Despite the fact that mats of the filamentous sulfide oxidizing bacteria Beggiatoa are quite extensive below the neritic zone, very little is known about the eukaryotic organisms inhabiting these mats. Specimen loss and destruction of spatial information are significant obstacles to past approaches used to study these fragile sedimentary communities. To overcome these limitations, a new sampling technique was developed in which sediment cores are incubated with a fluorogenic probe to label the contained biota, and then chemically fixed, dehydrated, and embedded with low viscosity epoxy resin. Combined with novel thick sectioning methods, confocal microscopy, and state of the art digital image processing, this fluorescently labeled embedded core (FLEC) technique has provided unparalleled views of the fine scale structure of the Beggiatoa mat community in the Santa Barbara Basin (SBB). Based on initial studies using the FLEC method, it is hypothesized that Beggiatoa structures the chemical microenvironment to allow microaerophiles to live in close proximity to anaerobes and aerobes (i.e., these mats might be considered analogous to bacterial biofilms in this respect). To advance this hypothesis, the major objective of this study is to correlate meiofaunal life positions and their physiological adaptations with finescale chemical and spatial information. Furthermore, the initial FLEC studies of SBB Beggiatoa mats yielded two undescribed species or higher taxa, as well as three new and unexpected bacterial eukaryote symbioses, suggesting that the Santa Barbara Basin provides habitat for yet more undescribed species or symbioses. It is hypothesized that meiofauna possessing chemoautotrophs inhabit zones below the Beggiatoa mat, meiofauna possessing metabolic adaptations or heterotrophic symbionts co exist with the Beggiatoa, and meiofauna without special adaptations inhabit space available above the Beggiatoa mat.
