1
|
Perazzolli M, Vicelli B, Antonielli L, Longa CMO, Bozza E, Bertini L, Caruso C, Pertot I. Simulated global warming affects endophytic bacterial and fungal communities of Antarctic pearlwort leaves and some bacterial isolates support plant growth at low temperatures. Sci Rep 2022; 12:18839. [PMID: 36336707 PMCID: PMC9637742 DOI: 10.1038/s41598-022-23582-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/02/2022] [Indexed: 11/07/2022] Open
Abstract
Antarctica is one of the most stressful environments for plant life and the Antarctic pearlwort (Colobanthus quitensis) is adapted to the hostile conditions. Plant-associated microorganisms can contribute to plant survival in cold environments, but scarce information is available on the taxonomic structure and functional roles of C. quitensis-associated microbial communities. This study aimed at evaluating the possible impacts of climate warming on the taxonomic structure of C. quitensis endophytes and at investigating the contribution of culturable bacterial endophytes to plant growth at low temperatures. The culture-independent analysis revealed changes in the taxonomic structure of bacterial and fungal communities according to plant growth conditions, such as the collection site and the presence of open-top chambers (OTCs), which can simulate global warming. Plants grown inside OTCs showed lower microbial richness and higher relative abundances of biomarker bacterial genera (Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Aeromicrobium, Aureimonas, Hymenobacter, Novosphingobium, Pedobacter, Pseudomonas and Sphingomonas) and fungal genera (Alternaria, Cistella, and Vishniacozyma) compared to plants collected from open areas (OA), as a possible response to global warming simulated by OTCs. Culturable psychrotolerant bacteria of C. quitensis were able to endophytically colonize tomato seedlings and promote shoot growth at low temperatures, suggesting their potential contribution to plant tolerance to cold conditions.
Collapse
Affiliation(s)
- Michele Perazzolli
- grid.11696.390000 0004 1937 0351Centre Agriculture, Food and the Environment (C3A), University of Trento, Via E. Mach 1, 38098 San Michele all’Adige, Italy ,grid.424414.30000 0004 1755 6224Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Bianca Vicelli
- grid.11696.390000 0004 1937 0351Centre Agriculture, Food and the Environment (C3A), University of Trento, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Livio Antonielli
- grid.4332.60000 0000 9799 7097Center for Health and Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430 Tulln an der Donau, Austria
| | - Claudia M. O. Longa
- grid.424414.30000 0004 1755 6224Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Elisa Bozza
- grid.424414.30000 0004 1755 6224Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Laura Bertini
- grid.12597.380000 0001 2298 9743Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università s.n.c., 01100 Viterbo, Italy
| | - Carla Caruso
- grid.12597.380000 0001 2298 9743Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università s.n.c., 01100 Viterbo, Italy
| | - Ilaria Pertot
- grid.11696.390000 0004 1937 0351Centre Agriculture, Food and the Environment (C3A), University of Trento, Via E. Mach 1, 38098 San Michele all’Adige, Italy ,grid.424414.30000 0004 1755 6224Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| |
Collapse
|
2
|
Chahed A, Nesler A, Esmaeel Q, Barka EA, Perazzolli M. The Amount of the Rare Sugar Tagatose on Tomato Leaves Decreases after Spray Application under Greenhouse Conditions. PLANTS (BASEL, SWITZERLAND) 2022; 11:2781. [PMID: 36297805 PMCID: PMC9607558 DOI: 10.3390/plants11202781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Tagatose is a rare sugar that suppresses plant diseases, such as late blight of tomato, caused by Phytophthora infestans. Tagatose can be metabolized by some microorganisms and no information is available on its persistence on tomato leaves. The aim of this study was to assess the persistence of tagatose on tomato leaves under commercial greenhouse conditions. The amount of tagatose on tomato leaves and the inhibitory activity against P. infestans decreased seven days after spray application in the absence of rain wash-off. Potential tagatose-degrading bacteria were isolated from tomato leaves, and they belonged to Acinetobacter sp., Bacillus sp., Comamonas sp., Enterobacter sp., Methylobacterium sp., Microbacterium sp., Pantoea sp., Plantibacter sp., Pseudomonas sp., Ralstonia sp., Rhodococcus sp., Sphingobium sp., and Sphingomonas sp. Thus, indigenous phyllosphere microorganisms could partially metabolize tagatose laid on plant leaves after spray application, reducing the persistence of this fungal inhibitor on tomato leaves.
Collapse
Affiliation(s)
- Abdessalem Chahed
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
- Bi-PA nv, Technologielaan 7, 1840 Londerzeel, Belgium
- Induced Resistance and Plant Bioprotection, USC INRAE 1488, University of Reims, UFR Sciences, CEDEX 02, 51687 Reims, France
| | - Andrea Nesler
- Bi-PA nv, Technologielaan 7, 1840 Londerzeel, Belgium
| | - Qassim Esmaeel
- Induced Resistance and Plant Bioprotection, USC INRAE 1488, University of Reims, UFR Sciences, CEDEX 02, 51687 Reims, France
| | - Essaid Ait Barka
- Induced Resistance and Plant Bioprotection, USC INRAE 1488, University of Reims, UFR Sciences, CEDEX 02, 51687 Reims, France
| | - Michele Perazzolli
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
- Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| |
Collapse
|
3
|
Clark CM, Hernandez A, Mullowney MW, Fitz-Henley J, Li E, Romanowski SB, Pronzato R, Manconi R, Sanchez LM, Murphy BT. Relationship between bacterial phylotype and specialized metabolite production in the culturable microbiome of two freshwater sponges. ISME COMMUNICATIONS 2022; 2:22. [PMID: 37938725 PMCID: PMC9723699 DOI: 10.1038/s43705-022-00105-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/09/2023]
Abstract
Microbial drug discovery programs rely heavily on accessing bacterial diversity from the environment to acquire new specialized metabolite (SM) lead compounds for the therapeutic pipeline. Therefore, knowledge of how commonly culturable bacterial taxa are distributed in nature, in addition to the degree of variation of SM production within those taxa, is critical to informing these front-end discovery efforts and making the overall sample collection and bacterial library creation process more efficient. In the current study, we employed MALDI-TOF mass spectrometry and the bioinformatics pipeline IDBac to analyze diversity within phylotype groupings and SM profiles of hundreds of bacterial isolates from two Eunapius fragilis freshwater sponges, collected 1.5 km apart. We demonstrated that within two sponge samples of the same species, the culturable bacterial populations contained significant overlap in approximate genus-level phylotypes but mostly nonoverlapping populations of isolates when grouped lower than the level of genus. Further, correlations between bacterial phylotype and SM production varied at the species level and below, suggesting SM distribution within bacterial taxa must be analyzed on a case-by-case basis. Our results suggest that two E. fragilis freshwater sponges collected in similar environments can exhibit large culturable diversity on a species-level scale, thus researchers should scrutinize the isolates with analyses that take both phylogeny and SM production into account to optimize the chemical space entering into a downstream bacterial library.
Collapse
Affiliation(s)
- Chase M Clark
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Antonio Hernandez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Michael W Mullowney
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Jhewelle Fitz-Henley
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Emma Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Sean B Romanowski
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Roberto Pronzato
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università di Genova, Genova, Italy
| | - Renata Manconi
- Dipartimento Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Brian T Murphy
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA.
| |
Collapse
|
4
|
Oceanographic setting influences the prokaryotic community and metabolome in deep-sea sponges. Sci Rep 2022; 12:3356. [PMID: 35233042 PMCID: PMC8888554 DOI: 10.1038/s41598-022-07292-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/16/2022] [Indexed: 11/09/2022] Open
Abstract
Marine sponges (phylum Porifera) are leading organisms for the discovery of bioactive compounds from nature. Their often rich and species-specific microbiota is hypothesised to be producing many of these compounds. Yet, environmental influences on the sponge-associated microbiota and bioactive compound production remain elusive. Here, we investigated the changes of microbiota and metabolomes in sponges along a depth range of 1232 m. Using 16S rRNA gene amplicon sequencing and untargeted metabolomics, we assessed prokaryotic and chemical diversities in three deep-sea sponge species: Geodia barretti, Stryphnus fortis, and Weberella bursa. Both prokaryotic communities and metabolome varied significantly with depth, which we hypothesized to be the effect of different water masses. Up to 35.5% of microbial ASVs (amplicon sequence variants) showed significant changes with depth while phylum-level composition of host microbiome remained unchanged. The metabolome varied with depth, with relative quantities of known bioactive compounds increasing or decreasing strongly. Other metabolites varying with depth were compatible solutes regulating osmolarity of the cells. Correlations between prokaryotic community and the bioactive compounds in G. barretti suggested members of Acidobacteria, Proteobacteria, Chloroflexi, or an unclassified prokaryote as potential producers.
Collapse
|
5
|
Dat TTH, Steinert G, Cuc NTK, Smidt H, Sipkema D. Bacteria Cultivated From Sponges and Bacteria Not Yet Cultivated From Sponges-A Review. Front Microbiol 2021; 12:737925. [PMID: 34867854 PMCID: PMC8634882 DOI: 10.3389/fmicb.2021.737925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022] Open
Abstract
The application of high-throughput microbial community profiling as well as "omics" approaches unveiled high diversity and host-specificity of bacteria associated with marine sponges, which are renowned for their wide range of bioactive natural products. However, exploration and exploitation of bioactive compounds from sponge-associated bacteria have been limited because the majority of the bacteria remains recalcitrant to cultivation. In this review, we (i) discuss recent/novel cultivation techniques that have been used to isolate sponge-associated bacteria, (ii) provide an overview of bacteria isolated from sponges until 2017 and the associated culture conditions and identify the bacteria not yet cultured from sponges, and (iii) outline promising cultivation strategies for cultivating the uncultivated majority of bacteria from sponges in the future. Despite intensive cultivation attempts, the diversity of bacteria obtained through cultivation remains much lower than that seen through cultivation-independent methods, which is particularly noticeable for those taxa that were previously marked as "sponge-specific" and "sponge-enriched." This poses an urgent need for more efficient cultivation methods. Refining cultivation media and conditions based on information obtained from metagenomic datasets and cultivation under simulated natural conditions are the most promising strategies to isolate the most wanted sponge-associated bacteria.
Collapse
Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Nguyen Thi Kim Cuc
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| |
Collapse
|