Microbes represent the most diverse group of organisms on our planet. It is all the more surprising that microbial biodiversity studies are still in their infancy. The majority of environmental microorganisms remain essentially unknown and represent the largest source of unexplored biodiversity on Earth. This creates immense opportunities for microbial discovery, and we are exploring these opportunities from three interrelated angles.
Search for novel forms of microbial life
For several years, we have been using the rRNA approach to discover the
hidden diversity of microbial eukaryotes. The geography of our studies
is substantial and include temperate areas (Northwest Atlantic coast,
Mediterranean Sea), tropics (Caribbean Sea, Hawaii), and High Arctic
(Greenland). The completed studies focus on anoxic and suboxic habitats
in Northwest Atlantic and Caribbean. We chose these environments
because anoxic habitats have occurred continuously throughout the
Earth’s history, and are promising to harbor organisms relevant to the
early evolution of eukaryotes. Our surveys have indeed detected a vast
assemblage of novel protists at all levels of taxonomic hierarchy,
including several clades not related to any known eukaryotic lineage
(Stoeck & Epstein 2003; Stoeck et al. 2003a.).
The present focus of our search for novel microbial species, supported
by a large Microbial Observatory grant from NSF, is on the Cariaco
Basin in the Caribbean off the coast of Venezuela. In collaboration
with Virginia Edgcomb (WHOI), Gordon Taylor (SYNU Stony Brook), and
Venezuelan colleagues Ramon Variela and Paula Suarez from Simon
Bolivar University in Caracas, we are conducting the largest to date
rRNA survey of microbial eukaryotes. This Basin harbors the ocean’s
largest body of permanently anoxic water, and provides a convenient
model to study the role of geochemical gradients in microbial
speciation. From this environment, we already recovered approximately
20,000 18S rRNA gene sequences. This dataset is a substantial portion
of all rRNA gene sequences collected to date world-wide. We recovered
representatives of all major protistan taxa (Figure ...). The breakdown
of our collection is presented in Fig. 1. Notable findings include
several deeply rooted excavate clades of various relatedness to
Euglenozoa, and what appears to be a new class of ciliates. The latter
is particularly noteworthy because ciliates are admittedly the best
protistan group studied, and some researchers maintain that most of the
ciliate species, let alone higher taxa, have been discovered. Because
of this, the sequences of putatively novel ciliate class are
particularly interesting, and we are spending major efforts recovering
cells from this putative class (Fig....)< insert image of car-h>.
In addition, we are continuously seeing wonderfully diverse cells of
unknown origin, some representing interesting cases of microbial
symbioses (Fig. ...
Novel protistan lineages (in red) from a salt marsh on Cape Cod in Massachusetts (left) and anoxic water column in the Cariaco Basin, Caribbean (right)