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- ItemImpact of Cultivation and Origin on the Fruit Microbiome of Apples and Blueberries and Implications for the Exposome(Berlin : Springer, 2022) Wicaksono, Wisnu Adi; Buko, Aisa; Kusstatscher, Peter; Cernava, Tomislav; Sinkkonen, Aki; Laitinen, Olli H.; Virtanen, Suvi M.; Hyöty, Heikki; Berg, GabrieleVegetables and fruits are a crucial part of the planetary health diet, directly affecting human health and the gut microbiome. The objective of our study was to understand the variability of the fruit (apple and blueberry) microbiome in the frame of the exposome concept. The study covered two fruit-bearing woody species, apple and blueberry, two countries of origin (Austria and Finland), and two fruit production methods (naturally grown and horticultural). Microbial abundance, diversity, and community structures were significantly different for apples and blueberries and strongly influenced by the growing system (naturally grown or horticultural) and country of origin (Austria or Finland). Our results indicated that bacterial communities are more responsive towards these factors than fungal communities. We found that fruits grown in the wild and within home gardens generally carry a higher microbial diversity, while commercial horticulture homogenized the microbiome independent of the country of origin. This can be explained by horticultural management, including pesticide use and post-harvest treatments. Specific taxonomic indicators were identified for each group, i.e., for horticultural apples: Pseudomonas, Ralstonia, and Stenotrophomonas. Interestingly, Ralstonia was also found to be enriched in horticultural blueberries in comparison to such that were home and wildly grown. Our study showed that the origin of fruits can strongly influence the diversity and composition of their microbiome, which means that we are exposed to different microorganisms by eating fruits from different origins. Thus, the fruit microbiome needs to be considered an important but relatively unexplored external exposomic factor.
- ItemFunction-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea(Washington, DC : American Society for Microbiology, 2022) Wicaksono, Wisnu Adi; Egamberdieva, Dilfuza; Berg, Christian; Mora, Maximilian; Kusstatscher, Peter; Cernava, Tomislav; Berg, GabrieleThe desiccation of the Aral Sea represents one of the largest human-made environmental regional disasters. The salt- and toxin-enriched dried-out basin provides a natural laboratory for studying ecosystem functioning and rhizosphere assembly under extreme anthropogenic conditions. Here, we investigated the prokaryotic rhizosphere communities of the native pioneer plant Suaeda acuminata (C.A.Mey.) Moq. in comparison to bulk soil across a gradient of desiccation (5, 10, and 40 years) by metagenome and amplicon sequencing combined with quantitative PCR (qPCR) analyses. The rhizosphere effect was evident due to significantly higher bacterial abundances but less diversity in the rhizosphere compared to bulk soil. Interestingly, in the highest salinity (5 years of desiccation), rhizosphere functions were mainly provided by archaeal communities. Along the desiccation gradient, we observed a significant change in the rhizosphere microbiota, which was reflected by (i) a decreasing archaeon-bacterium ratio, (ii) replacement of halophilic archaea by specific plant-associated bacteria, i.e., Alphaproteobacteria and Actinobacteria, and (iii) an adaptation of specific, potentially plant-beneficial biosynthetic pathways. In general, both bacteria and archaea were found to be involved in carbon cycling and fixation, as well as methane and nitrogen metabolism. Analysis of metagenome-assembled genomes (MAGs) showed specific signatures for production of osmoprotectants, assimilatory nitrate reduction, and transport system induction. Our results provide evidence that rhizosphere assembly by cofiltering specific taxa with distinct traits is a mechanism which allows plants to thrive under extreme conditions. Overall, our findings highlight a function-based rhizosphere assembly, the importance of plant-microbe interactions in salinated soils, and their exploitation potential for ecosystem restoration approaches.
- ItemBog ecosystems as a playground for plant-microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria(London : Biomed Central, 2021) Wicaksono, Wisnu Adi; Cernava, Tomislav; Berg, Christian; Berg, GabrieleBackground: Bogs are unique ecosystems inhabited by distinctive, coevolved assemblages of organisms, which play a global role for carbon storage, climate stability, water quality and biodiversity. To understand ecology and plant–microbe co-occurrence in bogs, we selected 12 representative species of bryophytes and vascular plants and subjected them to a shotgun metagenomic sequencing approach. We explored specific plant–microbe associations as well as functional implications of the respective communities on their host plants and the bog ecosystem. Results: Microbial communities were shown to be functionally adapted to their plant hosts; a higher colonization specificity was found for vascular plants. Bryophytes that commonly constitute the predominant Sphagnum layer in bogs were characterized by a higher bacterial richness and diversity. Each plant group showed an enrichment of distinct phylogenetic and functional bacterial lineages. Detailed analyses of the metabolic potential of 28 metagenome-assembled genomes (MAGs) supported the observed functional specification of prevalent bacteria. We found that novel lineages of Betaproteobacteria and Actinobacteria in the bog environment harboured genes required for carbon fixation via RuBisCo. Interestingly, several of the highly abundant bacteria in both plant types harboured pathogenicity potential and carried similar virulence factors as found with corresponding human pathogens. Conclusions: The unexpectedly high specificity of the plant microbiota reflects intimate plant–microbe interactions and coevolution in bog environments. We assume that the detected pathogenicity factors might be involved in coevolution processes, but the finding also reinforces the role of the natural plant microbiota as a potential reservoir for human pathogens. Overall, the study demonstrates how plant–microbe assemblages can ensure stability, functioning and ecosystem health in bogs. It also highlights the role of bog ecosystems as a playground for plant–microbe coevolution. [MediaObject not available: see fulltext.] © 2021, The Author(s).