A review of: Gilbert, JA. Steele, JA. Caporaso, JG. Steinbruck, L. Reeder, J. Temperton, B. Huse, S. McHardy, AC. Knight, R. Joint, I. Somerfield, P. Furhman, JA. Field, D. (2011), Defining seasonal marine microbial community dynamics. International society for Microbial ecology: 1 – 11.
The Western English Channel has been extensively studied for the last 100 years, providing a wealth of data on temporal microbiological complexity. With the recent introduction of molecular techniques, satisfactory descriptions of natural microbial assemblages have been generated.
Previous efforts to determine which factors might affect microbial communities have largely focused on the importance of temperature and nutrient concentrations, understandably so because of the strong effect temperature has upon biological processes and because nutrient concentrations can drive niche structure through resource partitioning. This study however goes beyond the initial 1 year study by Gilbert et al (2009) to test the influence of three competing alternative factors: (1) varying concentration of inorganic nutrients; (2) annual water-temperature cycle; and (3) population structure of phytoplankton and zooplankton and summarizes in this paper a 6-year time series of 16S rRNA tag pyrosequencing taken from a station in the English Channel.
From the observations, the authors divided the different micro-organisms found into three broad categories. The first group was the ‘most abundant’ OTU’s, such as Rickettsiales and Rhodobacterals. The second group was dubbed ‘most common’ OTU’s, containing those organisms that had the highest persistence over the six year sampling time. The third and final group was the ‘most variable’ OTU’s containing organisms that would be rare during certain times and bloom uncontrollably at others.
Overall they concluded that, throughout the 6-year period, the monthly pattern and broad seasonal changes in microbial assemblages indicate that the ‘most abundant’ and the ‘most common’ OTU’s have temporally defined niches. In contrast however, the most variable OTU’s have niches that can be defined temporally as well as by nutrient pulses and changes in currents.
This study highlights the added value of much longer temporal observations of natural communities as subtle changes in certain individual taxa were only detectable because of the long time series. It is quick to point out limitations of studying communities influenced by hydrography and the difficulty it causes in interpreting results. It also calls into question the relative effect of the currents and, by association, wind speeds and directions in the English Channel and its role on microbial community dynamics, admitting that more research needs to be done to fully take into account its potential effect.
2 comments:
Thanks for the review Nikie. It might be helpful to remind everyone that OTUs stands for operation taxoniomic units - a term derived from 16s rRNA analysis. This is typically based differences of less than 3% in sequence identity. Do the authors discuss the fact that this can hide a great deal of microdiversity? For example, ecotypes of Prochlorococcus marinus grwoing at different depths have less than 2% diference in 16s rRNA gene sequences and are considered as one species (or OTU). However, they have vast differences in the genome and physiological properites.
Yes, the authors do mention that in order to compensate for potential overestimation in diversity resulting from pyrosequencing and amplification errors they used several ‘noise reduction strategies’ such as SLP (Single- Linkage Preclustering) which grouped the OTU’s at 2% sequence identity. This reduced the number of OUT’s counted dramatically. Later comparisons between the techniques used (SLP, Denoiser and non-denoising/ filtering) indicated that overall, the same patterns of community diversity were evident with each technique but that SLP was the most conservative and therefore used for subsequent analysis.
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