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Novello G, Bona E, Nasuelli M, Massa N, Sudiro C, Campana DC, Gorrasi S, Hochart ML, Altissimo A, Vuolo F, Gamalero E. The Impact of Nitrogen-Fixing Bacteria-Based Biostimulant Alone or in Combination with Commercial Inoculum on Tomato Native Rhizosphere Microbiota and Production: An Open-Field Trial. BIOLOGY 2024; 13:400. [PMID: 38927280 PMCID: PMC11200462 DOI: 10.3390/biology13060400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
The agricultural sector is currently encountering significant challenges due to the effects of climate change, leading to negative consequences for crop productivity and global food security. In this context, traditional agricultural practices have been inadequate in addressing the fast-evolving challenges while maintaining environmental sustainability. A possible alternative to traditional agricultural management is represented by using beneficial micro-organisms that, once applied as bioinoculants, may enhance crop resilience and adaptability, thereby mitigating the adverse effects of environmental stressors and boosting productivity. Tomato is one of the most important crops worldwide, playing a central role in the human diet. The aim of this study was to evaluate the impact of a nitrogen-fixing bacterial-based biostimulant (Azospirillum sp., Azotobacter sp., and Rhizobium sp.) in combination or not with a commercial inoculum Micomix (Rhizoglomus irregulare, Funnelliformis mosseae, Funnelliformis caledonium, Bacillus licheniformis, and Bacillus mucilaginosus) (MYC) on the native rhizosphere communities and tomato production. Bacterial populations in the different samples were characterized using an environmental metabarcoding approach. The bioinocula effect on the native rhizosphere microbiota resulted in significant variation both in alpha and beta diversity and in a specific signature associated with the presence of biostimulants.
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Affiliation(s)
- Giorgia Novello
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (G.N.); (N.M.); (D.C.C.); (E.G.)
| | - Elisa Bona
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica (DISSTE), Università del Piemonte Orientale, 13100 Vercelli, Italy;
- Center on Autoimmune and Allergic Diseases (CAAD), Università del Piemonte Orientale, 28100 Novara, Italy
| | - Martina Nasuelli
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica (DISSTE), Università del Piemonte Orientale, 13100 Vercelli, Italy;
| | - Nadia Massa
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (G.N.); (N.M.); (D.C.C.); (E.G.)
| | - Cristina Sudiro
- Landlab S.r.l., 36050 Quinto Vicentino, Italy; (C.S.); (M.L.H.); (A.A.)
| | - Daniela Cristina Campana
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (G.N.); (N.M.); (D.C.C.); (E.G.)
| | - Susanna Gorrasi
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, 01100 Viterbo, Italy;
| | | | - Adriano Altissimo
- Landlab S.r.l., 36050 Quinto Vicentino, Italy; (C.S.); (M.L.H.); (A.A.)
| | | | - Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (G.N.); (N.M.); (D.C.C.); (E.G.)
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Mellai M, Allesina M, Edoardo B, Cascella F, Nobile V, Spina A, Amone F, Zaccaria V, Insolia V, Perri A, Lofaro D, Puoci F. A Randomized, Double-Blind, Placebo-Controlled Trial: Efficacy of Opuntia ficus- indica Prebiotic Supplementation in Subjects with Gut Dysbiosis. Nutrients 2024; 16:586. [PMID: 38474715 DOI: 10.3390/nu16050586] [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: 01/08/2024] [Revised: 02/06/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Gut dysbiosis refers to an imbalance in gut microbiota composition and function. Opuntia ficus-indica extract has been shown to modulate gut microbiota by improving SCFA production in vivo and gastrointestinal discomfort (GD) in humans. The aim of this study was to demonstrate the efficacy of OdiliaTM on gastrointestinal health by changing the microbial diversity of species involved in inflammation, immunity, oxidation, and the brain-gut-muscle axis. A randomized, double-blind clinical trial was conducted in 80 adults with gut dysbiosis. The intervention consisted of a 300 mg daily intake of OdiliaTM (n = 40) or maltodextrin as a placebo (n = 40), administered for 8 weeks. Intervention effect was evaluated using 16S metagenomics and GIQLI/GSAS scores at baseline, at 4 and 8 weeks. Eight weeks of OdiliaTM supplementation positively modulates gut microbiota composition with a significant reduction in the Firmicutes to Bacteroidetes ratio (p = 0.0012). Relative abundances of beneficial bacteria (Bacteroides and Clostridium_XIVa) were significantly increased (p < 0.001), in contrast to a significant reduction in pro-inflammatory bacteria (p < 0.001). Accordingly, GIQLI and GSAS scores revealed successful improvement in GD. OdiliaTM may represent an effective and well-tolerated treatment in subjects with gut dysbiosis.
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Affiliation(s)
- Marta Mellai
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy
- Genomics & Transcriptomics Unit, Center for Translational Research on Autoimmune and Allergic Disease, 28100 Novara, Italy
| | - Marta Allesina
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy
| | - Benedetto Edoardo
- GIGA-CP Italian Association for Primary Care Gastroenterology, 87036 Rende, Italy
| | - Federica Cascella
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy
| | - Vincenzo Nobile
- R&D Department, Complife Italia S.r.l., 27028 San Martino Siccomario, Italy
| | - Amelia Spina
- Nutratech S.r.l., Spin-Off of University of Calabria, 87036 Rende, Italy
| | - Fabio Amone
- Nutratech S.r.l., Spin-Off of University of Calabria, 87036 Rende, Italy
| | | | | | - Anna Perri
- Department of Experimental and Clinical Medicine, Magna Grecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Danilo Lofaro
- Department of Mechanical, Energy, Management Engineering, University of Calabria, 87036 Rende, Italy
| | - Francesco Puoci
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87100 Cosenza, Italy
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Conesa HM, Párraga-Aguado I, Jiménez-Cárceles FJ, Risueño Y. Evaluation of the rhizospheric microbiome of the native colonizer Piptatherum miliaceum in semiarid mine tailings. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:9359-9371. [PMID: 36074214 PMCID: PMC10673988 DOI: 10.1007/s10653-022-01357-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
The study of the rhizospheric microbiome in native plants should be a prerequisite before carrying out the phytomanagement of mine tailings. The goal of this work was to evaluate the rhizospheric microbiome of Piptatherum miliaceum in semiarid mine tailings. A comprehensive edaphic characterization was performed including the description of soil microbial composition in the rhizosphere of P. miliaceum growing at a mine tailings pile and at a control site. Plant nutritional and isotopic compositions were also determined. Neutral pH of the tailings (7.3) determined low metal extractability in 0.01 M CaCl2 (e.g. < 1 mg/kg for Zn). In spite of the contrasting edaphic fertility conditions of both sites, N (~ 15 g kg-1) and P (~ 400 mg kg-1) leaf concentrations were similar. The lower δ15N at the tailings plants (- 4.50‰) compared to the control (6.42‰) indicated greater efficiency of P. miliaceum for uptaking N under the low fertility conditions of the tailings (0.1% total soil nitrogen). The presence at the tailings of bacterial orders related to the cycling of N, such as Rhizobiales, could have contributed to enhance N acquisition. The lower leaf δ13C values at the tailings (- 30.22‰) compared to the control (- 28.47‰) indicated lower water use efficiency of the tailing plants. Some organotrophic bacterial and fungal groups in the tailings' rhizospheres were also found in the control site (e.g. Cytophagales, Sphingobacteriales for bacteria; Hypocreales, Pleosporales for fungi). This may indicate that P. miliaceum is able to shape its own specific microbiome at the tailings independently from the initial microbial composition of the tailings.
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Affiliation(s)
- Héctor M Conesa
- Departamento de Ingeniería Agronómica, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, Paseo Alfonso XIII, 48, 30203, Cartagena, Spain
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4
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Nasuelli M, Novello G, Gamalero E, Massa N, Gorrasi S, Sudiro C, Hochart M, Altissimo A, Vuolo F, Bona E. PGPB and/or AM Fungi Consortia Affect Tomato Native Rhizosphere Microbiota. Microorganisms 2023; 11:1891. [PMID: 37630451 PMCID: PMC10458106 DOI: 10.3390/microorganisms11081891] [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: 06/30/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Tomatoes are one of the most important crops worldwide and also play a central role in the human diet. Microbial consortia are microorganism associations, often employed as bioinoculants, that can interact with the native rhizosphere microbiota. The aim of this study was to evaluate the impact of a bacterial-based biostimulant (Pseudomonas fluorescens and Bacillus amyloliquefaciens) (PSBA) in combination, or not, with a commercial inoculum Micomix (Rhizoglomus irregulare, Funnelliformis mosseae, Funnelliformis caledonium, Bacillus licheniformis, Bacillus mucilaginosus) (MYC) on the native rhizosphere communities and on tomato production. The trial was carried out using Solanum lycopersicum in an open field as follows: control full NPK (CFD), control reduced NPK (CRD), MYC, PSBA, PSBA + MYC. Bacterial population in the different samples were characterized using a next generation sequencing approach. The bioinocula effect on the native rhizosphere microbiota resulted in significant variation both in alpha and beta diversity and in a specific signature associated with the presence of biostimulants, especially in the presence of co-inoculation (PSBA + MYC). In particular, the high initial biodiversity shifts in the community composition occurred and consisted in the increase in the abundance of genera correlated to the soil acidification and in an enhanced density of nitrogen-fixing microbes. The results also highlighted the well-known rhizosphere effect.
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Affiliation(s)
- Martina Nasuelli
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica (DISSTE), Università del Piemonte Orientale, 13100 Vercelli, Italy;
| | - Giorgia Novello
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (E.G.); (N.M.)
| | - Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (E.G.); (N.M.)
| | - Nadia Massa
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (E.G.); (N.M.)
| | - Susanna Gorrasi
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, 01100 Viterbo, Italy;
| | - Cristina Sudiro
- Landlab S.r.l., 36050 Quinto Vicentino, Italy; (C.S.); (M.H.); (A.A.)
| | - Marie Hochart
- Landlab S.r.l., 36050 Quinto Vicentino, Italy; (C.S.); (M.H.); (A.A.)
| | - Adriano Altissimo
- Landlab S.r.l., 36050 Quinto Vicentino, Italy; (C.S.); (M.H.); (A.A.)
| | | | - Elisa Bona
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica (DISSTE), Università del Piemonte Orientale, 13100 Vercelli, Italy;
- Center on Autoimmune and Allergic Diseases (CAAD), Università del Piemonte Orientale, 28100 Novara, Italy
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Pulcini L, Bona E, Vaudano ET, Tsolakis C, Garcia-Moruno E, Costantini A, Gamalero E. The Impact of a Commercial Biostimulant on the Grape Mycobiota of Vitis vinifera cv. Barbera. Microorganisms 2023; 11:1873. [PMID: 37630432 PMCID: PMC10457965 DOI: 10.3390/microorganisms11081873] [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: 06/01/2023] [Revised: 07/22/2023] [Accepted: 07/23/2023] [Indexed: 08/27/2023] Open
Abstract
Reducing the use of fungicides, insecticides, and herbicides in order to limit environmental pollution and health risks for agricultural operators and consumers is one of the goals of European regulations. In fact, the European Commission developed a package of measures (the European Green Deal) to promote the sustainable use of natural resources and strengthen the resilience of European agri-food systems. As a consequence, new plant protection products, such as biostimulants, have been proposed as alternatives to agrochemicals. Their application in agroecosystems could potentially open new scenarios regarding the microbiota. In particular, the vineyard microbiota and the microbiota on the grape surface can be affected by biostimulants and lead to different wine features. The aim of this work was to assess the occurrence of a possible variation in the mycobiota due to the biostimulant application. Therefore, our attention has been focused on the yeast community of grape bunches from vines subjected to the phytostimulant BION®50WG treatment. This work was carried out in the CREA-VE experimental vineyard of Vitis vinifera cv. Barbera in Asti (Piedmont, Italy). The composition of fungal communities on grapes from three experimental conditions such as IPM (integrated pest management), IPM+BION®50WG, and IPM+water foliar nebulization was compared by a metabarcoding approach. Our results revealed the magnitude of alpha and beta diversity, and the microbial biodiversity index and specific fungal signatures were highlighted by comparing the abundance of yeast and filamentous fungi in IPM and BION®50WG treatments. No significant differences in the mycobiota of grapevines subjected to the three treatments were detected.
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Affiliation(s)
- Laura Pulcini
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy;
| | - Elisa Bona
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica (DISSTE), Università del Piemonte Orientale, Piazza San Eusebio 5, 13100 Vercelli, Italy;
| | - Enrico Tommaso Vaudano
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Christos Tsolakis
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Emilia Garcia-Moruno
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Antonella Costantini
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy;
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Clavenna MG, La Vecchia M, Sculco M, Joseph S, Barberis E, Amede E, Mellai M, Brossa S, Borgonovi G, Occhipinti P, Boldorini R, Robotti E, Azzimonti B, Bona E, Pasolli E, Ferrante D, Manfredi M, Aspesi A, Dianzani I. Distinct Signatures of Tumor-Associated Microbiota and Metabolome in Low-Grade vs. High-Grade Dysplastic Colon Polyps: Inference of Their Role in Tumor Initiation and Progression. Cancers (Basel) 2023; 15:3065. [PMID: 37370676 DOI: 10.3390/cancers15123065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
According to the driver-passenger model for colorectal cancer (CRC), the tumor-associated microbiota is a dynamic ecosystem of bacterial species where bacteria with carcinogenic features linked to CRC initiation are defined as "drivers", while opportunistic bacteria colonizing more advanced tumor stages are known as "passengers". We reasoned that also gut microbiota-associated metabolites may be differentially enriched according to tumor stage, and be potential determinants of CRC development. Thus, we characterized the mucosa- and lumen-associated microbiota (MAM and LAM, respectively) and mucosa-associated metabolites in low- vs. high-grade dysplastic colon polyps from 78 patients. We show that MAM, obtained with a new biopsy-preserving approach, and LAM differ in composition and α/β-diversity. By stratifying patients for polyp histology, we found that bacteria proposed as passengers by previous studies colonized high-grade dysplastic adenomas, whereas driver taxa were enriched in low-grade polyps. Furthermore, we report altered "mucosa-associated metabolite" levels in low- vs. high-grade groups. Integrated microbiota-metabolome analysis suggests the involvement of the gut microbiota in the production and consumption of these metabolites. Altogether, our findings support the involvement of bacterial species and associated metabolites in CRC mucosal homeostasis in a tumor-stage-specific manner. These distinct signatures may be used to distinguish low-grade from high-grade dysplastic polyps.
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Affiliation(s)
| | - Marta La Vecchia
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Marika Sculco
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Soni Joseph
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Elettra Barberis
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Elia Amede
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Marta Mellai
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Silvia Brossa
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Giulia Borgonovi
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Pietro Occhipinti
- Department of Gastroenterology, "Maggiore della Carità" Hospital, 28100 Novara, Italy
| | - Renzo Boldorini
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Elisa Robotti
- Department of Sciences and Technological Innovation, Università del Piemonte Orientale, 15121 Alessandria, Italy
| | - Barbara Azzimonti
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Elisa Bona
- Department for Sustainable Development and Ecological Transition, Università del Piemonte Orientale, 13100 Vercelli, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Daniela Ferrante
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Marcello Manfredi
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Anna Aspesi
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Irma Dianzani
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
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Liu KL, Chen BY, Zhang B, Wang RH, Wang CS. Understory vegetation diversity, soil properties and microbial community response to different thinning intensities in Cryptomeria japonica var. sinensis plantations. Front Microbiol 2023; 14:1117384. [PMID: 36925469 PMCID: PMC10011715 DOI: 10.3389/fmicb.2023.1117384] [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: 12/06/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Introduction Soil microorganisms are the key factors in elucidating the effects of thinning on tree growth performance, but the effects of vegetation and soil on the species composition and function of soil microorganisms after thinning are still not well elaborated. Methods The effects of thinning on understory vegetation diversity, soil physicochemical properties and soil microbial community composition were investigated in a thinning trial plantation of Cryptomeria japonica var. sinensis, including four thinning intensities (control: 0%, LIT: 20%, MIT: 30% and HIT: 40%), and the relationships of the microbial community structure with the understory vegetation diversity and soil properties were assessed. Results The results showed that thinning had a greater effect on the diversity of the shrub layer than the herb layer. The soil bulk density and the contents of soil organic matter, total potassium and nitrogen increased with increasing thinning intensities. The Shannon and Chao indices of soil bacteria and fungi were significantly lower in the LIT, MIT and HIT treatments than in the control. Thinning can significantly increase the abundance of Proteobacteria and Actinobacteria, and higher thinning intensities led to a higher relative abundance of Ascomycota and a lower relative abundance of Basidiomycota, Rozellomycota, and Mortierellomycota. Redundancy analysis indicated that soil physicochemical properties rather than understory vegetation diversity were the main drivers of microbial communities, and fungi were more sensitive to soil properties than bacteria. Functional prediction showed that thinning significantly reduced the potential risk of human diseases and plant pathogens, and the nitrogen fixation capacity of bacteria was the highest in the HIT treatment. Thinning significantly increased the relative abundance of cellulolysis and soil saprotrophs in bacteria and fungi. Conclusion The findings provide important insights into the effects of thinning on C. japonica var. sinensis plantation ecosystems, which is essential for developing thinning strategies to promote their ecological and economic benefits.
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Affiliation(s)
- Kai-Li Liu
- College of Forestry, Central South University of Forestry & Technology, Changsha, China.,Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China.,National Long-term Scientific Research Base of Central and Subtropical Forestry, Changsha, China
| | - Bo-Yao Chen
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Bin Zhang
- College of Forestry, Central South University of Forestry & Technology, Changsha, China.,National Long-term Scientific Research Base of Central and Subtropical Forestry, Changsha, China
| | - Rui-Hui Wang
- College of Forestry, Central South University of Forestry & Technology, Changsha, China.,National Long-term Scientific Research Base of Central and Subtropical Forestry, Changsha, China
| | - Chun-Sheng Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
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Robert C, Cascella F, Mellai M, Barizzone N, Mignone F, Massa N, Nobile V, Bona E. Influence of Sex on the Microbiota of the Human Face. Microorganisms 2022; 10:microorganisms10122470. [PMID: 36557723 PMCID: PMC9786802 DOI: 10.3390/microorganisms10122470] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/24/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
The role of the microbiota in health and disease has long been recognized and, so far, the cutaneous microbiota in humans has been widely investigated. The research regarded mainly the microbiota variations between body districts and disease skin states (i.e., atopic dermatitis, psoriasis, acne). In fact, relatively little information is available about the composition of the healthy skin microbiota. The cosmetic industry is especially interested in developing products that maintain and/or improve a healthy skin microbiota. Therefore, in the present work, the authors chose to investigate in detail the structure and composition of the basal bacterial community of the face. Ninety-six cheek samples (48 women and 48 men) were collected in the same season and the same location in central northern Italy. Bacterial DNA was extracted, the 16S rDNA gene was amplified by PCR, the obtained amplicons were subjected to next generation sequencing. The principal members of the community were identified at the genus level, and statistical analyses showed significant variations between the two sexes. This study identified abundant members of the facial skin microbiota that were rarely reported before in the literature and demonstrated the differences between male and female microbiota in terms of both community structure and composition.
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Affiliation(s)
- Clémence Robert
- R&D Department, Complife Italia c/a Centre for Autoimmune and Allergic Diseases (CAAD), 22100 Novara, Italy
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
- Correspondence: (C.R.); (E.B.)
| | - Federica Cascella
- R&D Department, Complife Italia c/a Centre for Autoimmune and Allergic Diseases (CAAD), 22100 Novara, Italy
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
| | - Marta Mellai
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy
| | - Nadia Barizzone
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy
| | - Flavio Mignone
- Department of Science and Technologic Innovation, University of Eastern Piedmont, 15121 Alessandria, Italy
- SmartSeq s.r.l., 28100 Novara, Italy
| | - Nadia Massa
- Department of Science and Technologic Innovation, University of Eastern Piedmont, 15121 Alessandria, Italy
| | - Vincenzo Nobile
- R&D Department, Complife Italia c/a Centre for Autoimmune and Allergic Diseases (CAAD), 22100 Novara, Italy
| | - Elisa Bona
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
- Department for Sustainable Development and Ecological Transition, University of Eastern Piedmont, 13100 Vercelli, Italy
- Correspondence: (C.R.); (E.B.)
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Study of Wetland Soils of the Salar de Atacama with Different Azonal Vegetative Formations Reveals Changes in the Microbiota Associated with Hygrophile Plant Type on the Soil Surface. Microbiol Spectr 2022; 10:e0053322. [PMID: 36121227 DOI: 10.1128/spectrum.00533-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salar de Atacama is located approximately 55 km south of San Pedro de Atacama in the Antofagasta region, Chile. The high UV irradiation and salt concentration and extreme drought make Salar de Atacama an ideal site to search for novel soil microorganisms with unique properties. Here, we used a metataxonomic approach (16S rRNA V3-V4) to identify and characterize the soil microbiota associated with different surface azonal vegetation formations, including strict hygrophiles (Baccharis juncea, Juncus balticus, and Schoenoplectus americanus), transitional hygrophiles (Distichlis spicata, Lycium humile, and Tessaria absinthioides), and their various combinations. We detected compositional differences among the soil surface microbiota associated with each plant formation in the sampling area. There were changes in soil microbial phylogenetic diversity from the strict to the transitional hygrophiles. Moreover, we found alterations in the abundance of bacterial phyla and genera. Halobacteriota and Actinobacteriota might have facilitated water uptake by the transitional hygrophiles. Our findings helped to elucidate the microbiota of Salar de Atacama and associate them with the strict and transitional hygrophiles indigenous to the region. These findings could be highly relevant to future research on the symbiotic relationships between microbiota and salt-tolerant plants in the face of climate change-induced desertification. IMPORTANCE The study of the composition and diversity of the wetland soil microbiota associated with hygrophilous plants in a desert ecosystem of the high Puna in northern Chile makes it an ideal approach to search for novel extremophilic microorganisms with unique properties. These microorganisms are adapted to survive in ecological niches, such as those with high UV irradiation, extreme drought, and high salt concentration; they can be applied in various fields, such as biotechnology and astrobiology, and industries, including the pharmaceutical, food, agricultural, biofuel, cosmetic, and textile industries. These microorganisms can also be used for ecological conservation and restoration. Extreme ecosystems are a unique biological resource and biodiversity hot spots that play a crucial role in maintaining environmental sustainability. The findings could be highly relevant to future research on the symbiotic relationships between microbiota and extreme-environment-tolerant plants in the face of climate change-induced desertification.
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Cabral-Miramontes JP, Olmedo-Monfil V, Lara-Banda M, Zúñiga-Romo ER, Aréchiga-Carvajal ET. Promotion of Plant Growth in Arid Zones by Selected Trichoderma spp. Strains with Adaptation Plasticity to Alkaline pH. BIOLOGY 2022; 11:biology11081206. [PMID: 36009833 PMCID: PMC9405189 DOI: 10.3390/biology11081206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022]
Abstract
Trichoderma species are filamentous fungi that support plant health and confer improved growth, disease resistance, and abiotic stress tolerance. The objective of this study is to describe the physiological characteristics of the abundance and structure of Trichoderma model strains from arid zones and evaluate and describe their possible adaptation and modulation in alkaline pH. The presence of biotic factors such as phytopathogens forces farmers to take more actions such as using pesticides. In addition, factors such as the lack of water worldwide lead to losses in agricultural production. Therefore, the search for biocontrol microorganisms that support drought opens the door to the search for variations in the molecular mechanisms involved in these phenomena. In our case, we isolated 11 tested Trichoderma fungal strains from samples collected both from the rhizosphere and roots from two endemic plants. We probed their molecular markers to obtain their identity and assessed their resistance to alkaline conditions, as well as their response to mycoparasitism, plant growth promotion, and drought stress. The findings were worthy of being analyzed in depth. Three fungal taxa/species were grouped by phylogenetic/phenotypic characteristics; three T. harzianum strains showed outstanding capabilities to adapt to alkalinity stress. They also showed antagonistic activity against three phytopathogenic fungi. Additionally, we provided evidence of significant growth promotion in Sorghum bicolor seedlings under endemic agriculture conditions and a reduction in drought damage with Trichoderma infection. Finally, beneficial fungi adapted to specific ambient niches use various molecular mechanisms to survive and modulate their metabolism.
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Affiliation(s)
- Juan Pablo Cabral-Miramontes
- Unidad de Manipulación Genética, Laboratorio de Micología y Fitopatología, Facultad de Ciencias Biologicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66451, Nuevo León, Mexico
- Correspondence: (J.P.C.-M.); (E.T.A.-C.)
| | - Vianey Olmedo-Monfil
- Departamento de Biología, Division de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 38116, Gto., Mexico
| | - María Lara-Banda
- FIME-Centro de Investigación e Innovación en Ingeniería Aeronáutica (CIIIA), Universidad Autónoma de Nuevo Leon, Av. Universidad s/n, Ciudad Universitaria, San Nicolás de los Garza 66455, Mexico
| | - Efrén Ricardo Zúñiga-Romo
- Departamento de Biología, Division de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 38116, Gto., Mexico
| | - Elva Teresa Aréchiga-Carvajal
- Unidad de Manipulación Genética, Laboratorio de Micología y Fitopatología, Facultad de Ciencias Biologicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66451, Nuevo León, Mexico
- Correspondence: (J.P.C.-M.); (E.T.A.-C.)
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Current Techniques to Study Beneficial Plant-Microbe Interactions. Microorganisms 2022; 10:microorganisms10071380. [PMID: 35889099 PMCID: PMC9317800 DOI: 10.3390/microorganisms10071380] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria and plants. Some of these methods focus on changes to the plant and others are directed towards assessing the physiology and biochemistry of the beneficial plant growth-promoting bacteria (PGPB). Here, we provide an overview of some of the current techniques that have been employed to study the interaction of plants with PGPB. These techniques include the study of plant microbiomes; the use of DNA genome sequencing to understand the genes encoded by PGPB; the use of transcriptomics, proteomics, and metabolomics to study PGPB and plant gene expression; genome editing of PGPB; encapsulation of PGPB inoculants prior to their use to treat plants; imaging of plants and PGPB; PGPB nitrogenase assays; and the use of specialized growth chambers for growing and monitoring bacterially treated plants.
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Plant Diversity and Fungal Richness Regulate the Changes in Soil Multifunctionality in a Semi-Arid Grassland. BIOLOGY 2022; 11:biology11060870. [PMID: 35741391 PMCID: PMC9220314 DOI: 10.3390/biology11060870] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/18/2022]
Abstract
Simple Summary Understanding relationships between biodiversity and ecosystem functions is important in the context of global plant diversity loss. We evaluated the relationships between soil bacterial and fungal diversity, rare microbial taxa, and soil multifunctionality in a semi-arid grassland with varied plant diversity levels. The fungal richness rather than bacterial richness was positively related to soil multifunctionality. The relative abundance of saprotrophs was positively correlated with soil multifunctionality, and the relative abundance of pathogens was negatively correlated with soil multifunctionality. Furthermore, the rare fungal taxa played a disproportionate role in regulating soil multifunctionality. The shift of plant biomass allocation patterns increased plant below-ground biomass in the high diversity plant assemblages, which can alleviate soil microbial carbon limitations and enhance the fungal richness, thus promoting soil multifunctionality. This study provides a new perspective for evaluating the relative roles of fungal and bacterial diversity in maintaining multiple soil functions under global plant diversity loss scenarios. Abstract Loss in plant diversity is expected to impact biodiversity and ecosystem functioning (BEF) in terrestrial ecosystems. Soil microbes play essential roles in regulating ecosystem functions. However, the important roles and differences in bacterial and fungal diversity and rare microbial taxa in driving soil multifunctionality based on plant diversity remain poorly understood in grassland ecosystems. Here, we carried out an experiment in six study sites with varied plant diversity levels to evaluate the relationships between soil bacterial and fungal diversity, rare taxa, and soil multifunctionality in a semi-arid grassland. We used Illumina HiSeq sequencing to determine soil bacterial and fungal diversity and evaluated soil functions associated with the nutrient cycle. We found that high diversity plant assemblages had a higher ratio of below-ground biomass to above-ground biomass, soil multifunctionality, and lower microbial carbon limitation than those with low diversity. Moreover, the fungal richness was negatively and significantly associated with microbial carbon limitations. The fungal richness was positively related to soil multifunctionality, but the bacterial richness was not. We also found that the relative abundance of saprotrophs was positively correlated with soil multifunctionality, and the relative abundance of pathogens was negatively correlated with soil multifunctionality. In addition, the rare fungal taxa played a disproportionate role in regulating soil multifunctionality. Structural equation modeling showed that the shift of plant biomass allocation patterns increased plant below-ground biomass in the highly diverse plant plots, which can alleviate soil microbial carbon limitations and enhance the fungal richness, thus promoting soil multifunctionality. Overall, these findings expand our comprehensive understanding of the critical role of soil fungal diversity and rare taxa in regulating soil multifunctionality under global plant diversity loss scenarios.
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Dong C, Shao Q, Ren Y, Ge W, Yao T, Hu H, Huang J, Liang Z, Han Y. Assembly, Core Microbiota, and Function of the Rhizosphere Soil and Bark Microbiota in Eucommia ulmoides. Front Microbiol 2022; 13:855317. [PMID: 35591983 PMCID: PMC9110929 DOI: 10.3389/fmicb.2022.855317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022] Open
Abstract
Medicinal plants are inhabited by diverse microbes in every compartment, and which play an essential role in host growth and development, nutrient absorption, synthesis of secondary metabolites, and resistance to biological and abiotic stress. However, the ecological processes that manage microbiota assembly and the phenotypic and metabolic characteristics of the core microbiota of Eucommia ulmoides remain poorly explored. Here, we systematically evaluated the effects of genotypes, compartment niches, and environmental conditions (climate, soil nutrition, and secondary metabolites) on the assembly of rhizosphere soil and bark associated bacterial communities. In addition, phenotypic and metabolic characteristics of E. ulmoides core microbiota, and their relationship with dominant taxa, rare taxa, and pharmacologically active compounds were deciphered. Results suggested that microbiota assembly along the two compartments were predominantly shaped by the environment (especially pH, relative humidity, and geniposide acid) and not by host genotype or compartment niche. There were 690 shared genera in the rhizosphere soil and bark, and the bark microbiota was mainly derived from rhizosphere soil. Core microbiota of E. ulmoides was a highly interactive “hub” microbes connecting dominant and rare taxa, and its phenotypic characteristics had a selective effect on compartment niches. Metabolic functions of the core microbiota included ammonia oxidation, nitrogen fixation, and polyhydroxybutyrate storage, which are closely related to plant growth or metabolism. Moreover, some core taxa were also significantly correlated with three active compounds. These findings provide an important scientific basis for sustainable agricultural management based on the precise regulation of the rhizosphere soil and bark microbiota of E. ulmoides.
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Affiliation(s)
- Chunbo Dong
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Yulian Ren
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Wei Ge
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Ting Yao
- Analysis and Test Center, Huangshan University, Huangshan, China
| | - Haiyan Hu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
| | - Jianzhong Huang
- Engineering Research Centre of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Zongqi Liang
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China.,Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, China
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Glick BR, Gamalero E. Recent Developments in the Study of Plant Microbiomes. Microorganisms 2021; 9:microorganisms9071533. [PMID: 34361969 PMCID: PMC8306116 DOI: 10.3390/microorganisms9071533] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/11/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
To date, an understanding of how plant growth-promoting bacteria facilitate plant growth has been primarily based on studies of individual bacteria interacting with plants under different conditions. More recently, it has become clear that specific soil microorganisms interact with one another in consortia with the collective being responsible for the positive effects on plant growth. Different plants attract different cross-sections of the bacteria and fungi in the soil, initially based on the composition of the unique root exudates from each plant. Thus, plants mostly attract those microorganisms that are beneficial to plants and exclude those that are potentially pathogenic. Beneficial bacterial consortia not only help to promote plant growth, these consortia also protect plants from a wide range of direct and indirect environmental stresses. Moreover, it is currently possible to engineer plant seeds to contain desired bacterial strains and thereby benefit the next generation of plants. In this way, it may no longer be necessary to deliver beneficial microbiota to each individual growing plant. As we develop a better understanding of beneficial bacterial microbiomes, it may become possible to develop synthetic microbiomes where compatible bacteria work together to facilitate plant growth under a wide range of natural conditions.
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Affiliation(s)
- Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel, 11, 15121 Alessandria, Italy
- Correspondence:
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