Table 3.
Microbial Reference Systems for Investigations of Elemental Economy
| Domain:Phylum | Organism (abbreviation) | Environment | Nutrition | Notable mechanisms for elemental economy |
|---|---|---|---|---|
| A. Model systems for molecular genetic studies | ||||
| B: Proteobacteria | Escherichia coli (Eco) | mammalian intestine | facultative anaerobe | C/N - elemental optimization; recycling by ribophagy S - elemental optimization Fe - Fur regulon; Fe-sparing (RyhB sRNA); isozyme substitution, MnSOD vs. FeSOD; Mn RNR vs. Fe RNR |
| B: Firmicutes | Bacillus subtilis (Bsu) | soil, rhizosphere | facultative anaerobe | C/N - recycling by cannibalism P - P-sparing and recycling by cell wall remodeling Fe - Fur regulon; Fe sparing (FsrA sRNA); flavodoxin substitution for ferredoxin Zn - Zur regulon; ribosomal protein mobilization, FolE2 |
| A: Euryarchaeota | Halobacterium salinarum (Hsa) | halophilic archaeon | Fe - Fe acclimation response defined | |
| A: Euryarchaeota | Methanococcus maripaludis (Mma); Methanosarcina acetivorans (Mac) | methanogenesis | Ni - Ni sparing response for methanogenesis enzymes Mo/W-isozymes of formylmethanofuran dehydrogenases |
|
| E: Ascomycota | Saccharomyces cerevisiae (Sce) | yeast, model eukaryote | respiration, fermentation | C/N - elemental optimization; recycling S - S-sparing, substitution with S-depleted isozymes Fe - Fe-sparing (Aft1/Aft2 and Cth1/Cth2 regulons); isozyme substitution Zn - Zn-sparing by Zap1 repression of Adh1 and Adh3 |
| E: Chlorophyta | Chlamydomonas reinhardtii (Cre) | soil | photosynthetic and heterotrophic | N - ribophagy during gametogenesis S - S-sparing, substitution with isozymes; recycling of S from sulfolipids P - substitute P-lipids with S-lipids; recycle P from chloroplast DNA by copy number reduction Fe – down-regulation of PS I and Fd, prioritizing respiration over photosynthesis under heterotrophic conditions, chloroplast MnSOD induced Cu – Cyt c6 for plastocyanin, flavin amine oxidase instead of Cu amine oxidase |
| B. Reference systems for environmental and genomics-based studies in marine ecosystems | ||||
| B: Cyanobacteria | Prochlorococcus marinus (Pma) | oligotrophic open ocean | smallest known phototroph, | P - substitute P-lipids with S-lipids Fe - PS I remodeling |
| B: Cyanobacteria | Trichodesmium (Tri) | oligotrophic open ocean | phototroph, diazotroph | Fe- Fe-sparing by down-regulation of nitrogen fixation; Fe mobilization from Dps miniferritin |
| B: Cyanobacteria | Synechococcus (Syn) | mesophilic ocean and freshwater species | phototroph | N - recycling by phycobilisome degradation Fe - Fe sparing; flavodoxin substitution for ferredoxin Ni - recycling of Ni from urease to SodN (proposed) |
| B. Cyanobacteria | Synechocystis (Syc) | freshwater lake | phototroph | Cu - Cyt c6 for plastocyanin |
| B: Cyanobacteria | Crocosphaera watsonii (Cwa) | oligotrophic open ocean | phototroph, diazotroph | Fe - diurnal cycling of iron between photosynthetic and nitrogen fixation complexes (reduces Fe quota by 40%) |