Here is a good, short and critical description of her work

As eloquently but succinctly explained in Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth by Lynn Margulis & Karlene Schwartz, the current, most prevalent taxonomic model holds that there are five "kingdoms" of life on Earth: bacteria, protoctista, animals, fungi and plants, in order of evolutionary origins. All but bacteria are eukaryotic (meaning that most of their DNA is organized into chromosomes and found within a nucleus).

ProtoTista is named after the Protoctista: the kingdom of single-celled animal-, plant- and fungus-like eukaryotes. Famous Protoctistans studied in high school and college biology classes are amoebas, paramecia, volvox, euglena, diatoms and the slime mold Dictyostelium.

(Despite their name, slime molds are not only biological examples of self-organization par excellence, but also just incredible organisms that strattle the boundary between single-celled and multicellular. In fact, both forms exist in their life cycle.)

There are currently 30 phyla of Protoctista, but it's taxonomy is rapidly changing as more knowledge is gathered about them.

The name Protoctista is taken from the Greek 'protos' (very first) and 'ktistos' (to establish) because they were the first eukaryotes to evolve on Earth. They have existed for approximately 1.2 billion years.

A few decades ago, University of Massachusetts' biologist Lynn Margulis proposed that eukaryotic cells - cells of protoctists, animals, plants & fungi - are the product of symbiosis between three (animal, fungus, most protoctistan) or four (plant, photosynthetic protoctistan) types of bacterial cells. Specifically, undulipodia and mitochondria were once free-living bacteria (spirochetes and aerobic bacteria, respectively), whereas chloroplasts of plants and photosynthetic protoctistans were once free-living cyanobacteria. All symbionts are now so integrated into their host cell that they function as a single cell.

This theory is called the Serial Endosymbiotic Theory or SET. The term "serial" is included because the symbioses were established serially, one before the other.

The evolutionary process that it describes - the origin of new organs or life forms via close-contact relationships (symbiosis) between previously independent organisms (symbionts) - is called symbiogenesis. Symbionts are often from different taxonomic groups (including different kingdoms), each contributing some particular ability to the symbiosis (movement, aerobic respiration, photosynthesis, etc.).

The scientific evidence supporting SET with regard to mitochondria and chloroplasts is solid. The verdict about the origins of undulipodia is still out, but evidence is mounting.

SET is described eloquently for lay readers in one of Margulis' latest books, Symbiotic Planet: A New View of Evolution in which she also ties symbiogenesis to Gaia theory.

She has also contributed two other, more technically oriented books about symbiogenesis. One is Symbiosis in Cell Evolution: Microbial Communities in the Archean and Proterozoic Eons. The second, an edited volume, is Symbiosis as a Source of Evolutionary Innovation: Speciation and Morphogenesis, with René Fester.

Because of the view offered by SET, Margulis argues that Protoctista - and for that matter all eukaryotes - are perhaps better conceived as microbial communities than individuals, even though the symbionts have evolved to a point where they cannot live independently.

But the importance of SET doesn't stop with cell evolution. Margulis argues that symbiogenesis has played a more important role in the evolution of all eukaryotes than Darwin's theory of natural selection acting on random genetic mutation. Darwin's theory is important, but more so among bacteria (with higher mutation rates) than among eukaryotes.

But in terms of explaining macroevolution in more complex organisms than bacteria, symbiogenesis is likely to be equally, if not more, important.

The most famous and well-studied organisms larger than protoctistans that evolved via symbiogenesis are lichens, symbiotic associations between algae and fungi that are so biologically intertwined that they coexist as a single organism with its own species name. (There are many species of lichens.) Lichens often form a colorful, crusty coating on rocks and trees in dry and high altitude climates.

Whether symbiogenesis is indeed as important as natural selection in the evolution of multicellular organisms, although very compelling, is very controversial to say the least.