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Hirakawa MP, Rodriguez A, Tran-Gyamfi MB, Light YK, Martinez S, Diamond-Pott H, Simmons BA, Sale KL. Phenothiazines Rapidly Induce Laccase Expression and Lignin-Degrading Properties in the White-Rot Fungus Phlebia radiata. J Fungi (Basel) 2023; 9:jof9030371. [PMID: 36983539 PMCID: PMC10053029 DOI: 10.3390/jof9030371] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
Phlebia radiata is a widespread white-rot basidiomycete fungus with significance in diverse biotechnological applications due to its ability to degrade aromatic compounds, xenobiotics, and lignin using an assortment of oxidative enzymes including laccase. In this work, a chemical screen with 480 conditions was conducted to identify chemical inducers of laccase expression in P. radiata. Among the chemicals tested, phenothiazines were observed to induce laccase activity in P. radiata, with promethazine being the strongest laccase inducer of the phenothiazine-derived compounds examined. Secretomes produced by promethazine-treated P. radiata exhibited increased laccase protein abundance, increased enzymatic activity, and an enhanced ability to degrade phenolic model lignin compounds. Transcriptomics analyses revealed that promethazine rapidly induced the expression of genes encoding lignin-degrading enzymes, including laccase and various oxidoreductases, showing that the increased laccase activity was due to increased laccase gene expression. Finally, the generality of promethazine as an inducer of laccases in fungi was demonstrated by showing that promethazine treatment also increased laccase activity in other relevant fungal species with known lignin conversion capabilities including Trametes versicolor and Pleurotus ostreatus.
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Affiliation(s)
- Matthew P. Hirakawa
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94550, USA
- Correspondence: (M.P.H.); (K.L.S.)
| | - Alberto Rodriguez
- Biomaterials and Biomanufacturing Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Mary B. Tran-Gyamfi
- Bioresource and Environmental Security Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Yooli K. Light
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Salvador Martinez
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Henry Diamond-Pott
- Bioresource and Environmental Security Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Blake A. Simmons
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Kenneth L. Sale
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Computational Biology and Biophysics Department, Sandia National Laboratories, Livermore, CA 94550, USA
- Correspondence: (M.P.H.); (K.L.S.)
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Dang H, Zhang T, Wang Z, Li G, Zhao W, Lv X, Zhuang L. Differences in the endophytic fungal community and effective ingredients in root of three Glycyrrhiza species in Xinjiang, China. PeerJ 2021; 9:e11047. [PMID: 33854843 PMCID: PMC7953873 DOI: 10.7717/peerj.11047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Background Endophytic fungi influence the quality and quantity of the medicinal plant’s bioactive compounds through specific fungus-host interactions. Nevertheless, due to the paucity of information, the composition of endophytic fungal communities and the mechanism by which effective ingredients regulate endophytic fungal communities in roots remains unclear. Methods In this study, we collected root and soil samples (depth range: 0–20, 20–40, and 40–60 cm) of three Glycyrrhiza species (Glycyrrhiza uralensis, Glycyrrhiza inflata, and Glycyrrhiza glabra). Glycyrrhizic acid and liquiritin content were determined using high-performance liquid chromatography (HPLC), and total flavonoid content was determined using ultraviolet spectrophotometry. High-throughput sequencing technology was employed to explore the composition and diversity of the endophytic fungal community in different root segments of three Glycyrrhiza species. Furthermore, soil samples were subjected to physicochemical analyses. Results We observed that the liquiritin content was not affected by the root depth (0–20 cm, 20–40 cm, and 40–60 cm). Still, it was significantly affected by the Glycyrrhiza species (Glycyrrhiza uralensis, Glycyrrhiza inflata, Glycyrrhiza glabra) (P < 0.05). In Glycyrrhiza root, a total of eight phyla and 140 genera were annotated so far, out of which Ascomycota and Basidiomycota phyla, and the Fusarium, Paraphoma, and Helminthosporium genera were found to be significantly dominant. Spearman correlation analysis revealed that liquiritin content was accountable for the differences in the diversity of the endophytic fungal community. Furthermore, distance-based redundancy analysis (db-RDA) showed that physicochemical properties of the soil (available potassium and ammonium nitrogen) and the root factors (liquiritin and water content) were the main contributing factors for the variations in the overall structure of the endophytic fungal community. Our results showed that the effective ingredients of Glycyrrhiza root and physicochemical properties of the soil regulated the endophytic fungal community composition and medicinal licorice diversity.
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Affiliation(s)
- Hanli Dang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Tao Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Zhongke Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Guifang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Wenqin Zhao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Xinhua Lv
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Li Zhuang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
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3
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Hano T, Ito M, Ito K, Uchida M. Alterations of stool metabolome, phenome, and microbiome of the marine fish, red sea bream, Pagrus major, following exposure to phenanthrene: A non-invasive approach for exposure assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 752:141796. [PMID: 32898801 DOI: 10.1016/j.scitotenv.2020.141796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/12/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
The present study aimed to assess the impact of phenanthrene (Phe) on fish health by addressing the alteration of fecal characteristics, in lieu of collecting biomarkers that often involves injurious or even fatal sampling of organisms. The marine fish red sea bream, Pagrus major, was exposed to Phe at a concentration of 18 μg/L for 16 days followed by depuration for 13 days. We collected feces from Phe-exposed or control (Phe-free) fish and then analyzed the fecal metabolite profile (metabolome), carbon utilization of microbiota (phenome), and bacterial 16s rRNA gene sequence (microbiome). Along with the increase in physiological stress markers (SOD and EROD) in serum and liver, we noted the possible role of intestine as a Phe reservoir. Furthermore, abnormal fecal appearance (green coloration) and remarkable changes in fecal characteristics were observed. These changes include alterations of cholesterol and putrescine metabolism and the enhanced utilization of putrescine as a carbon source. Phe also altered the microbial community, with an increase in Phe-degrading bacteria such as Pseudomonas. Interestingly, these enteric impairments were ameliorated by depuration. Taken together, our findings suggest that these alterations in feces were associated with adaptive responses to environmentally relevant Phe exposure scenarios, and that stool samples are potential candidates for exposure assessment in fish.
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Affiliation(s)
- Takeshi Hano
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan.
| | - Mana Ito
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Katsutoshi Ito
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Motoharu Uchida
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
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4
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Jałowiecki Ł, Krzymińska I, Górska M, Płaza G, Ratman-Kłosińska I. Effect of the freeze-drying process on the phenotypic diversity of Pseudomonas putida strains isolated from the interior of healthy roots of Sida hermaphrodita: Phenotype microarrays (PMs). Cryobiology 2020; 96:145-151. [PMID: 32702362 DOI: 10.1016/j.cryobiol.2020.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 11/30/2022]
Abstract
The objective of this study was to research the effect of the freeze-drying process on the metabolic changes of Pseudomonas putida strains (E41, E42, R85) isolated from the interior of Sida hermaphrodita roots with the use of the phenotypic microarrays (PM) technology. The proposed method of the freeze-drying process with inulin as component lycoprotectant demonstrated a high bacterial survival ratio (BSR) immediately after freeze-drying and storage after 12 months. While, after 360 days of freeze-drying BSR decreased to value of 74.38. Pseudomonas putida strains were assayed on microplates PM1-PM5, and PM9-PM13 testing 664 different substrates. However, no significant differences in the use of C substrates were observed either before or after the freeze drying process. An insignificant negative effect of the freeze-drying on the use of these substrates was observed. The utilization of N, P and S sources was low or showed no metabolic activity for most of the compounds after freeze-drying. The freeze-drying process increased the sensitivity of the bacteria to antibiotics and selected chemicals. In this study, the freeze-drying process decreased the metabolic activities of the tested strains and their resistance to antibiotics and chemicals.
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Affiliation(s)
- Łukasz Jałowiecki
- Environmental Microbiology Unit, Institute for Ecology of Industrial Areas, Kossutha 6, 40-844, Katowice, Poland
| | - Izabela Krzymińska
- Department of Microbiology, Institute of Microbial Technologies, NSZZ Solidarnosc 9 Av., 62-700, Turek, Poland
| | - Magdalena Górska
- ProBiotics Polska Magdalena Górska, Bratuszyn 21, 62-720, Brudzew, Poland
| | - Grażyna Płaza
- Environmental Microbiology Unit, Institute for Ecology of Industrial Areas, Kossutha 6, 40-844, Katowice, Poland.
| | - Izabela Ratman-Kłosińska
- Office of Projects Coordination, Marketing and Research Commercialisation, Institute for Ecology of Industrial Areas, Kossutha 6, 40-844, Katowice, Poland
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5
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How Do Trichoderma Genus Fungi Win a Nutritional Competition Battle against Soft Fruit Pathogens? A Report on Niche Overlap Nutritional Potentiates. Int J Mol Sci 2020; 21:ijms21124235. [PMID: 32545883 PMCID: PMC7352470 DOI: 10.3390/ijms21124235] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/17/2022] Open
Abstract
We present a case study report into nutritional competition between Trichoderma spp. isolated from wild raspberries and fungal phytopathogenic isolates (Colletotrichum sp., Botrytis sp., Verticillium sp. and Phytophthora sp.), which infect soft fruit ecological plantations. The competition was evaluated on the basis of nutritional potentiates. Namely, these were consumption and growth, calculated on the basis of substrate utilization located on Biolog® Filamentous Fungi (FF) plates. The niche size, total niche overlap and Trichoderma spp. competitiveness indices along with the occurrence of a stressful metabolic situation towards substrates highlighted the unfolding step-by-step approach. Therefore, the Trichoderma spp. and pathogen niche characteristics were provided. As a result, the substrates in the presence of which Trichoderma spp. nutritionally outcompete pathogens were denoted. These were adonitol, D-arabitol, i-erythritol, glycerol, D-mannitol and D-sorbitol. These substrates may serve as additives in biopreparations of Trichoderma spp. dedicated to plantations contaminated by phytopathogens of the genera Colletotrichum sp., Botrytis sp., Verticillium sp. and Phytophthora sp.
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Dunkley EJ, Chalmers JD, Cho S, Finn TJ, Patrick WM. Assessment of Phenotype Microarray plates for rapid and high-throughput analysis of collateral sensitivity networks. PLoS One 2019; 14:e0219879. [PMID: 31851668 PMCID: PMC6919586 DOI: 10.1371/journal.pone.0219879] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/23/2019] [Indexed: 11/29/2022] Open
Abstract
The crisis of antimicrobial resistance is driving research into the phenomenon of collateral sensitivity. Sometimes, when a bacterium evolves resistance to one antimicrobial, it becomes sensitive to others. In this study, we have investigated the utility of Phenotype Microarray (PM) plates for identifying collateral sensitivities with unprecedented throughput. We assessed the relative resistance/sensitivity phenotypes of nine strains of Staphylococcus aureus (two laboratory strains and seven clinical isolates) towards the 72 antimicrobials contained in three PM plates. In general, the PM plates reported on resistance and sensitivity with a high degree of reproducibility. However, a rigorous comparison of PM growth phenotypes with minimum inhibitory concentration (MIC) measurements revealed a trade-off between throughput and accuracy. Small differences in PM growth phenotype did not necessarily correlate with changes in MIC. Thus, we conclude that PM plates are useful for the rapid and high-throughput assessment of large changes in collateral sensitivity phenotypes during the evolution of antimicrobial resistance, but more subtle examples of cross-resistance or collateral sensitivity cannot be identified reliably using this approach.
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Affiliation(s)
- Elsie J Dunkley
- Centre for Biodiscovery, School of Biological Sciences, Victoria University, Wellington, New Zealand
| | - James D Chalmers
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Stephanie Cho
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Thomas J Finn
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Wayne M Patrick
- Centre for Biodiscovery, School of Biological Sciences, Victoria University, Wellington, New Zealand.,Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Deng Y, Su Y, Liu S, Bei L, Guo Z, Li H, Chen C, Feng J. A novel sRNA srvg17985 identified in Vibrio alginolyticus involving into metabolism and stress response. Microbiol Res 2019; 229:126295. [PMID: 31450184 DOI: 10.1016/j.micres.2019.126295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 06/23/2019] [Accepted: 06/26/2019] [Indexed: 11/28/2022]
Abstract
Vibrio alginolyticus is an opportunistic pathogen that is a threat to the aquaculture industry. Evidence has revealed critical roles for small RNAs (sRNAs) in bacterial physiology and pathology by modulating gene expression post transcription. However, little information about sRNA-mediated regulation in V. alginolyticus is available. We experimentally verified the existence and characterized the function of sRNA srvg17985 in V. alginolyticus ZJ-T. We identified a 179 nt and growth-phase-dependent transcript with a σ70 promoter and a ρ-independent terminator. The transcript consisted of five stem-loops and was conserved in Vibrio spp. Phenotype microarray assays showed that deletion of srvg17985 led to less use of Gly-Glu as a carbon source but a gain in ability to use l-phenylalanine as a nitrogen source. Srvg17985 regulated the osmotic stress response with stronger tolerance to NaCl but weaker tolerance to urea. In addition, srvg17985 inhibited the deamination of l-serine at pH 9.5 and promoted the hydrolysis of X-beta-d-glucuronide, thus affecting the pH stress response. Bioinformatics by IntaRNA and TargetRNA2 identified 45 common target mRNAs, some of which probably contributed to the observed phenotypes. These results indicated that srvg17985 regulated environmental adaptation. The results provide valuable information for in-depth studies of sRNA-mediated regulation mechanisms of the complex physiological processes of V alginolyticus and provide new targets for antibacterial therapeutics or attenuated vaccines for Vibrio spp.
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Affiliation(s)
- Yiqin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Tropical Aquaculture Research and Development Centre, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hainan, China
| | - Youlu Su
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lei Bei
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Zhixun Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Huo Li
- Jinyang Tropical Haizhen Aquaculture Co., Ltd., Maoming, China
| | - Chang Chen
- Xisha/Nansha Ocean Observation and Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Juan Feng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Tropical Aquaculture Research and Development Centre, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hainan, China.
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9
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Forest Tree Microbiomes and Associated Fungal Endophytes: Functional Roles and Impact on Forest Health. FORESTS 2019. [DOI: 10.3390/f10010042] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Terrestrial plants including forest trees are generally known to live in close association with microbial organisms. The inherent features of this close association can be commensalism, parasitism or mutualism. The term “microbiota” has been used to describe this ecological community of plant-associated pathogenic, mutualistic, endophytic and commensal microorganisms. Many of these microbiota inhabiting forest trees could have a potential impact on the health of, and disease progression in, forest biomes. Comparatively, studies on forest tree microbiomes and their roles in mutualism and disease lag far behind parallel work on crop and human microbiome projects. Very recently, our understanding of plant and tree microbiomes has been enriched due to novel technological advances using metabarcoding, metagenomics, metatranscriptomics and metaproteomics approaches. In addition, the availability of massive DNA databases (e.g., NCBI (USA), EMBL (Europe), DDBJ (Japan), UNITE (Estonia)) as well as powerful computational and bioinformatics tools has helped to facilitate data mining by researchers across diverse disciplines. Available data demonstrate that plant phyllosphere bacterial communities are dominated by members of only a few phyla (Proteobacteria, Actinobacteria, Bacteroidetes). In bulk forest soil, the dominant fungal group is Basidiomycota, whereas Ascomycota is the most prevalent group within plant tissues. The current challenge, however, is how to harness and link the acquired knowledge on microbiomes for translational forest management. Among tree-associated microorganisms, endophytic fungal biota are attracting a lot of attention for their beneficial health- and growth-promoting effects, and were preferentially discussed in this review.
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10
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Deng Y, Su Y, Liu S, Guo Z, Cheng C, Ma H, Wu J, Feng J, Chen C. Identification of a Novel Small RNA srvg23535 in Vibrio alginolyticus ZJ-T and Its Characterization With Phenotype MicroArray Technology. Front Microbiol 2018; 9:2394. [PMID: 30349521 PMCID: PMC6186989 DOI: 10.3389/fmicb.2018.02394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 09/18/2018] [Indexed: 01/28/2023] Open
Abstract
Small non-coding RNAs (sRNAs) are important modulators of gene expression and are involved in the pathogenesis and survival of prokaryotes. However, few studies have been conducted with Vibrio alginolyticus, which limits our ability to probe the regulation of virulence and environmental adaptation by sRNAs in this opportunistic pathogen. In this study, the sRNA candidate srvg23535 was identified in V. alginolyticus ZJ-T. The precise transcript end, secondary structure, and sequence conservation were determined. A srvg23535 null mutant was constructed and characterized by using Phenotype MicroArray (PM) technology. In silico target prediction was conducted by IntaRNA and TargetRNA2. Subsequently, a 107 nt transcript was validated with a sigma70 promoter at the 5' end and a Rho-independent terminator at the 3' end. The sRNA srvg23535 had four stem-loop structures and was conserved among Vibrio harveyi, Vibrio parahaemolyticus, and Vibrio splendidus. Deletion of srvg23535 in V. alginolyticus ZJ-T led to a weaker utilization of D-mannose, D-melibiose, lactulose, and inosine as carbon sources but stronger utilization of L-cysteine as nitrogen source. Moreover, the srvg2353 mutant showed stronger resistance to osmotic stress but weaker resistance to pH stress. Additionally, a total of 22 common targets were identified and several were related to the observed phenotype of the mutant. This study indicated that the novel sRNA, srvg23535, is conserved and restricted to Vibrio spp., affecting the utilization of several carbon and nitrogen sources and the response to osmotic and pH stress. These results extend our understanding of sRNA regulation in V. alginolyticus and provide a significant resource for the further study of the precise target mRNAs of srvg23535, which may provide targets for antibacterial therapeutic or attenuated vaccines against Vibrio spp.
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Affiliation(s)
- Yiqin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Youlu Su
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Zhixun Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Changhong Cheng
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Hongling Ma
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jinjun Wu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Juan Feng
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chang Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Xisha/Nansha Ocean Observation and Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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11
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Agostinelli M, Cleary M, Martín JA, Albrectsen BR, Witzell J. Pedunculate Oaks ( Quercus robur L.) Differing in Vitality as Reservoirs for Fungal Biodiversity. Front Microbiol 2018; 9:1758. [PMID: 30123200 PMCID: PMC6085435 DOI: 10.3389/fmicb.2018.01758] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/13/2018] [Indexed: 11/13/2022] Open
Abstract
Ecological significance of trees growing in urban and peri-urban settings is likely to increase in future land-use regimes, calling for better understanding of their role as potential reservoirs or stepping stones for associated biodiversity. We studied the diversity of fungal endophytes in woody tissues of asymptomatic even aged pedunculate oak trees, growing as amenity trees in a peri-urban setting. The trees were classified into three groups according to their phenotypic vitality (high, medium, and low). Endophytes were cultured on potato dextrose media from surface sterilized twigs and DNA sequencing was performed to reveal the taxonomic identity of the morphotypes. In xylem tissues, the frequency and diversity of endophytes was highest in oak trees showing reduced vitality. This difference was not found for bark samples, in which the endophyte infections were more frequent and communities more diverse than in xylem. In general, most taxa were shared across the samples with few morphotypes being recovered in unique samples. Leaf phenolic profiles were found to accurately classify the trees according to their phenotypic vitality. Our results confirm that xylem is more selective substrate for endophytes than bark and that endophyte assemblages in xylem are correlated to the degree of host vitality. Thus, high vitality of trees may be associated with reduced habitat quality to wood-associated endophytes.
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Affiliation(s)
- Marta Agostinelli
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Michelle Cleary
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Juan A Martín
- Department of Natural Systems and Resources, School of Forest Engineers, Technical University of Madrid, Madrid, Spain
| | - Benedicte R Albrectsen
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Johanna Witzell
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden
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12
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Ceapă CD, Vázquez-Hernández M, Rodríguez-Luna SD, Cruz Vázquez AP, Jiménez Suárez V, Rodríguez-Sanoja R, Alvarez-Buylla ER, Sánchez S. Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions. PLoS One 2018; 13:e0192618. [PMID: 29447216 PMCID: PMC5813959 DOI: 10.1371/journal.pone.0192618] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/27/2018] [Indexed: 12/17/2022] Open
Abstract
Endophytic bacteria are wide-spread and associated with plant physiological benefits, yet their genomes and secondary metabolites remain largely unidentified. In this study, we explored the genome of the endophyte Streptomyces scabrisporus NF3 for discovery of potential novel molecules as well as genes and metabolites involved in host interactions. The complete genomes of seven Streptomyces and three other more distantly related bacteria were used to define the functional landscape of this unique microbe. The S. scabrisporus NF3 genome is larger than the average Streptomyces genome and not structured for an obligate endosymbiotic lifestyle; this and the fact that can grow in R2YE media implies that it could include a soil-living stage. The genome displays an enrichment of genes associated with amino acid production, protein secretion, secondary metabolite and antioxidants production and xenobiotic degradation, indicating that S. scabrisporus NF3 could contribute to the metabolic enrichment of soil microbial communities and of its hosts. Importantly, besides its metabolic advantages, the genome showed evidence for differential functional specificity and diversification of plant interaction molecules, including genes for the production of plant hormones, stress resistance molecules, chitinases, antibiotics and siderophores. Given the diversity of S. scabrisporus mechanisms for host upkeep, we propose that these strategies were necessary for its adaptation to plant hosts and to face changes in environmental conditions.
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Affiliation(s)
- Corina Diana Ceapă
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Melissa Vázquez-Hernández
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Stefany Daniela Rodríguez-Luna
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Angélica Patricia Cruz Vázquez
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
- Instituto Tecnológico de Tuxtla Gutiérrez,Tuxtla, Gutiérrez, Chiapas, México
| | - Verónica Jiménez Suárez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Romina Rodríguez-Sanoja
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Elena R. Alvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Sergio Sánchez
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
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13
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Shaffer JP, U'Ren JM, Gallery RE, Baltrus DA, Arnold AE. An Endohyphal Bacterium ( Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum ( F. solani Species Complex, Nectriaceae). Front Microbiol 2017; 8:350. [PMID: 28382021 PMCID: PMC5361657 DOI: 10.3389/fmicb.2017.00350] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 02/20/2017] [Indexed: 01/12/2023] Open
Abstract
Bacterial endosymbionts occur in diverse fungi, including members of many lineages of Ascomycota that inhabit living plants. These endosymbiotic bacteria (endohyphal bacteria, EHB) often can be removed from living fungi by antibiotic treatment, providing an opportunity to assess their effects on functional traits of their fungal hosts. We examined the effects of an endohyphal bacterium (Chitinophaga sp., Bacteroidetes) on substrate use by its host, a seed-associated strain of the fungus Fusarium keratoplasticum, by comparing growth between naturally infected and cured fungal strains across 95 carbon sources with a Biolog® phenotypic microarray. Across the majority of substrates (62%), the strain harboring the bacterium significantly outperformed the cured strain as measured by respiration and hyphal density. These substrates included many that are important for plant- and seed-fungus interactions, such as D-trehalose, myo-inositol, and sucrose, highlighting the potential influence of EHB on the breadth and efficiency of substrate use by an important Fusarium species. Cases in which the cured strain outperformed the strain harboring the bacterium were observed in only 5% of substrates. We propose that additive or synergistic substrate use by the fungus-bacterium pair enhances fungal growth in this association. More generally, alteration of the breadth or efficiency of substrate use by dispensable EHB may change fungal niches in short timeframes, potentially shaping fungal ecology and the outcomes of fungal-host interactions.
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Affiliation(s)
| | - Jana M U'Ren
- School of Plant Sciences, University of ArizonaTucson, AZ, USA; Department of Agricultural and Biosystems Engineering, University of ArizonaTucson, AZ, USA
| | - Rachel E Gallery
- School of Natural Resources and the Environment, University of ArizonaTucson, AZ, USA; Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
| | - David A Baltrus
- School of Plant Sciences, University of Arizona Tucson, AZ, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of ArizonaTucson, AZ, USA; Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
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14
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Shubin M, Schaufler K, Tedin K, Vehkala M, Corander J. Identifying Multiple Potential Metabolic Cycles in Time-Series from Biolog Experiments. PLoS One 2016; 11:e0162276. [PMID: 27676629 PMCID: PMC5038949 DOI: 10.1371/journal.pone.0162276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 08/20/2016] [Indexed: 11/26/2022] Open
Abstract
Biolog Phenotype Microarray (PM) is a technology allowing simultaneous screening of the metabolic behaviour of bacteria under a large number of different conditions. Bacteria may often undergo several cycles of metabolic activity during a Biolog experiment. We introduce a novel algorithm to identify these metabolic cycles in PM experimental data, thus increasing the potential of PM technology in microbiology. Our method is based on a statistical decomposition of the time-series measurements into a set of growth models. We show that the method is robust to measurement noise and captures accurately the biologically relevant signals from the data. Our implementation is made freely available as a part of an R package for PM data analysis and can be found at www.helsinki.fi/bsg/software/Biolog_Decomposition.
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Affiliation(s)
- Mikhail Shubin
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Katharina Schaufler
- Institute of Microbiology and Epizootics, Freie Univerität Berlin, Berlin, Germany
| | - Karsten Tedin
- Institute of Microbiology and Epizootics, Freie Univerität Berlin, Berlin, Germany
| | - Minna Vehkala
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Faculty of Medicine, University of Oslo, Oslo, Norway
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15
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Pinzari F, Ceci A, Abu-Samra N, Canfora L, Maggi O, Persiani A. Phenotype MicroArray™ system in the study of fungal functional diversity and catabolic versatility. Res Microbiol 2016; 167:710-722. [PMID: 27283363 DOI: 10.1016/j.resmic.2016.05.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 05/18/2016] [Accepted: 05/26/2016] [Indexed: 11/30/2022]
Abstract
Fungi cover a range of important ecological functions associated with nutrient and carbon cycling in leaf litter and soil. As a result, research on existing relationships between fungal functional diversity, decomposition rates and competition is of key interest. Indeed, availability of nutrients in soil is largely the consequence of organic matter degradation dynamics. The Biolog® Phenotype MicroArrays™ (PM) system allows for the testing of fungi against many different carbon sources at any one time. The use and potential of the PM system as a tool for studying niche overlap and catabolic versatility of saprotrophic fungi is discussed here, and examples of its application are provided.
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Affiliation(s)
- Flavia Pinzari
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia agraria, Centro di Ricerca per lo Studio delle Relazioni tra Pianta e Suolo (CREA-RPS), Via della Navicella 2-4, 00184 Rome, Italy; Natural History Museum, Life Sciences Department, Cromwell Road, London SW7 5BD, UK.
| | - Andrea Ceci
- Dipartimento di Biologia ambientale, Sapienza Università di Roma, P.le Aldo Moro, 00185 Rome, Italy.
| | - Nadir Abu-Samra
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia agraria, Centro di Ricerca per lo Studio delle Relazioni tra Pianta e Suolo (CREA-RPS), Via della Navicella 2-4, 00184 Rome, Italy.
| | - Loredana Canfora
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia agraria, Centro di Ricerca per lo Studio delle Relazioni tra Pianta e Suolo (CREA-RPS), Via della Navicella 2-4, 00184 Rome, Italy.
| | - Oriana Maggi
- Dipartimento di Biologia ambientale, Sapienza Università di Roma, P.le Aldo Moro, 00185 Rome, Italy.
| | - Annamaria Persiani
- Dipartimento di Biologia ambientale, Sapienza Università di Roma, P.le Aldo Moro, 00185 Rome, Italy.
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