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Li X, Fu T, Li H, Zhang B, Li W, Zhang B, Wang X, Wang J, Chen Q, He X, Chen H, Zhang Q, Zhang Y, Yang R, Peng Y. Safe Production Strategies for Soil-Covered Cultivation of Morel in Heavy Metal-Contaminated Soils. J Fungi (Basel) 2023; 9:765. [PMID: 37504753 PMCID: PMC10381497 DOI: 10.3390/jof9070765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Morel is a popular edible mushroom with considerable medicinal and economic value which has garnered global popularity. However, the increasing heavy metal (HM) pollution in the soil presents a significant challenge to morels cultivation. Given the susceptibility of morels to HM accumulation, the quality and output of morels are at risk, posing a serious food safety concern that hinders the development of the morel industry. Nonetheless, research on the mechanism of HM enrichment and mitigation strategies in morel remains scarce. The morel, being cultivated in soil, shows a positive correlation between HM content in its fruiting body and the HM content in the soil. Therefore, soil remediation emerges as the most practical and effective approach to tackle HM pollution. Compared to physical and chemical remediation, bioremediation is a low-cost and eco-friendly approach that poses minimal threats to soil composition and structure. HMs easily enriched during morels cultivation were examined, including Cd, Cu, Hg, and Pb, and we assessed soil passivation technology, microbial remediation, strain screening and cultivation, and agronomic measures as potential approaches for HM pollution prevention. The current review underscores the importance of establishing a comprehensive system for preventing HM pollution in morels.
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Affiliation(s)
- Xue Li
- School of Pharmacy, Zunyi Medical University, Zunyi 563006, China
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Tianhong Fu
- School of Pharmacy, Zunyi Medical University, Zunyi 563006, China
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Hongzhao Li
- Faculty of Food Science and Engineering, Foshan University, Foshan 258000, China
- Key Laboratory for New Technology Research of Vegetable, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Bangxi Zhang
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Wendi Li
- School of Pharmacy, Zunyi Medical University, Zunyi 563006, China
| | - Baige Zhang
- Key Laboratory for New Technology Research of Vegetable, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiaomin Wang
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Jie Wang
- Qiandongnan Academy of Agricultural Sciences, Kaili 556000, China
| | - Qing Chen
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xuehan He
- School of Pharmaceutical Sciences, Sun Yat-sen University, Shenzhen 518107, China
| | - Hao Chen
- School of Agriculture, Sun Yat-sen University, Shenzhen 518107, China
| | - Qinyu Zhang
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Yujin Zhang
- School of Pharmacy, Zunyi Medical University, Zunyi 563006, China
| | - Rende Yang
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Yutao Peng
- School of Agriculture, Sun Yat-sen University, Shenzhen 518107, China
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Wang YH, Yang XY, Wan LZ, Ren HX, Qu L, Guo HD, Dong LL, Lu X, Ren PF. Influence of the casing layer on the specific volatile compounds and microorganisms by Agaricus bisporus. Front Microbiol 2023; 14:1154903. [PMID: 37266010 PMCID: PMC10229858 DOI: 10.3389/fmicb.2023.1154903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/27/2023] [Indexed: 06/03/2023] Open
Abstract
One of the major variables affecting yield of the mushroom Agaricus bisporus is the casing layer, which directly affects the productivity and mass. Here, volatile organic compounds were extracted by headspace solid-phase microextraction and high-throughput sequencing was used to analyze the microbial community diversity. The relationship between mushroom yield at different cropping stages and the contents of volatile organic compounds and microorganisms in three different casing layers: peat, peat + soil and soil were systematically evaluated. The result shows that Benzaldehyde and (E)-2-octenal which stimulate yield, obviously increased as mushrooms grew, while 3-octanone, which inhibits yield, decreased over time in all three casing layers. However, there was not a strong correlation between the concentration of volatile compounds and yield. In addition, more than 3,000 bacterial operational taxonomic units (OTUs) by performing high throughput sequencing of the microbes were obtained in the three casing layers. Interestingly, the microbial community compositions were very similar between the three casing layers at a later cropping stage, but the community richness varied significantly in different casing layers and at different cropping stages. At the phylum level, the communities had similar structures but were quantitively very different, and this was even more obvious at the genus level. Principal component analysis revealed significant alterations in microbial community structure in different casing layers. Sphingomonas, Dongia and Achromobacter were the dominant genera at cropping stage 1, and the stage 3 were abundant in Saccharibacteria_norank, Pseudomonas, Flavobacterium and Brevundimonas, which was positively correlated with yield, while the abundance of Pseudomonas at stage 1 and Lactococcus and Bacillus at stage 3 was negatively correlated with yield. These results provide a guide for the development and agricultural application of microbial agents for yield improvement in the production of A. bisporus.
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Affiliation(s)
- Yong-Hui Wang
- Key Laboratory of Wastes Matrix Utilization, Ministry of Agriculture, Institute of Agricultural Resource and Environment, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiao-Ying Yang
- College of Food Science and Technology, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Lu-Zhang Wan
- Key Laboratory of Wastes Matrix Utilization, Ministry of Agriculture, Institute of Agricultural Resource and Environment, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hai-Xia Ren
- Key Laboratory of Wastes Matrix Utilization, Ministry of Agriculture, Institute of Agricultural Resource and Environment, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ling Qu
- Key Laboratory of Wastes Matrix Utilization, Ministry of Agriculture, Institute of Agricultural Resource and Environment, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hui-Dong Guo
- Key Laboratory of Wastes Matrix Utilization, Ministry of Agriculture, Institute of Agricultural Resource and Environment, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Li-Li Dong
- Key Laboratory of Wastes Matrix Utilization, Ministry of Agriculture, Institute of Agricultural Resource and Environment, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiao Lu
- Key Laboratory of Wastes Matrix Utilization, Ministry of Agriculture, Institute of Agricultural Resource and Environment, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Peng-Fei Ren
- Key Laboratory of Wastes Matrix Utilization, Ministry of Agriculture, Institute of Agricultural Resource and Environment, Shandong Academy of Agricultural Sciences, Jinan, China
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Zhang C, Shi X, Zhang J, Zhang Y, Wang W. Dynamics of soil microbiome throughout the cultivation life cycle of morel ( Morchella sextelata). Front Microbiol 2023; 14:979835. [PMID: 36910237 PMCID: PMC9992412 DOI: 10.3389/fmicb.2023.979835] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 02/02/2023] [Indexed: 02/24/2023] Open
Abstract
Although Morchella sextelata (morel) is a well-known, edible, and medicinal fungus widely cultivated in China, the dynamics and roles of its soil microbiome during cultivation are unclear. Using rhizosphere soil samples collected throughout the M. sextelata cultivation life cycle, we conducted a high-throughput metagenomic sequencing analysis, with an emphasis on variations in soil microbial composition, characteristic biomarkers, and ecological functions. We found that microbial relative abundance, alpha diversity, and structure varied significantly among fungal growth stages. A total of 47 stage-associated biomarkers were identified through a linear discriminant analysis of effect size. In addition, horizontal comparison of soil microbiomes exhibiting successful and failed primordium formation further confirmed primordium-associated microbes with possible key roles in primordium formation. A microbial function analysis revealed that nutrient metabolism-related pathways were enriched during mycelium and fruiting body stages, whereas the signal transduction pathway was enriched during the primordium stage. This result indicates that diverse microbes are required at different growth stages of M. sextelata. Our research has revealed the dynamic scenario of the soil microbiome throughout the cultivation life cycle of M. sextelata. The high-resolution microbial profiles uncovered in the present study provide novel insights that should contribute to the improvement of morel cultivation using microbial inoculants.
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Affiliation(s)
- Chen Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xiaofei Shi
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jiexiong Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yesheng Zhang
- Shandong Junsheng Biotechnologies Co., Ltd., Liaocheng, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
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Orban A, Jerschow JJ, Birk F, Suarez C, Schnell S, Rühl M. Effect of bacterial volatiles on the mycelial growth of mushrooms. Microbiol Res 2023; 266:127250. [DOI: 10.1016/j.micres.2022.127250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
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Phylogenesis of the Functional 1-Aminocyclopropane-1-Carboxylate Oxidase of Fungi and Plants. J Fungi (Basel) 2022; 9:jof9010055. [PMID: 36675876 PMCID: PMC9866368 DOI: 10.3390/jof9010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023] Open
Abstract
The 1-aminocyclopropane-1-carboxylic acid (ACC) pathway that synthesizes ethylene is shared in seed plants, fungi and probably other organisms. However, the evolutionary relationship of the key enzyme ACC oxidase (ACO) in the pathway among organisms remains unknown. Herein, we cloned, expressed and characterized five ACOs from the straw mushroom (Volvariella volvacea) and the oyster mushroom (Pleurotus ostreatus): VvACO1-4 and PoACO. The five mushroom ACOs and the previously identified AbACO of the button mushroom contained all three conserved residues that bound to Fe(II) in plant ACOs. They also had variable residues that were conserved and bound to ascorbate and bicarbonate in plant ACOs and harbored only 1-2 of the five conserved ACO motifs in plant ACOs. Particularly, VvACO2 and AbACO had only one ACO motif 2. Additionally, VvACO4 shared 44.23% sequence identity with the cyanobacterium Hapalosiphon putative functional ACO. Phylogenetic analysis showed that the functional ACOs of monocotyledonous and dicotyledonous plants co-occurred in Type I, Type II and Type III, while putative functional gymnosperm ACOs also appeared in Type III. The putative functional bacterial ACO, functional fungi and slime mold ACOs were clustered in ancestral Type IV. These results indicate that ACO motif 2, ACC and Fe(II) are essential for ACO activity. The ACOs of the other organisms may come from the horizontal transfer of fungal ACOs, which were found ordinarily in basidiomycetes. It is mostly the first case for the horizontal gene transfers from fungi to seed plants. The horizontal transfer of ACOs from fungi to plants probably facilitates the fungal-plant symbioses, plant-land colonization and further evolution to form seeds.
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Zhang C, Shang D, Zhang Y, Gao X, Liu D, Gao Y, Li Y, Qi Y, Qiu L. Two Hybrid Histidine Kinases Involved in the Ethylene Regulation of the Mycelial Growth and Postharvest Fruiting Body Maturation and Senescence of Agaricus bisporus. Microbiol Spectr 2022; 10:e0241122. [PMID: 36125274 PMCID: PMC9603746 DOI: 10.1128/spectrum.02411-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/02/2022] [Indexed: 01/04/2023] Open
Abstract
Ethylene regulates mycelial growth, primordium formation, and postharvest mushroom maturation and senescence in the white button mushroom, Agaricus bisporus. However, it remains unknown how ethylene is detected by the mushroom. In this study, we found that two hybrid histidine kinases in the mushroom, designated AbETR1 and AbETR2, showed domain structures similar to those of plant ethylene receptors. The transmembrane helices of AbETR1 and AbETR2 were expressed in yeast cells and showed ethylene-binding activities. Mushroom strains with downregulated expressions of AbETR1 and AbETR2 showed reduced sensitivity to the ethylene inhibition of mycelial growth, ethylene regulation of their own synthesis, postharvest mushroom maturation, and senescence and expression of maturation- and senescence-related genes. Therefore, AbETR1 and AbETR2 are expected to be biologically functional ethylene receptors and exhibit a different mode of action from that of the receptors of plants. Here, we fill gaps in the knowledge pertaining to higher fungus ethylene receptors, discover a novel mode of action of ethylene receptors, confirm ethylene as a novel fungal hormone, and provide a facilitated approach for preventing the maturation and senescence of postharvest button mushrooms. IMPORTANCE Ethylene regulates diverse physiological activities in bacteria, cyanobacteria, fungi, and plants, but how to perceive ethylene by fungi only remains unknown. In this study, we identify two biologically functional ethylene receptors in the basidiomycete fungus Agaricus bisporus, which fills the gaps of deficient fungal ethylene receptors. Furthermore, we found that decreased expression of the ethylene receptors facilitates preventing the maturation and senescence of postharvest button mushrooms, indicating that the two fungal ethylene receptors positively regulate the ethylene response, in contrast to that in plants.
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Affiliation(s)
- Chaohui Zhang
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
- College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Di Shang
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Yan Zhang
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Xiyang Gao
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Dehai Liu
- Institute of Biology Co., Ltd., Henan Academy of Science, Zhengzhou, China
| | - Yuqian Gao
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Yanan Li
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Yuancheng Qi
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Liyou Qiu
- College of Life Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
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Liu Q, Kong W, Cui X, Hu S, Shi Z, Wu J, Zhang Y, Qiu L. Dynamic succession of microbial compost communities and functions during Pleurotus ostreatus mushroom cropping on a short composting substrate. Front Microbiol 2022; 13:946777. [PMID: 36060741 PMCID: PMC9433973 DOI: 10.3389/fmicb.2022.946777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Cultivating oyster mushrooms (Pleurotus ostreatus), a typical primary decomposer of lignocellulose, on a short composting substrate is a novel procedure which possesses energy conserves, reduced the chance of infection by competitive species, shorter production duration and achieved high production efficiency. However, the microbiome and microbial metabolic functions in the composting substrate during the mushroom cropping is unknown. In the present study, the contents of hemicellulose, cellulose and lignin and the activities of protease, laccase and cellulase were evaluated in the corncob short composting substrate from before oyster mushroom spawning to first flush fructification; meanwhile the changes in the microbiome and microbial metabolic functions were surveyed by using metagenomic sequencing. Results showed that the hemicellulose, cellulose and lignin in the short composting substrate were decomposed of 42.76, 34.01, and 30.18%, respectively, during the oyster mushroom cropping process. In addition, the contents of hemicellulose, cellulose and lignin in the composting substrate were reduced rapidly and negatively correlated with the abundance of the Actinobacteria phylum. The activities of protease, laccase and cellulase fastly increased in the period of before oyster mushroom spawning to full colonization and were positively correlated to the abundance of Actinobacteria phylum. The total abundance of bacteria domain gradually decreased by only approximately 15%, while the abundance of Actinobacteria phylum increased by 68% and was positively correlated with that of oyster mushroom. The abundance of oyster mushroom increased by 50 times from spawning to first flush fructification. The dominant genera, all in the order of Actinomycetales, were Cellulosimicrobium, Mycobacterium, Streptomyces and Saccharomonospora. The total abundance of genes with functions annotated in the Clusters of Orthologous Groups of proteins (COG) for Bacteria and Archaea and Kyoto Encyclopedia of Genes and Genomes (KEGG) database for all three life domains was positively correlated.The three metabolic pathways for carbohydrates, amino acids and energy were the primary enrichment pathways in KEGG pathway, accounting for more than 30% of all pathways, during the mushroom cropping in which the glycine metabolic pathway, carbon fixation pathways in prokaryotes and methane metabolism were all dominated by bacteria. The genes of cellulolytic enzymes, hemicellulolytic enzymes, laccase, chitinolytic enzymes, peptidoglycanlytic enzymes and ammonia assimilation enzymes with abundances from 0.28 to 0.24%, 0.05 to 0.02%, 0.02 to 0.01%, 0.14 to 0.08%, 0.39 to 0.16%, and 0.13 to 0.12% during the mushroom cropping identified in the Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (eggNOG) database for all three life domains were all aligned to COG database. These results indicated that bacteria, especially Actinomycetales, were the main metabolism participants in the short composting substrate during the oyster mushroom cropping. The relationship between oyster mushrooms and bacteria was cooperative, Actinomycetales were oyster mushroom growth promoting bacteria (OMGPB).
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Affiliation(s)
- Qin Liu
- Institute of Plant Nutrition, Agricultural Resources and Environmental Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Weili Kong
- Institute of Plant Nutrition, Agricultural Resources and Environmental Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
- *Correspondence: Weili Kong,
| | - Xiao Cui
- Institute of Plant Nutrition, Agricultural Resources and Environmental Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Sujuan Hu
- Institute of Plant Nutrition, Agricultural Resources and Environmental Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Ziwen Shi
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jie Wu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yuting Zhang
- Institute of Plant Nutrition, Agricultural Resources and Environmental Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Liyou Qiu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Liyou Qiu,
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Hua Z, Liu T, Han P, Zhou J, Zhao Y, Huang L, Yuan Y. Isolation, genomic characterization, and mushroom growth-promoting effect of the first fungus-derived Rhizobium. Front Microbiol 2022; 13:947687. [PMID: 35935222 PMCID: PMC9354803 DOI: 10.3389/fmicb.2022.947687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/27/2022] [Indexed: 12/12/2022] Open
Abstract
Polyporus umbellatus is a well-known edible and medicinal mushroom, and some bacteria isolated from mushroom sclerotia may have beneficial effects on their host. These mushroom growth-promoting bacteria (MGPBs) are of great significance in the mushroom production. In this work, we aimed to isolate and identify MGPBs from P. umbellatus sclerotia. Using the agar plate dilution method, strain CACMS001 was isolated from P. umbellatus sclerotia. The genome of CACMS001 was sequenced using PacBio platform, and the phylogenomic analysis indicated that CACMS001 could not be assigned to known Rhizobium species. In co-culture experiments, CACMS001 increased the mycelial growth of P. umbellatus and Armillaria gallica and increased xylanase activity in A. gallica. Comparative genomic analysis showed that CACMS001 lost almost all nitrogen fixation genes but specially acquired one redox cofactor cluster with pqqE, pqqD, pqqC, and pqqB involved in the synthesis of pyrroloquinoline quinone, a peptide-derived redox participating in phosphate solubilization activity. Strain CACMS001 has the capacity to solubilize phosphate using Pikovskaya medium, and phnA and phoU involved in this process in CACMS001 were revealed by quantitative real-time PCR. CACMS001 is a new potential Rhizobium species and is the first identified MGPB belonging to Rhizobium. This novel bacterium would play a vital part in P. umbellatus, A. gallica, and other mushroom cultivation.
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Affiliation(s)
- Zhongyi Hua
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Tianrui Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Pengjie Han
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Junhui Zhou
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuyang Zhao
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuan Yuan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Yuan Yuan,
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Large-scale commercial cultivation of morels: current state and perspectives. Appl Microbiol Biotechnol 2022; 106:4401-4412. [PMID: 35731306 DOI: 10.1007/s00253-022-12012-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022]
Abstract
Since morels were first successfully cultivated commercially in Sichuan in 2012, morel cultivation has expanded to more than 20 provinces in China. The highest yield currently reaches 15,000 kg/ha. Morel cultivation is characterized by its environmental friendliness, short cycle length, and high profit. However, the yield obtained is unstable which makes morel cultivation a high-risk industry. Although 10 production cycles have passed, there is still a gap between morel cultivation practice and our basic knowledge of morel biology. This mini-review concentrates on the development needs of morel cultivation. We illustrate the key techniques used in the large-scale commercial cultivation of morels and their relevant studies, including nutritional requirements, mechanisms of nutrient bag, soil type, vegetative and reproductive growth conditions, and disease control. This review will be a useful practical reference for the commercial artificial cultivation of morels and promoting the vital technologies required. KEY POINTS: •Unstable yield still exists after commercial cultivation of morels realized. •There is a gap between cultivation practice and our knowledge of morel biology. •Key techniques are illustrated for morel cultivation practice.
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Braat N, Koster MC, Wösten HA. Beneficial interactions between bacteria and edible mushrooms. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2021.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Baars JJP, Scholtmeijer K, Sonnenberg ASM, van Peer A. Critical Factors Involved in Primordia Building in Agaricus bisporus: A Review. Molecules 2020; 25:molecules25132984. [PMID: 32610638 PMCID: PMC7411738 DOI: 10.3390/molecules25132984] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 11/19/2022] Open
Abstract
The button mushroom Agaricus bisporus is an economically important crop worldwide. Many aspects of its cultivation are well known, except for the precise biological triggers for its fructification. By and large, for most basidiomycete species, nutrient availability, light and a drop in temperature are critical factors for fructification. A. bisporus deviates from this pattern in the sense that it does not require light for fructification. Furthermore its fructification seems to be inhibited by a self-generated factor which needs to be removed by microorganisms in order to initiate fruiting. This review explores what is known about the morphogenesis of fruiting initiation in A. bisporus, the microflora, the self-inhibitors for fruiting initiation and transcription factors involved. This information is subsequently contrasted with an overall model of the regulatory system involved in the initiation of the formation of primordia in basidiomycetes. The comparison reveals a number of the blank spots in our understanding of the fruiting process in A. bisporus.
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12
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Yu F, Liang JF, Song J, Wang SK, Lu JK. Bacterial Community Selection of Russula griseocarnosa Mycosphere Soil. Front Microbiol 2020; 11:347. [PMID: 32269551 PMCID: PMC7109302 DOI: 10.3389/fmicb.2020.00347] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 02/17/2020] [Indexed: 11/13/2022] Open
Abstract
Russula griseocarnosa is a wild, ectomycorrhizal, edible, and medicinal fungus with high economic value in southern China. R. griseocarnosa fruiting bodies cannot be artificially cultivated. To better understand the effects of abiotic and biotic factors on R. griseocarnosa growth, the physicochemical properties of R. griseocarnosa and its associated bacterial communities were investigated in two soil types (mycosphere and bulk soil) from Fujian, Guangdong, and Guangxi Provinces. The results revealed that the diversity, community structure, and functional characteristics of the dominant mycosphere bacteria in all geographical locations were similar. Soil pH and available nitrogen (AN) are the major factors influencing the mycosphere-soil bacterial communities' structure. The diversity of soil bacteria is decreased in R. griseocarnosa mycosphere when compared with the bulk soil. Burkholderia-Paraburkholderia, Mycobacterium, Roseiarcus, Sorangium, Acidobacterium, and Singulisphaera may also be mycorrhiza helper bacteria (MHB) of R. griseocarnosa. The functional traits related to the two-component system, bacterial secretion system, tyrosine metabolism, biosynthesis of unsaturated fatty acids, and metabolism of cofactors and vitamins were more abundant in R. griseocarnosa mycosphere soil. The mycosphere soil bacteria of R. griseocarnosa play a key role in R. griseocarnosa growth. Application of management strategies, such as N fertilizer and microbial fertilizer containing MHB, may promote the conservation, propagation promotion, and sustainable utilization of R. griseocarnosa.
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Affiliation(s)
| | - Jun-Feng Liang
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
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13
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Gao X, Li T, Liu W, Zhang Y, Shang D, Gao Y, Qi Y, Qiu L. Enhancing the 1-Aminocyclopropane-1-Carboxylate Metabolic Rate of Pseudomonas sp. UW4 Intensifies Chemotactic Rhizocompetence. Microorganisms 2020; 8:microorganisms8010071. [PMID: 31906548 PMCID: PMC7023479 DOI: 10.3390/microorganisms8010071] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 12/27/2019] [Accepted: 12/31/2019] [Indexed: 11/16/2022] Open
Abstract
1-aminocyclopropane-1-carboxylic acid (ACC) is a strong metabolism-dependent chemoattractant for the plant beneficial rhizobacterium Pseudomonas sp. UW4. It is unknown whether enhancing the metabolic rate of ACC can intensify the chemotaxis activity towards ACC and rhizocompetence. In this study, we selected four promoters to transcribe the UW4 ACC deaminase (AcdS) gene in the UW4 ΔAcdS mutant. PA is the UW4 AcdS gene promoter, PB20, PB10 and PB1 are synthetic promoters. The order of the AcdS gene expression level and AcdS activity of the four strains harboring the promoters were PB20 > PA > PB10 > PB1. Interestingly, the AcdS activity of the four strains and their parent strain UW4 was significantly positively correlated with their chemotactic activity towards ACC, rhizosphere colonization, roots elongation and dry weight promotion. The results released that enhancing the AcdS activity of PGPRenable them to achieve strong chemotactic responses to ACC, rhizocompetence and plant growth promotion.
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14
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Zhang C, Zhang G, Wen Y, Li T, Gao Y, Meng F, Qiu L, Ai Y. Pseudomonas sp. UW4 acdS gene promotes primordium initiation and fruiting body development of Agaricus bisporus. World J Microbiol Biotechnol 2019; 35:163. [PMID: 31637600 DOI: 10.1007/s11274-019-2741-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/04/2019] [Indexed: 01/28/2023]
Abstract
To simplify industrial mushroom cultivation, we introduced a bacterial Pseudomonas sp. UW4 acdS gene, encoding 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (AcdS), into fungus Agaricus bisporus. Transformant A. bisporus-acdS14 cased with sterilized-vermiculite generated primordia 5 days sooner than wild-type strain, confirming the specific role of the AcdS enzyme. Being consistent with the AcdS enzyme activity increased by 84%, the mycelium growth rate was increased by 25%; but, the ACC and ethylene concentrations were reduced by 71% and 36%, respectively, in the A. bisporus-acdS14 transformant. And the bacterium P. sp. UW4 attachment on the mycelium of the A. bisporus-acdS14 transformant was drastically reduced. We conclude that the heterogeneously expressed bacterial acdS gene degrades ACC and reduces ethylene-synthesis, eliminating ethylene inhibition on the mycelium growth and primordium formation in A. bisporus. Our results provide new insights into the mechanism underlying casing soil bacterium, and help formulate a casing-less cultivation for the next-generation mushroom industry.
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Affiliation(s)
- Chaohui Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 135 Xingang Xi Road, Guangzhou, 510275, People's Republic of China.,College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China
| | - Guang Zhang
- College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China
| | - Yamei Wen
- Zhoukou Academy of Agricultural Sciences, Zhoukou, 466000, People's Republic of China
| | - Tao Li
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, College of Life Sciences, Henan Agricultural University, No. 63 Nongye Road, 450002, Henan, People's Republic of China
| | - Yuqian Gao
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, College of Life Sciences, Henan Agricultural University, No. 63 Nongye Road, 450002, Henan, People's Republic of China
| | - Fanmei Meng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 135 Xingang Xi Road, Guangzhou, 510275, People's Republic of China
| | - Liyou Qiu
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, College of Life Sciences, Henan Agricultural University, No. 63 Nongye Road, 450002, Henan, People's Republic of China.
| | - Yuncan Ai
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 135 Xingang Xi Road, Guangzhou, 510275, People's Republic of China.
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15
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Benucci GMN, Longley R, Zhang P, Zhao Q, Bonito G, Yu F. Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses. PeerJ 2019; 7:e7744. [PMID: 31579614 PMCID: PMC6766373 DOI: 10.7717/peerj.7744] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/25/2019] [Indexed: 12/28/2022] Open
Abstract
Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production.
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Affiliation(s)
| | - Reid Longley
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Peng Zhang
- CAS Key Laboratory for East Asia Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
| | - Qi Zhao
- CAS Key Laboratory for East Asia Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
| | - Gregory Bonito
- Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.,Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Fuqiang Yu
- CAS Key Laboratory for East Asia Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
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16
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Carrasco J, Preston GM. Growing edible mushrooms: a conversation between bacteria and fungi. Environ Microbiol 2019; 22:858-872. [DOI: 10.1111/1462-2920.14765] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Jaime Carrasco
- Department of Plant SciencesUniversity of Oxford, S Parks Rd Oxford OX1 3RB UK
- Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH) Autol Spain
| | - Gail M. Preston
- Department of Plant SciencesUniversity of Oxford, S Parks Rd Oxford OX1 3RB UK
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17
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Yang RH, Bao DP, Guo T, Li Y, Ji GY, Ji KP, Tan Q. Bacterial Profiling and Dynamic Succession Analysis of Phlebopus portentosus Casing Soil Using MiSeq Sequencing. Front Microbiol 2019; 10:1927. [PMID: 31507552 PMCID: PMC6716355 DOI: 10.3389/fmicb.2019.01927] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/05/2019] [Indexed: 11/13/2022] Open
Abstract
Phlebopusportentosus (Berk. and Broome) Boedijin is a popular edible mushroom found in China and Thailand. To date, P. portentosus is the only species in the order Boletales that can be successfully cultivated worldwide. The use of a casing layer or casing soil overlaying the substrate is a crucial step in the production of this mushroom. In this study, bacterial profiling and dynamic succession analyses of casing soil during the cultivation of P. portentosus were performed. One hundred and fifty samples were collected, and MiSeq sequencing of the V3-V4 region of the 16S rRNA gene was conducted. After performing a decontamination procedure, only 38 samples were retained, including 6 casing soil-originated samples (OS), 6 casing soil samples (FHCS) and 5 upper substrate samples (FHCU) from the period of complete colonization by mycelia; 6 casing soil samples (PCS) and 5 upper substrate samples (PCU) from the primordium period; and 6 casing soil samples (FCS) and 4 upper substrate samples (FCU) from fruit body period. The results revealed that bacterial diversity increased sharply from the hyphal to the primordium stage and then decreased during harvesting. The non-metric multidimensional scaling (NMDS) ordination and analysis of similarities (ANOSIM) analysis suggested that the community composition during different stages was significantly different in casing soil. The most abundant phyla in all of the samples were Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Saccharibacteria, and Bacteroidetes. Burkholderia was the most abundant genus in all the samples except the OS samples. The relative abundance of Burkholderia in the FHCS samples (55.79%) decreased to 35.14% in the PCS samples and then increased to 45.60% in the FCS samples. The abundances of Acidobacterium, Rhizobium, Acidisphaera, Bradyrhizobium, and Bacillus increased from the FHCS to PCS samples. The linear discriminant analysis (LDA) effect size (LEfSe) suggested that Acidobacterium and Acidisphaera are micromarkers for PCS, whereas Bradyrhizobium, Roseiarcus, and Pseudolabrys were associated with fruit body stages. The network analyses resulted in 23 edges, including 4 negative and 19 positive edges. Extensive mutualistic interactions may occur among casing soil bacteria. Furthermore, these bacteria play important roles in mycelial elongation, primordium formations, and the production of increased yields.
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Affiliation(s)
- Rui-Heng Yang
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Shanghai Academy of Agricultural Sciences, Institute of Edible Fungi, Shanghai, China.,Key Laboratory of Agricultural Genetics and Breeding of Shanghai, National Engineering Research Center of Edible Fungi, Shanghai Academy of Agricultural Sciences, Institute of Edible Fungi, Shanghai, China
| | - Da-Peng Bao
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Shanghai Academy of Agricultural Sciences, Institute of Edible Fungi, Shanghai, China.,Key Laboratory of Agricultural Genetics and Breeding of Shanghai, National Engineering Research Center of Edible Fungi, Shanghai Academy of Agricultural Sciences, Institute of Edible Fungi, Shanghai, China
| | - Ting Guo
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Shanghai Academy of Agricultural Sciences, Institute of Edible Fungi, Shanghai, China.,Key Laboratory of Agricultural Genetics and Breeding of Shanghai, National Engineering Research Center of Edible Fungi, Shanghai Academy of Agricultural Sciences, Institute of Edible Fungi, Shanghai, China
| | - Yan Li
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Shanghai Academy of Agricultural Sciences, Institute of Edible Fungi, Shanghai, China.,Key Laboratory of Agricultural Genetics and Breeding of Shanghai, National Engineering Research Center of Edible Fungi, Shanghai Academy of Agricultural Sciences, Institute of Edible Fungi, Shanghai, China
| | - Guang-Yan Ji
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Kai-Ping Ji
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Qi Tan
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Shanghai Academy of Agricultural Sciences, Institute of Edible Fungi, Shanghai, China.,Key Laboratory of Agricultural Genetics and Breeding of Shanghai, National Engineering Research Center of Edible Fungi, Shanghai Academy of Agricultural Sciences, Institute of Edible Fungi, Shanghai, China
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18
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Zhang F, Long L, Hu Z, Yu X, Liu Q, Bao J, Long Z. Analyses of artificial morel soil bacterial community structure and mineral element contents in ascocarp and the cultivated soil. Can J Microbiol 2019; 65:738-749. [PMID: 31206319 DOI: 10.1139/cjm-2018-0600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This study explored the differences among various artificial morel cultivations as well as the factors that influence these differences, including soil bacterial community structure, yield, and mineral element contents of ascocarp and the cultivated soil. High-throughput sequencing results revealed that the dominant bacterial phyla in all the samples, including Proteobacteria, Acidobacteria, Chloroflexi, Bacteroides, and Gemmatimonadetes, were found not only in morel soils (experimental group) but also in wheat soil (control group); the highest richness and diversity in the soil bacteria were observed during the primordial differentiation stage. The M6 group exhibited the highest yield (271.8 g/m2) and had an unexpectedly high proportion of Pseudomonas (25.30%) during the primordial differentiation stage, which was 1.77∼194.62 times more than the proportion of Pseudomonas in other samples. Pseudomonas may influence the growth of morel. The mineral element contents of the different soil groups and the ascocarp were determined by electrothermal digestion and inductively coupled plasma mass spectrometry. The results revealed that morel had high enrichment effects on phosphorus (P, bioconcentration factor = 16.83), potassium (K, 2.18), boron (B, 1.47), zinc (Zn, 1.36), copper (Cu, 1.15), and selenium (Se, 2.27). P levels were the highest followed by Se and K, and the mineral element contents in ascocarp were positively correlated with the soil element contents.
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Affiliation(s)
- Fusheng Zhang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
| | - Li Long
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
| | - Zongyue Hu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China.,Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
| | - Xiaorui Yu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China.,Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
| | - Qingya Liu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China.,Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
| | - Jinku Bao
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China.,Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
| | - Zhangfu Long
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China.,Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
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19
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The nematicide Serratia plymuthica M24T3 colonizes Arabidopsis thaliana, stimulates plant growth, and presents plant beneficial potential. Braz J Microbiol 2019; 50:777-789. [PMID: 31177380 DOI: 10.1007/s42770-019-00098-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/27/2019] [Indexed: 01/28/2023] Open
Abstract
Nine bacterial strains were previously isolated in association with pinewood nematode (PWN) from wilted pine trees. They proved to be nematicidal in vitro, and one of the highest activities, with potential to control PWN, was showed by Serratia sp. M24T3. Its ecology in association with plants remains unclear. This study aimed to evaluate the ability of strain M24T3 to colonize the internal tissues of the model plant Arabidopsis thaliana using confocal microscopy. Plant growth-promoting bacteria (PGPB) functional traits were tested and retrieved in the genome of strain M24T3. In greenhouse conditions, the bacterial effects of all nematicidal strains were also evaluated, co-inoculated or not with Bradyrhizobium sp. 3267, on Vigna unguiculata fitness. Inoculation of strain M24T3 increased the number of A. thaliana lateral roots and the confocal analysis confirmed effective bacterial colonization in the plant. Strain M24T3 showed cellulolytic activity, siderophores production, phosphate and zinc solubilization ability, and indole acetic acid production independent of supplementation with L-tryptophan. In the genome of strain M24T3, genes involved in the interaction with the plants such as 1-aminocyclopropane-1-carboxylate (ACC) deaminase, chitinolytic activity, and quorum sensing were also detected. The genomic organization showed ACC deaminase and its leucine-responsive transcriptional regulator, and the activity of ACC deaminase was 594.6 nmol α-ketobutyrate μg protein-1 μl-1. Strain M24T3 in co-inoculation with Bradyrhizobium sp. 3267 promoted the growth of V. unguiculata. In conclusion, this study demonstrated the ability of strain M24T3 to colonize other plants besides pine trees as an endophyte and displays PGPB traits that probably increased plant tolerance to stresses.
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20
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Li T, Zhang J, Shen C, Li H, Qiu L. 1-Aminocyclopropane-1-Carboxylate: A Novel and Strong Chemoattractant for the Plant Beneficial Rhizobacterium Pseudomonas putida UW4. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:750-759. [PMID: 30640574 DOI: 10.1094/mpmi-11-18-0317-r] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) and fungi-bacterial biofilms are both important biofertilizer inoculants for sustainable agriculture. However, the strongest chemoattractant for bacteria to colonize the rhizosphere and mycelia is not clear. Coincidentally, almost all the PGPRs possess 1-aminocyclopropane-1-carboxylate (ACC) deaminase (AcdS) and can utilize ACC as the sole nitrogen source. Here, we found that ACC was a novel, metabolic dependent and methyl-accepting chemoreceptor-involved chemoattractant for Pseudomonas putida UW4. The chemotactic response of UW4 to ACC is significantly greater than that to the amino acids and organic acids identified in the plant root and fungal hyphal exudates. The colonization counts of the UW4 acdS or cheR deletion mutants in the wheat rhizosphere and on Agaricus bisporus mycelia were reduced one magnitude compared with those of UW4. The colonization counts of UW4 on A. bisporus antisense ACC oxidase mycelia with a high ACC production significantly increased compared with A. bisporus, followed by the UW4 cheR complementary strain and the ethylene chemoreceptor gene-deletion mutant. The colonization counts of the UW4 strains on A. bisporus acdS+ mycelia with a low ACC production decreased significantly compared with A. bisporus wild type. These results suggested that ACC and not ethylene should be the strongest chemoattractant for the PGPR that contain AcdS.
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Affiliation(s)
- Tao Li
- College of Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Jun Zhang
- College of Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Chaohui Shen
- College of Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Huiru Li
- College of Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Liyou Qiu
- College of Sciences, Henan Agricultural University, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, 450002, China
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21
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Near-Complete Genome Sequence of Pseudomonas palleroniana MAB3, a Beneficial 1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Bacterium Able To Promote the Growth of Mushrooms and Plants. GENOME ANNOUNCEMENTS 2018; 6:6/16/e00242-18. [PMID: 29674537 PMCID: PMC5908933 DOI: 10.1128/genomea.00242-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The near-complete genome sequence of Pseudomonas palleroniana MAB3, a 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from an environmental soil Amanita mushroom, is presented here. The genome of P. palleroniana MAB3 contains a single circular chromosome of 6.29 Mb and an average GC content of 60.5%.
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22
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Bahram M, Vanderpool D, Pent M, Hiltunen M, Ryberg M. The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:155-166. [PMID: 29327481 DOI: 10.1111/1758-2229.12612] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/19/2017] [Accepted: 01/04/2018] [Indexed: 06/07/2023]
Abstract
Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.
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Affiliation(s)
- Mohammad Bahram
- Department of Organismal Biology, Evolutionary Biology Centre Uppsala University, Norbyvägen 18D, Uppsala, 75236 Sweden
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, 51005 Estonia
| | - Dan Vanderpool
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Mari Pent
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, 51005 Estonia
| | - Markus Hiltunen
- Department of Organismal Biology, Evolutionary Biology Centre Uppsala University, Norbyvägen 18D, Uppsala, 75236 Sweden
| | - Martin Ryberg
- Department of Organismal Biology, Evolutionary Biology Centre Uppsala University, Norbyvägen 18D, Uppsala, 75236 Sweden
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23
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Compost bacteria and fungi that influence growth and development of Agaricus bisporus and other commercial mushrooms. Appl Microbiol Biotechnol 2018; 102:1639-1650. [PMID: 29362825 DOI: 10.1007/s00253-018-8777-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/07/2018] [Accepted: 01/09/2018] [Indexed: 10/18/2022]
Abstract
Mushrooms are an important food crop for many millions of people worldwide. The most important edible mushroom is the button mushroom (Agaricus bisporus), an excellent example of sustainable food production which is cultivated on a selective compost produced from recycled agricultural waste products. A diverse population of bacteria and fungi are involved throughout the production of Agaricus. A range of successional taxa convert the wheat straw into compost in the thermophilic composting process. These initially break down readily accessible compounds and release ammonia, and then assimilate cellulose and hemicellulose into compost microbial biomass that forms the primary source of nutrition for the Agaricus mycelium. This key process in composting is performed by a microbial consortium consisting of the thermophilic fungus Mycothermus thermophilus (Scytalidium thermophilum) and a range of thermophilic proteobacteria and actinobacteria, many of which have only recently been identified. Certain bacterial taxa have been shown to promote elongation of the Agaricus hyphae, and bacterial activity is required to induce production of the mushroom fruiting bodies during cropping. Attempts to isolate mushroom growth-promoting bacteria for commercial mushroom production have not yet been successful. Compost bacteria and fungi also cause economically important losses in the cropping process, causing a range of destructive diseases of mushroom hyphae and fruiting bodies. Recent advances in our understanding of the key bacteria and fungi in mushroom compost provide the potential to improve productivity of mushroom compost and to reduce the impact of crop disease.
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24
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Xiang Q, Luo L, Liang Y, Chen Q, Zhang X, Gu Y. The Diversity, Growth Promoting Abilities and Anti-microbial Activities of Bacteria Isolated from the Fruiting Body of Agaricus bisporus. Pol J Microbiol 2017; 66:201-207. [DOI: 10.5604/01.3001.0010.7837] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Agaricus bisporus plays an important role in ecological processes and is one of the most widely cultivated mushrooms worldwide. Mushroom growth-promoting bacteria have been isolated from casing soil and compost, but microorganisms in the fruiting body have received only a little attention. To get an overview of phylogenetic diversity of microorganisms in the fruiting body of A. bisporus, as well as to screen antimicrobial and mushroom growth-promoting strains, and eventually intensify mushroom production, we isolated and characterized microorganisms from the fruiting body of A. bisporus. In total, 55 bacterial strains were isolated, among which nine isolates represented Actinomycetes. All the isolates were analyzed by 16S rRNA gene RFLP and sixteen representative strains by 16S rRNA gene sequencing. According to the phylogenetic analysis, eleven isolates represented the Gram positive Bacillus, Lysinibacillus, Paenibacillus, Pandorea and Streptomyces genera, and five isolates belonged to the Gram negative Alcaligenes and Pseudomonas genera. The bacteria isolated from the fruiting body of A. bisporus had broad-spectrum antimicrobial activities and potential mushroom growth-promoting abilities.
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Affiliation(s)
- Quanju Xiang
- College of Resource, Sichuan Agricultural University, Wenjiang District, Chengdu, Sichuan, P.R. China
| | - Lihua Luo
- College of Resource, Sichuan Agricultural University, Wenjiang District, Chengdu, Sichuan, P.R. China
| | - Yuhuan Liang
- College of Resource, Sichuan Agricultural University, Wenjiang District, Chengdu, Sichuan, P.R. China
| | - Qiang Chen
- College of Resource, Sichuan Agricultural University, Wenjiang District, Chengdu, Sichuan, P.R. China
| | - Xiaoping Zhang
- College of Resource, Sichuan Agricultural University, Wenjiang District, Chengdu, Sichuan, P.R. China
| | - Yunfu Gu
- College of Resource, Sichuan Agricultural University, Wenjiang District, Chengdu, Sichuan, P.R. China
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Liu Q, Liu H, Chen C, Wang J, Han Y, Long Z. Effects of element complexes containing Fe, Zn and Mn on artificial morel's biological characteristics and soil bacterial community structures. PLoS One 2017; 12:e0174618. [PMID: 28350840 PMCID: PMC5370159 DOI: 10.1371/journal.pone.0174618] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 03/12/2017] [Indexed: 12/29/2022] Open
Abstract
This study described the effects of elements (including Fe, Zn, Mn and their complexes) on the following factors in artificial morel cultivation: the characteristics of mycelia and sclerotia, soil bacterial community structures, yields and contents of microelements. The results indicated that the groups containing Mn significantly promoted mycelia growth rates, and all the experimental groups resulted in higher yields than the control (P<0.01), although their mycelia and sclerotia did not show obvious differences. It was also found that Proteobacteria, Chloroflexi, Bacteroides, Firmicutes, Actinobacteria, Acidobacteria and Nitrospirae were the dominated bacterial phyla. The Zn·Fe group had an unexpectedly high proportion (75.49%) of Proteobacteria during the primordial differentiation stage, while Pseudomonas also occupied a high proportion (5.52%) in this group. These results suggested that different trace elements clearly affected morel yields and soil bacterial community structures, particularly due to the high proportions of Pseudomonas during the primordial differentiation stage.
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Affiliation(s)
- Qingya Liu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Huimei Liu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Ciqiong Chen
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Jinmei Wang
- Sichuan Tongfeng Science & Technology Co. Ltd, Chengdu, P.R. China
| | - Yu Han
- Sichuan Tongfeng Science & Technology Co. Ltd, Chengdu, P.R. China
| | - Zhangfu Long
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
- * E-mail:
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Li Z, Chang S, Ye S, Chen M, Lin L, Li Y, Li S, An Q. Differentiation of 1-aminocyclopropane-1-carboxylate (ACC) deaminase from its homologs is the key for identifying bacteria containing ACC deaminase. FEMS Microbiol Ecol 2015; 91:fiv112. [PMID: 26362924 DOI: 10.1093/femsec/fiv112] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2015] [Indexed: 01/28/2023] Open
Abstract
1-Aminocyclopropane-1-carboxylate (ACC) deaminase-mediated reduction of ethylene generation in plants under abiotic stresses is a key mechanism by which bacteria can promote plant growth. Misidentification of ACC deaminase and the ACC deaminase structure gene (acdS) can lead to overestimation of the number of bacteria containing ACC deaminase and their function in ecosystems. Previous non-specific amplification of acdS homologs has led to an overestimation of the horizontal transfer of acdS genes. Here, we designed consensus-degenerate hybrid oligonucleotide primers (acdSf3, acdSr3 and acdSr4) based on differentiating the key residues in ACC deaminases from those of homologs for specific amplification of partial acdS genes. PCR amplification, sequencing and phylogenetic analysis identified acdS genes from a wide range of proteobacteria and actinobacteria. PCR amplification and a genomic search did not find the acdS gene in bacteria belonging to Pseudomonas stutzeri or in the genera Enterobacter, Klebsiella or Bacillus. We showed that differentiating the acdS gene and ACC deaminase from their homologs was crucial for the molecular identification of bacteria containing ACC deaminase and for understanding the evolution of the acdS gene. We provide an effective method for screening and identifying bacteria containing ACC deaminase.
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Affiliation(s)
- Zhengyi Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Siping Chang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shuting Ye
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mingyue Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Li Lin
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yuanyuan Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shuying Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qianli An
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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New insights into 1-aminocyclopropane-1-carboxylate (ACC) deaminase phylogeny, evolution and ecological significance. PLoS One 2014; 9:e99168. [PMID: 24905353 PMCID: PMC4048297 DOI: 10.1371/journal.pone.0099168] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 05/09/2014] [Indexed: 01/13/2023] Open
Abstract
The main objective of this work is the study of the phylogeny, evolution and ecological importance of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, the activity of which represents one of the most important and studied mechanisms used by plant growth–promoting microorganisms. The ACC deaminase gene and its regulatory elements presence in completely sequenced organisms was verified by multiple searches in diverse databases, and based on the data obtained a comprehensive analysis was conducted. Strain habitat, origin and ACC deaminase activity were taken into account when analyzing the results. In order to unveil ACC deaminase origin, evolution and relationships with other closely related pyridoxal phosphate (PLP) dependent enzymes a phylogenetic analysis was also performed. The data obtained show that ACC deaminase is mostly prevalent in some Bacteria, Fungi and members of Stramenopiles. Contrary to previous reports, we show that ACC deaminase genes are predominantly vertically inherited in various bacterial and fungal classes. Still, results suggest a considerable degree of horizontal gene transfer events, including interkingdom transfer events. A model for ACC deaminase origin and evolution is also proposed. This study also confirms the previous reports suggesting that the Lrp-like regulatory protein AcdR is a common mechanism regulating ACC deaminase expression in Proteobacteria, however, we also show that other regulatory mechanisms may be present in some Proteobacteria and other bacterial phyla. In this study we provide a more complete view of the role for ACC deaminase than was previously available. The results show that ACC deaminase may not only be related to plant growth promotion abilities, but may also play multiple roles in microorganism's developmental processes. Hence, exploring the origin and functioning of this enzyme may be the key in a variety of important agricultural and biotechnological applications.
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