Beyond borders: investigating microbiome interactivity and diversity for advanced biocontrol technologies.

Abstract

Recent, primarily technology-based advances in microbial ecology have opened an immense treasure chest of microbial diversity that has been observed in the vast majority of all investigated habitats. Additionally, habitats which were assumed to be sterile for a long time are now known to be colonized by diverse microorganisms; e.g. within the placenta and stomach of humans or reproductive organs of plants. Through the implementation of new techniques, deeper insights into the structure of microbiomes mainly by amplicon sequencing and microscopy have been gained. Now the current focus of research is on analysis of their function implementing meta-(genomic/epigenomic/transcriptomic/proteomic) techniques. The management of the accumulated metadata and the gleaning of new information is the challenge we are facing, but that challenge will be solved in the near future (Jansson, 2013). By looking into the proverbial crystal ball, my intention is to highlight two scientific aspects in particular, which I believe have been overlooked in current approaches to ecological research: (i) the interactivity of microbiomes and (ii) the interplay between microorganisms derived from different kingdoms – in particular archaea, bacteria and fungi. Both aspects could inspire the future course of biotechnology. In recent decades, deeper insight into many aquatic and terrestrial microbial communities was gained using omics approaches. Although this is now possible, considerable time must be invested in the future in order to assemble all pathways and understand the interactions within microbiomes (Jansson, 2013). In contrast to single microbiomes, the connection between microbiomes as well as mutual exchange between them is less understood. Although we live in a highly interconnected world, up to the present date, there are only a few examples of synergistic microbiomes, which have shown that there are important relationships between single microbiomes. The three presented here are the rhizosphere (root–soil connection), the gut microbiome (food–human connection) and the indoor microbiome (plant–inhabitant connection). First, the rhizosphere is one well-investigated example; the root–soil interface is influenced by the plant metabolism via root exudates (Philippot et al., 2013). After assessing many experimental data and a lengthy discussion, it was accepted that both the plant as well as the soil influence the composition of the rhizosphere community (Berg and Smalla, 2009). The extent of impact depends on the plant species/genotype, its metabolites and the soil quality. While the rhizosphere is an example of particular importance for plant health, another interesting example which is important for human health is the gut microbiome. David and colleagues (2014) recently provided evidence for the survival of food-borne microbes (both animal and plant-based diet) after transit through the digestive system, and that food-borne strains may have been metabolically active in the gut. Microbial diversity in our gut ecosystem has an enormous impact on the host and vice versa connected by gut–brain cross-talk, which was revealed as a complex, bidirectional communication system (Mayer, 2011). Interesting relationships were detected recently, such as those between the gut microbiome and the development of obesity, cardiovascular disease and metabolic syndromes (Blaser et al., 2013) and also on motivation and higher cognitive functions, including intuitive decision making (Mayer, 2011). However, less is known about the food microbiome, although in many countries food is monitored for the occurrence of pathogens while beneficials are often ignored. First studies show that the vegetable and fruit microbiome is highly diverse, and Enterobacteriaceae play a substantial role within the vegetable microbiome (Leff and Fierer, 2013; Berg et al., 2014). Hanski and colleagues (2012) found a correlation between environmental biodiversity, human microbiota, especially Enterobacteriaceae, and allergy, and showed an experimental correlation between bacterial diversity and atopy as shown through significant interactions with enteric bacteria. The current focus of research is placed on the impact of our diet on the composition of the gut microbiome (of particular importance); however, the microbiome in/on our diet opens many more potential insights into the complex interactions. A third example is the indoor microbiome, which has enjoyed enormous attention during the last years due to the fact that we Microbial Biotechnology (2015) 8(1), 5–7 doi:10.1111/1751-7915.12235 bs_bs_banner