Small Cell, Big Potential

Actinobacteria are one of the most abundant bacteria in freshwater ecosystems, however are still yet to be cultured. Other studies have focused on the abundance and distribution of this bacteria over time and space, however this was the first study that aimed to gain an insight into the physiology of the acI lineage of Acintobacteria using single-cell genomics.

Water samples were taken from Lake Mendota, USA at 1m depth in May 2009. The samples were prepared and a single amplified genome was selected, this particular one being from the acI-B1 clade. This was chosen as it is one of the most abundant in the acI lineage and also had a low multiple displacement amplification critical point, suggesting there was a significant amount of DNA readily available. This seemed an appropriate choice, given past experiments were unsuccessful in physiology analysis when using acl-A, due to the low abundance of this clade.

Core gene analysis was used to estimate a genome size of 1.2Mb. Furthermore, 118 cell membrane transporters were found in the genome, which is relatively small in comparison to other marine microorganisms. This may be due to the small genome size. However this does demonstrate that this cell is highly specialised, as despite the small size it is still capable of utilising a range of metabolic pathways. The genome codes for glycolysis, the pentose phosphate pathway, the citrate cycle and oxidative phosphorylation, suggesting Actinobacteria function by aerobic respiration. However, genes were also present for the fermentation of pyruvate to lactate, indicating that anaerobic respiration can be adopted, an advantageous trait given that oxygen levels in lakes can rapidly change depending on the season. Moreover, the acI-B1 lineage was found to contain actinorhodopsin genes, suggesting they may be able to produce energy from light. Another interesting find was a range of carbohydrate active enzymes that hydrolyse polysaccharides, in particular a chitinase-like protein. These enzymes enable the uptake and degradation of chitin, which is a major component of freshwater ecosystems. This further demonstrates the versatility of Actinobacteria, as they can become primary polysaccharide degraders or take up monosaccharides released when other heterotrophs degrade polysaccharides, depending on the varying substrate availability.

Many mechanisms associated with stress resistance were also discovered, with 6.5% of the overall genome being dedicated to DNA repair. This may be due to the bacteria living so close to the water surface, with continuous exposure to reactive oxygen, meaning repair is essential to enable such oxidative stress to be endured. Many other enzymes, thought to come into play during times of increased competition, were also found. For example, released lysozymes break down the cell wall of other microbes and cyanophycinase can cause cyanophycin to release aspartic acid and arginine. These amino acids can then be taken up by ABC transporters in acI-B1 cells and used for basal cellular metabolism. This is thought to be an important factor in the niche separation of acI-B1 cells during summer as there is a significant carbon and energy source provided by decaying cyanobacterial blooms at this time.

Although this was the first study to analyse the whole genome of the acI lineage, two other studies have sequenced large fragments of the acI-A6 and acI-B1 clade. These studies showed a 77% and 88% protein sequence similarity, respectively, with the current study. The relatively high level of similarity of the acI-A clade suggests future comparative analysis of metagenomic studies from samples containing diverse members of the acI lineage should be possible.

I found this a very interesting study as it is the first to achieve an almost complete genome of the previously uncultured Actinobacteria. Since this is the most abundant bacterioplankton in freshwater ecosystems, these findings help gain an understanding of the metabolic potential and ecological niche this microorganism occupies and can also be used to aid genomic analysis of other members of the acI lineage in the future. 

Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton

Sarahi L Garcia¹, Katherine D McMahon^2,3, Manuel Martinez-Garcia^4,9, Abhishek Srivastava⁵, Alexander Sczyrba^6,7, Ramunas Stepanauskas⁴, Hans-Peter Grossart^5,8, Tanja Woyke⁷ and Falk Warnecke¹

The ISME Journal (2013) 7, 137–147; doi:10.1038/ismej.2012.86; published online 19 July 2012

http://www.nature.com/ismej/journal/v7/n1/full/ismej201286a.html