prokaryotic community and its relationship to host traits across wheat varieties. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2740-2753. [PMID: 36807675 DOI: 10.1093/jxb/erad066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/17/2023] [Indexed: 06/06/2023]
Abstract
The root-associated microbiomes play important roles in plant growth. However, it is largely unknown how wheat variety evolutionary relatedness shapes each subcommunity in the root microbiome and, in turn, how these microbes affect wheat yield and quality. Here we studied the prokaryotic communities associated with the rhizosphere and root endosphere in 95 wheat varieties at regreening and heading stages. The results indicated that the less diverse but abundant core prokaryotic taxa occurred among all varieties. Among these core taxa, we identified 49 and 108 heritable amplicon sequence variants, whose variations in relative abundances across the root endosphere and rhizosphere samples were significantly affected by wheat variety. The significant correlations between phylogenetic distance of wheat varieties and prokaryotic community dissimilarity were only observed in non-core and abundant subcommunities in the endosphere samples. Again, wheat yield was only significantly associated with root endosphere microbiota at the heading stage. Additionally, wheat yield could be predicted using the total abundance of 94 prokaryotic taxa as an indicator. Our results demonstrated that the prokaryotic communities in the root endosphere had higher correlations with wheat yield and quality than those in the rhizosphere; thus, managing root endosphere microbiota, especially core taxa, through agronomic practices and crop breeding, is important for promoting wheat yield and quality.
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Affiliation(s)
- Yuyin Zheng
- Engineering Research Center of Soil Remediation of Fujian Province University; College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jialong Wang
- Engineering Research Center of Soil Remediation of Fujian Province University; College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xue Zhang
- Engineering Research Center of Soil Remediation of Fujian Province University; College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li Lei
- Engineering Research Center of Soil Remediation of Fujian Province University; College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rui Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Minjie Yao
- Engineering Research Center of Soil Remediation of Fujian Province University; College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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7
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Abstract
The concept of a core microbiome has been broadly used to refer to the consistent presence of a set of taxa across multiple samples within a given habitat. The assignment of taxa to core microbiomes can be performed by several methods based on the abundance and occupancy (i.e., detection across samples) of individual taxa. These approaches have led to methodological inconsistencies, with direct implications for ecological interpretation. Here, we reviewed a set of methods most commonly used to infer core microbiomes in divergent systems. We applied these methods using large data sets and analyzed simulations to determine their accuracy in core microbiome assignments. Our results show that core taxa assignments vary significantly across methods and data set types, with occupancy-based methods most accurately defining true core membership. We also found the ability of these methods to accurately capture core assignments to be contingent on the distribution of taxon abundance and occupancy in the data set. Finally, we provide specific recommendations for further studies using core taxa assignments and discuss the need for unifying methodical approaches toward data processing to advance ecological synthesis. IMPORTANCE Different methods are commonly used to assign core microbiome membership, leading to methodological inconsistencies across studies. In this study, we review a set of the most commonly used core microbiome assignment methods and compare their core assignments using both simulated and empirical data. We report inconsistent classifications from commonly applied core microbiome assignment methods. Furthermore, we demonstrate the implication that variable core assignments may have on downstream ecological interpretations. Although we still lack a standardized approach to core taxa assignments, our study provides a direction to properly test core assignment methods and offers advances in model parameterization and method choice across distinct data types.
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8
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Li P, Zong D, Gan P, Li H, Wu Z, Li F, Zhao C, Li L, He C. Comparison of the diversity and structure of the rhizosphere microbial community between the straight and twisted trunk types of Pinus yunnanensis. Front Microbiol 2023; 14:1066805. [PMID: 36910200 PMCID: PMC9995709 DOI: 10.3389/fmicb.2023.1066805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
Background Pinus yunnanensis is a major silvicultural species in Southwest China. Currently, large areas of twisted-trunk Pinus yunnanensis stands severely restrict its productivity. Different categories of rhizosphere microbes evolve alongside plants and environments and play an important role in the growth and ecological fitness of their host plant. However, the diversity and structure of the rhizosphere microbial communities between P. yunnanensis with two different trunk types-straight and twisted-remain unclear. Methods We collected the rhizosphere soil of 5 trees with the straight and 5 trees with the twisted trunk type in each of three sites in Yunnan province. We assessed and compared the diversity and structure of the rhizosphere microbial communities between P. yunnanensis with two different trunk types by Illumina sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions. Results The available phosphorus in soil differed significantly between P. yunnanensis with straight and twisted trunks. Available potassium had a significant effect on fungi. Chloroflexi dominated the rhizosphere soils of the straight trunk type, while Proteobacteria was predominant in the rhizosphere soils of the twisted trunk type. Trunk types significantly explained 6.79% of the variance in bacterial communities. Conclusion This study revealed the composition and diversity of bacterial and fungal groups in the rhizosphere soil of P. yunnanensis with straight and twisted trunk types, providing proper microbial information for different plant phenotypes.
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Affiliation(s)
- Peiling Li
- Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan, Southwest Forestry University, Kunming, China.,Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Dan Zong
- Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan, Southwest Forestry University, Kunming, China.,Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China.,Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Peihua Gan
- Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan, Southwest Forestry University, Kunming, China.,Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Hailin Li
- Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan, Southwest Forestry University, Kunming, China.,Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Zhiyang Wu
- Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan, Southwest Forestry University, Kunming, China.,Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Fahong Li
- Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan, Southwest Forestry University, Kunming, China.,Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Changlin Zhao
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China.,College of Biodiversity Conservation, Southwest Forestry University, Kunming, Yunnan, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Chengzhong He
- Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan, Southwest Forestry University, Kunming, China.,Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China.,Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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9
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Wang P, Ding L, Zou C, Zhang Y, Wang M. Rhizosphere element circling, multifunctionality, aboveground productivity and trade-offs are better predicted by rhizosphere rare taxa. FRONTIERS IN PLANT SCIENCE 2022; 13:985574. [PMID: 36161026 PMCID: PMC9495442 DOI: 10.3389/fpls.2022.985574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Microbes, especially abundant microbes in bulk soils, form multiple ecosystem functions, which is relatively well studied. However, the role of rhizosphere microbes, especially rhizosphere rare taxa vs. rhizosphere abundant taxa in regulating the element circling, multifunctionality, aboveground net primary productivity (ANPP) and the trade-offs of multiple functions remains largely unknown. Here, we compared the multiple ecosystem functions, the structure and function of rhizosphere soil bacterial and fungal subcommunities (locally rare, locally abundant, regionally rare, regionally abundant, and entire), and the role of subcommunities in the Zea mays and Sophora davidii sole and Z. mays/S. davidii intercropping ecosystems in subtropical China. Results showed that intercropping altered multiple ecosystem functions individually and simultaneously. Intercropped Z. mays significantly decreased the trade-off intensity compared to sole Z. mays, the trade-off intensity under intercropped S. davidii was significantly higher than under intercropped Z. mays. The beta diversities of bacterial and fungal communities, and fungal functions in each subcommunity significantly differed among groups. Network analysis showed intercropping increased the complexity and positive links of rare bacteria in Z. mays rhizosphere, but decreased the complexity and positive links of rare bacteria in S. davidii rhizosphere and the complexity and positive links of fungi in both intercropped plants rhizosphere. Mantel test showed significant changes in species of locally rare bacteria were most strongly related to nitrogen-cycling multifunctionality, ANPP and trade-offs intensity, significant changes in species of locally rare fungus were most strongly related to carbon-cycling multifunctionality, phosphorus-cycling multifunctionality, and average ecosystem multifunctionality. This research highlights the potential and role of rare rhizosphere microorganisms in predicting and regulating system functions, productivity, and trade-offs.
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Affiliation(s)
- Puchang Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Leilei Ding
- Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Chao Zou
- College of Animal Science, Guizhou University, Guiyang, China
| | - Yujun Zhang
- Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Mengya Wang
- College of Animal Science, Guizhou University, Guiyang, China
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10
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Chen KH, Nelson J. A scoping review of bryophyte microbiota: diverse microbial communities in small plant packages. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4496-4513. [PMID: 35536989 DOI: 10.1093/jxb/erac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
Plant health depends not only on the condition of the plant itself but also on its diverse community of microbes, or microbiota. Just like the better-studied angiosperms, bryophytes (mosses, liverworts, and hornworts) harbor diverse communities of bacteria, archaea, fungi, and other microbial eukaryotes. Bryophytes are increasingly recognized as important model systems for understanding plant evolution, development, physiology, and symbiotic interactions. Much of the work on bryophyte microbiota in the past focused on specific symbiont types for each bryophyte group, but more recent studies are taking a broader view acknowledging the coexistence of diverse microbial communities in bryophytes. Therefore, this review integrates studies of bryophyte microbes from both perspectives to provide a holistic view of the existing research for each bryophyte group and on key themes. The systematic search also reveals the taxonomic and geographic biases in this field, including a severe under-representation of the tropics, very few studies on viruses or eukaryotic microbes beyond fungi, and a focus on mycorrhizal fungi studies in liverworts. Such gaps may have led to errors in conclusions about evolutionary patterns in symbiosis. This analysis points to a wealth of future research directions that promise to reveal how the distinct life cycles and physiology of bryophytes interact with their microbiota.
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Affiliation(s)
- Ko-Hsuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jessica Nelson
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
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Kilbourn KJ, Green J, Zacharewski N, Aferzon J, Lawlor M, Jaffa M. Intracranial fungal Cladophialophora bantiana infection in a nonimmunocompromised patient: A case report and review of the literature. Surg Neurol Int 2022; 13:165. [PMID: 35509580 PMCID: PMC9062923 DOI: 10.25259/sni_116_2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/01/2022] [Indexed: 11/04/2022] Open
Abstract
Background:
Cladophialophora bantiana is a dematiaceous fungus that rarely infects the central nervous system (CNS). It is associated with a mortality rate of over 70% despite treatment.
Case Description:
An 81-year-old female with a remote history of renal cell carcinoma presented with progressive headache and an expressive aphasia for 3 days. Computed tomography imaging revealed a left frontotemporal mass with surrounding vasogenic edema. A left frontotemporal craniotomy was performed and cultures revealed C. bantiana. The initial management with IV voriconazole was unsuccessful and the patient had a recurrence of the cranial infection and developed pulmonary abscesses. Following the addition of oral flucytosine, the patient showed a significant improvement with a complete radiographic resolution of both the cranial and pulmonary lesions.
Conclusion:
C. bantiana involving the CNS is a rare and often fatal disease. Surgical management along with standard antifungal treatment may not provide definitive therapy. The addition of flucytosine to IV voriconazole resulted in a positive outcome for this patient who is alive, living independently 1 year from the original diagnosis. In this rare fungal infection, standard antifungal treatment may not provide adequate coverage and the utilization of additional therapy may be required.
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Affiliation(s)
- Kent J. Kilbourn
- Department of Neurosurgery, Hartford Hospital, Hartford, Connecticut, United States,
| | - Jaquise Green
- Department of Neurosurgery, Hartford Hospital, Hartford, Connecticut, United States,
| | - Nicholas Zacharewski
- Department of Neurosurgery, Hartford Hospital, Hartford, Connecticut, United States,
| | - Joseph Aferzon
- Department of Neurosurgery, Hartford Hospital, Hartford, Connecticut, United States,
| | - Michael Lawlor
- Department of Infectious Disease, Hartford Hospital, Hartford, Connecticut, United States,
| | - Matthew Jaffa
- Department of Neurointensive Care, Hartford Hospital, Hartford, Connecticut, United States
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12
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Rajulu MBG, Suryanarayanan TS, Murali TS, Thirunavukkarasu N, Venkatesan G. Minor species of foliar fungal endophyte communities: do they matter? Mycol Prog 2021. [DOI: 10.1007/s11557-021-01740-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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