Scanning electron micrographs of cells of (left) Heliobacterium modesticaldum, and (right) an unclassified coiled Heliorestis species        from an Egyptian soda lake.

The Heliobacteria: Heliobacterium modesticaldum

Heliobacteria are anoxygenic phototrophs that contain Bchl g (Madigan and Ormerod 1995). Heliobacteria are the most recently discovered of the major groups of anoxygenic phototrophs, with the first species described only 20 years ago (Gest and Favinger 1983). Heliobacteria are primarily soil residents (Stevenson et al. 1997) and are phylogenetic relatives of the endospore-forming gram-positive Bacteria (Woese et al. 1885). True to their evolutionary roots, heliobacteria produce heat-resistant endospores complete with the signature molecule of these structures, dipicolinic acid (Ormerod et al. 1996; Kimble and Madigan 2001). Collectively, these features make heliobacteria unique, because all other phototrophic prokaryotes are gram-negative, nonsporulating and aquatic bacteria.

Heliobacteria produce the simplest known photosynthetic apparatus, with a homodimeric reaction center of the Fe-S type, containing both Bchl g and OH-Chl (not Bchl) a (Amesz 1995).

Because of this, the heliobacterial reaction center has become an excellent model for structure/function analyses of green plant photosystem (PS) I (Heathcoate et al. 2003). Bchl g is similar in structure to Chl a in that it has a vinyl group in the 3 position of ring A (Brockmann and Lipinski 1983; Michalski et al. 1987). Sequence analysis has revealed a photosynthesis gene cluster from the species Heliobacillus mobilis similar to that found in the proteobacteria, although in other respects the two groups are not closely related (Xiong et al. 1998). Several species of heliobacteria are known, including species from extreme environments. Extremophilic species include thermophiles, such as Heliobacterium modesticaldum (Kimble et al. 1995) and alkaliphiles, such as Heliorestis species (Bryantseva et al. 1999) (Fig. 2). Because of their unique assemblage of properties, the heliobacteria constitute their own taxonomic family of Bacteria, the Heliobacteriaceae (Madigan 1992; 2001a,b).

All heliobacteria isolated to date have a similar physiology. They are obligate anaerobes that grow best as photoheterotrophs (light as energy source and organic compounds as carbon sources). Photoautotrophic growth (light as an energy source with CO 2 as a carbon source) has not been observed but dark growth is possible by fermentation of pyruvate (Kimble et al. 1994). Heliobacteria are robust nitrogen-fixers (Kimble and Madigan 1992a), with some species containing multiple forms of nitrogenase (Kimble and Madigan 1992b). Although no genetic transfer system yet exists for the heliobacteria, these phototrophs are closely related to gram-positive bacteria. Many of the latter are genetically amenable by natural transformation and thus the prospects for future genetic manipulation of heliobacteria are encouraging.

Enrichment and isolation studies have shown the habitat of heliobacteria to be soil. Heliobacteria are common in agricultural soils, in particular, paddy soils (Stevenson et al. 1997). Since paddies experience alternating periods of flooding and desiccation, it is likely that the capacity to sporulate is a survival strategy for heliobacteria when flooded anoxic paddy soils turn oxic during the dry season. It is likely that heliobacteria thrive in paddy soils by catabolizing the organic exudates of rice plants in exchange for supplying fixed nitrogen to the plants via nitrogen fixation (Madigan and Ormerod 1995; Ormerod et al. 1996; Stevenson et al. 1997).

Significance of the Heliobacterium modesticaldum Genome Sequence

There are many compelling reasons to sequence a heliobacterium genome, both general and specific. An overarching justification is that our current understanding of the heliobacteria has raised fundamental questions concerning their role in the evolution of photosynthesis and their impact on modern plant agriculture. A heliobacterium genome sequence could provide stimulating new insights in both these areas.

Specifically, a heliobacterium genome sequence would: (1) reveal the extent of the genetic links between heliobacteria and gram-positive bacteria, links that have been forged primarily on phylogenetic grounds thus far; (2) expose key metabolic processes in heliobacteria not yet identified through physiological studies, for example, the capacity for autotrophy; (3) determine whether in addition to their photosynthetic reaction center, heliobacteria encode other proteins in common with other anoxygenic photosynthetic bacteria; (4) help explain the unusually high light requirements and low pigment contents of the heliobacteria (Kimble and Madigan 2002); (5) uncover hidden metabolic patterns in the heliobacteria of importance to their ecology, including potential alternative energy-generating mechanisms, catabolic pathways for organic carbon, and mechanisms for dealing with oxic conditions during plant associations; (6) yield insight on the sporulation process in heliobacteria, including clues for why sporulation seems tightly repressed in laboratory cultures (Kimble and Madigan 2001) and the nature of environmental cues (light, oxygen?) that signal the onset of sporulation or germination in these phototrophs; (7) identify the genetics behind the biosynthesis of the novel carotenoids of heliobacteria, including the glycosylated pigments of extremophilic species (Takaichi et al. 1997; 2003); (8) reveal whether the observed associations between heliobacteria and agricultural crops are merely casual ones, or are more like true symbioses involving recognition molecules and other specific plant/bacterial interactions; and finally, (9) fill the last remaining hole in the genomic picture of phototrophic bacteria. Indeed, with a heliobacterial genome in hand, issues surrounding the evolution of photosynthesis (Gupta et al. 1999; Gupta 2000, 2003; Xiong et al. 1998, 2000) and identification of the “common core” of photosynthesis genes (Raymond et al. 2002, 2003), could finally be addressed from the perspective of the genes of all known photosynthetic prokaryotes.

Why sequence the genome of this particular species of heliobacteria? H. modesticaldum is representative of the family Heliobacteriaceae (Kimble et al. 1995) and is closely related to paddy field species (Ormerod et al. 1996). Moreover, the genome of H. modesticaldum should be relatively easy to sequence; its G+C content is 54.5% and it is only ~3 Mb in size based on pulsed field gel electrophoresis (unpublished data). The H. modesticaldum genome sequence would be the first genetic blueprint of a thermophilic anoxygenic phototroph. In this connection the H. modesticaldum genome could potentially reveal structural principles governing the thermal stability of key proteins, such as its PSI-like reaction center and heat-active nitrogenase, of importance to both basic studies of photosynthesis and future agricultural productivity.