SAR86 is a ubiquitous clade of 16S rRNA which is highly resistant to cultivation in the lab. In previous studies the genomes of some sub-classes have been shown to include genes for rhodopsin, allowing the bacteria to use light to supplement ATP production. However no work has been done on the metabolic capabilities of the clade.
SAR86 genomes were sequenced by combination of flowcytometry and PCR, and then gene fragments from across the clade were compared to genetic libraries to investigate their metabolism. This revealed four main assemblies of genes for the clade, named A, B, C and D. The genomes of A and B were 90% complete, whereas the genomes for C and D were roughly 50% complete. Comparing gene segments to the GOS metagenomic library (sampled from around the world) revealed ecotypes for each group; A segments were found in the open ocean, B segments were found in warm coastal waters, gene fragments from both C and D were found in the colder coastal sites. This is similar to what Colin was teaching, a small streamlined genome reducing the overall maintenance of the genes, but reducing the adaptability of the bacteria leaving a narrow environment in which it can live.
Dupont et al. (2012) found SAR86 to be free living aerobic heterotrophs with a buffering capacity of phototrophic ATP (via proteorhodopsin). All SAR86 were found to be largely auxotrophic in regards to vitamins and some animo acids (except from sub-class B having a Vitamin B1 biosynthesis pathway). However the authors point out that this could be due to either; the use of alternative biosynthetic routes yet undiscovered or the genes coding for the proteins were on fragments lost in analysis.
Two clades which recruited the largest portions of GOS were SAR86 and SAR11 which are often found in the same environment, so the authors made comparisons between the two most abundant bacterial clades. SAR11 uses protein compounds as primary energy source, whereas SAR86 utilises fats and carbohydrates as primary energy source. Both SAR11 and SAR86 contained sulphur reducing metabolic pathways, but SAR86 has a putative transporter for glutathione and ϒ-glutamyl transferases (allows the break down of glutathione into cysteine) which means SAR86 has a relatively larger pool of organic sulphur to metabolise than SAR11.
To conclude Dupont et al. (2012) draws attention to the relatively small overlap between the niches of both SAR11 and SAR86, and ties the abundance of both Clades to the ratios of protein, carbohydrate and lipids found within the sea.
Hi Myles,
ReplyDeleteI was just wondering what the reasoning was behind the genomes being only 50% complete - was this that they didn't know what the other 50% of genes coded for or that they only had 50% of the genome for some reason or another? You mention later on about fragments lost in analysis; was this what happened to the other 50%?
Thanks,
Robyn
Hi Robyn,
ReplyDeleteThe only explanation the authors give to the missing fragments are either the extraction process or through PCR.
The way they estimated the genomes was by comparing the genomes to a catalog of 107 single copy genes that are ubiquitous to all free living bacteria. 'A' had 100 of the 107 genes, 'B' had 99, etc. leading to >90% complete genomes for 'A'&'B'. The paper doesnt give the exact numbers for groups 'C'&'D' but just the percentages, i assume they were worked out in the same way. However it is worth noting that the seven of the missing genes from 'A' werent found in B,C or D either. Which to me suggests either; a streamlining in the clade, or an issue in the authors technique which excludes certain DNA fragments.
Thanks, Myles