Interplay between selenium hyperaccumulator plants and their microbiome

Abstract

The plant microbiome includes all microorganisms that occur on the plant root (rhizosphere) and shoot (phyllosphere) or inside plants (endosphere). Many of these microbes benefit their host by promoting growth, helping acquire nutrients or by alleviating biotic or abiotic stress. In addition to its intellectual merit, better knowledge of plant-microbiome interactions is important for agriculture and medicine. Microbiome studies are gaining popularity in multiple research areas, particularly due to advances in next generation sequencing, which has advantages over cultivable methods by revealing the complete microbial community. Still relatively little is known about the microbiomes of plants with extreme properties, including plants that hyperaccumulate (HA) toxic elements such as selenium (Se). Selenium HAs may contain up to 1.5% of their dry weight in Se, which can cause toxicity to herbivores and pathogens as well as neighboring plants. Many advances are yet to be made with regard to the interaction of Se and the plant microbiome: does plant Se affect microbial diversity and composition, and do plant-associated microbes affect plant Se accumulation? The first chapter of this thesis will discuss aspects of the plant microbiome as well as the discoveries to date with regard to plant-associated microbes and Se, mostly explored through culture-dependent methods. Selenium HA appear to harbor equally diverse endophytic microbial communities as non-hyperaccumulators. Thus, plant Se does not impair associations with microbes. A variety of microbes have been isolated from plants or soil in seleniferous areas, including some bacteria and fungi with extreme Se tolerance. Inoculation of plants with individual strains or consortia of microbes was able to promote plant growth, Se uptake and/or Se volatilization. Thus, microbes may facilitate their host’s fitness in seleniferous areas. Exploiting and optimizing plant-microbe associations may facilitate applications like phytoremediation (bio-based environmental cleanup) or biofortification (nutritionally fortified crops). Plant-derived microbial isolates may also be applicable without their plant host, e.g. for cleanup of wastewaters. Culture-dependent studies have dominated the plant-microbe interactions research in regards to hyperaccumulators thus far, painting an elaborate but incomplete picture. In the second chapter of this thesis, we use a mix of culture based and culture-independent methods to investigate the bacterial rhizobiome of selenium Se HAs. Using 16S rRNA Illumina sequencing, we show that the rhizobiomes of Se HAs are significantly different from non-accumulators from the same naturally seleniferous site, with a higher occurrence of Pedobacter and Deviosa surrounding HAs. In addition, we found that HAs harbor a higher species richness when compared to non-accumulators on the same seleniferous site. Thus, hyperaccumulation does not appear to negatively affect rhizobiome diversity, and may select for certain bacterial taxa in the rhizobiome. The bacterial isolates, independent from site or host plant species were in general extremely resistant to toxic concentrations of Se (up to 200mM selenate or selenite) and could reduce selenite to elemental Se. Thus, microbial Se resistance may be widespread and not be under selection by Se HAs. In future studies it will be interesting to further investigate the mechanisms by which Se HA species similarly shape their rhizobiome; this is perhaps due to Se-related root exudates. Future studies may also focus on elucidating the effects of microbes on plant Se accumulation and tolerance.