Domestication caused taxonomical and functional shifts in the wheat rhizosphere microbiota, and weakened the natural bacterial biocontrol against fungal pathogens.

Modern crops might have lost some of their functional traits, required for interacting with beneficial microbes, as a result of the genotypic/phenotypic modifications that occurred during domestication. Here, we studied the bacterial and fungal microbiota in the rhizosphere of two cultivated wheat species (Triticum aestivum and T. durum) and their respective ancestors (Aegilops tauschii and T. dicoccoides), in three experimental fields, by using metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. Moreover, the abundance of bacterial genes involved in N- and P-cycles was estimated by quantitative PCR, and urease, alkaline phosphatase and phosphomonoesterase activities were assessed by enzymatic tests. The relationships between microbiota and environmental metadata were tested by correlation analysis. The assemblage of core microbiota was affected by both site and plant species. No significant differences in the abundance of potential fungal pathogens between wild and cultivated wheat species were found; however, co-occurrence analysis showed more bacterial-fungal negative correlations in the wild species. Concerning functions, the nitrogen denitrification nirS gene was consistently more abundant in the rhizosphere of A. tauschii than T. aestivum. Urease activity was higher in the rhizosphere of each wild wheat species in at least two of the research locations. Several microbiota members, including potentially beneficial taxa such as Lysobacter and new taxa such as Blastocatellaceae, were found to be strongly correlated to rhizospheric soil metadata. Our results showed that a functional microbiome shift occurred as a result of wheat domestication. Notably, these changes also included the reduction of the natural biocontrol potential of rhizosphere-associated bacteria against pathogenic fungi, suggesting that domestication disrupted the equilibrium of plant-microbe relationships that had been established during million years of co-evolution.

Robbsia betulipollinis sp. nov., Isolated from Pollen of Birch (Betula pendula).

One gram-negative strain designated Bb-Pol-6 T was isolated from birch (Betula pendula) pollen at Giessen area, Germany. The analysis of 16S rRNA gene-based phylogenies indicated the next-relative genera were Robbsia, Chitinasiproducens, Pararobbsia and Paraburkholderia (96-95.6%). Further comparative genome analysis and phylogenetic tree-based methods revealed its phylogenetic position under the genus Robbsia. The genome of strain Bb-Pol-6 T was 5.04 Mbp with 4401 predicted coding sequences and a G + C content of 65.31 mol%. Average amino acid identity, average nucleotide identity, digital DNA-DNA hybridization and percentage of conserved proteins values to Robbsia andropogonis DSM 9511 T were 68.0, 72.5, 22.7 and 65.85%, respectively. Strain Bb-Pol-6 T was rod-shaped, non-motile, facultative anaerobic and grew optimally at 28 °C and pH 6-7. Ubiquinone 8 was the major respiratory quinone and the major cellular fatty acids were C16:0, C19:0 cyclo ω7c, C17:0 cyclo ω7c and C17:1 ω6c. The dominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. Based on the genomic physiological and phenotypic characteristics, strain Bb-Pol-6 T was considered a novel species under the genus Robbsia, for which the name Robbsia betulipollinis sp. nov. was proposed. The type strain is Bb-Pol-6 T (= LMG 32774 T = DSM 114812 T).

Bacterial Species Associated with Highly Allergenic Plant Pollen Yield a High Level of Endotoxins and Induce Chemokine and Cytokine Release from Human A549 Cells.

Sensitization to pollen allergens has been increasing in Europe every year. Most studies in this field are related to climate change, phenology, allergens associated with different pollens, and allergic disorders. As a plant microhabitat, pollen is colonized by diverse microorganisms, including endotoxin-producing bacteria which may contribute to pollen allergy (pollinosis). Therefore, bacteria isolated from high allergenic and low allergenic plant pollen, as well as the pollen itself with all microbial inhabitants, were used to assess the effect of the pollen by measuring the endotoxins lipopolysaccharides (LPS) and lipoteichoic acid (LTA) concentrations and their effect on chemokine and cytokine release from transwell cultured epithelial A549 cells as a model of epithelial lung barrier. High allergenic pollen showed a significantly higher level of bacterial endotoxins; interestingly, the endotoxin level found in the bacterial isolates from high allergenic pollen was significantly higher compared to that of bacteria from low allergenic pollen. Moreover, bacterial LPS concentrations across different pollen species positively correlated with the LPS concentration across their corresponding bacterial isolates. Selected bacterial isolates from hazel pollen (HA5, HA13, and HA7) co-cultured with A549 cells induced a potent concentration-dependent release of the chemokine interleukin-8 and monocyte chemotactic protein-1 as well as the cytokine TNF-alpha and interleukin-2 to both apical and basal compartments of the transwell model. This study clearly shows the role of bacteria and bacterial endotoxins in the pollen allergy as well as seasonal allergic rhinitis.

Domestication affects the composition, diversity, and co-occurrence of the cereal seed microbiota.

Introduction: The seed-associated microbiome has a strong influence on plant ecology, fitness, and productivity. Plant microbiota could be exploited for a more responsible crop management in sustainable agriculture. However, the relationships between seed microbiota and hosts related to the changes from ancestor species to breeded crops still remain poor understood. Objectives: Our aims were i) to understand the effect of cereal domestication on seed endophytes in terms of diversity, structure and co-occurrence, by comparing four cereal crops and the respective ancestor species; ii) to test the phylogenetic coherence between cereals and their seed microbiota (clue of co-evolution). Methods: We investigated the seed microbiota of four cereal crops (Triticum aestivum, Triticum monococcum, Triticum durum, and Hordeum vulgare), along with their respective ancestors (Aegilops tauschii, Triticum baeoticum, Triticum dicoccoides, and Hordeum spontaneum, respectively) using 16S rRNA gene metabarcoding, Randomly Amplified Polymorphic DNA (RAPD) profiling of host plants and co-evolution analysis. Results: The diversity of seed microbiota was generally higher in cultivated cereals than in wild ancestors, suggesting that domestication lead to a bacterial diversification. On the other hand, more microbe-microbe interactions were detected in wild species, indicating a better-structured, mature community. Typical human-associated taxa, such as Cutibacterium, dominated in cultivated cereals, suggesting an interkingdom transfers of microbes from human to plants during domestication. Co-evolution analysis revealed a significant phylogenetic congruence between seed endophytes and host plants, indicating clues of co-evolution between hosts and seed-associated microbes during domestication. Conclusion: This study demonstrates a diversification of the seed microbiome as a consequence of domestication, and provides clues of co-evolution between cereals and their seed microbiota. This knowledge is useful to develop effective strategies of microbiome exploitation for sustainable agriculture.

Domestication Impacts the Wheat-Associated Microbiota and the Rhizosphere Colonization by Seed- and Soil-Originated Microbiomes, Across Different Fields.

The seed-transmitted microorganisms and the microbiome of the soil in which the plant grows are major drivers of the rhizosphere microbiome, a crucial component of the plant holobiont. The seed-borne microbiome can be even coevolved with the host plant as a result of adaptation and vertical transmission over generations. The reduced genome diversity and crossing events during domestication might have influenced plant traits that are important for root colonization by seed-borne microbes and also rhizosphere recruitment of microbes from the bulk soil. However, the impact of the breeding on seed-transmitted microbiome composition and the plant ability of microbiome selection from the soil remain unknown. Here, we analyzed both endorhiza and rhizosphere microbiome of two couples of genetically related wild and cultivated wheat species (Aegilops tauschii/Triticum aestivum and T. dicoccoides/T. durum) grown in three locations, using 16S rRNA gene and ITS2 metabarcoding, to assess the relative contribution of seed-borne and soil-derived microbes to the assemblage of the rhizosphere microbiome. We found that more bacterial and fungal ASVs are transmitted from seed to the endosphere of all species compared with the rhizosphere, and these transmitted ASVs were species-specific regardless of location. Only in one location, more microbial seed transmission occurred also in the rhizosphere of A. tauschii compared with other species. Concerning soil-derived microbiome, the most distinct microbial genera occurred in the rhizosphere of A. tauschii compared with other species in all locations. The rhizosphere of genetically connected wheat species was enriched with similar taxa, differently between locations. Our results demonstrate that host plant criteria for soil bank's and seed-originated microbiome recruitment depend on both plants' genotype and availability of microorganisms in a particular environment. This study also provides indications of coevolution between the host plant and its associated microbiome resulting from the vertical transmission of seed-originated taxa.

Spirosoma endbachense sp. nov., isolated from a natural salt meadow.

A Gram-stain-negative bacterium, designated I-24T, was isolated from soil of a natural salt meadow. Strain I-24T was aerobic, non-motile, rod-shaped, catalase-positive, oxidase-positive and grew optimally at pH 7 and 25 °C. Comparative 16S rRNA gene analysis indicated that strain I-24T has closest similarities to Spirosoma agri KCTC 52727T (95.9 %) and Spirosoma terrae KCTC 52035T (95.5 %). Strain I-24T contained summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and C16 : 1 ω5c as the major fatty acids, the predominant respiratory quinone was menaquinone MK-7, and the major polar lipids were phosphatidylethanolamine as well as an unidentified phosphoaminolipid. The draft genome of strain I-24T consists of 10 326 072 base pairs with 9153 predicted coding sequences and a G+C content of 47.7 mol%. Clear distinctions between strain I-24T and S. agri KCTC 52727T or S. terrae KCTC 52035T were shown in the pairwise average nucleotide identity results with values of 76.71 and 74.01 %, respectively. Moreover, the digital DNA-DNA relatedness values to these strains were 20.8 and 19.0 %. Based on its phenotypic, genotypic and chemotaxonomic characteristics, strain I-24T represents a novel species of the genus Spirosoma, for which the name Spirosoma endbachense sp. nov. is proposed. The type strain is I-24T (DSM 111055T=KCTC 72613T).

Draft Genome Sequences of Spirosoma agri KCTC 52727 and Spirosoma terrae KCTC 52035.

Spirosoma agri S7-3-3 (KCTC 52727) and Spirosoma terrae 15J9-4 (KCTC 52035) are type strains isolated from an apple orchard and beach soil in South Korea, respectively; their draft genome sequences were assembled and annotated. The draft genome sequences of S7-3-3T (7,239,915 bp; G+C content, 50.6%) and 15J9-4T (7,551,610 bp; G+C content, 47.3%) are reported.

Spirosoma pollinicola sp. nov., isolated from pollen of common hazel (Corylus avellana L.).

A Gram-negative bacterium, strain HA7T, was isolated from the microhabitat of common hazel (Corylus avellana L.) pollen. HA7T was found to be an aerobic, rod-shaped, catalase-positive, oxidase-negative bacterium with an optimum growth temperature of 25 °C and pH of 7. The nearly complete 16S rRNA gene sequence of HA7T strain showed the closest similarities to Spirosoma linguale DSM 74T (97.4 %) and Spirosoma fluviale DSM 29961T (97.43 %). The major fatty acids (>5 %) were C16 : 1ω5c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were an unidentified aminophospholipid and phosphatidylethanolamine. The major respiratory quinone detected was menaquinone MK-7 (95 %). The draft genome sequence included 8 794 837 bases, which contained 3665 predicted coding sequences and had a G+C content of 47.9 mol%. The genome-based comparison between HA7T and S. linguale DSM 74T and S. fluviale DSM 29961T with pairwise average nucleotide identity indicated a clear distinction, between 76.2-76.3 %. Moreover, the digital DNA-DNA relatedness of HA7T to these strains was 26.5 and 25.1 %. Based on the differential genotypic, phenotypic and chemotaxonomic properties to closely related type strains, strain HA7T ought to be assigned with the status of a new species, for which the name Spirosomapollinicola sp. nov. is proposed. The type strain is HA7T (DSM 105799T=LMG 30282T).

Bacterial microbiota associated with flower pollen is influenced by pollination type, and shows a high degree of diversity and species-specificity.

Diverse microorganisms colonise the different plant-microhabitats, such as rhizosphere and phyllosphere, and play key roles for the host. However, bacteria associated with pollen are poorly investigated, despite its ecological, commercial and medical relevance. Due to structure and nutritive composition, pollen provides a unique microhabitat. Here the bacterial abundance, community structure, diversity and colonization pattern of birch, rye, rapes and autumn crocus pollens were examined, by using cultivation, high-throughput sequencing and microscopy. Cultivated bacteria belonged to Proteobacteria, Actinobacteria and Firmicutes, with remarkable differences at species level between pollen species. High-throughput sequencing of 16S rRNA gene amplicon libraries showed Proteobacteria as the dominant phylum in all pollen species, followed by Actinobacteria, Acidobacteria and Firmicutes. Both plant species and pollination type significant influenced structure and diversity of the pollen microbiota. The insect-pollinated species possessed a more similar microbiota in comparison to the wind-pollinated ones, suggesting a levelling effect by insect vectors. Scanning electron microscopy as well as fluorescent in situ hybridisation coupled with confocal laser scanning microscopy (FISH-CLSM) indicated the tectum surface as the preferred niche of bacterial colonisation. This work is the most comprehensive study of pollen microbiology, and strongly increases our knowledge on one of the less investigated plant-microhabitats.