Heme auxotrophy in abundant aquatic microbial lineages

Abstract

Heme, a porphyrin ring complexed with iron, is a metalloprosthetic group of numerous proteins involved in diverse metabolic and respiratory processes across all domains of life, and is thus considered essential for respiring organisms1,2. Several microbial groups are known to lack the de novo heme biosynthetic pathway and therefore require exogenous heme from the environment3. These heme auxotroph groups are largely limited to pathogens4,5, symbionts6,7, or microorganisms living in nutrient-replete conditions8, whereas the complete absence of heme biosynthesis is extremely rare in free-living organisms9. Here, we show that the acI lineage, a predominant and ubiquitous free-living bacterial group in freshwater habitats, is auxotrophic for heme. We found that two recently cultivated acI isolates10 require exogenous heme for their growth. According to whole-genome analyses, all (n=20) isolated acI strains lacked essential enzymes necessary for heme biosynthesis, indicating that heme auxotrophy is a conserved trait in this lineage. Analyses of >24,000 representative genomes for species clusters of the Genome Taxonomy Database (GTDB) revealed that heme auxotrophy is widespread across abundant but not-yet-cultivated microbial groups, including Patescibacteria, Marinisomatota (SAR406), Actinomarinales (OM1), and marine group III Euryarchaeota. Our findings indicate that heme auxotrophy is a more common phenomenon than previously thought, and may lead to use of heme as a growth factor to increase the cultured microbial diversity.

Emerging connections between gut microbiome bioenergetics and chronic metabolic diseases

“…However, lack of heme biosynthesis in free-living organisms is considered extremely rare. Challenging this long-standing belief, a recent screen of more than 24,000 bacterial genomes (GTDB database r95) showed that heme auxotrophy is in fact highly prevalent across many ubiquitous bacterial groups found in freshwater habitats (Kim et al, 2021). Another study supporting this also detected the presence of nanomolar levels of the iron(III) protoporphyrin IX (heme precursor)-like compounds in natural estuarine water bodies (Vong et al, 2007).…”

Regulation of heme biosynthesis via the coproporphyrin dependent pathway in bacteria

“…In some monoderm bacteria, the terminal heme biosynthesis enzyme coproheme decarboxylase (ChdC) and other enzymes of the CPD are found, but the CPD does not appear to be the predominant heme biosynthesis pathway across these phyla. In the Chloroflexota, for example, combinations of enzymes of the protoporphyrin dependent pathway (PDP), Siroheme and CPD pathways are found, with some species having enzymes from all three pathways (Kim et al, 2021). Though several genomes have the terminal heme synthesis enzyme coproheme decarboxylase (ChdC see Figure 1), no species that have been found to have a complete heme biosynthesis pathway utilizes only the CPD pathway (Kim et al, 2021).…”

“…In the Chloroflexota, for example, combinations of enzymes of the protoporphyrin dependent pathway (PDP), Siroheme and CPD pathways are found, with some species having enzymes from all three pathways (Kim et al, 2021). Though several genomes have the terminal heme synthesis enzyme coproheme decarboxylase (ChdC see Figure 1), no species that have been found to have a complete heme biosynthesis pathway utilizes only the CPD pathway (Kim et al, 2021). The first enzyme unique to the CPD, coproporphyrinogen III oxidase (CgoX see Figure 1), and the last, ChdC, have also been found in multiple bacteria of the Deinococcota, suggesting that the CPD may be utilized by these bacteria, though further studies are needed to verify that heme is synthesized via this pathway (Dailey et al, 2015).…”