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Yadav A, Yadav R, Sharma V, Dutta U. A comprehensive guide to assess gut mycobiome and its role in pathogenesis and treatment of inflammatory bowel disease. Indian J Gastroenterol 2024; 43:112-128. [PMID: 38409485 DOI: 10.1007/s12664-023-01510-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/20/2023] [Indexed: 02/28/2024]
Abstract
Inflammatory bowel disease (IBD) is an immune mediated chronic inflammatory disorder of gastrointestinal tract, which has underlying multifactorial pathogenic determinants such as environmental factors, susceptibility genes, gut microbial dysbiosis and a dysregulated immune response. Human gut is a frequent inhabitant of complex microbial ecosystem encompassing bacteria, viruses, parasites, fungi and other microorganisms that have an undisputable role in maintaining balanced homeostasis. All of these microbes interact with immune system and affect human gut physiology either directly or indirectly with interaction of each other. Intestinal fungi represent a smaller but crucial component of the human gut microbiome. Besides interaction with bacteriome and virome, it helps in balancing homoeostasis between pathophysiological and physiological processes, which is often dysregulated in patients with IBD. Understanding of gut mycobiome and its clinical implications are still in in its infancy as opposed to bacterial component of gut microbiome, which is more often focused. Modulation of gut mycobiome represents a novel and promising strategy in the management of patients with IBD. Emerging mycobiome-based therapies such as diet interventions, fecal microbiota transplantation (FMT), probiotics (both fungal and bacterial strains) and antifungals exhibit substantial effects in calibrating the gut mycobiome and restoring dysbalanced immune homeostasis by restoring the core gut mycobiome. In this review, we summarized compositional and functional diversity of the gut mycobiome in healthy individuals and patients with IBD, gut mycobiome dysbiosis in patients with IBD, host immune-fungal interactions and therapeutic role of modulation of intestinal fungi in patients with IBD.
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Affiliation(s)
- Amit Yadav
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160 012, India
| | - Renu Yadav
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Vishal Sharma
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160 012, India
| | - Usha Dutta
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160 012, India.
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Zhao X, Hu X, Han J, Yin R, Zhang S, Liu H. Gut mycobiome: A "black box" of gut microbiome-host interactions. WIREs Mech Dis 2023; 15:e1611. [PMID: 37157158 DOI: 10.1002/wsbm.1611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/01/2023] [Accepted: 04/12/2023] [Indexed: 05/10/2023]
Abstract
Fungi, being a necessary component of the gut microbiome, potentially have direct or indirect effects on the health and illness status of the host. The gut mycobiome is an inducer of the host's immunity, maintaining intestinal homeostasis, and protecting against infections, as well as a reservoir of opportunistic microorganisms and a potential cofactor when the host is immunocompromised. In addition, gut fungi interact with a diverse range of microbes in the intestinal niches. In this article, we reviewed the composition of gut mycobiome, their association with host health and illness, and summarized the specific Candida albicans-host interactions, in order to provide insights and directions for the ongoing study of fungi. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Xinyue Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xiaomin Hu
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Junjie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ruopeng Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Shuyang Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Hongwei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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Abstract
Liver and biliary diseases affect more than a billion people worldwide, with high associated morbidity and mortality. The impact of the intestinal bacterial microbiome on liver diseases has been well established. However, the fungal microbiome, or mycobiome, has been overlooked for a long time. Recently, several studies have shed light on the role of the mycobiome in the development and progression of hepatobiliary diseases. In particular, the fungal genus Candida has been found to be involved in the pathogenesis of multiple hepatobiliary conditions. Herein, we compare colonisation and infection, describe mycobiome findings in the healthy state and across the various hepatobiliary conditions, and point toward communalities. We detail how quantitation of immune responses to fungal antigens can be employed to predict disease severity, e.g. using antibodies to Saccharomyces cerevisiae or specific anti-Candida albicans antibodies. We also show how fungal products (e.g. beta-glucans, candidalysin) activate the host's immune system to exacerbate liver and biliary diseases. Finally, we describe how the gut mycobiome can be modulated to ameliorate hepatobiliary conditions.
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Affiliation(s)
- Phillipp Hartmann
- Department of Medicine, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Division of Gastroenterology, Hepatology & Nutrition, Rady Children's Hospital San Diego, San Diego, CA, USA
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA.
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Corona Ramirez A, Bregnard D, Junier T, Cailleau G, Dorador C, Bindschedler S, Junier P. Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis. BMC Microbiol 2023; 23:68. [PMID: 36918804 PMCID: PMC10015814 DOI: 10.1186/s12866-023-02809-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/01/2023] [Indexed: 03/15/2023] Open
Abstract
At particular stages during their life cycles, fungi use multiple strategies to form specialized structures to survive unfavorable environmental conditions. These strategies encompass sporulation, as well as cell-wall melanization, multicellular tissue formation or even dimorphism. The resulting structures are not only used to disperse to other environments, but also to survive long periods of time awaiting favorable growth conditions. As a result, these specialized fungal structures are part of the microbial seed bank, which is known to influence the microbial community composition and contribute to the maintenance of diversity. Despite the importance of the microbial seed bank in the environment, methods to study the diversity of fungal structures with improved resistance only target spores dispersing in the air, omitting the high diversity of these structures in terms of morphology and environmental distribution. In this study, we applied a separation method based on cell lysis to enrich lysis-resistant fungal structures (for instance, spores, sclerotia, melanized yeast) to obtain a proxy of the composition of the fungal seed bank. This approach was first evaluated in-vitro in selected species. The results obtained showed that DNA from fungal spores and from yeast was only obtained after the application of the enrichment method, while mycelium was always lysed. After validation, we compared the diversity of the total and lysis-resistant fractions in the polyextreme environment of the Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano. Environmental samples were collected from the salt flat and from microbial mats in small surrounding ponds. Both the lake sediments and microbial mats were dominated by Ascomycota and Basidiomycota, however, the diversity and composition of each environment differed at lower taxonomic ranks. Members of the phylum Chytridiomycota were enriched in the lysis-resistant fraction, while members of the phylum Rozellomycota were never detected in this fraction. Moreover, we show that the community composition of the lysis-resistant fraction reflects the diversity of life cycles and survival strategies developed by fungi in the environment. To the best of our knowledge this is the first time that the fungal diversity is explored in the Salar de Huasco. In addition, the method presented here provides a simple and culture independent approach to assess the diversity of fungal lysis-resistant cells in the environment.
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Affiliation(s)
- Andrea Corona Ramirez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Danaé Bregnard
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Cristina Dorador
- Department of Biotechnology, University of Antofagasta, Antofagasta, Chile
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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Tan H, Liu T, Yu Y, Tang J, Jiang L, Martin FM, Peng W. Morel Production Related to Soil Microbial Diversity and Evenness. Microbiol Spectr 2021; 9:e0022921. [PMID: 34643439 PMCID: PMC8515941 DOI: 10.1128/spectrum.00229-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/10/2021] [Indexed: 01/23/2023] Open
Abstract
Black morel is a widely prized ascomycetous mushroom with culinary value. It was once uncultivable but can now be cultivated routinely in ordinary farmland soils. Large-scale morel farming sometimes encounters nonfructification for unknown reasons. In spring 2020, many morel farms in the area of Chengdu-Plain, China, exhibited no fructification at all, causing disastrous economic loss to the farmers. To determine potential ecological factors associated with the different performance of morel production in these farms, 21 affected sites versus 11 sites with normal fructification performance were analyzed to compare soil microbiota and physiochemical characteristics during fructification. The results indicated that soil physiochemical characteristics were unlikely to be a major reason for the difference between successful fructification and nonfructification. The soils with successful fructification had significantly higher diversity in both the fungal and bacterial communities than those with nonfructification. Morel yield was positively correlated with the α-diversity of fungal communities. The higher diversity of the successfully fructified soils was contributed by community evenness rather than taxonomic richness. In contrast, most nonfructification soils were dominated by a high proportion of a certain fungal genus, typically Acremonium or Mortierella, in the fungal communities. Our findings demonstrate the importance of microbial ecology to the large-scale agroindustry of soil-cultivated mushrooms. IMPORTANCE Saprotrophic mushrooms cultivated in soils are subject to complex influences from soil microbial communities. Research on growing edible mushrooms has revealed connections between fungi and a few species of growth-promoting bacteria colonizing the mycosphere. The composition and diversity of the whole microbial community may also have an influence on the growth and production of soil-saprotrophic mushrooms. Morel mushrooms (Morchella spp.) are economically and culturally important and are widely prized throughout the world. This study used the large-scale farming of morels as an example of an agroecosystem for soil-saprotrophic mushroom cultivation. It demonstrated a typical pattern of how the microbial ecology in soil agroecosystems, especially the α-diversity level and community evenness among soil fungal taxa, could affect the production of high-value cash crops and the income of farmers.
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Affiliation(s)
- Hao Tan
- Institute of Agricultural Resources and Environments, Sichuan Academy of Agricultural Sciences, Chengdu, China
- School of Bioengineering, Jiangnan University, Wuxi, China
- Scientific Observation and Experimental Station of Agro-microbial Resource and Utilization in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Tianhai Liu
- Institute of Agricultural Resources and Environments, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Scientific Observation and Experimental Station of Agro-microbial Resource and Utilization in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Yang Yu
- Institute of Agricultural Resources and Environments, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Scientific Observation and Experimental Station of Agro-microbial Resource and Utilization in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Jie Tang
- Institute of Agricultural Resources and Environments, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Scientific Observation and Experimental Station of Agro-microbial Resource and Utilization in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Lin Jiang
- Institute of Agricultural Resources and Environments, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Scientific Observation and Experimental Station of Agro-microbial Resource and Utilization in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Francis M. Martin
- Université de Lorraine, Institut National de la Recherche Agronomique, UMR Interactions Arbres/Microorganismes, Centre INRA-GrandEst-Lorraine, Champenoux, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Weihong Peng
- Institute of Agricultural Resources and Environments, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Scientific Observation and Experimental Station of Agro-microbial Resource and Utilization in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu, China
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Cai XW, Bao YQ, Hu MF, Liu JB, Zhu JM. Simulation and Prediction of Fungal Community Evolution Based on RBF Neural Network. Comput Math Methods Med 2021; 2021:7918192. [PMID: 34659448 PMCID: PMC8519688 DOI: 10.1155/2021/7918192] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/20/2021] [Indexed: 11/18/2022]
Abstract
Simulation and prediction of the scale change of fungal community. First, using the experimental data of a variety of fungal decomposition activities, a mathematical model of the decomposition rate and the relationship between the bacterial species was established, thereby revealing the internal mechanism of fungal decomposition activity in a complex environment. Second, based on the linear regression method and the principle of biodiversity, a model of fungal decomposition rate was constructed, and it was concluded that the interaction between mycelial elongation and moisture resistance could increase the fungal decomposition rate. Third, the differential equations are used to quantify the competitive relationship between different bacterial species, divide the boundaries of superior and inferior species, and simulate the long-term and short-term evolution trends of the community under the same initial environment. And an empirical analysis is made by taking the sudden change of the atmosphere affecting the evolution of the colony as an example. Finally, starting from summer, combining soil temperature, humidity, and fungal species data in five different environments such as arid and semiarid, a three-dimensional model and RBF neural network are introduced to predict community evolution. The study concluded that under given conditions, different strains are in short-term competition, and in the long-term, mutually beneficial symbiosis. Biodiversity is important for the biological regulation of nature.
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Affiliation(s)
- Xiao-Wei Cai
- School of Statistics and Applied Mathematics, Anhui University of Finance and Economics, Bengbu 233030, China
| | - Ya-Qian Bao
- School of Statistics and Applied Mathematics, Anhui University of Finance and Economics, Bengbu 233030, China
| | - Ming-Feng Hu
- School of Statistics and Applied Mathematics, Anhui University of Finance and Economics, Bengbu 233030, China
| | - Jia-Bao Liu
- School of Mathematics and Physics, Anhui Jianzhu University, Hefei 230601, China
| | - Jia-Ming Zhu
- School of Statistics and Applied Mathematics, Anhui University of Finance and Economics, Bengbu 233030, China
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Li J, Wang W, Chen S, Shao T, Tao X, Yuan X. Effect of Lactic Acid Bacteria on the Fermentation Quality and Mycotoxins Concentrations of Corn Silage Infested with Mycotoxigenic Fungi. Toxins (Basel) 2021; 13:toxins13100699. [PMID: 34678992 PMCID: PMC8537395 DOI: 10.3390/toxins13100699] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/06/2021] [Accepted: 09/28/2021] [Indexed: 12/05/2022] Open
Abstract
This study was conducted to evaluate the effect of lactic acid bacteria (LAB) on fermentation quality, mycotoxin concentrations, and microbial communities of whole-crop corn silages infested with mycotoxigenic fungi. Cultured spores (106 cfu/mL) of mycotoxigenic Aspergillus flavus and Fusarium graminearum were sprayed (5 mL) on corn forage on 27 July and 10 August 2018. On 21 August 2018, sprayed (FI; 3 plots) and unsprayed (NFI; 3 plots) corn forage were harvested at the 1/2 kernel milk line stage, followed by chopping and ensiling without inoculants (CON), or with Lactobacillus buchneri (LB, 1 × 106 cfu/g FW), Lactobacillus plantarum (LT, 1 × 106 cfu/g FW), or L. buchneri + L. plantarum (BT: both L. buchneri and L. plantarum applied at 0.5 × 106 cfu/g FW). After 90 d of ensiling, FI silages had a higher (p < 0.05) pH value and higher acetic acid (ACA), ethanol, and ammonia nitrogen (ammonia N) concentrations, but lower (p < 0.05) lactic acid (LA) concentrations than NFI silage. The inoculants decreased pH and increased LA concentration and LA/ACA compared with CON. The aflatoxin B1 (AFB1) was only detected in FI fresh corn and silages; ensiling decreased (p < 0.05) AFB1 concentration compared with fresh corn, and LB and BT decreased AFB1 concentration compared with CON. The zearalenone (ZEN), deoxynivalenol (DON), and fumonisin B1 (FB1) concentrations were similar (p < 0.05) for NFI silages, while ZEN concentration in BT was the lowest (p < 0.05) among all FI silages; DON and FB1 concentrations in LB, LT, and BT silages were significantly lower (p < 0.05) than those of CON in FI silages. The fungal infestation increased the bacterial and fungal diversity of silages compared with NFI silages. The FI silages had a higher relative abundance (RA) of Lactobacillus, Weissella, Wickerhamomyces, Pichia, and Epicoccum than the corresponding NFI silages. The RA of Aspergillus and Fusarium markedly decreased after 90 d of ensiling, and the inoculation expanded this trend irrespective of fungal infestation. The Penicillium in FI silages survived after 90 d of ensiling, while the inoculants decreased the RA of Penicillium. Inoculants mitigate the adverse effects of fungal infestation on corn silage quality by changing the bacterial and fungal communities.
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Xu S, Xiang C, Wu J, Teng Y, Wu Z, Wang R, Lu B, Zhan Z, Wu H, Zhang J. Tongue Coating Bacteria as a Potential Stable Biomarker for Gastric Cancer Independent of Lifestyle. Dig Dis Sci 2021; 66:2964-2980. [PMID: 33044677 DOI: 10.1007/s10620-020-06637-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Gastric cancer (GC) is one of the most common cancers, and the noninvasive diagnostic methods for monitoring GC are still lacking. Growing evidence shows that human microbiota has potential value for identifying digestive diseases. AIMS The present study aimed to explore the association of the tongue coating microbiota with the serum metabolic features and inflammatory cytokines in GC patients and seek a potential, noninvasive biomarker for diagnosing GC. METHODS The tongue coating microbiota was profiled by 16S rRNA and 18S rRNA genes sequencing technology in the original population with 181 GC patients and 112 healthy controls (HCs). Propensity score matching method was used to eliminate potential confounders including age, gender, and six lifestyle factors and a matching population with 66 GC patients and 66 HCs generated. Serum metabolomics profiling was performed by ultra-performance liquid chromatography tandem quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) in the matching population. Random forest model was constructed for the diagnosis of GC. RESULTS Linear discriminant analysis effect size (LEfSe) revealed that the differential bacterial taxa between GC patients and HCs in the matching population were similar to that in the original population, while the differential fungal taxa between GC patients and HCs dramatically changed before and after PSM. By random forest analysis, the combination of six bacterial genera (Peptostreptococcus, Peptococcus, Porphyromonas, Megamonas, Rothia, and Fusobacterium) was the optimal predictive model to distinguish GC patients from HCs effectively, with an area under the curve (AUC) value of 0.85. The model was verified with a high predictive potential (AUC = 0.76 to 0.96). In the matching population, eighteen specific HCs-enriched bacterial genera (Porphyromonas, Parvimonas, etc.) had negative correlations with lysophospholipids metabolites, and three of them had also negative correlations with serum IL-17α. CONCLUSIONS The alteration of tongue coating microbiota had a possible linkage with the inflammations and metabolome, and the tongue coating bacteria could be a potential noninvasive biomarker for diagnosing GC, which might be independent of lifestyle.
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Affiliation(s)
- Shuo Xu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Chunjie Xiang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Juan Wu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Yuhao Teng
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Zhenfeng Wu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Ruiping Wang
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Bin Lu
- Department of Oncology, Yangzhong People's Hospital, Yangzhong, 212200, Jiangsu, China
| | - Zhen Zhan
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Huangan Wu
- Shanghai Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Shanghai Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No. 110 Ganhe Road, Shanghai, 200000, China
| | - Junfeng Zhang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, No. 138 Xianlin Road, Nanjing, 210000, China.
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Olchowik J, Suchocka M, Jankowski P, Malewski T, Hilszczańska D. The ectomycorrhizal community of urban linden trees in Gdańsk, Poland. PLoS One 2021; 16:e0237551. [PMID: 33901193 PMCID: PMC8075230 DOI: 10.1371/journal.pone.0237551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/24/2020] [Accepted: 03/22/2021] [Indexed: 12/05/2022] Open
Abstract
The linden tree (Tilia spp.) is a popular tree for landscaping and urban environments in central and northwest European countries, and it is one of the most popular in cities in Poland. Ectomycorrhizal fungi form a symbiosis with many urban tree species and protect the host plant from heavy metals and against salinity. The aim of this study was to characterise the ECM fungal community of urban linden trees along the tree damage gradient. The study was performed on two sites located in the centre of the city of Gdańsk, in northern Poland. The vitality assessment of urban linden trees was made according to Roloff’s classification. Tree damage classes were related to soil characteristics using principal component analysis. The five ectomycorrhizal fungal species were shared among all four tree damage classes, and Cenococcum geophilum was found to be the most abundant and frequent ectomycorrhizal fungal species in each class. Soil samples collected in the vicinity of trees belonging to the R0 class had significantly lower pH Na, Cl and Pb content than other soils. Our knowledge of ectomycorrhizal communities in urban areas is still limited, and these findings provide new insights into ectomycorrhizal distribution patterns in urban areas.
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Affiliation(s)
- Jacek Olchowik
- Department of Plant Protection, Institute of Horticultural Sciences, Warsaw University of Life Sciences, Warsaw, Poland
- * E-mail:
| | - Marzena Suchocka
- Department of Landscape Architecture, Institute of Environmental Engineering, Warsaw University of Life Sciences, Warsaw, Poland
| | - Paweł Jankowski
- Department of Computer Information Systems, Institute of Information Technology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Tadeusz Malewski
- Department of Molecular and Biometric Techniques, Museum and Institute of Zoology, Polish Academy of Science, Warsaw, Poland
| | - Dorota Hilszczańska
- Department of Forest Ecology, Forest Research Institute, Sękocin Stary, Poland
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Rios-Navarro A, Gonzalez M, Carazzone C, Celis Ramírez AM. Learning about microbial language: possible interactions mediated by microbial volatile organic compounds (VOCs) and relevance to understanding Malassezia spp. metabolism. Metabolomics 2021; 17:39. [PMID: 33825999 PMCID: PMC8026438 DOI: 10.1007/s11306-021-01786-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/13/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Microorganisms synthesize and release a large diversity of small molecules like volatile compounds, which allow them to relate and interact with their environment. Volatile organic compounds (VOCs) are carbon-based compounds with low molecular weight and generally, high vapor pressure; because of their nature, they spread easily in the environment. Little is known about the role of VOCs in the interaction processes, and less is known about VOCs produced by Malassezia, a genus of yeasts that belongs to the human skin mycobiota. These yeasts have been associated with several dermatological diseases and currently, they are considered as emerging opportunistic yeasts. Research about secondary metabolites of these yeasts is limited. The pathogenic role and the molecular mechanisms involved in the infection processes of this genus are yet to be clarified. VOCs produced by Malassezia yeasts could play an important function in their metabolism; in addition, they might be involved in either beneficial or pathogenic host-interaction processes. Since these yeasts present differences in their nutritional requirements, like lipids to grow, it is possible that these variations of growth requirements also define differences in the volatile organic compounds produced in Malassezia species. AIM OF REVIEW We present a mini review about VOCs produced by microorganisms and Malassezia species, and hypothesize about their role in its metabolism, which would reveal clues about host-pathogen interaction. KEY SCIENTIFIC CONCEPTS OF REVIEW Since living organisms inhabit a similar environment, the interaction processes occur naturally; as a result, a signal and a response from participants of these processes become important in understanding several biological behaviors. The efforts to elucidate how living organisms interact has been studied from several perspectives. An important issue is that VOCs released by the microbiota plays a key role in the setup of relationships between living micro and macro organisms. The challenge is to determine what is the role of these VOCs produced by human microbiota in commensal/pathogenic scenarios, and how these allow understanding the species metabolism. Malassezia is part of the human mycobiota, and it is implicated in commensal and pathogenic processes. It is possible that their VOCs are involved in these behavioral changes, but the knowledge about this remains overlocked. For this reason, VOCs produced by microorganisms and Malassezia spp. and their role in several biological processes are the main topic in this review.
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Affiliation(s)
- Andrea Rios-Navarro
- grid.7247.60000000419370714Cellular and Molecular of Pathogenic Microorganisms Research Group (CeMoP), Biological Sciences Department, Universidad de Los Andes, Cra 1 No. 18A-12, Bogotá, 111711 Cundinamarca Colombia
| | - Mabel Gonzalez
- grid.7247.60000000419370714Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de Los Andes, Cra 1 No. 18A-12, Bogotá, 111711 Cundinamarca Colombia
| | - Chiara Carazzone
- grid.7247.60000000419370714Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de Los Andes, Cra 1 No. 18A-12, Bogotá, 111711 Cundinamarca Colombia
| | - Adriana Marcela Celis Ramírez
- grid.7247.60000000419370714Cellular and Molecular of Pathogenic Microorganisms Research Group (CeMoP), Biological Sciences Department, Universidad de Los Andes, Cra 1 No. 18A-12, Bogotá, 111711 Cundinamarca Colombia
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11
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Iliev ID, Cadwell K. Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases. Gastroenterology 2021; 160:1050-1066. [PMID: 33347881 PMCID: PMC7956156 DOI: 10.1053/j.gastro.2020.06.100] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
The intestinal microbiota comprises diverse fungal and viral components, in addition to bacteria. These microbes interact with the immune system and affect human physiology. Advances in metagenomics have associated inflammatory and autoimmune diseases with alterations in fungal and viral species in the gut. Studies of animal models have found that commensal fungi and viruses can activate host-protective immune pathways related to epithelial barrier integrity, but can also induce reactions that contribute to events associated with inflammatory bowel disease. Changes in our environment associated with modernization and the COVID-19 pandemic have exposed humans to new fungi and viruses, with unknown consequences. We review the lessons learned from studies of animal viruses and fungi commonly detected in the human gut and how these might affect health and intestinal disease.
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Affiliation(s)
- Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, New York; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, New York.
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine, Skirball Institute, New York University Grossman School of Medicine, New York, New York; Department of Microbiology, New York University Grossman School of Medicine, New York, New York; Division of Gastroenterology and Hepatology, Department of Medicine, New York University Langone Health, New York, New York.
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12
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Zhang C, Lin Z, Que Y, Fallah N, Tayyab M, Li S, Luo J, Zhang Z, Abubakar AY, Zhang H. Straw retention efficiently improves fungal communities and functions in the fallow ecosystem. BMC Microbiol 2021; 21:52. [PMID: 33596827 PMCID: PMC7890633 DOI: 10.1186/s12866-021-02115-3] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Straw retention is a substitute for chemical fertilizers, which effectively maintain organic matter and improve microbial communities on agricultural land. The purpose of this study was to provide sufficient information on soil fungal community networks and their functions in response to straw retention. Hence, we used quantitative real-time PCR (qRT-PCR), Illumina MiSeq (ITS rRNA) and FUNGuild to examine ITS rRNA gene populations, soil fungal succession and their functions under control (CK) and sugarcane straw retention (SR) treatments at different soil layers (0-10, 10-20, 20-30, and 30-40 cm) in fallow fields. RESULT The result showed that SR significantly enhanced ITS rRNA gene copy number and Shannon index at 0-10 cm soil depth. Fungi abundance, OTUs number and ACE index decreased with the increasing soil depth. The ANOSIM analysis revealed that the fungal community of SR significantly differed from that of CK. Similarly, significant difference was also observed between topsoil (0-20 cm) and subsoil (20-40 cm). Compared with CK, SR decreased the relative abundance of the pathogen, while increased the proportion of saprotroph. Regarding soil depth, pathogen relative abundance in topsoil was lower than that in subsoil. Besides, both sugarcane straw retention and soil depths (topsoil and subsoil) significantly altered the co-occurrence patterns and fungal keystone taxa closely related to straw decomposition. Furthermore, both SR and topsoil had higher average clustering coefficients (aveCC), negative edges and varied modularity. CONCLUSIONS Overall, straw retention improved α-diversity, network structure and fungal community, while reduced soil pathogenic microbes across the entire soil profile. Thus, retaining straw to improve fungal composition, community stability and their functions, in addition to reducing soil-borne pathogens, can be an essential agronomic practice in developing a sustainable agricultural system.
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Affiliation(s)
- Caifang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhaoli Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Muhammad Tayyab
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Shiyan Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jun Luo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zichu Zhang
- Fuzhou No.8 High School, Fuzhou, 350000 China
| | - Ahmad Yusuf Abubakar
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hua Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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13
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Floc'h JB, Hamel C, Harker KN, St-Arnaud M. Fungal Communities of the Canola Rhizosphere: Keystone Species and Substantial Between-Year Variation of the Rhizosphere Microbiome. Microb Ecol 2020; 80:762-777. [PMID: 31897569 DOI: 10.1007/s00248-019-01475-8] [Citation(s) in RCA: 12] [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] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/16/2019] [Indexed: 05/25/2023]
Abstract
Rhizosphere microbes influence one another, forming extremely complex webs of interactions that may determine plant success. Identifying the key factors that structure the fungal microbiome of the plant rhizosphere is a necessary step in optimizing plant production. In a long-term field experiment conducted at three locations in the Canadian prairies, we tested the following hypotheses: (1) diversification of cropping systems influences the fungal microbiome of the canola (Brassica napus) rhizosphere; (2) the canola rhizosphere has a core fungal microbiome, i.e., a set of fungi always associated with canola; and (3) some taxa within the rhizosphere microbiome of canola are highly interrelated and fit the description of hub taxa. Our results show that crop diversification has a significant effect on the structure of the rhizosphere fungal community but not on fungal diversity. We also discovered and described a canola core microbiome made up of one zero-radius operational taxonomic unit (ZOTU), cf. Olpidium brassicae, and an eco-microbiome found only in 2013 consisting of 47 ZOTUs. Using network analysis, we identified four hub taxa in 2013: ZOTU14 (Acremonium sp.), ZOTU28 (Sordariomycetes sp.), ZOTU45 (Mortierella sp.) and ZOTU179 (cf. Ganoderma applanatum), and one hub taxon, ZOTU17 (cf. Mortierella gamsii) in 2016. None of these most interacting taxa belonged to the core microbiome or eco-microbiome for each year of sampling. This temporal variability puts into question the idea of a plant core fungal microbiome and its stability. Our results provide a basis for the development of ecological engineering strategies for the improvement of canola production systems in Canada.
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Affiliation(s)
- Jean-Baptiste Floc'h
- Institut de recherche en biologie végétale, ,Université de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada
- Jardin Botanique de Montréal, Montreal, Canada
- Québec Research and Development Centre of Quebec, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - Chantal Hamel
- Institut de recherche en biologie végétale, ,Université de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada
- Jardin Botanique de Montréal, Montreal, Canada
- Québec Research and Development Centre of Quebec, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - K Neil Harker
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, ,Université de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada.
- Jardin Botanique de Montréal, Montreal, Canada.
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Jiang Y, Luan L, Hu K, Liu M, Chen Z, Geisen S, Chen X, Li H, Xu Q, Bonkowski M, Sun B. Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences. Microbiome 2020; 8:142. [PMID: 33008469 PMCID: PMC7532650 DOI: 10.1186/s40168-020-00918-6] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/07/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND The soil mycobiome is composed of a complex and diverse fungal community, which includes functionally diverse species ranging from plant pathogens to mutualists. Among the latter are arbuscular mycorrhizal fungi (AMF) that provide phosphorous (P) to plants. While plant hosts and abiotic parameters are known to structure AMF communities, it remains largely unknown how higher trophic level organisms, including protists and nematodes, affect AMF abundance and community composition. RESULTS Here, we explored the connections between AMF, fungivorous protists and nematodes that could partly reflect trophic interactions, and linked those to rhizosphere P dynamics and plant performance in a long-term manure application setting. Our results revealed that manure addition increased AMF biomass and the density of fungivorous nematodes, and tailored the community structures of AMF, fungivorous protists, and nematodes. We detected a higher abundance of AMF digested by the dominant fungivorous nematodes Aphelenchoides and Aphelenchus in high manure treatments compared to no manure and low manure treatments. Structural equation modeling combined with network analysis suggested that predation by fungivorous protists and nematodes stimulated AMF biomass and modified the AMF community composition. The mycorrhizal-fungivore interactions catalyzed AMF colonization and expression levels of the P transporter gene ZMPht1;6 in maize roots, which resulted in enhanced plant productivity. CONCLUSIONS Our study highlights the importance of predation as a key element in shaping the composition and enhancing the biomass of AMF, leading to increased plant performance. As such, we clarify novel biological mechanism of the complex interactions between AMF, fungivorous protists, and nematodes in driving P absorption and plant performance. Video Abstract.
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Affiliation(s)
- Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Kaijie Hu
- College of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Manqiang Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ziyun Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, 6700 ES, Wageningen, Netherlands.
| | - Xiaoyun Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huixin Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qinsong Xu
- College of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Michael Bonkowski
- Institute of Zoology, Terrestrial Ecology, University of Cologne and Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
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15
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Fan W, Wu J. Short-term effects of returning granulated straw on soil microbial community and organic carbon fractions in dryland farming. J Microbiol 2020; 58:657-667. [PMID: 32583286 DOI: 10.1007/s12275-020-9266-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 05/30/2019] [Revised: 04/16/2020] [Accepted: 05/12/2020] [Indexed: 11/25/2022]
Abstract
We conducted a 2-year field experiment which was comprised of five treatments, namely no straw returning (CK), straw mulching (SM), straw plowed into the soil (SP), and straw returned in granulated form (SG). The aim of this study was to investigate the effects of different straw returning modes on soil bacterial and fungal community structure and their relationships to soil organic carbon (SOC) fractions at three different soil depths (0-20, 20-40, and 40-60 cm) in a dryland under maize cultivation in Northeast (NE) China. SM, SP, and SG treatments significantly increased SOC content. Compared with SM and SP treatments, SG treatment significantly increased the content of SOC and easily oxidizable carbon (EOC) in the topsoil (0-20 cm depth), and increased dissolved organic carbon (DOC) and SOC content of the light fraction (LFOC) in the 20-40 cm layer. Meanwhile, SG treatment exhibited the highest microbial biomass C (MBC) content in all of the three soil depths. SG treatment also enhanced bacterial richness as well as fungal richness and diversity in the upper 40 cm of soil. In addition, SG treatment increased the relative abundance of Proteobacteria in all depths, and had the highest relative abundance of Basidiomycota in the first 20 cm of soil. SP treatment showed the lowest soil organic carbon content in all fractions and soil microbial community composition. SM treatment exhibited similar results to SG treatment in SOC, DOC, and LFOC contents, and bacterial diversity in the topsoil and subsoil. As a whole, treatment SG improved soil quality and maize yield, hence we recommend returning granulated straw as the most effective practice for enhancing labile SOC fractions as well as maintaining soil diversity and microbial richness of arid farmlands in NE China.
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Affiliation(s)
- Wei Fan
- College of Resources and Environment Sciences, Jilin Agricultural University, Changchun, 130118, P. R. China
| | - Jinggui Wu
- College of Resources and Environment Sciences, Jilin Agricultural University, Changchun, 130118, P. R. China.
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16
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Massa N, Bona E, Novello G, Todeschini V, Boatti L, Mignone F, Gamalero E, Lingua G, Berta G, Cesaro P. AMF communities associated to Vitis vinifera in an Italian vineyard subjected to integrated pest management at two different phenological stages. Sci Rep 2020; 10:9197. [PMID: 32514032 PMCID: PMC7280190 DOI: 10.1038/s41598-020-66067-w] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 05/14/2020] [Indexed: 11/10/2022] Open
Abstract
Vitis vinifera L. is an economically important crop that can be influenced by soil microorganisms, including arbuscular mycorrhizal fungi (AMF), that establish symbiotic associations with its roots. AMF have beneficial effects on grapevine performance improving water use efficiency and replant success. Most grapevine varieties are susceptible to various diseases, and integrated pest management (IPM) is one of the emerging approaches to perform pest control. In the present study, we examined the AMF communities present in the soil associated to the roots of V. vinifera cv. Pinot Noir (comparing them to those present in a soil not affected by grapevine roots), in a vineyard subjected to IPM at two different phenological stages, using 454 Roche sequencing technology. We proposed a new approach to analyze sequencing data. Most of the taxa were included in the family Glomeraceae. In particular, Glomus sp. Rhizophagus sp. and Septoglomus viscosum were present. The family Archeosporaceae was represented only by the genus Archeospora sp. Different AMF communities were found in the two soils and the importance of the phenological stage in regulating AMF biodiversity was assessed.
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Affiliation(s)
- N Massa
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - E Bona
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Piazza San Eusebio 5, 13100, Vercelli, Italy
| | - G Novello
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - V Todeschini
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Piazza San Eusebio 5, 13100, Vercelli, Italy
| | - L Boatti
- SmartSeq s.r.l., spin-off of the Università del Piemonte Orientale, Viale T. Michel 11, Alessandria, 15121, Italy
| | - F Mignone
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
- SmartSeq s.r.l., spin-off of the Università del Piemonte Orientale, Viale T. Michel 11, Alessandria, 15121, Italy
| | - E Gamalero
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - G Lingua
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - G Berta
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - P Cesaro
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy.
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17
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Liu L, Wang S, Chen J. Hysteretic response of Microbial Eukaryotic Communities to Gradually Decreased Nutrient Concentrations in Eutrophic Water. Microb Ecol 2020; 79:815-822. [PMID: 31720759 DOI: 10.1007/s00248-019-01457-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
External environments to microbial eukaryotic communities often change gradually with time. However, whether the responses of microbial eukaryotic communities to these gradually changed environments are continuous or hysteretic and the mechanisms underlying these responses are largely unknown. Here, we used a microcosm to investigate the temporal variation of microbial eukaryotic communities with the gradually decreased nutrient concentrations (nitrogen and phosphorus). We found the differences of microbial eukaryotic community composition and species richness between the control and treatment groups were low during the days 0 to 12, although the nutrient concentrations decreased rapidly during this period in treatment group. However, these differences were clear during the days 14 to 18, although the nutrient concentrations decreased slowly during this period in treatment group. The mechanisms for these results are that the strong homogenous selection (perhaps due to the biotic factors) during the days 8 to 10 in treatment group might enhance the stability of microbial eukaryotic communities. However, the continuously decreased nutrient concentrations weakened the homogenous selection and promoted the strength of environmental filtering, and therefore resulted in the distinct change of microbial eukaryotic communities during the days 14 to 18 in treatment group. Fungi, Chlorophyta and Chrysophyta which associated with the nutrient removal played important roles in this hysteretic change of microbial eukaryotic communities. Overall, our findings suggest that disentangling the non-linear response of communities to gradual environmental changes is essential for understanding ecosystem restoration and degradation in future.
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Affiliation(s)
- Lemian Liu
- Technical Innovation Service Platform for High Value and High Quality Utilization of Marine Organism, Fuzhou University, Fuzhou, 350108, China.
- Fujian Engineering and Technology Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fuzhou, 350108, China.
- Fuzhou Industrial Technology Innovation Center for High Value Utilization of Marine Products, Fuzhou University, Fuzhou, 350108, China.
| | - Shanshan Wang
- Technical Innovation Service Platform for High Value and High Quality Utilization of Marine Organism, Fuzhou University, Fuzhou, 350108, China
- Fujian Engineering and Technology Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fuzhou, 350108, China
- Fuzhou Industrial Technology Innovation Center for High Value Utilization of Marine Products, Fuzhou University, Fuzhou, 350108, China
| | - Jianfeng Chen
- Technical Innovation Service Platform for High Value and High Quality Utilization of Marine Organism, Fuzhou University, Fuzhou, 350108, China.
- Fujian Engineering and Technology Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fuzhou, 350108, China.
- Fuzhou Industrial Technology Innovation Center for High Value Utilization of Marine Products, Fuzhou University, Fuzhou, 350108, China.
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18
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Chen M, Zhang J, Liu H, Wang M, Pan L, Chen N, Wang T, Jing Y, Chi X, Du B. Long-term continuously monocropped peanut significantly disturbed the balance of soil fungal communities. J Microbiol 2020; 58:563-573. [PMID: 32329018 DOI: 10.1007/s12275-020-9573-x] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 01/30/2023]
Abstract
Balancing soil microbial diversity and abundance is critical to sustaining soil health, and understanding the dynamics of soil microbes in a monocropping system can help determine how continuous monocropping practices induce soil sickness mediated by microorganisms. This study used previously constructed gradient continuous monocropping plots and four varieties with different monocropping responses were investigated. The feedback responses of their soil fungal communities to short-term and long-term continuous monocropping were tracked using high-throughput sequencing techniques. The analyses indicated that soil samples from 1 and 2 year monocropped plots were grouped into one class, and samples from the 11 and 12 year plots were grouped into another, regardless of variety. At the species level, the F. solani, Fusarium oxysporum, Neocosmospora striata, Acrophialophora levis, Aspergillus niger, Aspergillus corrugatus, Thielavia hyrcaniae, Emericellopsis minima, and Scedosporium aurantiacum taxa showed significantly increased abundances in the long-term monocropping libraries compared to the short-term cropping libraries. In contrast, Talaromyces flavus, Talaromyces purpureogenus, Mortierella alpina, Paranamyces uniporus, and Volutella citrinella decreased in the long-term monocropping libraries compared to the short-term libraries. This study, combined with our previous study, showed that fungal community structure was significantly affected by the length of the monocropping period, but peanut variety and growth stages were less important. The increase in pathogen abundances and the decrease in beneficial fungi abundances seem to be the main cause for the yield decline and poor growth of long-term monocultured peanut. Simplification of fungal community diversity could also contribute to peanut soil sickness under long-term monocropping. Additionally, the different responses of peanut varieties to monocropping may be related to variations in their microbial community structure.
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Affiliation(s)
- Mingna Chen
- Shandong Peanut Research Institute, Qingdao, P. R. China
- College of Life Sciences, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Taian, P. R. China
| | | | - Hu Liu
- College of Life Sciences, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Taian, P. R. China
| | - Mian Wang
- Shandong Peanut Research Institute, Qingdao, P. R. China
| | - LiJuan Pan
- Shandong Peanut Research Institute, Qingdao, P. R. China
| | - Na Chen
- Shandong Peanut Research Institute, Qingdao, P. R. China
| | - Tong Wang
- Shandong Peanut Research Institute, Qingdao, P. R. China
| | - Yu Jing
- Shandong Peanut Research Institute, Qingdao, P. R. China
| | - Xiaoyuan Chi
- Shandong Peanut Research Institute, Qingdao, P. R. China.
| | - Binghai Du
- College of Life Sciences, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Taian, P. R. China.
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19
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Rojas EC, Sapkota R, Jensen B, Jørgensen HJL, Henriksson T, Jørgensen LN, Nicolaisen M, Collinge DB. Fusarium Head Blight Modifies Fungal Endophytic Communities During Infection of Wheat Spikes. Microb Ecol 2020; 79:397-408. [PMID: 31448388 PMCID: PMC7033075 DOI: 10.1007/s00248-019-01426-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 11/23/2018] [Accepted: 08/13/2019] [Indexed: 05/29/2023]
Abstract
Fusarium head blight (FHB) is a devastating disease of wheat heads. It is caused by several species from the genus Fusarium. Several endophytic fungi also colonize wheat spikes asymptomatically. Pathogenic and commensal fungi share and compete for the same niche and thereby influence plant performance. Understanding the natural dynamics of the fungal community and how the pre-established species react to pathogen attack can provide useful information on the disease biology and the potential use of some of these endophytic organisms in disease control strategies. Fungal community composition was assessed during anthesis as well as during FHB attack in wheat spikes during 2016 and 2017 in two locations. Community metabarcoding revealed that endophyte communities are dominated by basidiomycete yeasts before anthesis and shift towards a more opportunistic ascomycete-rich community during kernel development. These dynamics are interrupted when Fusarium spp. colonize wheat spikes. The Fusarium pathogens appear to exclude other fungi from floral tissues as they are associated with a reduction in community diversity, especially in the kernel which they colonize rapidly. Similarly, the presence of several endophytes was negatively correlated with Fusarium spp. and linked with spikes that stayed healthy despite exposure to the pathogen. These endophytes belonged to the genera Cladosporium, Itersonillia and Holtermanniella. These findings support the hypothesis that some naturally occurring endophytes could outcompete or prevent FHB and represent a source of potential biological control agents in wheat.
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Affiliation(s)
- Edward C Rojas
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences & Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark.
| | - Rumakanta Sapkota
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Birgit Jensen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences & Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Hans J L Jørgensen
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences & Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | | | - Lise Nistrup Jørgensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - David B Collinge
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences & Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
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20
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Vujanovic V, Islam MN, Daida P. Transgenerational role of seed mycobiome - an endosymbiotic fungal composition as a prerequisite to stress resilience and adaptive phenotypes in Triticum. Sci Rep 2019; 9:18483. [PMID: 31811154 PMCID: PMC6898677 DOI: 10.1038/s41598-019-54328-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/08/2019] [Indexed: 12/16/2022] Open
Abstract
Illumina-MiSeq next-generation sequencing of ITS 5.8S rRNA gene demonstrated the transgenerational transmission of fungal seed-endophytes (mycobiome) across three consecutive wheat host generations under standard-control and drought conditions in the greenhouse. Drought-stressed plants experienced a positive shift in the seed mycobiome's composition, moderated by the external acquisition of endophytic Penicillium (E+) at the seed level. Untreated (E-) and unstressed plants harbor a maximal fungal diversity of non-equilibrium ecological communities. While fungal composition in drought-stressed E- plants experienced important fluctuation, E+ plants maintained fungal ecological communities in phase equilibrium across generations. E+ plants hosted a relatively higher abundance of Ascomycota in the 2nd and 3rd seed generations of wheat, whereas higher abundance of Basidiomycota was detected in 1st generation seeds. The dynamic response of ecological communities to environmental stress is conducive to E+ plants' active recruitment of endosymbiotic consortia in seeds, benefiting host stress resilience and phenotype. In contrast, E- plants showed an erratic distribution of detected OTUs with an increased occurrence of phytopathogens and diminished plant performance under stress. The present study gives insight into the understanding of the seed-mycobiome composition and dynamics with the potential to improve plant host traits in an adverse environment.
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Affiliation(s)
- Vladimir Vujanovic
- Department of Food and Bioproduct Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - M Nazrul Islam
- Department of Food and Bioproduct Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Prasad Daida
- Department of Food and Bioproduct Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
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Lu N, Xu X, Wang P, Zhang P, Ji B, Wang X. Succession in arbuscular mycorrhizal fungi can be attributed to a chronosequence of Cunninghamia lanceolata. Sci Rep 2019; 9:18057. [PMID: 31792242 PMCID: PMC6889488 DOI: 10.1038/s41598-019-54452-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 11/14/2019] [Indexed: 02/02/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi play an important role in plant-fungi communities. It remains a central question of how the AM fungal community changes as plants grow. To establish an understanding of AM fungal community dynamics associated with Chinese fir, Chinese fir with five different growth stages were studied and 60 root samples were collected at the Jiangle National Forestry Farm, Fujian Province. A total of 76 AM fungal operational taxonomic units (OTUs) were identified by high-throughput sequencing on an Illumina Miseq platform. The genera covered by OTUs were Glomus, Archaeospora, Acaulospora, Gigaspora and Diversispora. Glomus dominated the community in the whole stage. The number and composition of OTUs varied along with the host plant growth. The number of OTUs showed an inverted V-shaped change with the host plant age, and the maximum occurred in 23-year. Overall, the basic species diversity and richness in this study were stable. Non-metric multi-dimensional scaling (NMDS) analysis based on bray-curtis distance revealed that there were remarkable differentiations between the 9-year and other stages. Besides, AM fungal community in 32-year had a significant difference with that of 23-year, while no significant difference with that of 45-year, suggesting that 32-year may be a steady stage for AM fungi associated with Chinese fir. The cutting age in 32-year may be the most favorable for microbial community. The pH, total N, total P, total K, available N, available P, available K, organic matter and Mg varied as the Chinese fir grows. According to Mantel test and redundancy analysis, available N, available P, K and Mg could exert significant influence on AM fungal communities, and these variables explained 31% of variance in the composition of AM fungal communities.
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Affiliation(s)
- Nini Lu
- College of Forestry, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Silviculture and Conservation Joint-constructed by Province and Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Xuelei Xu
- College of Forestry, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Silviculture and Conservation Joint-constructed by Province and Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Ping Wang
- College of Forestry, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Silviculture and Conservation Joint-constructed by Province and Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Peng Zhang
- College of Forestry, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Silviculture and Conservation Joint-constructed by Province and Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Experimental Forest Farm, Beijing Forestry University, Beijing, 100095, China
| | - Baoming Ji
- College of Forestry, Beijing Forestry University, Beijing, 100083, China
| | - Xinjie Wang
- College of Forestry, Beijing Forestry University, Beijing, 100083, China.
- Key Laboratory for Silviculture and Conservation Joint-constructed by Province and Ministry of Education, Beijing Forestry University, Beijing, 100083, China.
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Vieira LC, da Silva DKA, de Melo MAC, Escobar IEC, Oehl F, da Silva GA. Edaphic Factors Influence the Distribution of Arbuscular Mycorrhizal Fungi Along an Altitudinal Gradient of a Tropical Mountain. Microb Ecol 2019; 78:904-913. [PMID: 30976842 DOI: 10.1007/s00248-019-01354-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 11/30/2018] [Accepted: 03/04/2019] [Indexed: 06/09/2023]
Abstract
Changes in relief in montane areas, with increasing altitude, provide different biotic and abiotic conditions, acting on the species of arbuscular mycorrhizal fungi (AMF). The objective of this work was to determine the influence of altitude, edaphic factors, and vegetation on the AMF species in a mountainous area. The list of AMF species was obtained from morphological identification of the spores, with 72 species recovered from field samples and trap cultures. Lower levels of Shannon's diversity occurred only at lower altitude; however, there was no difference in AMF richness. The structure of the AMF assembly between the two highest altitudes was similar and differed in relation to the lower altitude. There was variation in the distribution of AMF species, which was related to soil texture and chemical factors along the altitude gradient. Some species, genera, and families were indicative of a certain altitude, showing the preference of fungi for certain environmental conditions, which may aid in decisions to conserve montane ecosystems.
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Affiliation(s)
- Larissa Cardoso Vieira
- Departamento de Micologia, Laboratório de Micorrizas, Universidade Federal de Pernambuco, Av. Prof. Nelson Chaves s/n. Cidade Universitária, CEP 50670-420, Recife, Pernambuco, Brazil.
| | - Danielle Karla Alves da Silva
- Centro de Ciências Aplicadas e Educação, Campus IV, Departamento de Engenharia e Meio Ambiente, Universidade Federal da Paraíba, Av. Santa Elizabete s/n. CEP 56300-990, Rio Tinto, Paraíba, Brazil
| | - Mayara Alice Correia de Melo
- Departamento de Micologia, Laboratório de Micorrizas, Universidade Federal de Pernambuco, Av. Prof. Nelson Chaves s/n. Cidade Universitária, CEP 50670-420, Recife, Pernambuco, Brazil
| | - Indra Elena Costa Escobar
- Departamento de Micologia, Laboratório de Micorrizas, Universidade Federal de Pernambuco, Av. Prof. Nelson Chaves s/n. Cidade Universitária, CEP 50670-420, Recife, Pernambuco, Brazil
| | - Fritz Oehl
- Agroscope, Competence Division for Plants and Plant Products, Ecotoxicology, Schloss 1, CH-8820, Wädenswil, Switzerland
| | - Gladstone Alves da Silva
- Departamento de Micologia, Laboratório de Micorrizas, Universidade Federal de Pernambuco, Av. Prof. Nelson Chaves s/n. Cidade Universitária, CEP 50670-420, Recife, Pernambuco, Brazil
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23
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Chen S, Waghmode TR, Sun R, Kuramae EE, Hu C, Liu B. Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization. Microbiome 2019; 7:136. [PMID: 31640813 PMCID: PMC6806522 DOI: 10.1186/s40168-019-0750-2] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 09/13/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant nutrition and productivity. Although it is known that increased synthetic fertilizer input in Chinese farmlands over the past 50 years has resulted in not only increased yields but also environmental problems, we lack a comprehensive understanding of how crops under elevated nutrient input shape root-associated microbial communities, especially through adjusting the quantities and compositions of root metabolites and exudates. METHODS The compositions of bacterial and fungal communities from the roots and rhizosphere of wheat (Triticum aestivum L.) under four levels of long-term inorganic nitrogen (N) fertilization were characterized at the tillering, jointing and ripening stages. The root-released organic carbon (ROC), organic acids in the root exudates and soil organic carbon (SOC) and soil active carbon (SAC) in the rhizosphere were quantified. RESULTS ROC levels varied dramatically across wheat growth stages and correlated more with the bacterial community than with the fungal community. Rhizosphere SOC and SAC levels were elevated by long-term N fertilization but varied only slightly across growth stages. Variation in the microbial community structure across plant growth stages showed a decreasing trend with N fertilization level in the rhizosphere. In addition, more bacterial and fungal genera were significantly correlated in the jointing and ripening stages than in the tillering stage in the root samples. A number of bacterial genera that shifted in response to N fertilization, including Arthrobacter, Bacillus and Devosia, correlated significantly with acetic acid, oxalic acid, succinic acid and tartaric acid levels. CONCLUSIONS Our results indicate that both plant growth status and N input drive changes in the microbial community structure in the root zone of wheat. Plant growth stage demostrated a stronger influence on bacterial than on fungal community composition. A number of bacterial genera that have been described as plant growth-promoting rhizobacteria (PGPR) responded positively to N fertilization, and their abundance correlated significantly with the organic acid level, suggesting that the secretion of organic acids may be a strategy developed by plants to recruit beneficial microbes in the root zone to cope with high N input. These results provide novel insight into the associations among increased N input, altered carbon availability, and shifts in microbial communities in the plant roots and rhizosphere of intensive agricultural ecosystems.
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Affiliation(s)
- Shuaimin Chen
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Tatoba R Waghmode
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, China
| | - Ruibo Sun
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, China
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, Wageningen, PB, Netherlands
| | - Chunsheng Hu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, China.
| | - Binbin Liu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, China.
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24
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Neuenkamp L, Zobel M, Lind E, Gerz M, Moora M. Arbuscular mycorrhizal fungal community composition determines the competitive response of two grassland forbs. PLoS One 2019; 14:e0219527. [PMID: 31291331 PMCID: PMC6620016 DOI: 10.1371/journal.pone.0219527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 04/23/2019] [Accepted: 06/25/2019] [Indexed: 01/08/2023] Open
Abstract
We performed a greenhouse experiment to assess how differences in AM fungal community composition affect competitive response of grassland plant species. We used a full factorial design to determine how inoculation with natural AM fungal communities from different habitats in Western Estonia affects the growth response of two grassland forbs (Leontodon hispidus L., Plantago lanceolata L.) to competition with a dominant grass (Festuca rubra L.). We used AM fungal inocula that were known to differ in AM fungal diversity and composition: more diverse AM fungal communities from open grasslands and less diverse AM fungal communities from former grassland densely overgrown by pines (young pine forest). The presence of AM fungi balanced competition between forb and grass species, by enhancing competitive response of the forbs. The magnitude of this effect was dependent on forb species identity and on the origin of the AM fungal inoculum in the soil. The grassland inoculum enhanced the competitive response of the forb species more effectively than the forest inoculum, but inoculum-specific competitive responses varied according to the habitat preference of the forb species. Our findings provide evidence that composition and diversity of natural AM fungal communities, as well as co-adaptation of plant hosts and AM-fungal communities to local habitat conditions, can determine plant-plant interactions and thus ultimately influence plant community structure in nature.
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Affiliation(s)
- Lena Neuenkamp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Eva Lind
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maret Gerz
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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25
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Pierart A, Maes AQ, Dumat C, Sejalon-Delmas N. Vermicompost addition influences symbiotic fungi communities associated with leek cultivated in metal-rich soils. Environ Sci Pollut Res Int 2019; 26:20040-20051. [PMID: 30109687 DOI: 10.1007/s11356-018-2803-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/19/2018] [Indexed: 06/08/2023]
Abstract
In the context of urban agriculture, where soils are frequently contaminated with metal(loid)s (TM), we studied the influence of vermicompost amendments on symbiotic fungal communities associated with plants grown in two metal-rich soils. Leek (Allium porrum L.) plants were grown with or without vermicompost in two metal-rich soils characterized by either geogenic or anthropogenic TM sources, to assess the influence of pollutant origin on soil-plant transfer. Fungal communities associated with the leek roots were identified by high throughput Illumina MiSeq and TM contents were measured using mass spectrometry. Vermicompost addition led to a dramatic change in the fungal community with a loss of diversity in the two tested soils. This effect could partially explain the changes in metal transfer at the soil-AMF-plant interface. Our results suggest being careful while using composts when growing edibles in contaminated soils. More generally, this study highlights the need for further research in the field of fungal communities to refine practical recommendations to gardeners. Graphical abstract.
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Affiliation(s)
- Antoine Pierart
- Ecotoxicology Lab, Fac. Environmental Science and Biochemistry, University of Castilla-La Mancha, Toledo, Spain
| | - Arthur QuyManh Maes
- LRSV, Laboratoire de recherche en sciences végétales, Université de Toulouse, UPS, CNRS, 24 chemin de Borderouge, 31326, Castanet-Tolosan, France
| | - Camille Dumat
- CERTOP, UMR 5044, CNRS-UT2J-UPS, Maison de la Recherche, Université Toulouse, Toulouse Cedex 9, France
- INP-ENSAT, Université de Toulouse, Toulouse, France
| | - Nathalie Sejalon-Delmas
- LRSV, Laboratoire de recherche en sciences végétales, Université de Toulouse, UPS, CNRS, 24 chemin de Borderouge, 31326, Castanet-Tolosan, France.
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Panpetch W, Somboonna N, Palasuk M, Hiengrach P, Finkelman M, Tumwasorn S, Leelahavanichkul A. Oral Candida administration in a Clostridium difficile mouse model worsens disease severity but is attenuated by Bifidobacterium. PLoS One 2019; 14:e0210798. [PMID: 30645630 PMCID: PMC6333342 DOI: 10.1371/journal.pone.0210798] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [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: 07/04/2018] [Accepted: 01/02/2019] [Indexed: 12/13/2022] Open
Abstract
Gut fungi may influence the course of Clostridium difficile infection either positively or negatively for the host. Fungi are not prominent in the mouse gut, and C. albicans, the major human gastrointestinal commensal yeast, is in low abundance or absent in mice. Bifidobacterium is one of the probiotics that may attenuate the severity of C. difficile infection. Inflammatory synergy between C. albicans and C. difficile, in gut, may provide a state that more closely resembles human infection and be more suitable for testing probiotic effects. We performed fecal mycobiota analysis and administered C. albicans at 1 day prior to C. difficile dosing. Fecal eukaryotic 18S rDNA analysis demonstrated the presence of Ascomycota, specifically, Candida spp., after oral antibiotics, despite negative fecal fungal culture. C. albicans administration enhanced the severity of the C. difficile infection model as determined by mortality rate, weight loss, gut leakage (FITC-dextran assay), and serum and intestinal tissue cytokines. This occurred without increased fecal C. difficile or bacteremia, in comparison with C. difficile gavage alone. Candida lysate with C. difficile increased IL-8 production from HT-29 and Caco-2 human intestinal epithelial cell-lines. Bifidobacterium attenuated the disease severity of the C. difficile plus Candida model. The reduced severity was associated with decreased Candida burdens in feces. In conclusion, gut C. albicans worsened C. difficile infection, possibly through exacerbation of inflammation. Hence, a mouse model of Clostridium difficile infection with C. albicans present in the gut may better model the human patient condition. Gut fungal mycobiome investigation in patients with C. difficile is warranted and may suggest therapeutic targets.
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Affiliation(s)
- Wimonrat Panpetch
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Matanee Palasuk
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Pratsanee Hiengrach
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Somying Tumwasorn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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27
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Patterson A, Flores-Rentería L, Whipple A, Whitham T, Gehring C. Common garden experiments disentangle plant genetic and environmental contributions to ectomycorrhizal fungal community structure. New Phytol 2019; 221:493-502. [PMID: 30009496 DOI: 10.1111/nph.15352] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 05/30/2018] [Accepted: 06/16/2018] [Indexed: 05/16/2023]
Abstract
The interactions among climate change, plant genetic variation and fungal mutualists are poorly understood, but probably important to plant survival under drought. We examined these interactions by studying the ectomycorrhizal fungal (EMF) communities of pinyon pine seedlings (Pinus edulis) planted in a wildland ecosystem experiencing two decades of climate change-related drought. We established a common garden containing P. edulis seedlings of known maternal lineages (drought tolerant, DT; drought intolerant, DI), manipulated soil moisture and measured EMF community structure and seedling growth. Three findings emerged: EMF community composition differed at the phylum level between DT and DI seedlings, and diversity was two-fold greater in DT than in DI seedlings. EMF communities of DT seedlings did not shift with water treatment and were dominated by an ascomycete, Geopora sp. By contrast, DI seedlings shifted to basidiomycete dominance with increased moisture, demonstrating a lineage by environment interaction. DT seedlings grew larger than DI seedlings in high (28%) and low (50%) watering treatments. These results show that inherited plant traits strongly influence microbial communities, interacting with drought to affect seedling performance. These interactions and their potential feedback effects may influence the success of trees, such as P. edulis, in future climates.
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Affiliation(s)
- Adair Patterson
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011-5640, USA
| | - Lluvia Flores-Rentería
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011-5640, USA
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Amy Whipple
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011-5640, USA
- Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff, AZ, 86011-5640, USA
| | - Thomas Whitham
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011-5640, USA
- Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff, AZ, 86011-5640, USA
| | - Catherine Gehring
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011-5640, USA
- Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff, AZ, 86011-5640, USA
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Veach AM, Stokes CE, Knoepp J, Jumpponen A, Baird R. Fungal Communities and Functional Guilds Shift Along an Elevational Gradient in the Southern Appalachian Mountains. Microb Ecol 2018; 76:156-168. [PMID: 29204781 DOI: 10.1007/s00248-017-1116-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/20/2017] [Indexed: 05/03/2023]
Abstract
Nitrogen deposition alters forest ecosystems particularly in high elevation, montane habitats where nitrogen deposition is greatest and continues to increase. We collected soils across an elevational (788-1940 m) gradient, encompassing both abiotic (soil chemistry) and biotic (vegetation community) gradients, at eight locations in the southern Appalachian Mountains of southwestern North Carolina and eastern Tennessee. We measured soil chemistry (total N, C, extractable PO4, soil pH, cation exchange capacity [ECEC], percent base saturation [% BS]) and dissected soil fungal communities using ITS2 metabarcode Illumina MiSeq sequencing. Total soil N, C, PO4, % BS, and pH increased with elevation and plateaued at approximately 1400 m, whereas ECEC linearly increased and C/N decreased with elevation. Fungal communities differed among locations and were correlated with all chemical variables, except PO4, whereas OTU richness increased with total N. Several ecological guilds (i.e., ectomycorrhizae, saprotrophs, plant pathogens) differed in abundance among locations; specifically, saprotroph abundance, primarily attributable to genus Mortierella, was positively correlated with elevation. Ectomycorrhizae declined with total N and soil pH and increased with total C and PO4 where plant pathogens increased with total N and decreased with total C. Our results demonstrate significant turnover in taxonomic and functional fungal groups across elevational gradients which facilitate future predictions on forest ecosystem change in the southern Appalachians as nitrogen deposition rates increase and regional temperature and precipitation regimes shift.
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Affiliation(s)
- Allison M Veach
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, 37831, USA.
| | - C Elizabeth Stokes
- Department of Forest Products, Mississippi State University, Starkville, MS, 39762, USA
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, 39762, USA
| | - Jennifer Knoepp
- USDA, Forest Service, Southern Research Station, Center for Forest Watershed Research, Coweeta Hydrologic Laboratory, Otto, NC, 28763, USA
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Richard Baird
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, 39762, USA
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Abstract
The fruit fly, Drosophila melanogaster, is preferentially found on fermenting fruits. The yeasts that dominate the microbial communities of these substrates are the primary food source for developing D. melanogaster larvae, and adult flies manifest a strong olfactory system-mediated attraction for the volatile compounds produced by these yeasts during fermentation. Although most work on this interaction has focused on the standard laboratory yeast Saccharomyces cerevisiae, a wide variety of other yeasts naturally ferment fallen fruit. Here we address the open question of whether D. melanogaster preferentially associates with distinct yeasts in different, closely-related environments. We characterized the spatial and temporal dynamics of Drosophila-associated fungi in Northern California wineries that use organic grapes and natural fermentation using high-throughput, short-amplicon sequencing. We found that there is nonrandom structure in the fungal communities that are vectored by flies both between and within vineyards. Within wineries, the fungal communities associated with flies in cellars, fermentation tanks, and pomace piles are distinguished by varying abundances of a small number of yeast species. To investigate the origins of this structure, we assayed Drosophila attraction to, oviposition on, larval development in, and longevity when consuming the yeasts that distinguish vineyard microhabitats from each other. We found that wild fly lines did not respond differentially to the yeast species that distinguish winery habitats in habitat specific manner. Instead, this subset of yeast shares traits that make them attractive to and ensure their close association with Drosophila.
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Affiliation(s)
- Allison S. Quan
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- * E-mail:
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30
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Guan M, Pan XC, Wang S, Wei XL, Zhang CB, Wang J, Liu WL, Liu SY, Chang J. Comparison of fungal communities among ten macrophyte rhizospheres. Fungal Biol 2018; 122:867-874. [PMID: 30115320 DOI: 10.1016/j.funbio.2018.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 05/26/2017] [Revised: 04/16/2018] [Accepted: 05/03/2018] [Indexed: 11/17/2022]
Abstract
The fungal community composition, size and several physico-chemical properties were individually investigated in ten macrophyte rhizospheric substrates using nested PCR-denaturing gradient gel electrophoresis and soil chemical methods. Results indicated that both Dothideomycetes and Sordariomycetes were dominant fungi in macrophyte rhizospheric substrates, and denitrifying fungi (Fusarium graminearum) was found in nine of ten macrophyte rhizospheres. Fungal Shannon-Wiener diversity index (H) and richness (S) in Thalia dealbata, Typha latifolia, Iris hexagona and Hemerocallis aurantiaca rhizospheres were higher than those in other six rhizospheres. Fungal number and biomass were 1.91 × 103 CFUs g-1 dw and 1.53 μg ergosterol g-1 dw in Iris pseudacor rhizosphere, and were greater than in other nine rhizospheres. The correlation analysis showed that fungal number and biomass significantly and positively correlated to total soil phosphorus, while fungal H and S were significantly and negatively correlated to total organic carbon. The principal components analysis (PCA) showed that the fungal community significantly divided ten macrophyte rhizospheres into four groups, showing the significant difference of fungal communities among ten rhizospheric substrates. The current study revealed for the first time the importance of rhizospheric fungal community in distinguishing macrophyte rhizospheres, thus will undoubtedly widen our insight into fungal communities in aquatic rhizospheres.
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Affiliation(s)
- Ming Guan
- Institute of Constructed Wetland Technology, Taizhou University, Taizhou, 318000, China; College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiao-Cui Pan
- Institute of Constructed Wetland Technology, Taizhou University, Taizhou, 318000, China
| | - Shuo Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiao-Lin Wei
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Chong-Bang Zhang
- Institute of Constructed Wetland Technology, Taizhou University, Taizhou, 318000, China.
| | - Jiang Wang
- Institute of Constructed Wetland Technology, Taizhou University, Taizhou, 318000, China
| | - Wen-Li Liu
- Institute of Constructed Wetland Technology, Taizhou University, Taizhou, 318000, China; School of Civil Engineering and Architecture, Taizhou University, Taizhou, 318000, China
| | - Shu-Yuan Liu
- School of Civil Engineering and Architecture, Taizhou University, Taizhou, 318000, China
| | - Jie Chang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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31
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Li J, Chen D, Yu B, He J, Zheng P, Mao X, Yu J, Luo J, Tian G, Huang Z, Luo Y. Fungi in Gastrointestinal Tracts of Human and Mice: from Community to Functions. Microb Ecol 2018; 75:821-829. [PMID: 29110065 DOI: 10.1007/s00248-017-1105-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [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: 07/13/2017] [Accepted: 10/30/2017] [Indexed: 05/10/2023]
Abstract
Fungi are often ignored in studies on gut microbes because of their low level of presence (making up only 0.1% of the total microorganisms) in the gastrointestinal tract (GIT) of monogastric animals. Recent studies using novel technologies such as next generation sequencing have expanded our understanding on the importance of intestinal fungi in humans and animals. Here, we provide a comprehensive review on the fungal community, the so-called mycobiome, and their functions from recent studies in humans and mice. In the GIT of humans, fungi belonging to the phyla Ascomycota, Basidiomycota and Chytridiomycota are predominant. The murine intestines harbor a more diverse assemblage of fungi. Diet is one of the major factors influencing colonization of fungi in the GIT. Presence of the genus Candida is positively associated with dietary carbohydrates, but are negatively correlated with dietary amino acids, proteins, and fatty acids. However, the relationship between diet and the fungal community (and functions), as well as the underlying mechanisms remains unclear. Dysbiosis of intestinal fungi can cause invasive infections and inflammatory bowel diseases (IBD). However, it is not clear whether dysbiosis of the mycobiome is a cause, or a result of IBD. Compared to non-inflamed intestinal mucosa, the abundance and diversity of fungi is significantly increased in the inflamed mucosa. The commonly observed commensal fungal species Candida albicans might contribute to occurrence and development of IBD. Limited studies show that Candida albicans might interact with immune cells of the host intestines through the pathways associated with Dectin-1, Toll-like receptor 2 (TLR2), and TLR4. This review is expected to provide new thoughts for future studies on intestinal fungi and for new therapies to fungal infections in the GIT of human and animals.
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Affiliation(s)
- Jiayan Li
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Daiwen Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Bing Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jun He
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Ping Zheng
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiangbing Mao
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jie Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Junqiu Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Gang Tian
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhiqing Huang
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuheng Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China.
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Stefanaki C, Peppa M, Mastorakos G, Chrousos GP. Examining the gut bacteriome, virome, and mycobiome in glucose metabolism disorders: Are we on the right track? Metabolism 2017; 73:52-66. [PMID: 28732571 DOI: 10.1016/j.metabol.2017.04.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/21/2017] [Accepted: 04/28/2017] [Indexed: 12/19/2022]
Abstract
Human gut microbiome is defined as the gene complement of the gut microbial community, measured via laboratory metagenomic techniques. It includes bacteriome, virome and mycobiome, which represent, respectively, the assemblages of bacteria, viruses and fungi, living in the human gut. Gut microbiota function as a living "organ" that interacts with the gastro-intestinal environment, provides nutrients and vitamins to the organism and transduces hormonal messages, essentially influencing the main metabolic pathways, including drug metabolism. A clear association between gut, and glucose metabolism disorders has recently emerged. Medications acting on glucose absorption in the gut, or enhancing gut hormone activity are already extensively employed in the therapy of diabetes. Moreover, the gut is characterized by immune, and autonomous neuronal features, which play a critical role in maintaining glucose metabolism homeostasis. Gut microbes respond to neuroendocrine, and immune biochemical messages, affecting the health, and behavior of the host. There is vast heterogeneity in the studies included in this review, hence a meta-analysis, or a systematic review were not applicable. In this article, we attempt to reveal the interplay between human gut microbiota physiology, and hyperglycemic states, synthesizing, and interpreting findings from human studies.
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Affiliation(s)
- Charikleia Stefanaki
- 1st Department of Pediatrics, Choremeio Research Laboratory, Athens University Medical School, National and Kapodistrian University of Athens, Medical School, Athens, Greece.
| | - Melpomeni Peppa
- Endocrine Unit, 2nd Department of Internal Medicine Propaedeutic, Research Institute and Diabetes Center, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
| | - George Mastorakos
- Department of Endocrinology, Metabolism and Diabetes, Aretaieion University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - George P Chrousos
- 1st Department of Pediatrics, Choremeio Research Laboratory, Athens University Medical School, National and Kapodistrian University of Athens, Medical School, Athens, Greece
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Blachowicz A, Mayer T, Bashir M, Pieber TR, De León P, Venkateswaran K. Human presence impacts fungal diversity of inflated lunar/Mars analog habitat. Microbiome 2017; 5:62. [PMID: 28693587 PMCID: PMC5504618 DOI: 10.1186/s40168-017-0280-8] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/02/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND An inflatable lunar/Mars analog habitat (ILMAH), simulated closed system isolated by HEPA filtration, mimics International Space Station (ISS) conditions and future human habitation on other planets except for the exchange of air between outdoor and indoor environments. The ILMAH was primarily commissioned to measure physiological, psychological, and immunological characteristics of human inhabiting in isolation, but it was also available for other studies such as examining its microbiological aspects. Characterizing and understanding possible changes and succession of fungal species is of high importance since fungi are not only hazardous to inhabitants but also deteriorate the habitats. Observing the mycobiome changes in the presence of human will enable developing appropriate countermeasures with reference to crew health in a future closed habitat. RESULTS Succession of fungi was characterized utilizing both traditional and state-of-the-art molecular techniques during the 30-day human occupation of the ILMAH. Surface samples were collected at various time points and locations to observe both the total and viable fungal populations of common environmental and opportunistic pathogenic species. To estimate the cultivable fungal population, potato dextrose agar plate counts method was utilized. The internal transcribed spacer region-based iTag Illumina sequencing was employed to measure the community structure and fluctuation of the mycobiome over time in various locations. Treatment of samples with propidium monoazide (PMA; a DNA intercalating dye for selective detection of viable microbial populations) had a significant effect on the microbial diversity compared to non-PMA-treated samples. Statistical analysis confirmed that viable fungal community structure changed (increase in diversity and decrease in fungal burden) over the occupation time. Samples collected at day 20 showed distinct fungal profiles from samples collected at any other time point (before or after). Viable fungal families like Davidiellaceae, Teratosphaeriaceae, Pleosporales, and Pleosporaceae were shown to increase during the occupation time. CONCLUSIONS The results of this study revealed that the overall fungal diversity in the closed habitat changed during human presence; therefore, it is crucial to properly maintain a closed habitat to preserve it from deteriorating and keep it safe for its inhabitants. Differences in community profiles were observed when statistically treated, especially of the mycobiome of samples collected at day 20. On a genus level Epiccocum, Alternaria, Pleosporales, Davidiella, and Cryptococcus showed increased abundance over the occupation time.
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Affiliation(s)
- A Blachowicz
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Dr., M/S 89-2, Pasadena, CA, 91109, USA
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | - T Mayer
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Dr., M/S 89-2, Pasadena, CA, 91109, USA
| | - M Bashir
- Division of Endocrinology and Metabolism, Medical University Graz, Graz, Austria
| | - T R Pieber
- Division of Endocrinology and Metabolism, Medical University Graz, Graz, Austria
| | - P De León
- Department of Space Studies, University of North Dakota, Grand Forks, ND, 58202, USA
| | - K Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Dr., M/S 89-2, Pasadena, CA, 91109, USA.
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Singh DK, Sharma VK, Kumar J, Mishra A, Verma SK, Sieber TN, Kharwar RN. Diversity of endophytic mycobiota of tropical tree Tectona grandis Linn.f.: Spatiotemporal and tissue type effects. Sci Rep 2017; 7:3745. [PMID: 28623306 PMCID: PMC5473821 DOI: 10.1038/s41598-017-03933-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 04/02/2016] [Accepted: 05/09/2017] [Indexed: 11/03/2022] Open
Abstract
Fungal endophytes were isolated from leaf, bark and stem of Tectona grandis Linn.f. sampled at four geographical locations in winter, summer and monsoon seasons. The recovered 5089 isolates were assigned to 45 distinct morphotypes based on morphology. The sequences of the internal transcribed spacers (ITS) of the nrDNA of some morphotypes were identical, but morphological differences were strong enough to consider these morphotypes as separate species. Forty-three morphotypes were assigned to ascomycotina and two to basidiomycotina. Ascomycotina was the predominating group with 99.7% of total isolates followed by basidiomycotina with only 0.3% of total isolates. Diaporthe (Phomopsis) species dominated the communities independently on tissue type, location or season. More than 60% of the examined tissue pieces were colonized by members of this species complex. While these endophytes are ubiquitous others were tissue or location specific. Tissue type had the strongest effect on the species evenness of the endophytic assemblage followed by geographical location and season. However, Shannon-Wiener index (H') significantly (p ≤ 0.001) varied with all three factors i.e. season, location and tissue type. Leaves supported the highest diversity across all the seasons and locations. In conclusion, all the three factors together determined the structure of endophytic mycobiota assemblage of T. grandis.
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Affiliation(s)
- Dheeraj K Singh
- Mycopathology and Microbial Technology Laboratory, Department of Botany, Banaras Hindu University (BHU), Varanasi, 221005, India
| | - Vijay K Sharma
- Mycopathology and Microbial Technology Laboratory, Department of Botany, Banaras Hindu University (BHU), Varanasi, 221005, India
| | - Jitendra Kumar
- Mycopathology and Microbial Technology Laboratory, Department of Botany, Banaras Hindu University (BHU), Varanasi, 221005, India
| | - Ashish Mishra
- Mycopathology and Microbial Technology Laboratory, Department of Botany, Banaras Hindu University (BHU), Varanasi, 221005, India
| | - Satish K Verma
- Mycopathology and Microbial Technology Laboratory, Department of Botany, Banaras Hindu University (BHU), Varanasi, 221005, India
| | - Thomas N Sieber
- ETH Zurich, Institute of Integrative Biology, Forest Pathology and Dendrology, 8092, Zurich, Switzerland
| | - Ravindra N Kharwar
- Mycopathology and Microbial Technology Laboratory, Department of Botany, Banaras Hindu University (BHU), Varanasi, 221005, India.
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Krause R, Halwachs B, Thallinger GG, Klymiuk I, Gorkiewicz G, Hoenigl M, Prattes J, Valentin T, Heidrich K, Buzina W, Salzer HJF, Rabensteiner J, Prüller F, Raggam RB, Meinitzer A, Moissl-Eichinger C, Högenauer C, Quehenberger F, Kashofer K, Zollner-Schwetz I. Characterisation of Candida within the Mycobiome/Microbiome of the Lower Respiratory Tract of ICU Patients. PLoS One 2016; 11:e0155033. [PMID: 27206014 PMCID: PMC4874575 DOI: 10.1371/journal.pone.0155033] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [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: 03/06/2016] [Accepted: 04/22/2016] [Indexed: 02/06/2023] Open
Abstract
Whether the presence of Candida spp. in lower respiratory tract (LRT) secretions is a marker of underlying disease, intensive care unit (ICU) treatment and antibiotic therapy or contributes to poor clinical outcome is unclear. We investigated healthy controls, patients with proposed risk factors for Candida growth in LRT (antibiotic therapy, ICU treatment with and without antibiotic therapy), ICU patients with pneumonia and antibiotic therapy and candidemic patients (for comparison of truly invasive and colonizing Candida spp.). Fungal patterns were determined by conventional culture based microbiology combined with molecular approaches (next generation sequencing, multilocus sequence typing) for description of fungal and concommitant bacterial microbiota in LRT, and host and fungal biomarkes were investigated. Admission to and treatment on ICUs shifted LRT fungal microbiota to Candida spp. dominated fungal profiles but antibiotic therapy did not. Compared to controls, Candida was part of fungal microbiota in LRT of ICU patients without pneumonia with and without antibiotic therapy (63% and 50% of total fungal genera) and of ICU patients with pneumonia with antibiotic therapy (73%) (p<0.05). No case of invasive candidiasis originating from Candida in the LRT was detected. There was no common bacterial microbiota profile associated or dissociated with Candida spp. in LRT. Colonizing and invasive Candida strains (from candidemic patients) did not match to certain clades withdrawing the presence of a particular pathogenic and invasive clade. The presence of Candida spp. in the LRT rather reflected rapidly occurring LRT dysbiosis driven by ICU related factors than was associated with invasive candidiasis.
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Affiliation(s)
- Robert Krause
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- * E-mail:
| | - Bettina Halwachs
- Bioinformatics, Institute for Knowledge Discovery, University of Technology, Graz, Austria and OMICS Center Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | | | - Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | | | - Martin Hoenigl
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Jürgen Prattes
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Thomas Valentin
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Katharina Heidrich
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Department of Medicine I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Walter Buzina
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Helmut J. F. Salzer
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibnitz Center for Medicine and Biosciences, Borstel, Germany
| | - Jasmin Rabensteiner
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Florian Prüller
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Reinhard B. Raggam
- Division of Angiology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Andreas Meinitzer
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Christoph Högenauer
- Theodor Escherich Laboratory for Microbiome Research, Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Franz Quehenberger
- Institute for Medical Informatics, Statistics, and Documentation, Medical University of Graz, Graz, Austria
| | - Karl Kashofer
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Ines Zollner-Schwetz
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
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