101
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Buresova‐Faitova A, Kopecky J, Sagova‐Mareckova M, Alonso L, Vautrin F, Moënne‐Loccoz Y, Rodriguez‐Nava V. Comparison of
Actinobacteria
communities from human‐impacted and pristine karst caves. Microbiologyopen 2022; 11:e1276. [PMID: 35478281 PMCID: PMC8988830 DOI: 10.1002/mbo3.1276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 11/07/2022] Open
Abstract
Actinobacteria are important cave inhabitants, but knowledge of how anthropization and anthropization‐related visual marks affect this community on cave walls is lacking. We compared Actinobacteria communities among four French limestone caves (Mouflon, Reille, Rouffignac, and Lascaux) ranging from pristine to anthropized, and within Lascaux Cave between marked (wall visual marks) and unmarked areas in different rooms (Sas‐1, Passage, Apse, and Diaclase). In addition to the 16S rRNA gene marker, 441 bp fragments of the hsp65 gene were used and an hsp65‐related taxonomic database was constructed for the identification of Actinobacteria to the species level by Illumina‐MiSeq analysis. The hsp65 marker revealed higher resolution for species and higher richness (99% operational taxonomic units cutoff) versus the 16S rRNA gene; however, more taxa were identified at higher taxonomic ranks. Actinobacteria communities varied between Mouflon and Reille caves (both pristine), and Rouffignac and Lascaux (both anthropized). Rouffignac displayed high diversity of Nocardia, suggesting human inputs, and Lascaux exhibited high Mycobacterium relative abundance, whereas Gaiellales were typical in pristine caves and the Diaclase (least affected area of Lascaux Cave). Within Lascaux, Pseudonocardiaceae dominated on unmarked walls and Streptomycetaceae (especially Streptomyces mirabilis) on marked walls, indicating a possible role in mark formation. A new taxonomic database was developed. Although not all Actinobacteria species were represented, the use of the hsp65 marker enabled species‐level variations of the Actinobacteria community to be documented based on the extent of anthropogenic pressure. This approach proved effective when comparing different limestone caves or specific conditions within one cave.
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Affiliation(s)
- Andrea Buresova‐Faitova
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
- Department of Ecology, Faculty of ScienceCharles University in PraguePrague 2PragueCzech Republic
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Jan Kopecky
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Marketa Sagova‐Mareckova
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Lise Alonso
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Florian Vautrin
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Yvan Moënne‐Loccoz
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Veronica Rodriguez‐Nava
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
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102
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Henagamage AP, Peries CM, Seneviratne G. Fungal-bacterial biofilm mediated heavy metal rhizo-remediation. World J Microbiol Biotechnol 2022; 38:85. [PMID: 35380298 DOI: 10.1007/s11274-022-03267-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/21/2022] [Indexed: 12/01/2022]
Abstract
Heavy metal pollution due to excessive use of chemical fertilizers (CF) causes major damage to the environment. Microbial biofilms, closely associated with the rhizosphere can remediate heavy metal-contaminated soil by reducing plant toxicity. Thus, this study was undertaken to examine the remedial effects of microbial biofilms against contaminated heavy metals. Fungi and bacteria isolated from soil were screened for their tolerance against Cd2+, Pb2+, and Zn2+. Three bacterial and two fungal isolates were selected upon the tolerance index (TI) percentage. Fungal-bacterial biofilms (FBBs) were developed with the most tolerant isolates and were further screened for their bioremediation capabilities against heavy metals. The best biofilm was evaluated for its rhizoremediation capability with different CF combinations using a pot experiment conducted under greenhouse conditions with potatoes. Significantly (P < 0.05), the highest metal removal percentage was observed in Trichoderma harzianum and Bacillus subtilis biofilm under in situ conditions. When compared to the 100% recommended CF, the biofilm with 50% of the recommended CF (50CB) significantly (P < 0.05) reduced soil available Pb2+ by 77%, Cd2+ by 78% and Zn2+ by 62%. In comparison to initial soil, it was 73%, 76%, and 57% lower of Pb2+, Cd2+, and Zn2+, respectively. In addition, 50CB treatment significantly (P < 0.05) reduced the metal penetration into the tuber tissues in comparison with 100 C. Thus, the function of the developed FBB with T. harzianum-B. subtilis can be used as a potential solution to remediate soil polluted with Pb2+ Cd2+ and Zn2+ metal contaminants.
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Affiliation(s)
- A P Henagamage
- Department of Science and Technology, Faculty of Applied Sciences, Uva Wellassa University, Passara Road, Badulla, Sri Lanka.
| | - C M Peries
- Department of Science and Technology, Faculty of Applied Sciences, Uva Wellassa University, Passara Road, Badulla, Sri Lanka
| | - G Seneviratne
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka
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103
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Wei G, Li M, Zhang G, Chen Z, Wei F, Jiao S, Qian J, Wang Y, Wei J, Wang Y, Meng X, Fitzgerald M, Yu Y, Dong L, Chen S. Temporal Dynamics of Rhizosphere Communities Across the Life Cycle of Panax notoginseng. Front Microbiol 2022; 13:853077. [PMID: 35432289 PMCID: PMC9010977 DOI: 10.3389/fmicb.2022.853077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/02/2022] [Indexed: 12/13/2022] Open
Abstract
Rhizosphere microbiome promotes plant growth; however, the succession of rhizosphere microbial community during the growth stages of perennial medicinal plant Panax notoginseng (P. notoginseng) is still unclear. Here, amplicon sequencing was performed to assess the succession characteristics of rhizosphere microbiomes during developmental stages. Results showed that bacterial and fungal communities were mainly shaped by the development stages. The microbial α-diversities first increased and then decreased with plant growth and the variation in microbial composition was active at the 3-year root growth (3YR) stage. The variation trend of cross-domain co-occurrence network complexity was similar to that of α-diversities. Cross-domain nodes decreased at the 3YR stage and fungal nodes increased at the 3YR stage. This study provided a detailed and systematic survey of rhizosphere microbiomes during the growth stages of P. notoginseng. The findings revealed that the development stages of P. notoginseng drove the temporal dynamics of rhizosphere communities. This study helps in harnessing the power of microbiomes to evaluate herbal medicine growth and provides valuable information to guide the microbial breeding of medical plants.
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Affiliation(s)
- Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mengzhi Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan University, Wenshan, China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co., Ltd., Wenshan, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Jun Qian
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan, China
| | - Jianhe Wei
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Yitao Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, China
| | - Xiangxiao Meng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | | | - Yuqi Yu
- Wenshan Miaoxiang Notoginseng Technology, Co., Ltd., Wenshan, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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104
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Complete Genome Sequence of Achromobacter sp. Strain 77, a Hyphosphere Isolate of Fusarium oxysporum f. sp. cucumerinum. Microbiol Resour Announc 2022; 11:e0113821. [PMID: 35357184 PMCID: PMC9022553 DOI: 10.1128/mra.01138-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome sequence of Achromobacter sp. strain 77, a bacterium isolated from the hyphosphere of Fusarium oxysporum f. sp. cucumerinum, is reported here. Genome sequencing and assembly yielded one chromosome consisting of 5,868,070 bases, with a G+C content of 65.89%.
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105
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Estoppey A, Weisskopf L, Di Francesco E, Vallat-Michel A, Bindschedler S, Chain PS, Junier P. Improved methods to assess the effect of bacteria on germination of fungal spores. FEMS Microbiol Lett 2022; 369:6553822. [PMID: 35325127 DOI: 10.1093/femsle/fnac034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/08/2021] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial-fungal interactions (BFI) play a major role on ecosystem functioning and might be particularly relevant at a specific development stage. For instance, in the case of biological control of fungal pathogens by bacteria, a highly relevant kind of BFI, in-vitro experiments often assess the impact of a bacterium on the inhibition of actively growing mycelia. However, this fails to consider other stages of plant infection such as the germination of a spore or a sclerotium. This study aims to present novel experimental platforms for in-vitro experiments with fungal spores, in order to assess the effect of bacteria on germination and fungal growth control, to recover the metabolites produced in the interaction, and to enhance direct visualisation of BFI. Botrytis cinerea, a phytopathogenic fungus producing oxalic acid (OA) as pathogenicity factor, was used as model. Given that oxalotrophic bacteria have been shown previously to control the growth of B. cinerea, the oxalotrophic bacteria Cupriavidus necator and Cupriavidus oxalaticus were used as models. The experiments performed demonstrated the suitability of the methods and confirmed that both bacteria were able to control the growth of B. cinerea, but only in media in which soluble OA was detected by the fungus. The methods presented here can be easily performed in any microbiology laboratory and are not only applicable to screen for potential biocontrol agents, but also to better understand BFI.
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Affiliation(s)
- Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Laure Weisskopf
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Eva Di Francesco
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Armelle Vallat-Michel
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Patrick S Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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106
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Gardner CM, Gerhard WA, Redfern LK, Gunsch CK. Evaluation of developing maize microbiomes and associations among nitrogen cyclers and key fungal taxa. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35319433 DOI: 10.1099/mic.0.001155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
More sustainable approaches to agriculture are urgently needed to protect existing resources and optimize crop yields and to provide food for a growing global human population. More sustainable agricultural practices that utilize plant-microbe relationships across cultivation are urgently needed. The main objectives of this study were to track the prokaryotic and fungal microbiomes associated with key growth stages of developing maize to evaluate the relationships among nitrogen cycling bacteria and major fungal genera including those known to contain arbuscular mycorrhizal fungi and other important taxa. Prokaryotic and fungal microbiomes associated with bulk soils, rhizosphere soils and tissues of developing maize were characterized using Illumina MiSeq sequencing. Similarities in microbiome diversity and abundance were compared to sample metadata to explore the influence of external factors on microbiome development. Correlations among target fungal taxa, bulk bacteria and nitrogen cycling bacteria were determined using non-parametric Spearman correlations. Important maize-associated fungal taxa were detected in all samples across growth stages, with Fusarium, Penicillium and Aspergillus fungi comprising up to 4.21, 4.26 and 0.28% of all fungal genera, respectively. Thirteen statistically significant correlations between nitrogen cycling genera and targeted fungal genera were also identified (r S≥0.70 or r S≤-0.70; P<0.05). This study is the first to note a strong positive association among several nitrifying bacteria and Fusarium (R=0.71; P=0.0046), Aspergillus (R=0.71; P=0.0055) and Cladosporium spcies (R=0.74; P=0.0038), suggesting the levels of soil nitrate, nitrite or nitrification intermediates may have large roles in the proliferation of important maize-associated fungi.
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Affiliation(s)
- Courtney M Gardner
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA.,Present address: Washington State University, Civil and Environmental Engineering, 405 Spokane St., PO Box 642910, Pullman, WA 99164, USA
| | - William A Gerhard
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA
| | - Lauren K Redfern
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA.,Present address: Florida Gulf Coast University, Environmental and Civil Engineering, 10501 FGCU Blvd. South, Ft. Myers, FL 33965, USA
| | - Claudia K Gunsch
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA.,Present address: Duke University, Durham, NC 27708, USA
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107
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Tao L, Wang M, Guan G, Zhang Y, Hao T, Li C, Li S, Chen Y, Huang G. Streptococcus mutans suppresses filamentous growth of Candida albicans through secreting mutanocyclin, an unacylated tetramic acid. Virulence 2022; 13:542-557. [PMID: 35311622 PMCID: PMC8942415 DOI: 10.1080/21505594.2022.2046952] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Li Tao
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Min Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guobo Guan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuwei Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Hao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chao Li
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuaihu Li
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guanghua Huang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms
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108
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Crystal structures of YeiE from Cronobacter sakazakii and the role of sulfite tolerance in gram-negative bacteria. Proc Natl Acad Sci U S A 2022; 119:e2118002119. [PMID: 35271389 PMCID: PMC8931317 DOI: 10.1073/pnas.2118002119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
YeiE has been identified as a master virulence factor of Cronobacter sakazakii. In this study, we determined the crystal structures of the regulatory domain of YeiE in complex with its physiological ligand sulfite ion (SO32−). The structure provides the basis for the molecular mechanisms for sulfite sensing and the ligand-dependent conformational changes of the regulatory domain. The genes under the control of YeiE in response to sulfite were investigated to reveal the functional roles of YeiE in the sulfite tolerance of the bacteria. We propose the molecular mechanism underlying the ability of gram-negative pathogens to defend against the innate immune response involving sulfite, thus providing a strategy to control the pathogenesis of bacteria. Cronobacter sakazakii is an emerging gram-negative pathogenic bacterium that causes meningitis, bacteremia, and necrotizing enterocolitis in infants and has a high mortality rate. The YeiE homolog (gpESA_01081) was identified as a global virulence regulator of bacterial pathogenesis in C. sakazakii. YeiE is a LysR-type transcriptional regulator (LTTR) composed of a DNA binding domain and a regulatory domain to recognize the unknown ligand. To reveal the molecular mechanism and function of YeiE, we determined the crystal structure of the regulatory domain of YeiE. A sulfite ion was bound at the putative ligand-binding site, and subsequent studies revealed that the sulfite is the physiological ligand for YeiE. Structural comparisons to its sulfite-free structure further showed the sulfite-dependent conformational change of YeiE. The essential role of YeiE in defending against toxicity from sulfite during the growth of C. sakazakii and Escherichia coli was examined. Furthermore, the target genes and functional roles of YeiE in H2S production and survival capability from neutrophils were investigated. Our findings provide insights into the sophisticated behaviors of pathogenic gram-negative bacteria in response to sulfite from the environment and host.
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109
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Singh D, Lee SH, Lee CH. Non-obligate pairwise metabolite cross-feeding suggests ammensalic interactions between Bacillus amyloliquefaciens and Aspergillus oryzae. Commun Biol 2022; 5:232. [PMID: 35293898 PMCID: PMC8924192 DOI: 10.1038/s42003-022-03181-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/18/2022] [Indexed: 11/17/2022] Open
Abstract
Bacterial-fungal metabolite trade-offs determine their ecological interactions. We designed a non-obligate pairwise metabolite cross-feeding (MCF) between Bacillus amyloliquefaciens and Aspergillus oryzae. Cross-feeding Aspergillus metabolites (MCF-1) affected higher growth and biofilm formation in Bacillus. LC-MS/MS-based multivariate analyses (MVA) showed variations in the endogenous metabolite profiles between the cross-fed and control Bacillus. We observed and validated that Aspergillus-derived oxylipins were rapidly depleted in Bacillus cultures concomitant with lowered secretion of cyclic lipopeptides (CLPs). Conversely, Bacillus extracts cross-fed to Aspergillus (MCF-2) diminished its mycelial growth and conidiation. Fungistatic effects of Bacillus-derived cyclic surfactins were temporally reduced following their hydrolytic linearization. MVA highlighted disparity between the cross-fed (MCF-2) and control Aspergillus cultures with marked variations in the oxylipin levels. We conclude that the pairwise MCF selectively benefitted Bacillus while suppressing Aspergillus, which suggests their ammensalic interaction. Widening this experimental pipeline across tailored communities may help model and simulate BFIs in more complex microbiomes. Metabolite trade-offs between Bacillus amyloliquefaciens and Aspergillus oryzae selectively benefit the bacterial partner and suppress fungal growth, showcasing their ammensalic interaction.
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Affiliation(s)
- Digar Singh
- Department of Bioscience and Biotechnology, Konkuk University, 05029, Seoul, Korea
| | - Sang Hee Lee
- Department of Bioscience and Biotechnology, Konkuk University, 05029, Seoul, Korea
| | - Choong Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, 05029, Seoul, Korea.
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110
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Itabangi H, Sephton-Clark PCS, Tamayo DP, Zhou X, Starling GP, Mahamoud Z, Insua I, Probert M, Correia J, Moynihan PJ, Gebremariam T, Gu Y, Ibrahim AS, Brown GD, King JS, Ballou ER, Voelz K. A bacterial endosymbiont of the fungus Rhizopus microsporus drives phagocyte evasion and opportunistic virulence. Curr Biol 2022; 32:1115-1130.e6. [PMID: 35134329 PMCID: PMC8926845 DOI: 10.1016/j.cub.2022.01.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 11/04/2021] [Accepted: 01/11/2022] [Indexed: 02/07/2023]
Abstract
Opportunistic infections by environmental fungi are a growing clinical problem, driven by an increasing population of people with immunocompromising conditions. Spores of the Mucorales order are ubiquitous in the environment but can also cause acute invasive infections in humans through germination and evasion of the mammalian host immune system. How they achieve this and the evolutionary drivers underlying the acquisition of virulence mechanisms are poorly understood. Here, we show that a clinical isolate of Rhizopus microsporus contains a Ralstonia pickettii bacterial endosymbiont required for virulence in both zebrafish and mice and that this endosymbiosis enables the secretion of factors that potently suppress growth of the soil amoeba Dictyostelium discoideum, as well as their ability to engulf and kill other microbes. As amoebas are natural environmental predators of both bacteria and fungi, we propose that this tri-kingdom interaction contributes to establishing endosymbiosis and the acquisition of anti-phagocyte activity. Importantly, we show that this activity also protects fungal spores from phagocytosis and clearance by human macrophages, and endosymbiont removal renders the fungal spores avirulent in vivo. Together, these findings describe a new role for a bacterial endosymbiont in Rhizopus microsporus pathogenesis in animals and suggest a mechanism of virulence acquisition through environmental interactions with amoebas.
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Affiliation(s)
- Herbert Itabangi
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Poppy C S Sephton-Clark
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Diana P Tamayo
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Xin Zhou
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Georgina P Starling
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Zamzam Mahamoud
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ignacio Insua
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mark Probert
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Joao Correia
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Patrick J Moynihan
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Teclegiorgis Gebremariam
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yiyou Gu
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ashraf S Ibrahim
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA; David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Gordon D Brown
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Jason S King
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Elizabeth R Ballou
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - Kerstin Voelz
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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111
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Chitlapilly Dass S, Wang R. Biofilm through the Looking Glass: A Microbial Food Safety Perspective. Pathogens 2022; 11:346. [PMID: 35335670 PMCID: PMC8954374 DOI: 10.3390/pathogens11030346] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
Food-processing facilities harbor a wide diversity of microorganisms that persist and interact in multispecies biofilms, which could provide an ecological niche for pathogens to better colonize and gain tolerance against sanitization. Biofilm formation by foodborne pathogens is a serious threat to food safety and public health. Biofilms are formed in an environment through synergistic interactions within the microbial community through mutual adaptive response to their long-term coexistence. Mixed-species biofilms are more tolerant to sanitizers than single-species biofilms or their planktonic equivalents. Hence, there is a need to explore how multispecies biofilms help in protecting the foodborne pathogen from common sanitizers and disseminate biofilm cells from hotspots and contaminate food products. This knowledge will help in designing microbial interventions to mitigate foodborne pathogens in the processing environment. As the global need for safe, high-quality, and nutritious food increases, it is vital to study foodborne pathogen behavior and engineer new interventions that safeguard food from contamination with pathogens. This review focuses on the potential food safety issues associated with biofilms in the food-processing environment.
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Affiliation(s)
| | - Rong Wang
- Roman L. Hruska U.S. Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, NE 68933, USA;
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Bacterial hitchhikers derive benefits from fungal housing. Curr Biol 2022; 32:1523-1533.e6. [PMID: 35235767 PMCID: PMC9009100 DOI: 10.1016/j.cub.2022.02.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 10/14/2021] [Accepted: 02/03/2022] [Indexed: 12/21/2022]
Abstract
Fungi and bacteria are ubiquitous constituents of all microbiomes, yet mechanisms of microbial persistence in polymicrobial communities remain obscure. Here, we examined the hypothesis that specialized fungal survival structures, chlamydospores, induced by bacterial lipopeptides serve as bacterial reservoirs. We find that symbiotic and pathogenic gram-negative bacteria from non-endosymbiotic taxa enter and propagate in chlamydospores. Internalized bacteria have higher fitness than planktonic bacteria when challenged with abiotic stress. Further, tri-cultures of Ralstonia solanacearum, Pseudomonas aeruginosa, and Aspergillus flavus reveal the unprecedented finding that chlamydospores are colonized by endofungal bacterial communities. Our work identifies a previously unknown ecological role of chlamydospores, provides an expanded view of microbial niches, and presents significant implications for the persistence of pathogenic and beneficial bacteria.
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113
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Senanayake IC, Pem D, Rathnayaka AR, Wijesinghe SN, Tibpromma S, Wanasinghe DN, Phookamsak R, Kularathnage ND, Gomdola D, Harishchandra D, Dissanayake LS, Xiang MM, Ekanayaka AH, McKenzie EHC, Hyde KD, Zhang HX, Xie N. Predicting global numbers of teleomorphic ascomycetes. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00498-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
AbstractSexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.
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Peng L, Liu CF, Wu H, Jin H, Deng XY, Zeng LT, Xiao Y, Deng C, Yang ZK. Complete Genome Sequencing and Comparative Analysis of the Clinically-Derived Apiotrichum mycotoxinivorans Strain GMU1709. Front Cell Infect Microbiol 2022; 12:834015. [PMID: 35186802 PMCID: PMC8855340 DOI: 10.3389/fcimb.2022.834015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/12/2022] [Indexed: 12/22/2022] Open
Abstract
Over the past decade, Apiotrichum mycotoxinivorans has been recognized globally as a source of opportunistic infections. It is a yeast-like fungus, and its association as an uncommon pulmonary pathogen with cystic fibrosis patients has been previously reported. Immunocompromised patients are at the highest risk of A. mycotoxinivorans infections. Therefore, to investigate the genetic basis for the pathogenicity of A. mycotoxinivorans, we performed whole-genome sequencing and comparative genomic analysis of A. mycotoxinivorans GMU1709 that was isolated from sputum specimens of a pneumonia patient receiving cardiac repair surgery. The assembly of Oxford Nanopore reads from the GMU1709 strain and its subsequent correction using Illumina paired-end reads yielded a high-quality complete genome with a genome size of 30.5 Mb in length, which comprised six chromosomes and one mitochondrion. Subsequently, 8,066 protein-coding genes were predicted based on multiple pieces of evidence, including transcriptomes. Phylogenomic analysis indicated that A. mycotoxinivorans exhibited the closest evolutionary affinity to A. veenhuisii, and both the A. mycotoxinivorans strains and the formerly Trichosporon cutaneum ACCC 20271 strain occupied the same phylogenetic position. Further comparative analysis supported that the ACCC 20271 strain belonged to A. mycotoxinivorans. Comparisons of three A. mycotoxinivorans strains indicated that the differences between clinical and non-clinical strains in pathogenicity and drug resistance may be little or none. Based on the comparisons with strains of other species in the Trichosporonaceae family, we identified potential key genetic factors associated with A. mycotoxinivorans infection or pathogenicity. In addition, we also deduced that A. mycotoxinivorans had great potential to inactivate some antibiotics (e.g., tetracycline), which may affect the efficacy of these drugs in co-infection. In general, our analyses provide a better understanding of the classification and phylogeny of the Trichosporonaceae family, uncover the underlying genetic basis of A. mycotoxinivorans infections and associated drug resistance, and provide clues into potential targets for further research and the therapeutic intervention of infections.
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Affiliation(s)
- Liang Peng
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Chen-Fei Liu
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hong Wu
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hai Jin
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiao-Yan Deng
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Li-Ting Zeng
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yi Xiao
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Cong Deng
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhi-Kai Yang
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhi-Kai Yang,
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Das P, Effmert U, Baermann G, Quella M, Piechulla B. Impact of bacterial volatiles on phytopathogenic fungi: an in vitro study on microbial competition and interaction. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:596-614. [PMID: 34718549 DOI: 10.1093/jxb/erab476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms in the rhizosphere are abundant and exist in very high taxonomic diversity. The major players are bacteria and fungi, and bacteria have evolved many strategies to prevail over fungi, among them harmful enzyme activities and noxious secondary metabolites. Interactions between plant growth promoting rhizobacteria and phytopathogenic fungi are potentially valuable since the plant would benefit from fungal growth repression. In this respect, the role of volatile bacterial metabolites in fungistasis has been demonstrated, but the mechanisms of action are less understood. We used three phytopathogenic fungal species (Sclerotinia sclerotiorum, Rhizoctonia solani, and Juxtiphoma eupyrena) as well as one non-phytopathogenic species (Neurospora crassa) and the plant growth promoting rhizobacterium Serratia plymuthica 4Rx13 in co-cultivation assays to investigate the influence of bacterial volatile metabolites on fungi on a cellular level. As a response to the treatment, we found elevated lipid peroxidation, which indirectly reflected the loss of fungal cell membrane integrity. An increase in superoxide dismutase, catalase, and laccase activities indicated oxidative stress. Acclimation to these adverse growth conditions completely restored fungal growth. One of the bioactive bacterial volatile compounds seemed to be ammonia, which was a component of the bacterial volatile mixture. Applied as a single compound in biogenic concentrations ammonia also caused an increase in lipid peroxidation and enzyme activities, but the extent and pattern did not fully match the effect of the entire bacterial volatile mixture.
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Affiliation(s)
- Piyali Das
- Institute of Biological Sciences, Biochemistry, Albert-Einstein-Strasse 3, University of Rostock, 18059 Rostock, Germany
| | - Uta Effmert
- Institute of Biological Sciences, Biochemistry, Albert-Einstein-Strasse 3, University of Rostock, 18059 Rostock, Germany
| | - Gunnar Baermann
- Institute of Biological Sciences, Biochemistry, Albert-Einstein-Strasse 3, University of Rostock, 18059 Rostock, Germany
| | - Manuel Quella
- Institute of Biological Sciences, Biochemistry, Albert-Einstein-Strasse 3, University of Rostock, 18059 Rostock, Germany
| | - Birgit Piechulla
- Institute of Biological Sciences, Biochemistry, Albert-Einstein-Strasse 3, University of Rostock, 18059 Rostock, Germany
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Harnessing phytomicrobiome signals for phytopathogenic stress management. J Biosci 2022. [DOI: 10.1007/s12038-021-00240-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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117
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Begum N, Harzandi A, Lee S, Uhlen M, Moyes DL, Shoaie S. Host-mycobiome metabolic interactions in health and disease. Gut Microbes 2022; 14:2121576. [PMID: 36151873 PMCID: PMC9519009 DOI: 10.1080/19490976.2022.2121576] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 02/04/2023] Open
Abstract
Fungal communities (mycobiome) have an important role in sustaining the resilience of complex microbial communities and maintenance of homeostasis. The mycobiome remains relatively unexplored compared to the bacteriome despite increasing evidence highlighting their contribution to host-microbiome interactions in health and disease. Despite being a small proportion of the total species, fungi constitute a large proportion of the biomass within the human microbiome and thus serve as a potential target for metabolic reprogramming in pathogenesis and disease mechanism. Metabolites produced by fungi shape host niches, induce immune tolerance and changes in their levels prelude changes associated with metabolic diseases and cancer. Given the complexity of microbial interactions, studying the metabolic interplay of the mycobiome with both host and microbiome is a demanding but crucial task. However, genome-scale modelling and synthetic biology can provide an integrative platform that allows elucidation of the multifaceted interactions between mycobiome, microbiome and host. The inferences gained from understanding mycobiome interplay with other organisms can delineate the key role of the mycobiome in pathophysiology and reveal its role in human disease.
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Affiliation(s)
- Neelu Begum
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Azadeh Harzandi
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Sunjae Lee
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Mathias Uhlen
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - David L. Moyes
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
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La Y, Kwon DE, Jeon S, Lee S, Lee KH, Han SH, Song YG. Clinical Implication of Candida Score in Multidrug-Resistant Pneumonia with Airway Candida Colonization. Infect Chemother 2022; 54:287-297. [PMID: 35706075 PMCID: PMC9259915 DOI: 10.3947/ic.2022.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/29/2022] [Indexed: 12/02/2022] Open
Abstract
Background The growth of Candida in respiratory secretions is usually considered colonization, and antifungal therapy is rarely required. The role of Candida colonization in the progression of bacterial pneumonia remains controversial. The aim of this study was to identify the clinical implication of Candida score by analyzinge the relationship with multidrug-resistant (MDR) pneumonia and prognosis in patients with airway Candida colonization. Materials and Methods This study was a retrospective review of patients with airway Candida colonization by bronchial washing or bronchoalveolar lavage. The Candida score was calculated according to the four factors (severe sepsis, surgery at baseline, total parenteral nutrition, and multifocal Candida colonization). Pneumonia related mortality or hopeless discharge expecting death was defined as a poor outcome. Results A total of 148 patients were enrolled in the study. In a multivariate analysis model, Candida score was identified as an independent predictor of poor outcomes (odds ratio 2.23; 95% confidential interval 1.57 – 3.17; P <0.001) in pneumonia patients with airway Candida colonization. With a Candida score of three or higher compared with low score group, it was associated with bacterial pneumonia, especially methicillin-resistant Staphylococcus aureus (MRSA) infection (0.0% vs. 15.2%, P = 0.004). In addition, patients with a high Candida score had a longer hospital stay (13 vs. 38 days, P <0.001), longer duration of intensive care (7 vs. 18 days, P <0.001), and higher pneumonia-related mortality (0.0% vs. 45.5%, P <0.001) as compared to the low Candida score group. The Candida score showed a positive correlation with other pneumonia severity scales such as CURB-65 (Confusion, Urea, Respiratory rate, Blood pressure, and age ≥65 years) (r = 0.461, P <0.001), Pneumonia Severity Index (r = 0.397, P <0.001), and predisposition, insult, response, and organ dysfunction (PIRO) score (r = 0.425, P <0.001). Conclusion This study revealed that Candida is no longer a bystander of airway colonization, and that it affects the progression of bacterial pneumonia, including multidrug-resistant pathogens, particularly MRSA infection. Also Candida score can be used to predict the prognosis of patients with pneumonia.
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Affiliation(s)
- Yeonju La
- Division of Infectious Diseases, Department of Internal Medicine, Kangwon National University Hospital, Chuncheon, Korea
| | - Da Eun Kwon
- Division of Infectious Diseases, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Soyoung Jeon
- Biostatistics Collaboration Unit, Yonsei University College of Medicine, Seoul, Korea
| | - Sujee Lee
- Biostatistics Collaboration Unit, Yonsei University College of Medicine, Seoul, Korea
| | - Kyoung Hwa Lee
- Division of Infectious Diseases, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Hoon Han
- Division of Infectious Diseases, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Young Goo Song
- Division of Infectious Diseases, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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Han Y, Guo C, Guan X, McMinn A, Liu L, Zheng G, Jiang Y, Liang Y, Shao H, Tian J, Wang M. Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench. MICROBIAL ECOLOGY 2022; 83:34-47. [PMID: 33811505 DOI: 10.1007/s00248-021-01747-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Diversity of microbial eukaryotes is estimated largely based on sequencing analysis of the hypervariable regions of 18S rRNA genes. But the use of different regions of 18S rRNA genes as molecular markers may generate bias in diversity estimation. Here, we compared the differences between the two most widely used markers, V4 and V9 regions of the 18S rRNA gene, in describing the diversity of epipelagic, bathypelagic, and hadal picoeukaryotes in the Challenger Deep of the Mariana Trench, which is a unique and little explored environment. Generally, the V9 region identified more OTUs in deeper waters than V4, while the V4 region provided greater Shannon diversity than V9. In the epipelagic zone, where Alveolata was the dominant group, picoeukaryotic community compositions identified by V4 and V9 markers are similar at different taxonomic levels. However, in the deep waters, the results of the two datasets show clear differences. These differences were mainly contributed by Retaria, Fungi, and Bicosoecida. The primer targeting the V9 region has an advantage in amplifying Bicosoecids in the bathypelagic and hadal zone of the Mariana Trench, and its high abundance in V9 dataset pointed out the possibility of Bicosoecids as a dominant group in this environment. Chrysophyceae, Fungi, MALV-I, and Retaria were identified as the dominant picoeukaryotes in the bathypelagic and hadal zone and potentially play important roles in deep-sea microbial food webs and biogeochemical cycling by their phagotrophic, saprotrophic, and parasitic life styles. Overall, the use of different markers of 18S rRNA gene allows a better assessment and understanding of the picoeukaryotic diversity in deep-sea environments.
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Affiliation(s)
- Yuye Han
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Xuran Guan
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Lu Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Guiliang Zheng
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, China
- Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
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Chen W, Cheung HK, McMillan M, Turkington TK, Izydorczyk MS, Gräfenhan T. The dynamics of indigenous epiphytic bacterial and fungal communities of barley grains through the commercial malting process in Western Canada. Curr Res Food Sci 2022; 5:1352-1364. [PMID: 36082140 PMCID: PMC9445228 DOI: 10.1016/j.crfs.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Wen Chen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Corresponding author. Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
| | - H.Y. Kitty Cheung
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Morgan McMillan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Thomas Kelly Turkington
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | | | - Tom Gräfenhan
- Grain Research Laboratory, Canadian Grain Commission, Winnipeg, MB, Canada
- Corresponding author.
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121
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Bell NL, Jeffers SN, Hitchcock DR, White SA. Potential Susceptibility of Six Aquatic Plant Species to Infection by Five Species of Phytophthora. PLANT DISEASE 2021; 105:4074-4083. [PMID: 34114888 DOI: 10.1094/pdis-10-20-2190-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Investigations of the susceptibility of aquatic plants to species of Phytophthora are limited. Therefore, the objective of this study was to assess the potential susceptibility of six aquatic plant species, frequently used in constructed wetlands or vegetated channels, to infection by five species of Phytophthora commonly found at nurseries in the southeastern United States. In a greenhouse experiment, roots of each plant species (Agrostis alba, Carex stricta, Iris ensata 'Rising Sun', Panicum virgatum, Pontederia cordata, and Typha latifolia) growing in aqueous solutions were exposed to zoospores of each of the species of Phytophthora (Phytophthora cinnamomi, Phytophthora citrophthora, Phytophthora cryptogea, Phytophthora nicotianae, and Phytophthora palmivora). Zoospore presence and activity in solution were monitored with a standard baiting bioassay with rhododendron leaf discs as baits. Experiments were initiated in 2016 and repeated in 2017 and 2018. During the 2016 trials, Phytophthora spp. were not isolated from the roots of any of the plants, but some roots of C. stricta, P. virgatum, and T. latifolia were infected with multiple species of Phytophthora during trials in 2017 and 2018. Presence of plant roots reduced the percentage of rhododendron leaf discs infected by zoospores of four of the species of Phytophthora but not those infected by P. cinnamomi, which suggested that roots of these plants negatively affected the presence or activity of zoospores of these four species of Phytophthora in the aqueous growing solution. Results from this study demonstrated that certain aquatic plant species may be sources of inoculum at ornamental plant nurseries if these plants are present naturally in waterways or used in constructed wetlands treating water flowing off production areas, which could be of concern to plant producers who recycle irrigation water.
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Affiliation(s)
- Natasha L Bell
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC 29634
- Department of Engineering, East Carolina University, Greenville, NC 27858
| | - Steven N Jeffers
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - Daniel R Hitchcock
- Department of Agricultural Sciences, Baruch Institute of Coastal Ecology and Forest Science, Clemson University, Georgetown, SC 29442
| | - Sarah A White
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
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Sun H, Liu X, Pei J, Hao D, Li X, Chen D, Shen Y, Xu Z. Identification, characterisation and inhibition of
Geotrichum pseudocandidum
spoilage microbe in
Gastrodia elata
tuber. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.15361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Haiyan Sun
- Key Laboratory of Life Resources of Shaanxi Province Shaanxi Key Laboratory of Resource Biology College of Biological Science and Engineering Shaanxi University of Technology Hanzhong China
| | - Xiao Liu
- Key Laboratory of Life Resources of Shaanxi Province Shaanxi Key Laboratory of Resource Biology College of Biological Science and Engineering Shaanxi University of Technology Hanzhong China
| | - Jinjin Pei
- Key Laboratory of Life Resources of Shaanxi Province Shaanxi Key Laboratory of Resource Biology College of Biological Science and Engineering Shaanxi University of Technology Hanzhong China
| | - Danqing Hao
- Key Laboratory of Life Resources of Shaanxi Province Shaanxi Key Laboratory of Resource Biology College of Biological Science and Engineering Shaanxi University of Technology Hanzhong China
| | - Xinsheng Li
- Key Laboratory of Life Resources of Shaanxi Province Shaanxi Key Laboratory of Resource Biology College of Biological Science and Engineering Shaanxi University of Technology Hanzhong China
| | - Dejing Chen
- Key Laboratory of Life Resources of Shaanxi Province Shaanxi Key Laboratory of Resource Biology College of Biological Science and Engineering Shaanxi University of Technology Hanzhong China
| | - Yixiao Shen
- College of Food Science Shenyang Agricultural University Shenyang China
- School of Nutrition and Food Sciences Louisiana State University Baton Rouge LA USA
| | - Zhimin Xu
- School of Nutrition and Food Sciences Louisiana State University Baton Rouge LA USA
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Pellegrini M, Ercole C, Gianchino C, Bernardi M, Pace L, Del Gallo M. Fusarium Oxysporum f. sp. Cannabis Isolated from Cannabis Sativa L.: In Vitro and In Planta Biocontrol by a Plant Growth Promoting-Bacteria Consortium. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112436. [PMID: 34834799 PMCID: PMC8623994 DOI: 10.3390/plants10112436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Industrial hemp (Cannabis sativa L.) is a multipurpose plant used in several fields. Several phytopathogens attack hemp crops. Fusarium oxysporum is a common fungal pathogen that causes wilt disease in nurseries and in field cultivation and causes high losses. In the present study, a pathogenic strain belonging to F. oxysporum f. sp. cannabis was isolated from a plant showing Fusarium wilt. After isolation, identification was conducted based on morphological and molecular characterizations and pathogenicity tests. Selected plant growth-promoting bacteria with interesting biocontrol properties-Azospirillum brasilense, Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae and Burkholderia ambifaria-were tested against this pathogen. In vitro antagonistic activity was determined by the dual culture method. Effective strains (in vitro inhibition > of 50%) G. diazotrophicus, H. seropedicae and B. ambifaria were combined in a consortium and screened for in planta antagonistic activity in pre-emergence (before germination) and post-emergence (after germination). The consortium counteracted Fusarium infection both in pre-emergence and post-emergence. Our preliminary results show that the selected consortium could be further investigated as an effective biocontrol agent for the management of this pathogen.
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Das J, Kumar R, Yadav SK, Jha G. The alternative sigma factors, rpoN1 and rpoN2 are required for mycophagous activity of Burkholderia gladioli strain NGJ1. Environ Microbiol 2021; 24:2781-2796. [PMID: 34766435 DOI: 10.1111/1462-2920.15836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/26/2022]
Abstract
Bacteria utilize RpoN, an alternative sigma factor (σ54) to grow in diverse habitats, including nitrogen-limiting conditions. Here, we report that a rice-associated mycophagous bacterium Burkholderia gladioli strain NGJ1 encodes two paralogues of rpoN viz. rpoN1 and rpoN2. Both of them are upregulated during 24 h of mycophagous interaction with Rhizoctonia solani, a polyphagous fungal pathogen. Disruption of either one of rpoNs renders the mutant NGJ1 bacterium defective in mycophagy, whereas ectopic expression of respective rpoN genes restores mycophagy in the complementing strains. NGJ1 requires rpoN1 and rpoN2 for efficient biocontrol to prevent R. solani to establish disease in rice and tomato. Further, we have identified 17 genes having RpoN regulatory motif in NGJ1, majority of them encode potential type III secretion system (T3SS) effectors, nitrogen assimilation, and cellular transport-related functions. Several of these RpoN regulated genes as well as certain previously reported T3SS apparatus (hrcC and hrcN) and effector (Bg_9562 and endo-β-1,3-glucanase) encoding genes are upregulated in NGJ1 but not in ΔrpoN1 or ΔrpoN2 mutant bacterium, during mycophagous interaction with R. solani. This highlights that RpoN1 and RpoN2 modulate T3SS, nitrogen assimilation as well as cellular transport systems in NGJ1 and thereby promote bacterial mycophagy.
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Affiliation(s)
- Joyati Das
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Rahul Kumar
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Sunil Kumar Yadav
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Gopaljee Jha
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, New Delhi, 110067, India
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Robinson AJ, House GL, Morales DP, Kelliher JM, Gallegos-Graves LV, LeBrun ES, Davenport KW, Palmieri F, Lohberger A, Bregnard D, Estoppey A, Buffi M, Paul C, Junier T, Hervé V, Cailleau G, Lupini S, Nguyen HN, Zheng AO, Gimenes LJ, Bindschedller S, Rodrigues DF, Werner JH, Young JD, Junier P, Chain PSG. Widespread bacterial diversity within the bacteriome of fungi. Commun Biol 2021; 4:1168. [PMID: 34621007 PMCID: PMC8497576 DOI: 10.1038/s42003-021-02693-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/20/2021] [Indexed: 02/08/2023] Open
Abstract
Knowledge of associations between fungal hosts and their bacterial associates has steadily grown in recent years as the number and diversity of examinations have increased, but current knowledge is predominantly limited to a small number of fungal taxa and bacterial partners. Here, we screened for potential bacterial associates in over 700 phylogenetically diverse fungal isolates, representing 366 genera, or a tenfold increase compared with previously examined fungal genera, including isolates from several previously unexplored phyla. Both a 16 S rDNA-based exploration of fungal isolates from four distinct culture collections spanning North America, South America and Europe, and a bioinformatic screen for bacterial-specific sequences within fungal genome sequencing projects, revealed that a surprisingly diverse array of bacterial associates are frequently found in otherwise axenic fungal cultures. We demonstrate that bacterial associations with diverse fungal hosts appear to be the rule, rather than the exception, and deserve increased consideration in microbiome studies and in examinations of microbial interactions.
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Affiliation(s)
- Aaron J Robinson
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Geoffrey L House
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Demosthenes P Morales
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Center of Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Julia M Kelliher
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - La Verne Gallegos-Graves
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Erick S LeBrun
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Karen W Davenport
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Andrea Lohberger
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Danaé Bregnard
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Matteo Buffi
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Christophe Paul
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Vincent Hervé
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Simone Lupini
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX, 77004, USA
| | - Hang N Nguyen
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX, 77004, USA
| | - Amy O Zheng
- Department of Chemical and Biomolecular Engineering and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235-1604, USA
| | - Luciana Jandelli Gimenes
- Center for Environmental Research and Training, University of São Paulo, Cubatão, São Paulo, 11.540 -990, Brazil
| | - Saskia Bindschedller
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Debora F Rodrigues
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX, 77004, USA
| | - James H Werner
- Center of Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235-1604, USA
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Patrick S G Chain
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
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Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11199182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.
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Purahong W, Wahdan SFM, Heinz D, Jariyavidyanont K, Sungkapreecha C, Tanunchai B, Sansupa C, Sadubsarn D, Alaneed R, Heintz-Buschart A, Schädler M, Geissler A, Kressler J, Buscot F. Back to the Future: Decomposability of a Biobased and Biodegradable Plastic in Field Soil Environments and Its Microbiome under Ambient and Future Climates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:12337-12351. [PMID: 34486373 DOI: 10.1021/acs.est.1c02695] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Decomposition by microorganisms of plastics in soils is almost unexplored despite the fact that the majority of plastics released into the environment end up in soils. Here, we investigate the decomposition process and microbiome of one of the most promising biobased and biodegradable plastics, poly(butylene succinate-co-adipate) (PBSA), under field soil conditions under both ambient and future predicted climates (for the time between 2070 and 2100). We show that the gravimetric and molar mass of PBSA is already largely reduced (28-33%) after 328 days under both climates. We provide novel information on the PBSA microbiome encompassing the three domains of life: Archaea, Bacteria, and Eukarya (fungi). We show that PBSA begins to decompose after the increase in relative abundances of aquatic fungi (Tetracladium spp.) and nitrogen-fixing bacteria. The PBSA microbiome is distinct from that of surrounding soils, suggesting that PBSA serves as a new ecological habitat. We conclude that the microbial decomposition process of PBSA in soil is more complex than previously thought by involving interkingdom relationships, especially between bacteria and fungi.
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Affiliation(s)
- Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale) D-06120, Germany
| | - Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale) D-06120, Germany
- Department of Botany, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Daniel Heinz
- Department of Chemistry, Martin Luther University Halle-Wittenberg, Halle (Saale) D-06099, Germany
| | - Katalee Jariyavidyanont
- Center of Engineering Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale) D-06099, Germany
| | - Chanita Sungkapreecha
- Center of Engineering Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale) D-06099, Germany
| | - Benjawan Tanunchai
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale) D-06120, Germany
| | - Chakriya Sansupa
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale) D-06120, Germany
| | - Dolaya Sadubsarn
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale) D-06120, Germany
| | - Razan Alaneed
- Department of Chemistry, Martin Luther University Halle-Wittenberg, Halle (Saale) D-06099, Germany
| | - Anna Heintz-Buschart
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale) D-06120, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig D-04103, Germany
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig D-04103, Germany
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale) D-06120, Germany
| | - Andreas Geissler
- Department of Macromolecular Chemistry and Paper Chemistry, Technical University of Darmstadt, Darmstadt D-64287, Germany
| | - Joerg Kressler
- Department of Chemistry, Martin Luther University Halle-Wittenberg, Halle (Saale) D-06099, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale) D-06120, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig D-04103, Germany
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129
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Rämä T, Quandt CA. Improving Fungal Cultivability for Natural Products Discovery. Front Microbiol 2021; 12:706044. [PMID: 34603232 PMCID: PMC8481835 DOI: 10.3389/fmicb.2021.706044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
The pool of fungal secondary metabolites can be extended by activating silent gene clusters of cultured strains or by using sensitive biological assays that detect metabolites missed by analytical methods. Alternatively, or in parallel with the first approach, one can increase the diversity of existing culture collections to improve the access to new natural products. This review focuses on the latter approach of screening previously uncultured fungi for chemodiversity. Both strategies have been practiced since the early days of fungal biodiscovery, yet relatively little has been done to overcome the challenge of cultivability of as-yet-uncultivated fungi. Whereas earlier cultivability studies using media formulations and biological assays to scrutinize fungal growth and associated factors were actively conducted, the application of modern omics methods remains limited to test how to culture the fungal dark matter and recalcitrant groups of described fungi. This review discusses the development of techniques to increase the cultivability of filamentous fungi that include culture media formulations and the utilization of known chemical growth factors, in situ culturing and current synthetic biology approaches that build upon knowledge from sequenced genomes. We list more than 100 growth factors, i.e., molecules, biological or physical factors that have been demonstrated to induce spore germination as well as tens of inducers of mycelial growth. We review culturing conditions that can be successfully manipulated for growth of fungi and visit recent information from omics methods to discuss the metabolic basis of cultivability. Earlier work has demonstrated the power of co-culturing fungi with their host, other microorganisms or their exudates to increase their cultivability. Co-culturing of two or more organisms is also a strategy used today for increasing cultivability. However, fungi possess an increased risk for cross-contaminations between isolates in existing in situ or microfluidics culturing devices. Technological improvements for culturing fungi are discussed in the review. We emphasize that improving the cultivability of fungi remains a relevant strategy in drug discovery and underline the importance of ecological and taxonomic knowledge in culture-dependent drug discovery. Combining traditional and omics techniques such as single cell or metagenome sequencing opens up a new era in the study of growth factors of hundreds of thousands of fungal species with high drug discovery potential.
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Affiliation(s)
- Teppo Rämä
- Marbio, Norwegian College of Fishery Science, University of Tromsø – The Arctic University of Norway, Tromsø, Norway
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
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Ramírez-Granillo A, Bautista-Hernández LA, Bautista-De Lucío VM, Magaña-Guerrero FS, Domínguez-López A, Córdova-Alcántara IM, Pérez NO, Martínez-Rivera MDLA, Rodríguez-Tovar AV. Microbial Warfare on Three Fronts: Mixed Biofilm of Aspergillus fumigatus and Staphylococcus aureus on Primary Cultures of Human Limbo-Corneal Fibroblasts. Front Cell Infect Microbiol 2021; 11:646054. [PMID: 34485167 PMCID: PMC8415486 DOI: 10.3389/fcimb.2021.646054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 07/19/2021] [Indexed: 11/08/2022] Open
Abstract
Background Coinfections with fungi and bacteria in ocular pathologies are increasing at an alarming rate. Two of the main etiologic agents of infections on the corneal surface, such as Aspergillus fumigatus and Staphylococcus aureus, can form a biofilm. However, mixed fungal–bacterial biofilms are rarely reported in ocular infections. The implementation of cell cultures as a study model related to biofilm microbial keratitis will allow understanding the pathogenesis in the cornea. The cornea maintains a pathogen-free ocular surface in which human limbo-corneal fibroblast cells are part of its cell regeneration process. There are no reports of biofilm formation assays on limbo-corneal fibroblasts, as well as their behavior with a polymicrobial infection. Objective To determine the capacity of biofilm formation during this fungal–bacterial interaction on primary limbo-corneal fibroblast monolayers. Results The biofilm on the limbo-corneal fibroblast culture was analyzed by assessing biomass production and determining metabolic activity. Furthermore, the mixed biofilm effect on this cell culture was observed with several microscopy techniques. The single and mixed biofilm was higher on the limbo-corneal fibroblast monolayer than on abiotic surfaces. The A. fumigatus biofilm on the human limbo-corneal fibroblast culture showed a considerable decrease compared to the S. aureus biofilm on the limbo-corneal fibroblast monolayer. Moreover, the mixed biofilm had a lower density than that of the single biofilm. Antibiosis between A. fumigatus and S. aureus persisted during the challenge to limbo-corneal fibroblasts, but it seems that the fungus was more effectively inhibited. Conclusion This is the first report of mixed fungal–bacterial biofilm production and morphological characterization on the limbo-corneal fibroblast monolayer. Three antibiosis behaviors were observed between fungi, bacteria, and limbo-corneal fibroblasts. The mycophagy effect over A. fumigatus by S. aureus was exacerbated on the limbo-corneal fibroblast monolayer. During fungal–bacterial interactions, it appears that limbo-corneal fibroblasts showed some phagocytic activity, demonstrating tripartite relationships during coinfection.
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Affiliation(s)
- Adrián Ramírez-Granillo
- Medical Mycology Laboratory, National School of Biological Sciences (ENCB)-Instituto Politécnico Nacional (IPN), Department of Microbiology, Mexico City, Mexico
| | - Luis Antonio Bautista-Hernández
- Ocular Microbiology and Proteomics Laboratory, Research Unit, "Conde de Valenciana Private Assistance Foundation", Mexico City, Mexico
| | - Víctor Manuel Bautista-De Lucío
- Ocular Microbiology and Proteomics Laboratory, Research Unit, "Conde de Valenciana Private Assistance Foundation", Mexico City, Mexico
| | - Fátima Sofía Magaña-Guerrero
- Cell Biology and Amniotic Membrane Laboratory, Research Unit, "Conde de Valenciana Private Assistance Foundation", Mexico City, Mexico
| | - Alfredo Domínguez-López
- Cell Biology and Amniotic Membrane Laboratory, Research Unit, "Conde de Valenciana Private Assistance Foundation", Mexico City, Mexico
| | - Itzel Margarita Córdova-Alcántara
- Medical Mycology Laboratory, National School of Biological Sciences (ENCB)-Instituto Politécnico Nacional (IPN), Department of Microbiology, Mexico City, Mexico
| | - Néstor O Pérez
- Research and Development Department Probiomed SA de CV, Tenancingo Edo de Mex, Mexico
| | - María de Los Angeles Martínez-Rivera
- Medical Mycology Laboratory, National School of Biological Sciences (ENCB)-Instituto Politécnico Nacional (IPN), Department of Microbiology, Mexico City, Mexico
| | - Aída Verónica Rodríguez-Tovar
- Medical Mycology Laboratory, National School of Biological Sciences (ENCB)-Instituto Politécnico Nacional (IPN), Department of Microbiology, Mexico City, Mexico
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131
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Influence of Trichoderma asperellum and Bacillus subtilis as biocontrol and plant growth promoting agents on soil microbiota. ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01647-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
The manipulation of soil microbiota can involve changes in microbial diversity and microbial activities, and it is carried out for practical purposes. The microbial diversity can be modified by the inoculation of beneficial microorganisms into soil or by agricultural management practices. This study provides information on the influence of introducing beneficial soil microorganisms on soil indigenous microbiota. The aim of this study was to determine how biocontrol and plant growth promoting agents Trichoderma asperellum and Bacillus subtilis and their consortium affect indigenous soil microbiota without placing emphasis on the plant as a determinant of change.
Methods
Experimental soil samples were treated with B. subtilis and T. asperellum and their consortium. The shift of number of bacterial and fungal CFUs in soil was determined. Biolog EcoPlate assay demonstrated the metabolic activity of microorganisms in soil. The concentration of Trichoderma genus, Firmicutes, Gammaproteobacteria and Acidobacteria DNA in soil samples was determined by molecular methods. A correlation analysis was performed between microbiological and molecular data.
Results
Soil treatment with T. asperellum, B. subtilis and the plant pathogenic fungus Botrytis cinerea changed the number of CFUs and amplified DNA fragments of certain taxa. The study showed that added microorganisms did not significantly affect the metabolic diversity of the community and Shannon-Wiener biodiversity index but change the utilization of carbohydrates, complex carbon compounds and organic phosphorus compounds.
Conclusion
Introduced biocontrol and plant growth promoting agents T. asperellum and B. subtilis survive in soil during a 60-day experiment and influence composition and functionality of indigenous populations. Whereas B. subtilis and T. asperellum and their consortium are inhibitors of the pathogenic fungus B. cinerea, this could further positively affect specific crops.
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132
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Harrison XA, McDevitt AD, Dunn JC, Griffiths SM, Benvenuto C, Birtles R, Boubli JP, Bown K, Bridson C, Brooks DR, Browett SS, Carden RF, Chantrey J, Clever F, Coscia I, Edwards KL, Ferry N, Goodhead I, Highlands A, Hopper J, Jackson J, Jehle R, da Cruz Kaizer M, King T, Lea JMD, Lenka JL, McCubbin A, McKenzie J, de Moraes BLC, O'Meara DB, Pescod P, Preziosi RF, Rowntree JK, Shultz S, Silk MJ, Stockdale JE, Symondson WOC, de la Pena MV, Walker SL, Wood MD, Antwis RE. Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome. Proc Biol Sci 2021; 288:20210552. [PMID: 34403636 PMCID: PMC8370808 DOI: 10.1098/rspb.2021.0552] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/14/2021] [Indexed: 12/30/2022] Open
Abstract
Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate marked variation across host taxonomy in patterns of covariation between bacterial and fungal abundances. Host phylogeny drives differences in the overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in the mammalian gut microbiome. Sample type, tissue storage and DNA extraction method also affected bacterial and fungal community composition, and future studies would benefit from standardized approaches to sample processing. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.
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Affiliation(s)
| | - Allan D. McDevitt
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jenny C. Dunn
- School of Life Sciences, Joseph Banks Laboratories, University of Lincoln, UK
| | - Sarah M. Griffiths
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Chiara Benvenuto
- School of Science, Engineering and Environment, University of Salford, UK
| | - Richard Birtles
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jean P. Boubli
- School of Science, Engineering and Environment, University of Salford, UK
| | - Kevin Bown
- School of Science, Engineering and Environment, University of Salford, UK
| | - Calum Bridson
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | - Darren R. Brooks
- School of Science, Engineering and Environment, University of Salford, UK
| | - Samuel S. Browett
- School of Science, Engineering and Environment, University of Salford, UK
| | - Ruth F. Carden
- School of Archaeology, University College Dublin, Ireland
- Wildlife Ecological and Osteological Consultancy, Wicklow, Ireland
| | - Julian Chantrey
- Institute of Veterinary Science, University of Liverpool, UK
| | - Friederike Clever
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
- Smithsonian Tropical Research Institute, Ancon, Republic of Panama
| | - Ilaria Coscia
- School of Science, Engineering and Environment, University of Salford, UK
| | - Katie L. Edwards
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Natalie Ferry
- School of Science, Engineering and Environment, University of Salford, UK
| | - Ian Goodhead
- School of Science, Engineering and Environment, University of Salford, UK
| | - Andrew Highlands
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jane Hopper
- The Aspinall Foundation, Port Lympne Reserve, Hythe, Kent, UK
| | - Joseph Jackson
- School of Science, Engineering and Environment, University of Salford, UK
| | - Robert Jehle
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Tony King
- The Aspinall Foundation, Port Lympne Reserve, Hythe, Kent, UK
- School of Anthropology and Conservation, University of Kent, UK
| | - Jessica M. D. Lea
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | - Jessica L. Lenka
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Jack McKenzie
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Denise B. O'Meara
- School of Science and Computing, Waterford Institute of Technology, Ireland
| | - Poppy Pescod
- School of Science, Engineering and Environment, University of Salford, UK
| | - Richard F. Preziosi
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Jennifer K. Rowntree
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Susanne Shultz
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | | | - Jennifer E. Stockdale
- School of Biosciences, University of Cardiff, UK
- School of Life Sciences, University of Nottingham, UK
| | | | | | - Susan L. Walker
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Michael D. Wood
- School of Science, Engineering and Environment, University of Salford, UK
| | - Rachael E. Antwis
- School of Science, Engineering and Environment, University of Salford, UK
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Fiala J, Schöbel H, Vrabl P, Dietrich D, Hammerle F, Artmann DJ, Stärz R, Peintner U, Siewert B. A New High-Throughput-Screening-Assay for Photoantimicrobials Based on EUCAST Revealed Unknown Photoantimicrobials in Cortinariaceae. Front Microbiol 2021; 12:703544. [PMID: 34421861 PMCID: PMC8375034 DOI: 10.3389/fmicb.2021.703544] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance is one of the biggest health and subsequent economic threat humanity faces. Next to massive global awareness campaigns, governments and NGOs alike stress the need for new innovative strategies to treat microbial infections. One of such innovative strategies is the photodynamic antimicrobial chemotherapy (PACT) in which the synergistic effects of photons and drugs are exploited. While many promising reports are available, PACT - and especially the drug-design part behind - is still in its infancy. Common best-practice rules, such as the EUCAST or CLSI protocols for classic antibiotics as well as high-throughput screenings, are missing, and this, in turn, hampers the identification of hit structures. Hit-like structures might come from synthetic approaches or from natural sources. They are identified via activity-guided synthesis or isolation strategies. As source for new antimicrobials, fungi are highly ranked. They share the same ecological niche with many other microbes and consequently established chemical strategies to combat with the others. Recently, in members of the Cortinariaceae, especially of the subgenus Dermocybe, photoactive metabolites were detected. To study their putative photoantimicrobial effect, a photoantimicrobial high-throughput screening (HTS) based on The European Committee on Antimicrobial Susceptibility Testing (EUCAST) was established. After validation, the established HTS was used to evaluate a sample set containing six colorful representatives from the genus Cortinarius (i.e., Cortinarius callisteus, C. rufo-olivaceus, C. traganus, C. trivialis, C. venetus, and C. xanthophyllus). The assay is built on a uniform, light-emitting diode (LED)-based light irradiation across a 96-well microtiter plate, which was achieved by a pioneering arrangement of the LEDs. The validation of the assay was accomplished with well-known photoactive drugs, so-called photosensitizers, utilizing six distinct emission wavelengths (λexc = 428, 478, 523, 598, or 640 nm) and three microbial strains (Candida albicans, Staphylococcus aureus, and Escherichia coli). Evaluating the extracts of six Cortinarius species revealed two highly promising species, i.e., C. rufo-olivaceus and C. xanthophyllus. Extracts from the latter were photoactive against the Gram-positive S. aureus (c = 7.5 μg/ml, H = 30 J/cm2, λ = 478 nm) and the fungus C. albicans (c = 75 μg/ml, H = 30 J/cm2, λ = 478 nm).
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Affiliation(s)
- Johannes Fiala
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
| | | | - Pamela Vrabl
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Dorothea Dietrich
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Fabian Hammerle
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | | | - Ronald Stärz
- MCI - The Entrepreneurial School, Innsbruck, Austria
| | - Ursula Peintner
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Bianka Siewert
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
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134
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Orlofsky E, Zabari L, Bonito G, Masaphy S. Changes in soil bacteria functional ecology associated with Morchella rufobrunnea fruiting in a natural habitat. Environ Microbiol 2021; 23:6651-6662. [PMID: 34327796 DOI: 10.1111/1462-2920.15692] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/04/2023]
Abstract
Morchella rufobrunnea is a saprobic edible mushroom, found in a range of ecological niches, indicating nutritional adjustment to different habitats and possible interaction with soil prokaryotic microbiome (SPM). Using the 16S rRNA gene, we examined the SPM of M. rufobrunnea that appeared in a natural habitat in Northern Israel. Three sample types were included: bare soil without mushroom, soil beneath young mushroom initials and soil beneath the mature fruiting body. Morchella rufobrunnea developmental stage was significantly associated with changes in bacterial populations (PERMANOVA, p < 0.0005). Indicator analysis with point-biserial correlation coefficient found 180 operational taxonomic units (OTU) uniquely associated with distinct stages of development. The Functional Annotation of Prokaryotic Taxonomy (FAPROTAX) database helped to infer ecological roles for indicator OTU. The functional ecological progression begins with establishment of a photoautotrophic N-fixing bacterial mat on bare soil. Pioneer heterotrophs including oligotrophs, acidifying nutrient mobilizers and nitrifiers are congruent with appearance of young M. rufobrunnea initials. Under the mature fruiting body, the population changed to saprobes, organic-N degraders, denitrifiers, insect endosymbionts and fungal antagonists. Based on this work, M. rufobrunnea may be able to influence SPM and change the soil nutritional profile.
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Affiliation(s)
- Ezra Orlofsky
- Applied Mycology and Microbiology, Migal, Kiryat Shemona, 11016, Israel
| | - Limor Zabari
- Applied Mycology and Microbiology, Migal, Kiryat Shemona, 11016, Israel
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Segula Masaphy
- Applied Mycology and Microbiology, Migal, Kiryat Shemona, 11016, Israel.,Tel Hai Academic College, Kiryat Shemona, 12210, Israel
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135
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Espinosa-Ortiz EJ, Rene ER, Gerlach R. Potential use of fungal-bacterial co-cultures for the removal of organic pollutants. Crit Rev Biotechnol 2021; 42:361-383. [PMID: 34325585 DOI: 10.1080/07388551.2021.1940831] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fungi and bacteria coexist in a wide variety of natural and artificial environments which can lead to their association and interaction - ranging from antagonism to cooperation - that can affect the survival, colonization, spatial distribution and stress resistance of the interacting partners. The use of polymicrobial cultivation approaches has facilitated a more thorough understanding of microbial dynamics in mixed microbial communities, such as those composed of fungi and bacteria, and their influence on ecosystem functions. Mixed (multi-domain) microbial communities exhibit unique associations and interactions that could result in more efficient systems for the degradation and removal of organic pollutants. Several previous studies have reported enhanced biodegradation of certain pollutants when using combined fungal-bacterial treatments compared to pure cultures or communities of either fungi or bacteria (single domain systems). This article reviews: (i) the mechanisms of pollutant degradation that can occur in fungal-bacterial systems (e.g.: co-degradation, production of secondary metabolites, enhancement of degradative enzyme production, and transport of bacteria by fungal mycelia); (ii) case studies using fungal-bacterial co-cultures for the removal of various organic pollutants (synthetic dyes, polycyclic aromatic hydrocarbons, pesticides, and other trace or volatile organic compounds) in different environmental matrices (e.g. water, gas/vapors, soil); (iii) the key aspects of engineering artificial fungal-bacterial co-cultures, and (iv) the current challenges and future perspectives of using fungal-bacterial co-cultures for environmental remediation.
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Affiliation(s)
- Erika J Espinosa-Ortiz
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Eldon R Rene
- Department of Water Supply, Sanitary and Environmental Engineering, IHE Delft Institute for Water Education, 2601DA Delft, The Netherlands
| | - Robin Gerlach
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
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136
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Sharma S, Compant S, Franken P, Ruppel S, Ballhausen MB. It Takes Two to Tango: A Bacterial Biofilm Provides Protection against a Fungus-Feeding Bacterial Predator. Microorganisms 2021; 9:microorganisms9081566. [PMID: 34442645 PMCID: PMC8398733 DOI: 10.3390/microorganisms9081566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 11/23/2022] Open
Abstract
Fungus-bacterium interactions are widespread, encompass multiple interaction types from mutualism to parasitism, and have been frequent targets for microbial inoculant development. In this study, using in vitro systems combined with confocal laser scanning microscopy and real-time quantitative PCR, we test whether the nitrogen-fixing bacterium Kosakonia radicincitans can provide protection to the plant-beneficial fungus Serendipita indica, which inhabits the rhizosphere and colonizes plants as an endophyte, from the fungus-feeding bacterium Collimonas fungivorans. We show that K. radicincitans can protect fungal hyphae from bacterial feeding on solid agar medium, with probable mechanisms being quick hyphal colonization and biofilm formation. We furthermore find evidence for different feeding modes of K. radicincitans and C. fungivorans, namely “metabolite” and “hyphal feeding”, respectively. Overall, we demonstrate, to our knowledge, the first evidence for a bacterial, biofilm-based protection of fungal hyphae against attack by a fungus-feeding, bacterial predator on solid agar medium. Besides highlighting the importance of tripartite microbial interactions, we discuss implications of our results for the development and application of microbial consortium-based bioprotectants and biostimulants.
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Affiliation(s)
- Shubhangi Sharma
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany; (S.S.); (P.F.); (S.R.)
| | - Stéphane Compant
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Konrad Lorenz Strasse 24, 3430 Tulln, Austria;
| | - Philipp Franken
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany; (S.S.); (P.F.); (S.R.)
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 24, 07743 Jena, Germany
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany; (S.S.); (P.F.); (S.R.)
| | - Max-Bernhard Ballhausen
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany; (S.S.); (P.F.); (S.R.)
- Correspondence:
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137
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Kim JH, Lee N, Hwang S, Kim W, Lee Y, Cho S, Palsson BO, Cho BK. Discovery of novel secondary metabolites encoded in actinomycete genomes through coculture. J Ind Microbiol Biotechnol 2021; 48:6119915. [PMID: 33825906 PMCID: PMC9113425 DOI: 10.1093/jimb/kuaa001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/02/2020] [Indexed: 01/23/2023]
Abstract
Actinomycetes are a rich source of bioactive natural products important for novel drug leads. Recent genome mining approaches have revealed an enormous number of secondary metabolite biosynthetic gene clusters (smBGCs) in actinomycetes. However, under standard laboratory culture conditions, many smBGCs are silent or cryptic. To activate these dormant smBGCs, several approaches, including culture-based or genetic engineering-based strategies, have been developed. Above all, coculture is a promising approach to induce novel secondary metabolite production from actinomycetes by mimicking an ecological habitat where cryptic smBGCs may be activated. In this review, we introduce coculture studies that aim to expand the chemical diversity of actinomycetes, by categorizing the cases by the type of coculture partner. Furthermore, we discuss the current challenges that need to be overcome to support the elicitation of novel bioactive compounds from actinomycetes.
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Affiliation(s)
- Ji Hun Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Namil Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,Intelligent Synthetic Biology Center, Daejeon 34141, Republic of Korea
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138
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Wang L, Huang D. Nitrogen and phosphorus losses by surface runoff and soil microbial communities in a paddy field with different irrigation and fertilization managements. PLoS One 2021; 16:e0254227. [PMID: 34242302 PMCID: PMC8274659 DOI: 10.1371/journal.pone.0254227] [Citation(s) in RCA: 5] [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: 12/09/2020] [Accepted: 06/22/2021] [Indexed: 11/24/2022] Open
Abstract
Rice cultivation usually involves high water and fertilizer application rates leading to the nonpoint pollution of surface waters with phosphorus (P) and nitrogen (N). Here, a 10-year field experiment was conducted to investigate N and P losses and their impact factors under different irrigation and fertilization regimes. Results indicated that T2 (Chemical fertilizer of 240 kg N ha-1, 52 kg P ha-1, and 198 kg K ha-1 combined with shallow intermittent irrigation) decreased N loss by 48.9% compared with T1 (Chemical fertilizer of 273 kg N ha-1, 59 kg P ha-1, and 112 kg K ha-1 combined with traditional flooding irrigation). The loss ratio (total N loss loading/amount of applied N) of N was 9.24-15.90%, whereas that of P was 1.13-1.31% in all treatments. Nitrate N (NO3--N) loss was the major proportion accounting for 88.30-90.65% of dissolved inorganic N loss through surface runoff. Moreover, the N runoff loss was mainly due to high fertilizer input, soil NO3--N, and ammonium N (NH4+-N) contents. In addition, the N loss was accelerated by Bacteroidetes, Proteobacteria, Planotomycetes, Nitrospirae, Firmicutes bacteria and Ascomycota fungi, but decreased by Chytridiomycota fungi whose contribution to the N transformation process. Furthermore, T2 increased agronomic N use efficiency (AEN) and rice yield by 32.81% and 7.36%, respectively, in comparison with T1. These findings demonstrated that T2 might be an effective approach to ameliorate soil chemical properties, regulate microbial community structure, increase AEN and consequently reduce N losses as well as maintaining rice yields in the present study.
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Affiliation(s)
- Limin Wang
- Soil and Fertilizer Institute, Fujian Academy of Agricultural Sciences,
Fuzhou, P. R. China
- Fujian Key Laboratory of Agro—products Quality & Safety, Fujian
Academy of Agricultural Sciences, Fuzhou, P. R. China
| | - Dongfeng Huang
- Soil and Fertilizer Institute, Fujian Academy of Agricultural Sciences,
Fuzhou, P. R. China
- Fujian Key Laboratory of Agro—products Quality & Safety, Fujian
Academy of Agricultural Sciences, Fuzhou, P. R. China
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139
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Influence of Taxonomic and Functional Content of Microbial Communities on the Quality of Fermented Cocoa Pulp-Bean Mass. Appl Environ Microbiol 2021; 87:e0042521. [PMID: 33990301 DOI: 10.1128/aem.00425-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial metabolism drives changes in the physicochemical properties and, consequently, the sensory characteristics of fermented cocoa beans. In this context, information regarding the structure, function, and metabolic potential of microbial communities' present during cocoa pulp-bean mass fermentation is limited, especially concerning the formation of aromatic compounds. To bridge the gap, the metagenome of fermented cocoa pulp-bean mass (Criollo and Forastero) has been investigated using shotgun metagenomics coupled with physicochemical, microbiological, quality, and sensory analyses to explore the impact of microbial communities on the quality of fermented cocoa pulp-bean mass on one farm in one season and in one region under the same environmental conditions. Our findings showed that the metagenomic diversity in cocoa, the fermentation length, and the diversity and function of metagenome-assembled genomes (MAGs) greatly influence the resulting distinctive flavors. From the metabolic perspective, multiple indicators suggest that the heterolactic metabolism was more dominant in Criollo fermentations. KEGG genes were linked with the biosynthesis of acetic acid, ethanol, lactic acid, acetoin, and phenylacetaldehyde during Criollo and Forastero fermentations. MAGs belonging to Lactiplantibacillus plantarum, Limosilactobacillus reuteri, and Acetobacter pasteurianus were the most prevalent. Fermentation time and roasting are the most important determinants of cocoa quality, while the difference between the two varieties are relatively minor. The assessment of microbiological and chemical analysis is urgently needed for developing fermentation protocols according to regions, countries, and cocoa varieties to guarantee safety and desirable flavor development. IMPORTANCE Monitoring the composition, structure, functionalities, and metabolic potential encoded at the level of DNA of fermented cocoa pulp-bean mass metagenome is of great importance for food safety and quality implications.
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140
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Jiménez-Gómez I, Barcoto MO, Montoya QV, Goes AC, Monteiro LSVE, Bueno OC, Rodrigues A. Host Susceptibility Modulates Escovopsis Pathogenic Potential in the Fungiculture of Higher Attine Ants. Front Microbiol 2021; 12:673444. [PMID: 34194409 PMCID: PMC8238408 DOI: 10.3389/fmicb.2021.673444] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/14/2021] [Indexed: 12/17/2022] Open
Abstract
Health and disease emerge from intricate interactions between genotypes, phenotypes, and environmental features. The outcomes of such interactions are context-dependent, existing as a dynamic continuum ranging from benefits to damage. In host-microbial interactions, both the host and environmental conditions modulate the pathogenic potential of a microorganism. Microbial interactions are the core of the agricultural systems of ants in the subtribe Attina, which cultivate basidiomycete fungi for food. The fungiculture environment harbors a diverse microbial community, including fungi in the genus Escovopsis that has been studied as damage-causing agent. Here, we consider the ant colony as a host and investigate to what extent its health impacts the dynamics and outcomes of host-Escovopsis interactions. We found that different ant fungal cultivars vary in susceptibility to the same Escovopsis strains in plate-assays interactions. In subcolony-Escovopsis interactions, while healthy subcolonies gradually recover from infection with different concentrations of Escovopsis conidia, insecticide-treated subcolonies evidenced traits of infection and died within 7 days. The opportunistic nature of Escovopsis infections indicates that diseases in attine fungiculture are a consequence of host susceptibility, rather than the effect of a single microbial agent. By addressing the host susceptibility as a major modulator of Escovopsis pathogenesis, our findings expand the understanding of disease dynamics within attine colonies.
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Affiliation(s)
- Irina Jiménez-Gómez
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil.,Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Mariana O Barcoto
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Quimi V Montoya
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Aryel C Goes
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Lana S V E Monteiro
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Odair C Bueno
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Andre Rodrigues
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
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141
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Li C, Tang D, Wang Y, Fan Q, Zhang X, Cui X, Yu H. Endogenous bacteria inhabiting the Ophiocordyceps highlandensis during fruiting body development. BMC Microbiol 2021; 21:178. [PMID: 34116633 PMCID: PMC8196446 DOI: 10.1186/s12866-021-02227-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 05/10/2021] [Indexed: 01/04/2023] Open
Abstract
Background The genus Ophiocordyceps, which includes Ophiocordyceps sinensis, has been demonstrated to be one of the most valuable medicinal taxa. The low rate of larval infection and slow development that characterize the cultivation of this genus should be urgently addressed. To identify potential bioinoculants that stimulate the growth of Ophiocordyceps, O. highlandensis was selected as a model system, and a total of 72 samples were collected to systematically compare the microbial communities present during fruiting body development. By applying high-throughput 16S and ITS2 amplicon sequencing technology, the bacterial and fungal communities were identified in O. highlandensis and its surrounding soil, and the functional dynamics of the bacteria were explored. Results The results indicate that the most abundant bacteria across all the samples from O. highlandensis were Proteobacteria, Firmicutes and Bacteroidetes, while members of Ascomycota were detected among the fungi. The pathways enriched in the developmental stages were associated with carbohydrate degradation, nucleotides and pyridoxal biosynthesis, and the TCA cycle. Compared with that in the fungal community, an unexpectedly high taxonomic and functional fluctuation was discovered in the bacterial community during the maturation of O. highlandensis. Furthermore, bipartite network analysis identified four potential supercore OTUs associated with O. highlandensis growth. Conclusions All the findings of this study suggest unexpectedly high taxonomic and functional fluctuations in the bacterial community of O. highlandensis during its maturation. O. highlandensis may recruit different endogenous bacteria across its life cycle to enhance growth and support rapid infection. These results may facilitate Ophiocordyceps cultivation and improve the development of strategies for the identification of potential bioinoculant resources. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02227-w.
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Affiliation(s)
- Chengpeng Li
- Yunnan Herbal Laboratory, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.,Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Dexiang Tang
- Yunnan Herbal Laboratory, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.,Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Yuanbing Wang
- Yunnan Herbal Laboratory, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.,Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China.,The Research Center of Cordyceps Development and Utilization of Kunming, Yunnan Herbal Biotech Co. Ltd, Kunming, 650106, China
| | - Qi Fan
- Yunnan Herbal Laboratory, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.,Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Xiaomei Zhang
- Yunnan Herbal Laboratory, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.,Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China.,The Research Center of Cordyceps Development and Utilization of Kunming, Yunnan Herbal Biotech Co. Ltd, Kunming, 650106, China.,College of Basic Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Xiaolong Cui
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China.
| | - Hong Yu
- Yunnan Herbal Laboratory, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.
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142
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Herczeg D, Ujszegi J, Kásler A, Holly D, Hettyey A. Host-multiparasite interactions in amphibians: a review. Parasit Vectors 2021; 14:296. [PMID: 34082796 PMCID: PMC8173923 DOI: 10.1186/s13071-021-04796-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/20/2021] [Indexed: 01/15/2023] Open
Abstract
Parasites, including viruses, bacteria, fungi, protists, helminths, and arthropods, are ubiquitous in the animal kingdom. Consequently, hosts are frequently infected with more than one parasite species simultaneously. The assessment of such co-infections is of fundamental importance for disease ecology, but relevant studies involving non-domesticated animals have remained scarce. Many amphibians are in decline, and they generally have a highly diverse parasitic fauna. Here we review the literature reporting on field surveys, veterinary case studies, and laboratory experiments on co-infections in amphibians, and we summarize what is known about within-host interactions among parasites, which environmental and intrinsic factors influence the outcomes of these interactions, and what effects co-infections have on hosts. The available literature is piecemeal, and patterns are highly diverse, so that identifying general trends that would fit most host–multiparasite systems in amphibians is difficult. Several examples of additive, antagonistic, neutral, and synergistic effects among different parasites are known, but whether members of some higher taxa usually outcompete and override the effects of others remains unclear. The arrival order of different parasites and the time lag between exposures appear in many cases to fundamentally shape competition and disease progression. The first parasite to arrive can gain a marked reproductive advantage or induce cross-reaction immunity, but by disrupting the skin and associated defences (i.e., skin secretions, skin microbiome) and by immunosuppression, it can also pave the way for subsequent infections. Although there are exceptions, detrimental effects to the host are generally aggravated with increasing numbers of co-infecting parasite species. Finally, because amphibians are ectothermic animals, temperature appears to be the most critical environmental factor that affects co-infections, partly via its influence on amphibian immune function, partly due to its direct effect on the survival and growth of parasites. Besides their importance for our understanding of ecological patterns and processes, detailed knowledge about co-infections is also crucial for the design and implementation of effective wildlife disease management, so that studies concentrating on the identified gaps in our understanding represent rewarding research avenues. ![]()
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Affiliation(s)
- Dávid Herczeg
- Lendület Evolutionary Ecology Research Group, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Herman Ottó út 15, Budapest, 1022, Hungary.
| | - János Ujszegi
- Lendület Evolutionary Ecology Research Group, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Herman Ottó út 15, Budapest, 1022, Hungary
| | - Andrea Kásler
- Lendület Evolutionary Ecology Research Group, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Herman Ottó út 15, Budapest, 1022, Hungary.,Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Dóra Holly
- Lendület Evolutionary Ecology Research Group, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Herman Ottó út 15, Budapest, 1022, Hungary.,Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Attila Hettyey
- Lendület Evolutionary Ecology Research Group, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Herman Ottó út 15, Budapest, 1022, Hungary.,Department of Ecology, Institute for Biology, University of Veterinary Medicine, Rottenbiller utca 50, Budapest, 1077, Hungary
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143
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Pellan L, Dieye CAT, Durand N, Fontana A, Strub C, Schorr-Galindo S. Biocontrol Agents: Toolbox for the Screening of Weapons against Mycotoxigenic Fusarium. J Fungi (Basel) 2021; 7:446. [PMID: 34205071 PMCID: PMC8226957 DOI: 10.3390/jof7060446] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/31/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022] Open
Abstract
The aim of this study was to develop a set of experiments to screen and decipher the mechanisms of biocontrol agents (BCAs), isolated from commercial formulation, against two major mycotoxigenic fungi in cereals, Fusarium graminearum and Fusarium verticillioides. These two phytopathogens produce mycotoxins harmful to human and animal health and are responsible for the massive use of pesticides, for the protection of cereals. It is therefore essential to better understand the mechanisms of action of alternative control strategies such as the use of BCAs in order to optimize their applications. The early and late stages of interaction between BCAs and pathogens were investigated from germination of spores to the effects on perithecia (survival form of pathogen). The analysis of antagonist activities of BCAs revealed different strategies of biocontrol where chronological, process combination and specialization aspects of interactions are discussed. Streptomyces griseoviridis main strategy is based on antibiosis with the secretion of several compounds with anti-fungal and anti-germination activity, but also a mixture of hydrolytic enzymes to attack pathogens, which compensates for an important deficit in terms of spatial colonization capacity. It has good abilities in terms of nutritional competition. Trichoderma asperellum is capable of activating a very wide range of defenses and attacks combining the synthesis of various antifungal compounds (metabolite, enzymes, VOCs), with different targets (spores, mycelium, mycotoxins), and direct action by mycoparasitism and mycophagy. Concerning Pythium oligandrum, its efficiency is mainly due to its strong capacity to colonize the environment, with a direct action via microbial predation, stimulation of its reproduction at the contact of pathogens and the reduction of perithecia formation.
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Affiliation(s)
- Lucile Pellan
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, 34095 Montpellier, France; (L.P.); (C.A.T.D.); (N.D.); (A.F.); (S.S.-G.)
| | - Cheikh Ahmeth Tidiane Dieye
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, 34095 Montpellier, France; (L.P.); (C.A.T.D.); (N.D.); (A.F.); (S.S.-G.)
| | - Noël Durand
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, 34095 Montpellier, France; (L.P.); (C.A.T.D.); (N.D.); (A.F.); (S.S.-G.)
- CIRAD, UMR Qualisud, 34398 Montpellier, France
| | - Angélique Fontana
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, 34095 Montpellier, France; (L.P.); (C.A.T.D.); (N.D.); (A.F.); (S.S.-G.)
| | - Caroline Strub
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, 34095 Montpellier, France; (L.P.); (C.A.T.D.); (N.D.); (A.F.); (S.S.-G.)
| | - Sabine Schorr-Galindo
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, 34095 Montpellier, France; (L.P.); (C.A.T.D.); (N.D.); (A.F.); (S.S.-G.)
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144
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Repeated Exposure of Aspergillus niger Spores to the Antifungal Bacterium Collimonas fungivorans Ter331 Selects for Delayed Spore Germination. Appl Environ Microbiol 2021; 87:e0023321. [PMID: 33811027 DOI: 10.1128/aem.00233-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The bacterial strain Collimonas fungivorans Ter331 (CfTer331) inhibits mycelial growth and spore germination in Aspergillus niger N402 (AnN402). The mechanisms underlying this antagonistic bacterial-fungal interaction have been extensively studied, but knowledge on the long-term outcome of this interaction is currently lacking. Here, we used experimental evolution to explore the dynamics of fungal adaptation to recurrent exposure to CfTer331. Specifically, five single-spore isolates (SSIs) of AnN402 were evolved under three selection scenarios in liquid culture, i.e., (i) in the presence of CfTer331 for 80 growth cycles, (ii) in the absence of the bacterium for 80 cycles, and (iii) in the presence of CfTer331 for 40 cycles and then in its absence for 40 cycles. The evolved SSI lineages were then evaluated for phenotypic changes from the founder fungal strain, such as germinability with or without CfTer331. The analysis showed that recurrent exposure to CfTer331 selected for fungal lineages with reduced germinability and slower germination, even in the absence of CfTer331. In contrast, when AnN402 evolved in the absence of the bacteria, lineages with increased germinability and faster germination were favored. SSIs that were first evolved in the presence of CfTer331 and then in its absence showed intermediate phenotypes but overall were more similar to SSIs that evolved in the absence of CfTer331 for 80 cycles. This suggests that traits acquired from exposure to CfTer331 were reversible upon removal of the selection pressure. Overall, our study provides insights into the effects on fungi from the long-term coculture with bacteria. IMPORTANCE The use of antagonistic bacteria for managing fungal diseases is becoming increasingly popular, and thus there is a need to understand the implications of their long-term use against fungi. Most efforts have so far focused on characterizing the antifungal properties and mode of action of the bacterial antagonists, but the possible outcomes of the persisting interaction between antagonistic bacteria and fungi are not well understood. In this study, we used experimental evolution in order to explore the evolutionary aspects of an antagonistic bacterial-fungal interaction, using the antifungal bacterium Collimonas fungivorans and the fungus Aspergillus niger as a model system. We show that evolution in the presence or absence of the bacteria selects for fungal lineages with opposing and conditionally beneficial traits, such as slow and fast spore germination, respectively. Overall, our studies reveal that fungal responses to biotic factors related to antagonism could be to some extent predictable and reversible.
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145
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An Overview of Antimicrobial Compounds from African Edible Insects and Their Associated Microbiota. Antibiotics (Basel) 2021; 10:antibiotics10060621. [PMID: 34067471 PMCID: PMC8224635 DOI: 10.3390/antibiotics10060621] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 01/26/2023] Open
Abstract
The need for easily biodegradable and less toxic chemicals in drug development and pest control continues to fuel the exploration and discovery of new natural molecules. Like certain plants, some insects can also respond rapidly to microbial infections by producing a plethora of immune-induced molecules that include antibacterial and antifungal peptides/polypeptides (AMPs), among other structurally diverse small molecules. The recent recognition that new natural product-derived scaffolds are urgently needed to tackle life-threatening pathogenic infections has been prompted by the health threats posed by multidrug resistance. Although many researchers have concentrated on the discovery of AMPs, surprisingly, edible insect-produced AMPs/small molecules have received little attention. This review will discuss the recent advances in the identification and bioactivity analysis of insect AMPs, with a focus on small molecules associated with the microbiota of selected African edible insects. These molecules could be used as templates for developing next-generation drugs to combat multidrug-resistant pathogens.
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146
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Santoyo G, Gamalero E, Glick BR. Mycorrhizal-Bacterial Amelioration of Plant Abiotic and Biotic Stress. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.672881] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Soil microbiota plays an important role in the sustainable production of the different types of agrosystems. Among the members of the plant microbiota, mycorrhizal fungi (MF) and plant growth-promoting bacteria (PGPB) interact in rhizospheric environments leading to additive and/or synergistic effects on plant growth and heath. In this manuscript, the main mechanisms used by MF and PGPB to facilitate plant growth are reviewed, including the improvement of nutrient uptake, and the reduction of ethylene levels or biocontrol of potential pathogens, under both normal and stressful conditions due to abiotic or biotic factors. Finally, it is necessary to expand both research and field use of bioinoculants based on these components and take advantage of their beneficial interactions with plants to alleviate plant stress and improve plant growth and production to satisfy the demand for food for an ever-increasing human population.
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147
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Niimi J, Deveau A, Splivallo R. Geographical-based variations in white truffle Tuber magnatum aroma is explained by quantitative differences in key volatile compounds. THE NEW PHYTOLOGIST 2021; 230:1623-1638. [PMID: 33555031 DOI: 10.1111/nph.17259] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
The factors that vary the aroma of Tuber magnatum fruiting bodies are poorly understood. The study determined the headspace aroma composition, sensory aroma profiles, maturity and bacterial communities from T. magnatum originating from Italy, Croatia, Hungary, and Serbia, and tested if truffle aroma is dependent on provenance and if fruiting body volatiles are explained by maturity and/or bacterial communities. Headspace volatile profiles were determined using gas chromatography-mass spectrometry-olfactometry (GC-MS-O) and aroma of fruiting body extracts were sensorially assessed. Fruiting body maturity was estimated through spore melanisation. Bacterial community was determined using 16S rRNA amplicon sequencing. Main odour active compounds were present in all truffles but varied in concentration. Aroma of truffle extracts were sensorially discriminated by sites. However, volatile profiles of individual fruiting bodies varied more within sites than across geographic area, while maturity level did not play a role. Bacterial communities varied highly and were partially explained by provenance. A few rare bacterial operational taxonomical units associated with a select few nonodour active volatile compounds. Specificities of the aroma of T. magnatum truffles are more likely to be linked to individual properties than provenance. Some constituents of bacteria may provide biomarkers of provenance and be linked to nonodour active volatiles.
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Affiliation(s)
- Jun Niimi
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, Frankfurt am Main, 60438, Germany
| | - Aurélie Deveau
- Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, Champenoux, 54280, France
| | - Richard Splivallo
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, Frankfurt am Main, 60438, Germany
- Nectariss Sàrl, Avenue de Senalèche 9, Pully, 1009, Switzerland
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148
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Vujanovic V. Tremellomycetes Yeasts in Kernel Ecological Niche: Early Indicators of Enhanced Competitiveness of Endophytic and Mycoparasitic Symbionts against Wheat Pathobiota. PLANTS 2021; 10:plants10050905. [PMID: 33946244 PMCID: PMC8145979 DOI: 10.3390/plants10050905] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/06/2023]
Abstract
Tremellomycetes rDNA sequences previously detected in wheat kernels by MiSeq were not reliably assigned to a genus or clade. From comparisons of ribosomal internal transcribed spacer region (ITS) and subsequent phylogenetic analyses, the following three basidiomycetous yeasts were resolved and identified: Vishniacozymavictoriae, V. tephrensis, and an undescribed Vishniacozyma rDNA variant. The Vishniacozyma variant’s clade is evolutionarily close to, but phylogenetically distinct from, the V. carnescens clade. These three yeasts were discovered in wheat kernel samples from the Canadian prairies. Variations in relative Vishniacozyma species abundances coincided with altered wheat kernel weight, as well as host resistance to chemibiotrophic Tilletia (Common bunt—CB) and necrotrophic Fusarium (Fusarium head blight—FHB) pathogens. Wheat kernel weight was influenced by the coexistence of Vishniacozyma with endophytic plant growth-promoting and mycoparasitic biocontrol fungi that were acquired by plants. Kernels were coated with beneficial Penicillium endophyte and Sphaerodes mycoparasite, each of which had different influences on the wild yeast population. Its integral role in the kernel microbiome renders Vishniacozyma a measurable indicator of the microbiome–plant interaction. The ability of NGS technology to detect specific endophytic DNA variants and early changes in dynamics among symbionts within the kernel ecological niche enables the prediction of crop disease emergence, suggesting that advanced microbiological testing may be a potentially useful tool for both phytoprotection and more efficient wheat breeding programs.
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Affiliation(s)
- Vladimir Vujanovic
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
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149
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Embacher J, Neuhauser S, Zeilinger S, Kirchmair M. Microbiota Associated with Different Developmental Stages of the Dry Rot Fungus Serpula lacrymans. J Fungi (Basel) 2021; 7:354. [PMID: 33946450 PMCID: PMC8147175 DOI: 10.3390/jof7050354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/19/2022] Open
Abstract
The dry rot fungus Serpula lacrymans causes significant structural damage by decaying construction timber, resulting in costly restoration procedures. Dry rot fungi decompose cellulose and hemicellulose and are often accompanied by a succession of bacteria and other fungi. Bacterial-fungal interactions (BFI) have a considerable impact on all the partners, ranging from antagonistic to beneficial relationships. Using a cultivation-based approach, we show that S. lacrymans has many co-existing, mainly Gram-positive, bacteria and demonstrate differences in the communities associated with distinct fungal parts. Bacteria isolated from the fruiting bodies and mycelia were dominated by Firmicutes, while bacteria isolated from rhizomorphs were dominated by Proteobacteria. Actinobacteria and Bacteroidetes were less abundant. Fluorescence in situ hybridization (FISH) analysis revealed that bacteria were not present biofilm-like, but occurred as independent cells scattered across and within tissues, sometimes also attached to fungal spores. In co-culture, some bacterial isolates caused growth inhibition of S. lacrymans, and vice versa, and some induced fungal pigment production. It was found that 25% of the isolates could degrade pectin, 43% xylan, 17% carboxymethylcellulose, and 66% were able to depolymerize starch. Our results provide first insights for a better understanding of the holobiont S. lacrymans and give hints that bacteria influence the behavior of S. lacrymans in culture.
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Affiliation(s)
| | | | | | - Martin Kirchmair
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria; (J.E.); (S.N.); (S.Z.)
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150
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Uncovering the hidden bacterial ghost communities of yeast and experimental evidences demonstrates yeast as thriving hub for bacteria. Sci Rep 2021; 11:9394. [PMID: 33931672 PMCID: PMC8087679 DOI: 10.1038/s41598-021-88658-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 04/15/2021] [Indexed: 11/09/2022] Open
Abstract
Our major concern was to address “yeast endobacteria” which was based on a few reports in the recent past where bacteria may find yeast as a niche for survival. In this study, we report the microbiota of twenty-nine axenic yeast cultures recovered from different habitats based on their 16S rRNA gene-amplicon metagenomes. Yeasts were identified based on D1/D2 or ITS gene sequences. Bacterial diversity was widespread, varied and rich among all yeasts except for four strains. Taxa belonging to the phylum Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes and the genera; Streptococcus, Propionibacterium were common to all the yeasts. Candida tropicalis was used as a model organism to confirm bacteria through fluorescence in situ hybridization (FISH), isolating and re-introducing the isolated bacteria into the yeast. FISH analysis confirmed the endobacteria of C. tropicalis and we have successfully isolated four bacteria only after lysis and disruption of yeast cells. These bacteria were identified as species of Pseudomonas, Chryseobacterium, Lysinibacillus and Propionibacterium. Guestimates indicate 95% of bacterial species of C. tropicalis are yet-to-be-cultivated. We have successfully reintroduced mCherry tagged Pseudomonas into C. tropicalis. Also, auto-fluorescent Prochlorococcus and Rhodopseudomonas could be introduced into C. tropicalis while mCherry tagged E. coli or Salmonella could not be introduced. FISH analysis confirmed the presence of both native and infected bacterial cells present in C. tropicalis. Our findings unveil the insights into the ghost microbiota associated with yeast, which otherwise are considered to be axenic cultures. Their inherent occurrence, together with co-cultivation experiments under laboratory conditions suggests that yeasts are a thriving hub for bacterial communities.
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