Are there any pathogenic archaeans?

Actually, there exist at least one reference to a negative effect of Nanoarchaeum towards its host. Jahn et al (2008) describes that single Ignicoccus cells wich had more than two Nanoarchaeum cells attached were unable to grow, while those with two or less could form a colony.

It's true that there isn't strong evidence to considere Nanoarchaeum as a parasite in the traditional sense, provided this is the only reference I have found to a negative (or positive) effect of this archeon. It's also true that even traditional symbiots such as micorhizic fungi can be harmful in certain conditions, and because of that, this lonely example wouldn't be representative. However, untill this reference there were the same evidence to consider this archaeon as a symbiot or as a parasite, and for unkown reasons the first hypothesis was assumed by default. This results sugest that Nanoarcheum is potentially harmful and, since there still isn't any evidence that demostrate that Nanoarchaeum has any benefit, I strongly believe the consideration of a putative parasite should be encouraged and used as the default hypothesis.

Some authors prefer to use the term "intimal association", and they define it as "a highly specialized system combining characteristics of symbiosis, commensalisms, and parasitism" wich tries to be something neutral beween the two hypothesis. However I find that expression unnecesary, confuse and with an strong lack of meaning; mainly because that kind of relationship can be described with classical ecologycal terms.

To date, there isn't a single species that may be considered pathogenic to animals or plants. There are archeon who live in association with animals (in the case of human, they have been found in the gut microbiota aswell as certain skin surfaces) that are mainly methanogens. This could lead to think that archaons could produce "pathologic farting", but that condition has never been described.

In the case of ascidians and other marine invertebrates, some archeon have been found living in symbiosis, with the microbe aiding the animal by means of nitrogen fixation. One could think that, since they're able to live inside the organisms, they could behave as opportunistic pathogens, but none has been described.

Furthermore, it actually exists at least one known species who could be classified as parasitic, the nanoarchaeota Nanoarchaeum equitans, which has been described as a symbiont of some hyperthermophilic archaeon. Despite that description as symbiont, Nanoarchaeum cannot live by its own, while its companion does. Moreover, its genome contains the typical traits associated to parasitism, with great reduction in genome size and loss of many key pathways and cell functions, including methabolic pathways an even some key components of its transcriptional and translational machinery. Since there is no known function of the Nanoarchaeum itself, it should be considered as a parasite.

However, the lack of evidence may be biased, since few people has used metagenomic approach to look for archeon in clinical samples, and some rare cases may be found in the future.