There are many groups of eukaryotes known that live in anaerobic environments. They do not possess textbook-like mitochondria: Some possess anaerobic mitochondria, some possess hydrogenosomes (hydrogen-producing mitochondria that usually lack a genome), and some possess no organelles of ATP-synthesis at all. The classical 'endosymbiont hypothesis' fails to account for the origin of these anaerobic organelles and their anaerobic biochemstry. We have put forward an alternative model for the origins of organelles, one that accounts both for oxygen-dependent and for anaerobic ATP-synthesis in eukaryotes (the 'hydrogen hypothesis'). We are currently testing the predictions of that model by investigating the enzymes of energy metabolism in two groups of eukaryotes that possess hydrogenosomes and in the photosynthetic protists Euglena gracilis, which has an unusual wax-ester fermentation in its facultatively anaerobic mitochondria. This work is currently flanked by proteom work (mass-spectrometry microsequencing of proteins from isolated organelles), by EST projects, and by DNA-microarray studies to examine gene expression profiles. Some papers on this topic are:

• Martin W, Müller M (1998) The hydrogen hypothesis for the first eukaryote. Nature 392:37-41.
  
• Embley TM, Martin W (1998) A hydrogen-producing mitochondrion. Nature 396: 517-519.
  
• Martin W (2000) A powerhouse divided. Science 287:1219.
  
• Rotte C, Martin W (2001) Endosymbiosis does not explain the origin of the nucleus. Nature Cell Biol. 8:E173-174.
  
• Rotte C, Stejskal F, Zhu G, Keithly JS, Martin W (2001) Pyruvate:NADP+ oxidoreductase from the mitochondrion of Euglena gracilis and from the apicomplexan Cryptosporidium parvum: A fusion of pyruvate:ferredoxin oxidoreductase and NADPH-cytochrome P450 reductase. Mol. Biol. Evol. 18: 710-720.
  
• Rotte C, Henze K, Müller M, Martin W (2000) Origins of hydrogenosomes and mitochondria. Curr. Opin. Microbiol. 3:481-486.
  
• Martin W (2000) Primitive anaerobic protozoa: The wrong host for mitochondria and hydrogenosomes? Microbiology 146:1021-1022.
  
• Martin W (1999) A briefly argued case that mitochondria and plastids are descendants of endosymbionts, but that the nuclear compartment is not. Proc. Roy. Soc. Lond. B. 266: 1387-1395.
  
• Müller M, Martin W (1999) The genome of Rickettsia prowazekii and some thoughts on the origins of mitochondria and hydrogenosomes. BioEssays 21:377-381.
  
• Dooijes D, Chaves I, Kieft R, Martin W, Borst P (2000) Conservation outside the order Kinetoplastida of base J as a constituent of nuclear but not nucleolar DNA in Euglena gracilis. Nucl. Acids Res. 28:3017-3021.
  
• Martin W, Hoffmeister M, Rotte C, Henze K (2001) An overview of endosymbiotic models for the origins of eukaryotes, their ATP-producing organelles (mitochondria and hydrogenosomes), and their heterotrophic lifestyle. Biol. Chem. 382: 1521-1539.