Group post: Composition and function of bacterial communities

Heterotrophic microbial communities are responsible for remineralising and transforming a considerable fraction of organic matter in marine systems and help shape the nature and quantity of carbon and nutrients that pass from surface waters to the deep ocean. The first step in this transformation is the release of extracellular enzymes to hydrolyse high molecular weight (MW) compounds to smaller substrates. A focal point for investigation has been the differences in the nature and composition of aggregate-associated and free living microbial communities. Low MW substrates have previously been used in these investigations to act as proxies when assessing the capabilities of microbial communities. However, these proxies provide no information on many enzyme processes. A study by D’Ambrosio et al. (2014) instead used high MW substrates and, for the first time, measured potential enzyme activity directly from the same filters used for community analysis. The focal point of this study was the potential polysaccharide hydrolysing endo-acting enzymes as high MW carbohydrates constitute a large percentage of phytoplankton detritus as well as marine POM and DOM.

Carboys were used to hold water samples collected from sampling sites. Inshore samples were collected at 3-4m depth (surface) on the North shore of Bogue Sound in late October and offshore samples were collected in early December at depths of 2m (surface), 146m (midwater), and 505m (deep/bottom water). The differences in sampling times and depths may have caused discrepancies in the consistency of the microbial communities collected due to high turnover rates. Changes in surface depth samples may also alter community composition.

Samples collected both on and offshore were gravity filtered over 17 hours to separate free living and particle associated communities. Onshore samples were filtered immediately after collection whereas offshore samples were filtered after 10 days. This again may result in changes to composition and enzyme function due to a long storage time.

Hydrolysis measurements were used to assess enzyme activities and specific substrate hydrolysis. Six different fluorescently labelled polysaccharides were used, however, the paper does not describe where they were found or at what concentrations they are normally found in the environment. This would allow for more accurate comparisons for abundance or hydrolysis rates. Potential rates were compared at day 2 and day 7 for the offshore samples and day 8 for coastal.

The experimental design of this study was able to link the potential substrate hydrolysis rates of a community functions to community composition using clone libraries which provided a measure of the extent and active members of the community at initiation of the hydrolysis experiments.

After two days of incubation, summed hydrolysis rates in whole water were higher in coastal than in offshore waters. The same pattern of hydrolysis rates can also be seen after 7/8 days of incubation. At the coastal station all six substrates were hydrolysed in whole water after 2 days while at the offshore station only 3/4 were hydrolysed depending on depth. Even after extended incubation, the offshore communities hydrolysed a narrower spectrum of substrate. Similar to the patterns of enzyme activities, patterns of 16S rDNA and rRNA sequences showed spatial distinctions. rDNA and rRNA clone libraries from coastal surface waters were dominated by SAR11 and Roseobacter respectively but offshore surface  libraries were dominated by the groups Pseudoalteromonas (particle-associated DNA library) and Thalassospira (free-living RNA library). The mid-depth and bottom libraries from colder water offshore were dominated by Gammaproteobacteria.

Although the bacterial communities changed extensively with depth, the ability to hydrolyse a particular substrate changed more gradually. Bottom water communities only hydrolysed laminarin, xylan and chondroitin. Depth-related changes in microbial community composition were quite distinct with a strong partitioning between surface water and the deepwater column communities. The DNA and RNA libraries also indicate bacterial populations with attenuated activity and rRNA content or entirely inactive populations.

It was found that compositional differences between particle-associated and free-living communities did not change with depth. The two types exhibited similar summed hydrolysis rates but the time point for enzyme detection differed. Overall, the particle and free-living communities hydrolysed the same spectrum of substrates as the unfiltered fraction.

Functional redundancy occurs when groups of bacteria share the capacity to use a certain substrate, so not all of the bacteria have to produce the enzyme to hydrolyse it otherwise it could result in a waste of resources. Laminarin, for example, was hydrolysed rapidly by all the samples used in the study because it has a wide distribution so many microbial phyla have the ability to hydrolyse it. Also it was found that cultured marine bacteria in close relation to Gamma- and Alpha-proteobacteria in the clone libraries can grow on laminarin and are able to use it as a sole carbon source.

Although the authors of this paper assume that the long filtration time is unlikely to affect the results it is possible that it might cause changes to the community composition and enzyme activity. Different filtration methods should be compared to ensure that this does not affect community composition and function. The samples were also kept for 10 days after collection at 4^oC. This could also affect the community structure and composition as many papers have showed that within a few days of collection bacterial community structure is likely to change drastically. There is also very little information present as to why these six carbon sources were chosen and their relevance. While laminarin and fuciodan might be very wide spread compounds, the other compounds are likely to be very rare so few bacteria would be expected to hydrolyse them.

(Group: B. Oliver, B. Sockett, M. Nisulescu)

D'Ambrosio, L., Ziervogel, K., MacGregor, B., Teske, A., & Arnosti, C. (2014). Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison. The ISME journal.

http://www.nature.com/ismej/journal/v8/n11/full/ismej201467a.html