‘Candidatus Thermochlorobacter aerophilum:’ an aerobic chlorophotoheterotrophic member of the phylum Chlorobi defined by metagenomics and metatranscriptomics

Abstract

An uncultured member of the phylum Chlorobi, provisionally named ‘Candidatus Thermochlorobacter aerophilum’, occurs in the microbial mats of alkaline siliceous hot springs at the Yellowstone National Park. ‘Ca. T. aerophilum’ was investigated through metagenomic and metatranscriptomic approaches. ‘Ca. T. aerophilum’ is a member of a novel, family-level lineage of Chlorobi, a chlorophototroph that synthesizes type-1 reaction centers and chlorosomes similar to cultivated relatives among the green sulfur bacteria, but is otherwise very different physiologically. ‘Ca. T. aerophilum’ is proposed to be an aerobic photoheterotroph that cannot oxidize sulfur compounds, cannot fix N2, and does not fix CO2 autotrophically. Metagenomic analyses suggest that ‘Ca. T. aerophilum’ depends on other mat organisms for fixed carbon and nitrogen, several amino acids, and other important nutrients. The failure to detect bchU suggests that ‘Ca. T. aerophilum’ synthesizes bacteriochlorophyll (BChl) d, and thus it occupies a different ecological niche than other chlorosome-containing chlorophototrophs in the mat. Transcription profiling throughout a diel cycle revealed distinctive gene expression patterns. Although ‘Ca. T. aerophilum’ probably photoassimilates organic carbon sources and synthesizes most of its cell materials during the day, it mainly transcribes genes for BChl synthesis during late afternoon and early morning, and it synthesizes and assembles its photosynthetic apparatus during the night.

BciD Is a Radical S-Adenosyl-l-methionine (SAM) Enzyme That Completes Bacteriochlorophyllide e Biosynthesis by Oxidizing a Methyl Group into a Formyl Group at C-7

“…In aquatic systems, organisms with chlorosomes containing BChl d typically occur at shallower depths than organisms containing BChl c (12, 54 -56). A similar pattern is observed in benthic mat systems in chlorophototrophic mats associated with alkaline siliceous hot springs in Yellowstone National Park (57,58). When BChl e assembles into supramolecular aggregates in chlorosomes, an emergent absorption band appears at about 525 nm (see Fig.…”

Role of Polyphosphate in Thermophilic Synechococcus sp. from Microbial Mats

“…Based on homology, some of these genes were identified as being from Synechococcus sp. while others were identified as putatively belonging to the filamentous anoxygenic phototrophs (FAPs) Roseiflexus and Chloroflexus spp., which are prominent members of the mat community (data not shown) (40). These FAPs also contain other enzymes associated with poly P metabolism, including the poly P-AMP-phosphotransferase (41).…”

A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer

“…We applied DNA sequencing with metagenomic assembly, constructed draft genomes, annotated the taxonomy and function of the ORFs, and subsequently performed read mapping of mRNA sequences to the metagenomic ORFs. Generally, this approach improves the number of mRNA reads used for analyses because they are mapped to an identical DNA template [31][32][33][34] . Additionally, this procedure allowed us to correlate gene expression results to specific strains in the community.…”

“…The success of this approach relies heavily on using simplified EET stimuli to induce gene expression changes, and the strength of using the same genetic background for metatranscriptomic analyses. Generally, metatranscriptomic analyses have demonstrated between 0.5 and 40% of mRNA reads mapped 15,16,[31][32][33][34][35][36][37] . We found that over 60% of mRNA reads were mapped to the reference metagenomic contigs (Supplementary Table S2), which indicates a higher representation of overall gene expression profiles within the microbial community.…”