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I know that microbes are not capable of sexual reproduction, thus sorting them into species according to "groups that can interbreed and generate fertile offspring" should not apply.

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  • $\begingroup$ I was reading on the topic of OTU's (Operational taxonomic units) and they might sound like a good definition for you. en.wikipedia.org/wiki/Operational_taxonomic_unit $\endgroup$
    – Ro Siv
    Commented Dec 16, 2017 at 12:39
  • $\begingroup$ Here is more info for bacteria, protozoa, and fungi. $\endgroup$
    – vkehayas
    Commented Dec 16, 2017 at 13:07
  • $\begingroup$ Microbe is not a taxonomic unit: there are no microbial species. --- "Microbe" is "an extremely minute living being"---one needs a microscope to see it. And what is the opposite of microbe? Macrobe, of course. Microbe (viz. microbiology, microbiome, etc.) is a very popular, but not very useful, concept. $\endgroup$
    – user37894
    Commented Dec 17, 2017 at 8:03

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Your question is relative to the species concept that you are using. Mayr's biological species concept (BSC) is based on the ability to interbreed; a process-based definition. Most biologists use it, but most taxonomists, who are the people who actually describe species, use some variation of the phylogenetic species concept. The phylogenetic species concept is not based on process, but on fixed differences. Fixed differences are evidence of a lack of interbreeding, but the concept is not explicitly based on reproduction. Fixed morphological differences have been used to classify microbes, most often in culture. But currently, microbes are most often classified with a combination of morphological and genetic characters. The small subunit rRNA is sequenced and put through an algorithm for estimating species based on genetic distances. In short, your question depends a lot on which species concept you are using, and whether you would accept a distance-based DNA definition. But species need not be defined reproductively.

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This question actually does not have an easy answer. As indicated in a previous answer, the 16S rRNA gene is used by many scientists. Since this is a fairly conserved genetic region, mutations in this region can differentiate species phylogenetically, but it is not a foolproof method. For example, several species of Shigella can yield nearly identical 16S sequences to those of Escherichia coli and debates rage as to whether they in fact should be classified as the same species. Some scientists even deny that there are such things as microbial species, or if there are, that being able to group microbes into taxonomical units is not worthwhile or informative (although these scientists are still in the minority). If you would like to know more about that viewpoint, you can check out the work of W.F. Doolittle. This one is a fun read:

Doolittle, W., & Zhaxybayeva, O. (2009). On the origin of prokaryotic species. Genome Research, 19(5), 744-756. http://dx.doi.org/10.1101/gr.086645.108

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