The great diversity of microbial assemblages

A Review of: J A Gilbert, et al. (2011). Defining seasonal
marine microbial community dynamics. The ISME Journal.

This paper explores the seasonal variability of microbial assemblages, focusing on the environmental factors which influence their varying diversity. The study summarises a 6-year time series of 16S rRNA tag pyrosequencing of samples taken from the English Channel. This topic has been widely researched before now where previous researchers have mainly focused on the importance of temperature and nutrient concentrations, and have rarely collected samples over such a long period. The introduction to this paper suggests that only very recently have molecular techniques been useful descriptions of these microbial assemblages. These techniques are also constantly being developed and improved in order to better map microbial communities.

It was recently shown in a previous 1-year study by Gilbert et al (2009) that bacterioplankton diversity followed a latitudinal gradient, with maximum potential richness being primarily fuelled by temperature. The main aim of the study is to expand on this discovery, by further characterising the potential drivers of seasonal patterns of bacterioplankton diversity in the Western English Channel. Three factors were chosen to be analysed for potential correlations with the observed seasonal patterns. These were varying concentrations of inorganic nutrients, annual water-temperature cycle, and the population structure of the eukaryotic phytoplankton and zooplankton. In order to test their theories samples were collected on 72 instances between January 2003 and December 2008 from the same site. Bacterial diversity was examined from each sample which included assessing a wide range of variables. These variables include phytoplankton and zooplankton species abundance, the concentrations of ammonia, nitrate and nitrite, phosphate, silicate, total organic carbon and nitrogen, salinity, chlorophyll, photosynthetically active radiation, North Atlantic Oscillation data, day length, primary productivity and temperature.

Bacterioplankton was found to be very diverse at the chosen sample site with a total of 8794 different OTUs (operational taxonomic units) found over the 6-year series. While this shows great diversity at this location, a common problem associated with studies of natural assemblages was faced – identifying sequences to species level. The taxonomic levels that were achieved for the remaining OTUs are as follows – Phylum (9%), Class (32%), Order (10%), Family (26%), Genus (21%). The study showed significant seasonal variations in OTU frequency throughout the 6-year period, but also strong repeating patterns. The Alphaproteobacteria were the most abundant Class, which was expected. OTUs most frequently recorded were of the Ricketsiales and Rhodobacteriales. Flavobacteriales were also found in high frequency.

Alpha diversity was relatively constant across the 6-year series, but showed distinct cyclical patterns with a maximum in winter and minimum in summer. This pattern was further confirmed by analysis of variance for all taxa. It is suggested that this seasonal cycle was also consistent across the 6-year series. Seasonal trends in the most abundant bacteria were very interesting, and also gave consistency to what is already known from single-strain-level studies. One of the most abundant Orders, Rickettsiales, tended to peak in winter, favouring low levels of light and primary production, but maximum concentrations of inorganic nutrients. In contrast, Rhodobacterales peaked in spring and autumn, where nutrient concentrations are lower, but primary production is higher.

Another interesting part of the study which I would have liked to see in more depth was the mention of bacterial ‘blooms’. At one stage during the study a single Vibrio species accounted for 54% of the sequences. However, at all other times, this taxon was rare, with an abundance of 0-2%. The peak also correlated with an increased abundance of the diatom, Chaetoceros compressus, which at all other times had a similarly low abundance. The study does not look at this in more depth, but it could be of interest to analyse the relationship.

This study has shown that strong seasonal patterns exist in this surface water microbial community. The patterns of most abundant, common and variable OTUs are also consistent with other reports. This suggests that seasonal succession patterns of marine surface water bacterial communities in temperate regions may be sustained across different regions also. The study has also identified key drivers of the communities varying diversity. Day length has proven to be an important factor for describing temporal community structure, being the variable which best supports overall bacterial richness. The taxa identified also present different seasonal cycles, relying on varying concentrations of inorganic nutrients. Also, blooms of rare OTUs may be linked to changes in population structure of eukaryotic species and environmental variables. The techniques used to monitor such driving forces still need to be greatly improved in order to better identify patterns in microbial community composition. Monitoring these patterns over a greater time scale is also important to confirm persistence. Despite this, the study has successfully highlighted the factors which influence the varying diversity in microbial assemblages. It is however important to consider that microbial communities are very diverse, fast-growing and dependent on local environmental conditions. These highly sensitive communities can be a great measure of the state of the microbial food web and are important to consider when looking at the bigger picture – they may well serve as important indicators, being the first reactors to the biologically critical effects of anthropogenic activities and global climate change.