The labyrinthulomycetes are a diverse group of marine heterokont protists with fungus-like lifestyles. They have been found in every marine habitat examined, and some are associated with devastating diseases of marine metazoans and metaphytes including bivalves and eelgrass [1,2]. There are representatives of four distinct labyrinthulomycete subgroups (labyrinthulids, aplanochytrids, oblongichytrids, and thraustochytrids; Figures 1 and 2) in cultivation, and environmental sequences indicate that additional distinct groups remain to be cultivated [3,4]. The thraustochytrids are frequently identified at the level of class (Thraustochytriaceae), and are clearly monophyletic, while the other three groups are usually placed in a second class (Labyrinthulaceae) although the monophyly of this grouping is less certain.
Recent efforts to resolve inconsistencies [5] in the classification of thraustochytrids have recognized numerous genera in which isolates share ~98% or greater 18S rRNA sequence identity [6,7], and there is typically <80% 18S rRNA sequence identity between thraustochytrid genera. Different labyrinthulid isolates, so far all assigned to the single genus Labyrinthula, can be less than 85% identical. 18S rRNA sequences within both the aplanochytrids (right now the single genus Aplanochytrium) and oblongichytrids (right now the single genus Oblongichytrium) generally have >95% identity, with <90% identity between the two groups. The recently sequenced genomes of three labyrinthulomycetes (work done in collaboration with the Joint Genome Institute) reveal extensive structural and gene content differences between thraustochytrids and aplanochytrids (Collier and others, work in progress). Cultivation-dependent work has suggested differences in substrate and habitat preferences among major groups of labyrinthulomycetes, particularly labyrinthulids vs thraustochytrids, and cultivation-independent 18S rDNA sequence-based approaches now make it possible to investigate differences in the ecology of previously unresolved genera and species. While thraustochytrids have historically been a major focus, evidence is accumulating that aplanochytrids and oblongichytrids may be more abundant in most marine habitats (e.g., [3,4,8-11]). It appears likely that the 18S sequence diversity of labyrinthulomycetes reflects diversity in their ecology; for example, different 18S sequence types of Labyrinthula (likely different species) show distinct distributions [12] and there also appear to be ecological differences among aplanochytrids and oblongichytrids ([13]; unpublished data of Collier and Honda groups). The ubiquity of labyrinthulomycetes means that they could be used to gain insights into ocean biogeochemistry and ecology everywhere from the sunlit surface to deep (oxic and anoxic) zones of the water column, and from littoral to deep ocean sediments. Importantly, their lifestyle offers a complement to that of diatoms, so having genetic tools for both would enable genetically-empowered investigations of marine food webs and elemental cycles from formation to remineralization of organic matter. That vision would be brought closer to reality by developing the ability to genetically manipulate a wide variety of labyrinthulomycetes. Progress has already been made in the genetic manipulation of some thraustochytrids (see below). Thus, we will prioritize our efforts by focusing initially on representatives of Labyrinthula, Aplanochytrium, and Oblongichytrium. As time and other resources allow, we will broaden our efforts to more strains in these three groups, and extend our study into the diverse thraustochytrid genera that have not yet been transformed, including as a first target the organism known as ‘QPX’, cause of QPX disease in the hard clam (quahog) Mercenaria mercenaria [14,15].