Cultivation and Genomic, Nutritional, and Lipid Biomarker Characterization of Roseiflexus Strains Closely Related to Predominant In Situ Populations Inhabiting Yellowstone Hot Spring Microbial Mats

Abstract

Roseiflexus sp. strains were cultivated from a microbial mat of an alkaline siliceous hot spring in Yellowstone National Park. These strains are closely related to predominant filamentous anoxygenic phototrophs found in the mat, as judged by the similarity of small-subunit rRNA, lipid distributions, and genomic and metagenomic sequences. Like a Japanese isolate, R. castenholzii, the Yellowstone isolates contain bacteriochlorophyll a, but not bacteriochlorophyll c or chlorosomes, and grow photoheterotrophically or chemoheterotrophically under dark aerobic conditions. The genome of one isolate, Roseiflexus sp. strain RS1, contains genes necessary to support these metabolisms. This genome also contains genes encoding the 3-hydroxypropionate pathway for CO 2 fixation and a hydrogenase, which might enable photoautotrophic metabolism, even though neither isolate could be grown photoautotrophically with H 2 or H 2 S as a possible electron donor. The isolates exhibit temperature, pH, and sulfide preferences typical of their habitat. Lipids produced by these isolates matched much better with mat lipids than do lipids produced by R. castenholzii or Chloroflexus isolates.We have investigated laminated cyanobacterial mats in alkaline siliceous hot springs of Yellowstone National Park (Octopus Spring and Mushroom Spring) as models for understanding principles of microbial community ecology (49, 51, 54) and as models of stromatolites (50, 55), which are important fossilized microbial communities of the Precambrian. These mats are dominated by unicellular cyanobacteria (Synechococcus spp.) and filamentous anoxygenic phototrophic bacteria (FAPs) (e.g., Chloroflexus spp. and Roseiflexus spp.); they also contain newly described anoxygenic phototrophic bacteria (8) and many organisms involved in mat decomposition (49). We have studied the composition and structure of the mat community using both nucleic acid and lipid biomarker approaches (50), as well as the functional contributions of and interactions among community members (34, 46, 47).A major finding from molecular analyses was that the predominant Synechococcus spp. of the mat are distantly related to readily cultivated strains (15, 49). Careful cultivation of predominant strains was necessary before we could observe phenotypic properties of Synechococcus sp. isolates that were useful for understanding the in situ ecology of native mat populations (2). Genomic analysis of relevant isolates has also vastly improved our ability to understand metagenomic Similarly, based on small-subunit rRNA (SSU rRNA) cloning and sequencing and fluorescent in situ hybridization (FISH) probing, the dominant FAPs of the community were found to be distantly related to readily cultivated Chloroflexus spp. but closely related to Roseiflexus castenholzii (35), a bacteriochlorophyll a-containing anoxygenic phototroph lacking chlorosomes, which was initially cultivated from a Japanese hot spring (20). Only one SSU rRNA sequence somewhat distantly related to that of Heliothrix oregonensis, the only ot...

Identification of the Bacteriochlorophylls, Carotenoids, Quinones, Lipids, and Hopanoids of "Candidatus Chloracidobacterium thermophilum"

“…Because wax esters were not analyzed separately, and wax esters can occur in significant amounts in chlorosomes (15,60), it is possible that some of the alcohols identified might be derived from these components. There is no precedent to suggest that the 14-methyl-pentadecanol (iso-C 16 alcohol) and 15-methylhexadecanol (iso-C 17 alcohol) could be esterifying alcohols for BChls, while they can be prominent components in wax esters of some FAPs (74) and, thus, may be derived from wax esters. Four isoprenoid alcohols were identified, including farnesol (i-C 15:3 -OH), geranylgeraniol (i-C 20:4 -OH), phytol (i-C 20:1 -OH), and phytadienol (i-C 20:2 -OH).…”

Coassimilation of Organic Substrates via the Autotrophic 3-Hydroxypropionate Bi-Cycle in Chloroflexus aurantiacus

“…Only members of the family of Chloroflexaceae (Chloroflexus aggregans and Roseiflexus spp.) harbor all the genes required to establish the complete 3-hydroxypropionate bi-cycle (22,40,44). Interestingly, Oscillochloris trichoides (also Chloroflexi) possesses only genes encoding malonyl-CoA reductase and propionyl-CoA synthase but lacks genes of the second glyoxylate assimilation cycle (21,25).…”

“…Key genes of the autotrophic pathway are indicated by a gray background and genes required for glyoxylate assimilation by a white background. Lowercase represents genes with low identities (less than 40 …”

In Situ Hydrogen Dynamics in a Hot Spring Microbial Mat during a Diel Cycle

“…Genomic and metagenomic analyses of microbial mats in Mushroom Spring and Octopus Spring have demonstrated that Roseiflexus (15,27), but not Synechococcus (28), possesses hydrogenases and might thus produce H 2 by fermentation. The lack of hydrogenases in Synechococcus means that any H 2 produced by Synechococcus nitrogen fixation is lost to the environment where other mat organisms may use it as an electron donor in anoxygenic photosynthesis or respiration.…”