Horsenettle (Solanum carolinense) fruit bacterial communities are not variable across fine spatial scales (original) (raw)
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BMC Microbiology, 2013
Background: Research to understand and control microbiological risks associated with the consumption of fresh fruits and vegetables has examined many environments in the farm to fork continuum. An important data gap however, that remains poorly studied is the baseline description of microflora that may be associated with plant anatomy either endemically or in response to environmental pressures. Specific anatomical niches of plants may contribute to persistence of human pathogens in agricultural environments in ways we have yet to describe. Tomatoes have been implicated in outbreaks of Salmonella at least 17 times during the years spanning 1990 to 2010. Our research seeks to provide a baseline description of the tomato microbiome and possibly identify whether or not there is something distinctive about tomatoes or their growing ecology that contributes to persistence of Salmonella in this important food crop.
Proceedings of the National Academy of Sciences, 2021
Significance The role of flowers as environmental filters for bacterial communities and the provenance of bacteria in the phyllosphere are currently poorly understood. We experimentally tested the effect of induced variation in soil communities on the microbiota of plant organs. We identified soil-derived bacteria in the phyllosphere and show a strong convergence of floral communities with an enrichment of members of the Burkholderiaceae family. This finding highlights a potential role of the flower in shaping the interaction between plants and a bacterial family known to harbor both plant pathogens and growth-promoting strains. Because the flower involves host–symbiont feedback, the selection of specific bacteria by the reproductive organs of angiosperms could be relevant for the modulation of fruit and seed production.
Microbiome diversity, composition and assembly in a California citrus orchard
Frontiers in Microbiology, 2023
The citrus root and rhizosphere microbiomes have been relatively well described in the literature, especially in the context of Huanglonbing disease. Yet questions addressing the assembly of root microbial endophytes have remained unanswered. In the above ground tree tissues, leaves and stems have been the research focus point, while flush and flower microbiomes, two important tissues in the vegetative and reproductive cycles of the tree, are not well described. In this study, the fungal and bacterial taxa in five biocompartments (bulk soil, rhizosphere, root endosphere, flower and flush) of citrus trees grown in a single California orchard were profiled using an amplicon-based metagenomic Illumina sequencing approach. Trees with no observable signs of abiotic or biotic stresses were sampled for two consecutive years during the floral development phase. The rhizosphere was the most biodiverse compartment compared to bulk soil, root endosphere, flower and flush microbiomes. In addition, the belowground bacteriome was more diverse than the mycobiome. Microbial richness decreased significantly from the root exosphere to the endosphere and was overall low in the above ground tissues. Root endophytic microbial community composition shared strong similarities to the rhizosphere but also contained few taxa from above ground tissues. Our data indicated compartmentalization of the microbiome with distinct profiles between above and below ground microbial communities. However, several taxa were present across all compartments suggesting the existence of a core citrus microbiota. These findings highlight key microbial taxa that could be engineered as biopesticides and biofertilizers for citriculture.
Shared and unique features of bacterial communities in native forest and vineyard phyllosphere
Ecology and Evolution, 2019
The aboveground parts of plants, so-called phyllosphere, not only are among one of the most prevalent bacterial habitats on Earth, but also support diverse bacterial communities (Bringel & Couée, 2015; Yang, Crowley, Borneman, & Keen, 2001). Phyllosphere microorganisms provide specific ecosystem services and potentially mediate plant biodiversity-ecosystem function relationships (Kembel et al., 2014; Laforest-Lapointe, Paquette, Messier, & Kembel, 2017; Vacher et al., 2016). For example, leaf-associated bacteria have been shown to affect host growth (Saleem, Meckes, Pervaiz, & Traw, 2017) and protection against pathogen infection (Innerebner, Knief, & Vorholt, 2011). In addition, phyllosphere bacteria can influence the physicochemical properties of the environment, such as climate dynamics and the dynamics of numerous gaseous compounds of the surrounding atmosphere (Bringel & Couée, 2015). Therefore, phyllosphere
Molecular Plant, 2018
The microbiome refers to the collective genomes of all resident microorganisms of a particular organism, environment, or ecosystem. Plant surfaces and interior parts are populated by myriads of bacteria, fungi, and microbes from other kingdoms, which can have considerable effects on plant growth, disease resistance, abiotic stress tolerance, and nutrient uptake. Hence, deep insight into the mechanisms underlying plant microbiome evolution, composition, and function would provide new opportunities to improve crop health and yield and thus benefit global food security. To bolster the promise and potential of microbiome research in agriculture, Jianbing Yan from Huazhong Agricultural University (HZAU, China) and Marcel Bucher from University of Cologne (UoC, Germany) developed the idea to organize an interdisciplinary workshop on plant microbiome late in 2017.
A latitudinal pattern of plant leaf-associated bacterial community assembly
bioRxiv (Cold Spring Harbor Laboratory), 2022
Plant-associated microbes influence plant ecology, evolution, and ecosystem function, while explaining the diversity and abundance of these microbes at broad geographic scales remains problematic. Here we quantified the contribution of biotic and abiotic factors to the diversity and biogeography of leaf-associated bacteria on woody plants across a latitudinal gradient. We show that host plant attributes, environments, space and neighborhood effects jointly explained the majority of variation in leaf bacterial diversity. With increasing latitude, the importance of host plant attributes for bacterial community assembly increased while the host specificity of bacteria decreased. Broad-scale plant-bacteria association networks were
Microbial Ecology, 2017
Microbial model systems are very useful in addressing macro-ecological questions. Two major theories exist to date, to explain the community structure of organisms: (1) the dispersal (neutral) assembly theory which predicts that community similarity decreases with increasing geographic distance, independent of any environmental variables, and (2) the niche assembly theory which predicts that the communities' compositions are more homogeneous among sites characterized by similar environmental conditions. Our study system offered a unique opportunity to investigate the relative role of environmental conditions and spatial factors in shaping community composition. We explored the bacterial community composition (BCC) of Nicotiana glauca floral nectar using the Illumina MiSeq technique at three spatial scales (plants, site, and region) and two taxonomic levels. Floral nectar samples were collected from 69 N. glauca plants at 11 different sites along a 200-km transect in Israel, along three biogeographic regions. A distance decay of BCC was found among all plants throughout Israel, but such pattern was not found among either sites or biogeographical regions. The BCC was also governed by environmental conditions in all examined scales (from the plant up to the biogeographical region). We also found that taxonomic resolution (89 and 97% sequence identity for clustering operational taxonomic units) affected the results of these BCC analyses. Hence, our study revealed that the BCC in N. glauca floral nectar is shaped by both the environmental conditions and the distance between plants, depending on the sampling scale under examination as well as by taxonomic resolution.