Bacterial community structures and ice recrystallization inhibition activity of bacteria isolated from the phyllosphere of the Antarctic vascular plant Deschampsia antarctica

Cid, Fernanda P.; Inostroza, Nitza G.; Graether, Steffen P.; Bravo, León A.; Jorquera, Milko A.

doi:10.1007/s00300-016-2036-5

Cited by 26 publications

(31 citation statements)

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“…Portions of tissues (1-2 g) were aseptically cut, frozen in liquid nitrogen, macerated and homogenized with a mortar and pestle, and stored at −80 • C until DNA extraction. In parallel, quadruplicate phyllosphere leaf samples were processed as described by Cid et al (2017). Briefly, 1 g portions of leaves were cut (aerial parts), gently washed, and vortexed for 10 min in 10 ml sterile saline solution (0.85% NaCl).…”

Section: Samplingmentioning

confidence: 99%

“…Similarly, the salt tolerance and ecophysiological performance of D. antarctica and C. quitensis was improved when plants were inoculated with Antarctic bacteria isolated from their rhizosphere (Gallardo-Cerda et al, 2018). Despite these advances, the contribution of microbiota from the endosphere (inner tissues of plants) and phyllosphere (the aerial part of plant leaves) to plant fitness have scarcely been considered, especially since these compartments are thought to be essential for plant success (Cid et al, 2017). In addition, new studies have revealed that the plant microbiome is structured and complex and interconnected by microbial networks (Turner et al, 2013;Vandenkoornhuyse et al, 2015;Banerjee et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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Niche Differentiation in the Composition, Predicted Function, and Co-occurrence Networks in Bacterial Communities Associated With Antarctic Vascular Plants

et al. 2020

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Climate change directly affecting the Antarctic Peninsula has been reported to induce the successful colonization of ice-free lands by two Antarctic vascular plants (Deschampsia antarctica and Colobanthus quitensis). While studies have revealed the importance of microbiota for plant growth and stress tolerance in temperate climates, the role that plant-associated microbes play in the colonization of ice-free lands remains unknown. Consequently, we used high-throughput DNA sequence analyses to explore the composition, predicted functions, and interactive networks of plant-associated microbial communities among the rhizosphere, endosphere, and phyllosphere niches of D. antarctica and C. quitensis. Here we report a greater number of operational taxonomic units (OTUs), diversity, and richness in the microbial communities from the rhizosphere, relative to endosphere and phyllosphere. While taxonomic assignments showed greater relative abundances of Proteobacteria, Bacteroidetes, and Actinobacteria in plant niches, principal coordinate analysis revealed differences among the bacterial communities from the other compartments examined. More importantly, however, our results showed that most of OTUs were exclusively found in each plant niche. Major predicted functional groups of these microbiota were attributed to heterotrophy, aerobic heterotrophy, fermentation, and nitrate reduction, independent of plant niches or plant species. Co-occurrences network analyses identified 5 (e.g., Microbacteriaceae, Pseudomonaceae, Lactobacillaceae, and Corynebacteriaceae), 23 (e.g., Chitinophagaceae and Sphingomonadaceae) and 7 (e.g., Rhodospirillaceae) putative keystone taxa present in endosphere, phyllosphere, and rhizosphere, respectively. Our results revealed niche differentiation in Antarctic vascular plants, highlighting some putative microbial indicators and keystone taxa in each niche. However, more studies are required to determine the pivotal role that these microbes play in the successful colonization of ice-free lands by Antarctic plants.

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Section: Samplingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Niche Differentiation in the Composition, Predicted Function, and Co-occurrence Networks in Bacterial Communities Associated With Antarctic Vascular Plants

et al. 2020

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“…In the rice phylloplane, the microbiome presented greater diversity in cultivated and controlled plants in pots than those cultivated in the open field [ 82 ]. Bacterial community composition in phylloplane of Deschampsia antarctica at different locations in open fields, revealed significant differences [ 83 ]. The phylloplane and its microbial communities are interrelated [ 84 ] and can provide a structural and functional model microenvironment [ 3 , 85 ] to understand plant-pathogen interactions and thus to select more resistant plants, which will contribute to the continuity of food production.…”

Section: Discussionmentioning

confidence: 99%

Witches’ broom resistant genotype CCN51 shows greater diversity of symbiont bacteria in its phylloplane than susceptible genotype catongo

et al. 2018

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BackgroundTheobroma cacao L. (cacao) is a perennial tropical tree, endemic to rainforests of the Amazon Basin. Large populations of bacteria live on leaf surfaces and these phylloplane microorganisms can have important effects on plant health. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated studies of the phylloplane microbiome. In this study, we characterized the bacterial microbiome of the phylloplane of the catongo genotype (susceptible to witch’s broom) and CCN51 (resistant). Bacterial microbiome was determined by sequencing the V3-V4 region of the bacterial 16S rRNA gene.ResultsAfter the pre-processing, a total of 1.7 million reads were considered. In total, 106 genera of bacteria were characterized. Proteobacteria was the predominant phylum in both genotypes. The exclusive genera of Catongo showed activity in the protection against UV radiation and in the transport of substrates. CCN51 presented genus that act in the biological control and inhibition in several taxonomic groups. Genotype CCN51 presented greater diversity of microorganisms in comparison to the Catongo genotype and the total community was different between both. Scanning electron microscopy analysis of leaves revealed that on the phylloplane, many bacterial occur in large aggregates in several regions of the surface and isolated nearby to the stomata.ConclusionsWe describe for the first time the phylloplane bacterial communities of T. cacao. The Genotype CCN51, resistant to the witch’s broom, has a greater diversity of bacterial microbioma in comparison to Catongo and a greater amount of exclusive microorganisms in the phylloplane with antagonistic action against phytopathogens.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1339-9) contains supplementary material, which is available to authorized users.

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“…In all eight sampled phyllospheres of the Antarctic grass Deschampsia antarctica E. Desv., DGGE revealed four common bands representing Agrobacterium , Aurantimonas , Pseudomonas , and Psychrobacter (Cid et al., ). For the Mediterranean seagrass Posidonia oceanica Delile sampled from 26 locations around the Balearic Islands, DGGE revealed patterns composed of 34 different bands that were differently distributed among tissues and sampling locations (Garcias‐Bonet et al., ).…”

Section: Comparing Dna‐based Methods For Studying Plant Microbiomes (mentioning

confidence: 99%

Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant‐associated communities of bacteria and fungi

Johnston‐Monje

Mejía

2020

Appl Plant Sci

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High‐throughput sequencing technologies have revolutionized the study of plant‐associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant‐associated microbiomes using molecular fingerprinting methodologies, including single‐strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), amplicon length heterogeneity PCR (LH‐PCR), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP). We also present data juxtaposing results from TRFLP methods with those generated using Illumina sequencing in the comparison of rhizobacterial populations of Brazilian maize and fungal surveys in Canadian tomato roots. In both cases, the TRFLP approach yielded the desired results at a level of resolution comparable to that of the MiSeq method, but at a fraction of the cost. Community fingerprinting methods (especially TRFLP) remain relevant for the identification of dominant microbes in a population, the observation of shifts in plant microbiome community diversity, and for screening samples before their use in more sensitive and expensive approaches.

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Bacterial community structures and ice recrystallization inhibition activity of bacteria isolated from the phyllosphere of the Antarctic vascular plant Deschampsia antarctica

Cited by 26 publications

References 54 publications

Niche Differentiation in the Composition, Predicted Function, and Co-occurrence Networks in Bacterial Communities Associated With Antarctic Vascular Plants

Niche Differentiation in the Composition, Predicted Function, and Co-occurrence Networks in Bacterial Communities Associated With Antarctic Vascular Plants

Witches’ broom resistant genotype CCN51 shows greater diversity of symbiont bacteria in its phylloplane than susceptible genotype catongo

Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant‐associated communities of bacteria and fungi

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