Microbial Associations formed and hosted by Protists, Algae, and Fungi

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Background

The analysis of microbiomes of animals and plants became one of the most rapidly developing fields of research. Some Eukaryotes, such as protists, algae and fungi, may be not only part of microbiomes of multicellular organisms, but they also host their own microbiomes which may include a broad spectrum of bacteria, archaea, and unicellular eukaryotes. At the same time, such microbial associations mostly remain out of focus. The role of obligate or facultative symbioses in survival and environmental adaptation of both hosts and symbionts still has to be elucidated. Actually, many protists and algae cannot be grown in axenic cultures but need prokaryotic co-habitants. Some pathogenic or opportunistic bacteria were occasionally found in protists. Anaerobic ciliates always host symbiotic bacteria or archaea. Fungi can form stable associations with numerous microorganisms; lichens are, probably, the most impressive evolutionary outcome of symbiosis between fungi and algae. Finally, some biofilms include both prokaryotes and eukaryotes, which share, form and shape the complex microbial community.

The studies of symbiotic systems formed by protists, algae, fungi and prokaryotes in last decade made a huge progress due to appearance of molecular methods allowing to characterize uncultivable microorganisms. Fast-developing HTS techniques opened up best possibilities to metabarcoding - quick and reliable identification of complete sets of prokaryotic microorganisms associated with the eukaryotic hosts based on deep sequencing of the 16S rRNA gene regions, and then to metagenomic analysis of symbiotic systems. Currently not only the complete genomes of all partners in symbiotic association can be obtained and assembled from one set of sequencing data, but the predictions of metabolic abilities of the microbial community can be inferred from metagenomic datasets. These tools allow to dissect the complex symbiotic systems and microbial communities, illuminating the modes of different organism’s co-existence in nature. Involvement of new research models and methodological improvements may contribute into the modern ‘holobiont concept’, thus elucidating some basic principles of evolution and diversity of life.

In the proposed Research Topic, we aim to highlight diverse aspects of existence and function of symbiotic systems where protists, algae and fungi were considered as hosts, and their microbiomes include specialized symbionts or facultative cohabitants (bacteria, archaea or other unicellular eukaryotes). The Research Topic will include but not be limited to issues such as:

- descriptions of new symbiotic associations;
- taxonomic and functional profiling of microbial communities associated with less-conventional eukaryotic hosts;
- analysis of the microbial symbiotic associations by metagenomics and other ‘-omics’ techniques;
- the descriptions and research of complex microbial communities where protists, algae and fungi play the key role.

The contributions in form of Original Research, Reviews, Mini Reviews, Hypothesis and Theory, Perspective, Opinion, Methods

Microbial Symbioses does not consider descriptive studies that are solely based on amplicon (eg. 16S rRNA) profiles, unless they are accompanied by a clear hypothesis and experimentation and provide insight into the microbiological system and symbiotic behaviors or process being studied. If your manuscript include amplicon profiles please make sure that your abstract include a clear statement on why we should consider your manuscript. Especially helpful would be to specify in your abstract the methods used to test the hypothesis and how the reported results support and validate this hypothesis.

Keywords: symbiosis, protists, algae, fungi, microbiome, metagenome, prokaryotic symbionts, ciliates, microbial communities

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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