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Bertrand C, Martins R, Nunes F, Brandão P, Nascimento FX. Genomic insights into indole-3-acetic acid catabolism in the marine algae-associated bacterium, Marinomonas sp. NFXS50. Access Microbiol 2024; 6:000856.v3. [PMID: 39239567 PMCID: PMC11373566 DOI: 10.1099/acmi.0.000856.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 08/02/2024] [Indexed: 09/07/2024] Open
Abstract
Auxins, mainly in the form of indole-3-acetic acid (IAA), regulate several aspects of plant and algal growth and development. Consequently, plant and algae-associated bacteria developed the ability to modulate IAA levels, including IAA catabolism. In this work, we present and analyse the genome sequence of the IAA-degrading and marine algae-associated bacterium, Marinomonas sp. NFXS50, analyse its IAA catabolism gene cluster and study the prevalence of IAA catabolism genes in other Marinomonas genomes. Our findings revealed the presence of homologs of the Pseudomonas iac gene cluster, implicated in IAA catabolism, in the genome of strain NFXS50; however, differences were observed in the content and organization of the Marinomonas iac gene cluster when compared to that of the model iac-containing Pseudomonas putida 1290. These variations suggest potential adaptations in the IAA catabolism pathway, possibly influenced by substrate availability and evolutionary factors. The prevalence of iac genes across several Marinomonas species underscores the significance of IAA catabolism in marine environments, potentially influencing plant/algae-bacteria interactions. This study provides novel insights into the IAA catabolism in Marinomonas, laying the groundwork for future investigations into the role of iac genes in Marinomonas physiology and the regulation of marine plant/algae-bacteria interactions.
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Affiliation(s)
- Constança Bertrand
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Rodrigo Martins
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Francisco Nunes
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Pedro Brandão
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Francisco X Nascimento
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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Wang Z, Sun J, Yang P, Zhang W, Jiang Y, Liu Q, Yang Y, Hao R, Guo G, Huo W, Zhang Q, Li Q. Molecular Analysis of Indole and Skatole Decomposition Metabolism in Acinetobacter piscicola p38 Utilizing Biochemical and Omics Approaches. Microorganisms 2024; 12:1792. [PMID: 39338467 PMCID: PMC11434297 DOI: 10.3390/microorganisms12091792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 08/24/2024] [Accepted: 08/26/2024] [Indexed: 09/30/2024] Open
Abstract
Indole and skatole (3-methylindole, C9H9N) are common nitrogen-containing heterocyclic pollutants found in waste, wastewater treatment plants, and public restrooms and are the most notorious compounds in animal feces. Biodegradation was considered a feasible method for the removal of indole and skatole, but a comprehensive understanding of the metabolic pathways under both aerobic and anaerobic conditions was lacking, and the functional genes responsible for skatole biodegradation remained a mystery. Through metagenomic and gene cluster functional analysis, Acinetobacter piscicola p38 (NCBI: CP167896), genes 1650 (styrene monooxygenase: ACDW34_08180), and 1687 (styrene monooxygenase: ACDW34_08350) were identified as having the potential to degrade indole and skatole. The heterologous expression results demonstrate that the genes 1650 and 1651 (flavin reductase: ACDW34_08185), when combined, are capable of degrading indole, while the genes 1687 and 1688 (flavin reductase: ACDW34_08355), in combination, can degrade indole as well as skatole. These reactions necessitate the involvement of flavin reductase and NAD(P)H to catalyze the oxygenation process. This work aimed to provide new experimental evidence for the biodegradation of indole and skatole. This study offered new insights into our understanding of skatole degradation. The Acinetobacter_piscicola p38 strain provided an effective bacterial resource for the bioremediation of fecal indole and skatole.
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Affiliation(s)
- Zhonghao Wang
- College of Animal Science, Shanxi Agricultural University, Taigu 030800, China; (Z.W.); (J.S.); (P.Y.); (W.Z.); (Y.J.); (Q.L.); (Y.Y.); (R.H.); (G.G.); (W.H.)
| | - Jiajin Sun
- College of Animal Science, Shanxi Agricultural University, Taigu 030800, China; (Z.W.); (J.S.); (P.Y.); (W.Z.); (Y.J.); (Q.L.); (Y.Y.); (R.H.); (G.G.); (W.H.)
| | - Pu Yang
- College of Animal Science, Shanxi Agricultural University, Taigu 030800, China; (Z.W.); (J.S.); (P.Y.); (W.Z.); (Y.J.); (Q.L.); (Y.Y.); (R.H.); (G.G.); (W.H.)
| | - Wanjun Zhang
- College of Animal Science, Shanxi Agricultural University, Taigu 030800, China; (Z.W.); (J.S.); (P.Y.); (W.Z.); (Y.J.); (Q.L.); (Y.Y.); (R.H.); (G.G.); (W.H.)
| | - Yihong Jiang
- College of Animal Science, Shanxi Agricultural University, Taigu 030800, China; (Z.W.); (J.S.); (P.Y.); (W.Z.); (Y.J.); (Q.L.); (Y.Y.); (R.H.); (G.G.); (W.H.)
| | - Qiang Liu
- College of Animal Science, Shanxi Agricultural University, Taigu 030800, China; (Z.W.); (J.S.); (P.Y.); (W.Z.); (Y.J.); (Q.L.); (Y.Y.); (R.H.); (G.G.); (W.H.)
| | - Yunqi Yang
- College of Animal Science, Shanxi Agricultural University, Taigu 030800, China; (Z.W.); (J.S.); (P.Y.); (W.Z.); (Y.J.); (Q.L.); (Y.Y.); (R.H.); (G.G.); (W.H.)
| | - Ruirong Hao
- College of Animal Science, Shanxi Agricultural University, Taigu 030800, China; (Z.W.); (J.S.); (P.Y.); (W.Z.); (Y.J.); (Q.L.); (Y.Y.); (R.H.); (G.G.); (W.H.)
| | - Gang Guo
- College of Animal Science, Shanxi Agricultural University, Taigu 030800, China; (Z.W.); (J.S.); (P.Y.); (W.Z.); (Y.J.); (Q.L.); (Y.Y.); (R.H.); (G.G.); (W.H.)
| | - Wenjie Huo
- College of Animal Science, Shanxi Agricultural University, Taigu 030800, China; (Z.W.); (J.S.); (P.Y.); (W.Z.); (Y.J.); (Q.L.); (Y.Y.); (R.H.); (G.G.); (W.H.)
| | - Qiang Zhang
- College of Resources and Environment, Shanxi Agricultural University, Taigu 030800, China;
| | - Qinghong Li
- College of Animal Science, Shanxi Agricultural University, Taigu 030800, China; (Z.W.); (J.S.); (P.Y.); (W.Z.); (Y.J.); (Q.L.); (Y.Y.); (R.H.); (G.G.); (W.H.)
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Zeng Y, Guo M, Wu Q, Tan X, Jiang C, Teng F, Chen J, Zhang F, Ma X, Li X, Gu J, Huang W, Zhang C, Yuen-Kwan Law B, Long Y, Xu Y. Gut microbiota-derived indole-3-propionic acid alleviates diabetic kidney disease through its mitochondrial protective effect via reducing ubiquitination mediated-degradation of SIRT1. J Adv Res 2024:S2090-1232(24)00361-8. [PMID: 39147198 DOI: 10.1016/j.jare.2024.08.018] [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: 03/17/2024] [Revised: 07/15/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024] Open
Abstract
INTRODUCTION Gut microbes and their metabolites play crucial roles in the pathogenesis of diabetic kidney disease (DKD). However, which one and how specific gut-derived metabolites affect the progression of DKD remain largely unknown. OBJECTIVES This study aimed to investigate the potential roles of indole-3-propionic acid (IPA), a microbial metabolite of tryptophan, in DKD. METHODS Metagenomic sequencing was performed to analyze the microbiome structure in DKD. Metabolomics screening and validation were conducted to identify characteristic metabolites associated with DKD. The protective effect of IPA on DKD glomerular endothelial cells (GECs) was assessed through in vivo and in vitro experiments. Further validation via western blot, immunoprecipitation, gene knockout, and site-directed mutation elucidated the mechanism of IPA on mitochondrial injury. RESULTS Alterations in gut microbial community structure and dysregulated tryptophan metabolism were evident in DKD mice. Serum IPA levels were significantly reduced in DKD patients and correlated with fasting blood glucose, HbA1c, urine albumin-to-creatinine ratio (UACR), and estimated glomerular filtration rate (eGFR). IPA supplementation ameliorated albuminuria, bolstered the integrity of the glomerular filtration barrier, and mitigated mitochondrial impairments in GECs. Mechanistically, IPA hindered SIRT1 phosphorylation-mediated ubiquitin-proteasome degradation, restoring SIRT1's role in promoting PGC-1α deacetylation and nuclear translocation, thereby upregulating genes associated with mitochondrial biosynthesis and antioxidant defense. CONCLUSION Our findings underscore the potential of the microbial metabolite IPA to attenuate DKD progression, offering novel insights and potential therapeutic strategies for its management.
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Affiliation(s)
- Yan Zeng
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, China; Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou 646000, Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000, Sichuan, China
| | - Man Guo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou 646000, Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000, Sichuan, China
| | - Qi Wu
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou 646000, Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000, Sichuan, China; Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Xiaozhen Tan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou 646000, Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000, Sichuan, China; Experimental Medicine Center, the Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Chunxia Jiang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, China; Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou 646000, Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000, Sichuan, China
| | - Fangyuan Teng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou 646000, Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000, Sichuan, China; Experimental Medicine Center, the Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Jiao Chen
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou 646000, Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000, Sichuan, China
| | - Fanjie Zhang
- Department of Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Xiumei Ma
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610000, Sichuan, China
| | - Xinyue Li
- Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu 610000, Sichuan, China
| | - Junling Gu
- Department of Endocrinology, Yibin Second People's Hospital-West China Yibin Hospital, Sichuan University, Yibin 644000, Sichuan, China
| | - Wei Huang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou 646000, Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000, Sichuan, China
| | - Chunxiang Zhang
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research, Basic Medicine Research Innovation Center for Cardiometabolic Diseases, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Betty Yuen-Kwan Law
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, China.
| | - Yang Long
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou 646000, Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000, Sichuan, China; Experimental Medicine Center, the Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China.
| | - Yong Xu
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, China; Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou 646000, Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000, Sichuan, China.
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Fu M, Tello E, Hatzakis E, Peterson DG. Identification of Compounds That Impact Consumer Flavor Liking of American-European Hazelnut Hybrids Using Nontargeted LC/MS Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8092-8102. [PMID: 38536005 DOI: 10.1021/acs.jafc.4c00304] [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: 04/11/2024]
Abstract
American-European (Corylus americana × Corylus avellana) hazelnut hybrids are being developed for the Midwest-growing region of the United States. However, an inadequate understanding of the compounds that impact the consumer acceptance of hazelnuts limits breeding programs. Nontargeted liquid chromatography/mass spectrometry (LC/MS) chemical profiles of 12 roasted hybrid hazelnut samples and the corresponding consumer flavor liking scores were modeled by orthogonal partial least squares with good fit and predictive ability (R2Y > 0.9, Q2 > 0.9) to identify compounds that impact nut liking. The five most predictive compounds (1-5) were negatively correlated to flavor liking, selected as putative markers, purified by multidimensional preparative LC/MS, structurally elucidated (nuclear magnetic resonance, MS), quantified, and validated for sensory relevance. Compound 1 was identified as 1″-O-3'-b-glucofuranosyl-1'-O-1-b-glucofuranosyl-(2,6-dihydroxyphenyl)-ethan-4-one. Compounds 2 and 4 were identified as rotamers of 2-(3-hydroxy-2-oxoindolin-3-yl) acetic acid 3-O-6'-galactopyranosyl-2″-(2″oxoindolin-3″yl) acetate, whereas compounds 3 and 5 were identified as rotamers of 1″-O-1'-b-glucofuranosyl-9-O-6'-b-glucopyranosyl-2″-(2″-oxoindolin-3″yl) acetate. Sensory evaluation determined that all compounds were characterized by bitterness and/or astringency. The sensory threshold values of compounds 1-5 were determined to be below the concentrations reported in 91, 83, 41, 25, and 41% of all 12 hybrid hazelnut samples, respectively, indicating they contributed to aversive flavor attributes.
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Affiliation(s)
- Mengying Fu
- Department of Food Science and Technology, 110 Parker Building, The Ohio State University, 2015 Fyffe Road, Columbus, Ohio 43210, United States
| | - Edisson Tello
- Department of Food Science and Technology, 110 Parker Building, The Ohio State University, 2015 Fyffe Road, Columbus, Ohio 43210, United States
| | - Emmanuel Hatzakis
- Department of Food Science and Technology, 110 Parker Building, The Ohio State University, 2015 Fyffe Road, Columbus, Ohio 43210, United States
| | - Devin G Peterson
- Department of Food Science and Technology, 110 Parker Building, The Ohio State University, 2015 Fyffe Road, Columbus, Ohio 43210, United States
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Gao J, Xie H. Daylily intercropping: Effects on soil nutrients, enzyme activities, and microbial community structure. FRONTIERS IN PLANT SCIENCE 2023; 14:1107690. [PMID: 36890887 PMCID: PMC9986260 DOI: 10.3389/fpls.2023.1107690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
The daylily (Hemerocallis citrina Baroni)/other crop intercropping system can be a specific and efficient cropping pattern in a horticultural field. Intercropping systems contribute to the optimization of land use, fostering sustainable and efficient agriculture. In the present study, high-throughput sequencing was employed to explore the diversity in the root-soil microbial community in the intercropping of four daylily intercropping systems [watermelon (Citrullus lanatus)/daylily (WD), cabbage (Brassica pekinensis)/daylily (CD), kale (Brassica oleracea)/daylily (KD), watermelon/cabbage/kale/daylily (MI)], and determine the physicochemical traits and enzymatic activities of the soil. The results revealed that the contents of available potassium (2.03%-35.71%), available phosphorus (3.85%-62.56%), available nitrogen (12.90%-39.52%), and organic matter (19.08%-34.53%), and the urease (9.89%-31.02%) and sucrase (23.63%-50.60%) activities, and daylily yield (7.43%- 30.46%) in different intercropping soil systems were significantly higher compared to those in the daylily monocropping systems (CK). The bacterial Shannon index increased significantly in the CD and KD compared to the CK. In addition, the fungi Shannon index was also increased significantly in the MI, while the Shannon indices of the other intercropping modes were not significantly altered. Different intercropping systems also caused dramatic architectural and compositional alterations in the soil microbial community. A prominently higher relative richness of Bacteroidetes was noted in MI compared to that in CK, while Acidobacteria in WD and CD and Chloroflexi in WD were pronouncedly less abundant compared to those in CK. Furthermore, the association between soil bacteria taxa and soil characteristic parameters was stronger than that between fungi and soil. In conclusion, the present study demonstrated that the intercropping of daylily with other crops could significantly improve the nutrient levels of the soil and optimize the soil bacterial microflora composition and diversity.
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Stanek M, Kushwaha P, Murawska-Wlodarczyk K, Stefanowicz AM, Babst-Kostecka A. Quercus rubra invasion of temperate deciduous forest stands alters the structure and functions of the soil microbiome. GEODERMA 2023; 430:116328. [PMID: 37600960 PMCID: PMC10438910 DOI: 10.1016/j.geoderma.2023.116328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Invasive plants can modify the diversity and taxonomical structure of soil microbiomes. However, it is difficult to generalize the underlying factors as their influence often seems to depend on the complex plant-soil-microbial interactions. In this paper, we investigated how Quercus rubra impacts on the soil microbiome across two soil horizons in relation to native woodland. Five paired adjacent invaded vs native vegetation plots in a managed forest in southern Poland were investigated. Soil microbial communities were assessed along with soil enzyme activities and soil physicochemical parameters, separately for both organic and mineral horizons, as well as forest stand characteristics to explore plant-soil-microbe interactions. Although Q. rubra did not significantly affect pH, organic C, total N, available nutrients nor enzymatic activity, differences in soil abiotic properties (except C to N ratio) were primarily driven by soil depth for both vegetation types. Further, we found significant differences in soil microbiome under invasion in relation to native vegetation. Microbial richness and diversity were lower in both horizons of Q. rubra vs control plots. Moreover, Q. rubra increased relative abundance of unique amplicon sequence variants in both horizons and thereby significantly changed the structure of the core soil microbial communities, in comparison to the control plots. In addition, predicted microbial functional groups indicated a predominant soil depth effect in both vegetation plots with higher abundance of aerobic chemoheterotrophic bacteria and endophytic fungi in the organic horizon and greater abundance of methanotrophic and methylotrophic bacteria, and ectomycorrhizal fungi in the mineral horizon. Overall, our results indicate strong associations between Q. rubra invasion and changes in soil microbiome and associated functions, a finding that needs to be further investigated to predict modifications in ecosystem functioning caused by this invasive species.
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Affiliation(s)
- Małgorzata Stanek
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Priyanka Kushwaha
- Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA
| | | | - Anna M. Stefanowicz
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Alicja Babst-Kostecka
- Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA
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Bai YC, Li BX, Xu CY, Raza M, Wang Q, Wang QZ, Fu YN, Hu JY, Imoulan A, Hussain M, Xu YJ. Intercropping Walnut and Tea: Effects on Soil Nutrients, Enzyme Activity, and Microbial Communities. Front Microbiol 2022; 13:852342. [PMID: 35369467 PMCID: PMC8971985 DOI: 10.3389/fmicb.2022.852342] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/08/2022] [Indexed: 11/21/2022] Open
Abstract
The practice of intercropping, which involves growing more than one crop simultaneously during the same growing season, is becoming more important for increasing soil quality, land-use efficiency, and subsequently crop productivity. The present study examined changes in soil physicochemical properties, enzymatic activity, and microbial community composition when walnut (Juglans spp.) was intercropped with tea (Camellia sinensis L.) plants in a forest and compared with a walnut and tea monocropping system. The results showed that walnut-tea intercropping improved the soil nutrient profile and enzymatic activity. The soil available nitrogen (AN), available phosphorus (AP), available potassium (AK), organic matter (OM) content, and sucrase activity were significantly boosted in intercropped walnut and tea than in monocropping forests. The interaction between crops further increased bacterial and fungal diversity when compared to monoculture tea forests. Proteobacteria, Bacteroidetes, Firmicutes, Chlamydiae, Rozellomycota, and Zoopagomycota were found in greater abundance in an intercropping pattern than in monoculture walnut and tea forest plantations. The walnut-tea intercropping system also markedly impacted the abundance of several bacterial and fungal operational taxonomic units (OTUs), which were previously shown to support nutrient cycling, prevent diseases, and ameliorate abiotic stress. The results of this study suggest that intercropping walnut with tea increased host fitness and growth by positively influencing soil microbial populations.
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Affiliation(s)
- Yong-Chao Bai
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bao-Xin Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | | | - Mubashar Raza
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Qi-Zhu Wang
- Center for Walnut Technology of Baokang County, Xiangyang, China
| | - Ya-Nan Fu
- Center for Walnut Technology of Baokang County, Xiangyang, China
| | - Jian-Yang Hu
- State Key Laboratory of the Discovery and Development of Novel Pesticides, Shenyang Sinochem Agrochemicals R&D Co., Ltd., Shenyang, China
| | - Abdessamad Imoulan
- Department of Biology, Faculty of Science and Technics of Errachidia, Mouly Ismail University, Meknes, Morocco
| | - Muzammil Hussain
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Syrova DS, Shaposhnikov AI, Yuzikhin OS, Belimov AA. Destruction and Transformation of Phytohormones By Microorganisms. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822010094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zhao S, Chen X, Sun Q, Wang F, Hu C, Guo L, Bai J, Yu H. Label-Free Quantitative Proteomic Analysis of the Global Response to Indole-3-Acetic Acid in Newly Isolated Pseudomonas sp. Strain LY1. Front Microbiol 2021; 12:694874. [PMID: 34447357 PMCID: PMC8383072 DOI: 10.3389/fmicb.2021.694874] [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: 04/13/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
Indole-3-acetic acid (IAA), known as a common plant hormone, is one of the most distributed indole derivatives in the environment, but the degradation mechanism and cellular response network to IAA degradation are still not very clear. The objective of this study was to elucidate the molecular mechanisms of IAA degradation at the protein level by a newly isolated strain Pseudomonas sp. LY1. Label-free quantitative proteomic analysis of strain LY1 cultivated with IAA or citrate/NH4Cl was applied. A total of 2,604 proteins were identified, and 227 proteins have differential abundances in the presence of IAA, including 97 highly abundant proteins and 130 less abundant proteins. Based on the proteomic analysis an IAA degrading (iad) gene cluster in strain LY1 containing IAA transformation genes (organized as iadHABICDEFG), genes of the β-ketoadipate pathway for catechol and protocatechuate degradation (catBCA and pcaABCDEF) were identified. The iadA, iadB, and iadE-disrupted mutants lost the ability to grow on IAA, which confirmed the role of the iad cluster in IAA degradation. Degradation intermediates were analyzed by HPLC, LC-MS, and GC-MS analysis. Proteomic analysis and identified products suggested that multiple degradation pathways existed in strain LY1. IAA was initially transformed to dioxindole-3-acetic acid, which was further transformed to isatin. Isatin was then transformed to isatinic acid or catechol. An in-depth data analysis suggested oxidative stress in strain LY1 during IAA degradation, and the abundance of a series of proteins was upregulated to respond to the stress, including reaction oxygen species (ROS) scavenging, protein repair, fatty acid synthesis, RNA protection, signal transduction, chemotaxis, and several membrane transporters. The findings firstly explained the adaptation mechanism of bacteria to IAA degradation.
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Affiliation(s)
- Shuxue Zhao
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xi Chen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Qianshu Sun
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Fei Wang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chunhui Hu
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lizhong Guo
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jie Bai
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Hao Yu
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
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10
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Wang X, Tello E, Peterson DG. Characterization of bitter compounds in native and hybrid American hazelnuts. Food Chem 2021; 363:130311. [PMID: 34175639 DOI: 10.1016/j.foodchem.2021.130311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/18/2022]
Abstract
The main objective of this study was to identify compounds that contribute to the bitter taste attributes of American hazelnuts (C. americana) and derived hybrids. Sensory-guided Prep-LC fractionation analysis selected four compounds as bitter that were further identified by MS and NMR as carpinontriol B, 2-(3-hydroxy-2-oxoindolin-3-yl)acetic acid 3-O-6'-galactopyranosyl-2″-(2″oxoindolin-3″yl) acetate, giffonin-2-O-[(α-d-glucopyranosyl)-6'-O-(3-hydroxy-3-methylglutaric acid) and Afzelin, termed compounds 1-4, respectively. The concentrations of compounds 1, 2, 3, and 4 were determined across 88 American hybrid hazelnut genotypes and reported to be present at levels above their bitter threshold values in 94, 75, 25, and 0% of the samples, respectively. Moreover, the concentrations of compounds 1 and 3 were significantly higher for nuts dehusked prior to drying during post-harvest handling, which is expected to result in a higher perceived bitter intensity.
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Affiliation(s)
- Xue Wang
- Department of Food Science and Technology, 317 Parker Food Science & Technology Building, The Ohio State University, 2015 Fyffe Rd., Columbus, OH 43210, United States
| | - Edisson Tello
- Department of Food Science and Technology, 317 Parker Food Science & Technology Building, The Ohio State University, 2015 Fyffe Rd., Columbus, OH 43210, United States
| | - Devin G Peterson
- Department of Food Science and Technology, 317 Parker Food Science & Technology Building, The Ohio State University, 2015 Fyffe Rd., Columbus, OH 43210, United States.
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11
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Paul CE, Eggerichs D, Westphal AH, Tischler D, van Berkel WJH. Flavoprotein monooxygenases: Versatile biocatalysts. Biotechnol Adv 2021; 51:107712. [PMID: 33588053 DOI: 10.1016/j.biotechadv.2021.107712] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.
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Affiliation(s)
- Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniel Eggerichs
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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12
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Molecular and physiological analysis of indole-3-acetic acid degradation in Bradyrhizobium japonicum E109. Res Microbiol 2021; 172:103814. [PMID: 33539931 DOI: 10.1016/j.resmic.2021.103814] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/20/2021] [Accepted: 01/26/2021] [Indexed: 11/21/2022]
Abstract
Bradyrhizobium japonicum E109 is a bacterium widely used for inoculants production in Argentina. It is known for its ability to produce several phytohormones and degrade indole-3-acetic acid (IAA). The genome sequence of B. japonicum E109 was recently analyzed and it showed the presence of genes related to the synthesis of IAA by indole-3-acetonitrile, indole-3-acetamide and tryptamine pathways. Nevertheless, B. japonicum E109 is not able to produce IAA and instead has the ability to degrade this hormone under saprophytic culture conditions. This work aimed to study the molecular and physiological features of IAA degradation and identify the genes responsible of this activity. In B. japonicum E109 we identified two sequences coding for a putative 3-phenylpropionate dioxygenase (subunits α and β) responsible for the IAA degradation that were homologous to the canonical cluster of iacC and iacD of Pseudomonas putida 1290. These genes form a separate cluster together with three additional genes with unknown functions. The degradation activity was found to be constitutively expressed in B. japonicum E109. As products of IAA degradation, we identified two compounds, 3-indoleacetic acid 2,3-oxide and 2-(2-hydroperoxy-3-hydroxyindolin-3-yl) acetic acid. Our report proposes, for the first time, a model for IAA degradation in Bradyrhizobium.
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13
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Rzemieniecki T, Kleiber T, Pernak J. Naturally based ionic liquids with indole-3-acetate anions and cations derived from cinchona alkaloids. RSC Adv 2021; 11:27530-27540. [PMID: 35480698 PMCID: PMC9037897 DOI: 10.1039/d1ra04805h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/05/2021] [Indexed: 12/31/2022] Open
Abstract
The use of highly efficient methods and natural raw materials in syntheses of new biologically active substances addresses the current challenges in this area: ensuring the highest possible efficacy at low concentrations and reducing negative environmental impact. In the present study, we applied this strategy to obtain a new group of ionic liquids containing the indole-3-acetate anion, which is a well-known plant growth hormone, and a cation derived from a cinchona alkaloid – quinine or quinidine. A comparison of the derivatization kinetics of both alkaloids was also carried out, and the use of a quaternary quinidine derivative as a source of biologically active ionic liquids is described here for the first time. The structures of the obtained compounds were fully confirmed based on spectral methods. According to analyses of the effects of the obtained compounds on the growth and development of lettuce plants (Lactuca sativa L.), the ionic liquids obtained with indole-3-acetate anions exhibited activity at a concentration of 0.5 mg dm−3, and the length of the alkyl substituent in the alkaloid-derived cation or the chirality of this cation is crucial in determining the biological activity of the compound. In the cases of several salts containing the 1-alkylquininium cation, we recorded significant, beneficial changes in micronutrient content, which directly translated into plant nutritional value, while no signs of phytotoxicity were observed. Analyses of relevant physicochemical properties (e.g., with differential scanning calorimetry, thermogravimetric analysis and solubility analysis) as well as microbial toxicity tests were also performed to evaluate the environmental impacts of the products. The promising results of our study indicate significant potential for application of these new ionic liquids derived from cinchona alkaloids. The transformation of a plant hormone into an alkaloid-based ionic liquid results in unique changes in physicochemical and biological properties.![]()
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Affiliation(s)
- Tomasz Rzemieniecki
- Department of Chemical Technology, Poznan University of Technology, Berdychowo 4, Poznan 60-965, Poland
| | - Tomasz Kleiber
- Department of Agronomy, Horticulture and Bioengineering, Poznan University of Life Sciences, Zgorzelecka 4, Poznan 60-198, Poland
| | - Juliusz Pernak
- Department of Chemical Technology, Poznan University of Technology, Berdychowo 4, Poznan 60-965, Poland
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14
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Laird TS, Flores N, Leveau JHJ. Bacterial catabolism of indole-3-acetic acid. Appl Microbiol Biotechnol 2020; 104:9535-9550. [PMID: 33037916 DOI: 10.1007/s00253-020-10938-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/21/2020] [Accepted: 09/27/2020] [Indexed: 12/18/2022]
Abstract
Indole-3-acetic acid (IAA) is a molecule with the chemical formula C10H9NO2, with a demonstrated presence in various environments and organisms, and with a biological function in several of these organisms, most notably in plants where it acts as a growth hormone. The existence of microorganisms with the ability to catabolize or assimilate IAA has long been recognized. To date, two sets of gene clusters underlying this property in bacteria have been identified and characterized: one (iac) is responsible for the aerobic degradation of IAA into catechol, and another (iaa) for the anaerobic conversion of IAA to 2-aminobenzoyl-CoA. Here, we summarize the literature on the products, reactions, and pathways that these gene clusters encode. We explore two hypotheses about the benefit that iac/iaa gene clusters confer upon their bacterial hosts: (1) exploitation of IAA as a source of carbon, nitrogen, and energy; and (2) interference with IAA-dependent processes and functions in other organisms, including plants. The evidence for both hypotheses will be reviewed for iac/iaa-carrying model strains of Pseudomonas putida, Enterobacter soli, Acinetobacter baumannii, Paraburkholderia phytofirmans, Caballeronia glathei, Aromatoleum evansii, and Aromatoleum aromaticum, more specifically in the context of access to IAA in the environments from which these bacteria were originally isolated, which include not only plants, but also soils and sediment, as well as patients in hospital environments. We end the mini-review with an outlook for iac/iaa-inspired research that addresses current gaps in knowledge, biotechnological applications of iac/iaa-encoded enzymology, and the use of IAA-destroying bacteria to treat pathologies related to IAA excess in plants and humans. KEY POINTS: • The iac/iaa gene clusters encode bacterial catabolism of the plant growth hormone IAA. • Plants are not the only environment where IAA or IAA-degrading bacteria can be found. • The iac/iaa genes allow growth at the expense of IAA; other benefits remain unknown.
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Affiliation(s)
- Tyler S Laird
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Neptali Flores
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Johan H J Leveau
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA.
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