Spatially explicit depiction of a floral epiphytic bacterial community reveals role for environmental filtering within petals

Hyperaccumulation of nickel but not selenium drives floral microbiome differentiation: A study with six species of Brassicaceae

PREMISE

Intraspecific variation in flower microbiome composition can mediate pollination and reproduction, and so understanding the community assembly processes driving this variation is critical. Yet the relative importance of trait-based host filtering and dispersal in shaping among-species variation in floral microbiomes remains unknown.

METHODS

Within two clades of Brassicaceae, we compared diversity and composition of floral microbiomes in natural populations of focal nickel and selenium hyperaccumulator species and two of their non-accumulating relatives. We assessed the relative strengths of floral elemental composition, plant phylogenetic distance (host filtering), and geography (dispersal) in driving floral microbiome composition.

RESULTS

Species in the nickel hyperaccumulator clade had strongly divergent floral microbiomes, the most of that variation driven by floral elemental composition, followed by geographic distance between plant populations and, lastly, phylogenetic distance. Conversely, within the selenium hyperaccumulator clade, floral microbiome divergence was much lower among the species and elemental composition, geography, and plant phylogeny were far weaker determinants of microbiome variation.

CONCLUSIONS

Our results show that the strength of elemental hyperaccumulation's effect on floral microbiomes differs substantially among plant clades, possibly due to variation in elements as selective filters or in long-distance dispersal probability in different habitats.

Do flower-colonizing microbes influence floral evolution? A test with fast-cycling Brassica

Pollinators are thought to be the main drivers of floral evolution. Flowers are also colonized by abundant communities of microbes that can affect the interaction between plants and their pollinators. Very little is known, however, about how flower-colonizing microbes influence floral evolution. Here we performed a 6-generation experimental evolution study using fast-cycling Brassica rapa, in which we factorially manipulated the presence of pollinators and flower microbes to determine how pollinators and microbes interact in driving floral evolution. We measured the evolution of 6 morphological traits, as well as the plant mating system and flower attractiveness. Only one of the 6 traits (flower number) evolved in response to pollinators, while microbes did not drive the evolution of any trait, nor did they interact with pollinators in driving the evolution of morphological traits. Moreover, we did not find evidence that pollinators or microbes affected the evolution of flower attractiveness to pollinators. However, we found an interactive effect of pollinators and microbes on the evolution of autonomous selfing, a trait that is expected to evolve in response to pollinator limitations. Overall, we found only weak evidence that microbes mediate floral evolution. However, our ability to detect an interactive effect of pollinators and microbes might have been limited by weak pollinator-mediated selection in our experimental setting. Our results contrast with previous (similar) experimental evolution studies, highlighting the susceptibility of such experiments to drift and to experimental artefacts.

Petal segmentation in CT images based on divide-and-conquer strategy

Manual segmentation of the petals of flower computed tomography (CT) images is time-consuming and labor-intensive because the flower has many petals. In this study, we aim to obtain a three-dimensional (3D) structure of Camellia japonica flowers and propose a petal segmentation method using computer vision techniques. Petal segmentation on the slice images fails by simply applying the segmentation methods because the shape of the petals in CT images differs from that of the objects targeted by the latest instance segmentation methods. To overcome these challenges, we crop two-dimensional (2D) long rectangles from each slice image and apply the segmentation method to segment the petals on the images. Thanks to cropping, it is easier to segment the shape of the petals in the cropped images using the segmentation methods. We can also use the latest segmentation method for the task because the number of images used for training is augmented by cropping. Subsequently, the results are integrated into 3D to obtain 3D segmentation volume data. The experimental results show that the proposed method can segment petals on slice images with higher accuracy than the method without cropping. The 3D segmentation results were also obtained and visualized successfully.

A quantitative survey of the blueberry (Vaccinium spp.) culturable nectar microbiome: variation between cultivars, locations, and farm management approaches

Microbes in floral nectar can impact both their host plants and floral visitors, yet little is known about the nectar microbiome of most pollinator-dependent crops. In this study, we examined the abundance and composition of the fungi and bacteria inhabiting Vaccinium spp. nectar, as well as nectar volume and sugar concentrations. We compared wild V. myrsinites with two field-grown V. corymbosum cultivars collected from two organic and two conventional farms. Differences in nectar traits and microbiomes were identified between V. corymbosum cultivars but not Vaccinium species. The microbiome of cultivated plants also varied greatly between farms, whereas management regime had only subtle effects, with higher fungal populations detected under organic management. Nectars were hexose-dominant, and high cell densities were correlated with reduced nectar sugar concentrations. Bacteria were more common than fungi in blueberry nectar, although both were frequently detected and co-occurred more often than would be predicted by chance. "Cosmopolitan" blueberry nectar microbes that were isolated in all plants, including Rosenbergiella sp. and Symmetrospora symmetrica, were identified. This study provides the first systematic report of the blueberry nectar microbiome, which may have important implications for pollinator and crop health.

Blueberry floral probiotics: nectar microbes inhibit the growth of Colletotrichum pathogens

AIMS

To identify whether microorganisms isolated from blueberry flowers can inhibit the growth of Colletotrichum, an opportunistic plant pathogen that infects flowers and threatens yields, and to assess the impacts of floral microbes and Colletotrichum pathogens on artificial nectar sugars and honey bee consumption.

METHODS AND RESULTS

The growth inhibition of Colletotrichum (Colletotrichum acutatum, Colletotrichum fioriniae, and Colletotrichum gloeosporioides) was screened using both artificial nectar co-culture and dual culture plate assays. All candidate nectar microbes were screened for antagonism against a single C. acutatum isolate. Then, the top four candidate nectar microbes showing the strongest inhibition of C. acutatum (Neokomagataea thailandica, Neokomagataea tanensis, Metschnikowia rancensis, and Symmetrospora symmetrica) were evaluated for antagonism against three additional C. acutatum isolates, and single isolates of both C. fioriniae and C. gloeosporioides. In artificial nectar assays, single and three-species cultures inhibited the growth of two of four C. acutatum isolates by ca. 60%, but growth of other Colletotrichum species was not affected. In dual culture plate assays, inhibition was observed for all Colletotrichum species for at least three of four selected microbial antagonists (13%‒53%). Neither honey bee consumption of nectar nor nectar sugar concentrations were affected by any microbe or pathogen tested.

CONCLUSIONS

Selected floral microbes inhibited growth of all Colletotrichum species in vitro, although the degree of inhibition was specific to the assay and pathogen examined. In all microbial treatments, nectar sugars were preserved, and honey bee preference was not affected.

New insights into engineered plant-microbe interactions for pesticide removal

Over the past decades, rapid industrialization along with the overutilization of organic pollutants/pesticides has altered the environmental circumstances. Moreover, various anthropogenic, xenobiotics and natural activities also affected plants, soil, and human health, in both direct and indirect ways. To counter this, several conventional methods are currently practiced, but are uneconomical, noxious, and is yet inefficient for large-scale application. Plant-microbe interactions are mediated naturally in an ecosystem and are practiced in several areas. Plant growth promoting rhizobacteria (PGPR) possess certain attributes affecting plant and soil consequently performing decontamination activity via a direct and indirect mechanism. PGPR also harbors indispensable genes stimulating the mineralization of several organic and inorganic compounds. This makes microbes potential candidates for contributing to sustainably remediating the harmful pesticide contaminants. There is a limited piece of information about the plant-microbe interaction pertaining predict and understand the overall interaction concerning a sustainable environment. Therefore, this review focuses on the plant-microbe interaction in the rhizosphere and inside the plant's tissues, along with the utilization augmenting the crop productivity, reduction in plant stress along with decontamination of pesticides/organic pollutants in soil for sustainable environmental management.

A metacommunity ecology approach to understanding microbial community assembly in developing plant seeds

Microorganisms have the potential to affect plant seed germination and seedling fitness, ultimately impacting plant health and community dynamics. Because seed-associated microbiota are highly variable across individual plants, plant species, and environments, it is challenging to identify the dominant processes that underlie the assembly, composition, and influence of these communities. We propose here that metacommunity ecology provides a conceptually useful framework for studying the microbiota of developing seeds, by the application of metacommunity principles of filtering, species interactions, and dispersal at multiple scales. Many studies in seed microbial ecology already describe individual assembly processes in a pattern-based manner, such as correlating seed microbiome composition with genotype or tracking diversity metrics across treatments in dispersal limitation experiments. But we see a lot of opportunities to examine understudied aspects of seed microbiology, including trait-based research on mechanisms of filtering and dispersal at the micro-scale, the use of pollination exclusion experiments in macro-scale seed studies, and an in-depth evaluation of how these processes interact via priority effect experiments and joint species distribution modeling.

Are microbes growing on flowers evil? Effects of old flower microbes on fruit set in a wild ginger with one-day flowers, Alpinia japonica (Zingiberaceae)

Flowers are colonized and inhabited by diverse microbes. Flowers have various mechanisms to suppress microbial growth, such as flower volatiles, reactive oxygen and secondary compounds. Besides, plants rapidly replace flowers that have a short lifespan, and old flowers senesce. They may contribute to avoiding adverse effects of the microbes. In this study, we investigate if the flower microbial community on old flowers impedes fruit and seed production in a wild ginger with one-day flowers. We focus on microbes on old flowers because they may be composed of microbes that would grow during flowering if the flowers did not have mechanisms to suppress microbial growth. We inoculated newly opened flowers with old flower microbes, and monitored the effects on fruit and seed set. We also assessed prokaryotic communities on the flowers using 16S rRNA amplicon sequencing. We found six bacterial amplicon sequence variants (ASVs) whose proportions were increased on the inoculated flowers. These ASVs were also found on flower buds and flowers that were bagged by net or paper during anthesis, suggesting that they had been present in small numbers prior to flowering. Fruit set was negatively associated with the proportions of these ASVs, while seed set was not. The results suggest that old flowers harbor microbial communities different from those at anthesis, and that the microbes abundant on old flowers negatively affect plant reproduction. Although it has received little attention, antagonistic microbes that rapidly proliferate on the flowers may have affected the evolution of various flower characteristics such as flower volatiles and life span.

Horsenettle (Solanum carolinense) fruit bacterial communities are not variable across fine spatial scales

Fruit house microbial communities that are unique from the rest of the plant. While symbiotic microbial communities complete important functions for their hosts, the fruit microbiome is often understudied compared to other plant organs. Fruits are reproductive tissues that house, protect, and facilitate the dispersal of seeds, and thus they are directly tied to plant fitness. Fruit microbial communities may, therefore, also impact plant fitness. In this study, we assessed how bacterial communities associated with fruit of Solanum carolinense, a native herbaceous perennial weed, vary at fine spatial scales (<0.5 km). A majority of the studies conducted on plant microbial communities have been done at large spatial scales and have observed microbial community variation across these large spatial scales. However, both the environment and pollinators play a role in shaping plant microbial communities and likely have impacts on the plant microbiome at fine scales. We collected fruit samples from eight sampling locations, ranging from 2 to 450 m apart, and assessed the fruit bacterial communities using 16S rRNA gene amplicon sequencing. Overall, we found no differences in observed richness or microbial community composition among sampling locations. Bacterial community structure of fruits collected near one another were not more different than those that were farther apart at the scales we examined. These fine spatial scales are important to obligate out-crossing plant species such as S. carolinense because they are ecologically relevant to pollinators. Thus, our results could imply that pollinators serve to homogenize fruit bacterial communities across these smaller scales.

Divergent assembly processes? A comparison of the plant and soil microbiome with plant communities in a glacier forefield

Community assembly is a result of dispersal, abiotic and biotic characteristics of the habitat as well as stochasticity. A direct comparison between the assembly of microbial and 'macrobial' organisms is hampered by the sampling of these communities in different studies, at different sites or on different scales. In a glacier forefield in the Austrian Alps, we recorded the soil and plant microbiome (bacteria and fungi) and plants that occurred in the same landscape and in close proximity in the same plots. We tested five predictions deduced from assembly processes and revealed deviating patterns of assembly in these community types. In short, microbes appeared to be less dispersal limited than plants and soil microbes, and plants strongly responded to abiotic factors whereas the leaf microbiome was plant species specific and well buffered from environmental conditions. The observed differences in community assembly processes may be attributed to the organisms' dispersal abilities, the exposure of the habitats to airborne propagules and habitat characteristics. The finding that assembly is conditional to the characteristics of the organisms, the habitat and the spatial scale under consideration is thus central for our understanding about the establishment and the maintenance of biodiversity.

Pollinators mediate floral microbial diversity and microbial network under agrochemical disturbance

How pollinators mediate microbiome assembly in the anthosphere is a major unresolved question of theoretical and applied importance in the face of anthropogenic disturbance. We addressed this question by linking visitation of diverse pollinator functional groups (bees, wasps, flies, butterflies, beetles, true bugs and other taxa) to the key properties of the floral microbiome (microbial α- and β-diversity and microbial network) under agrochemical disturbance, using a field experiment of bactericide and fungicide treatments on cultivated strawberries that differ in flower abundance. Structural equation modelling was used to link agrochemical disturbance and flower abundance to pollinator visitation to floral microbiome properties. Our results revealed that (i) pollinator visitation influenced the α- and β-diversity and network centrality of the floral microbiome, with different pollinator functional groups affecting different microbiome properties; (ii) flower abundance influenced the floral microbiome both directly by governing the source pool of microbes and indirectly by enhancing pollinator visitation; and (iii) agrochemical disturbance affected the floral microbiome primarily directly by fungicide, and less so indirectly via pollinator visitation. These findings improve the mechanistic understanding of floral microbiome assembly, and may be generalizable to many other plants that are visited by diverse insect pollinators in natural and managed ecosystems.