Synechococcus Population Dynamics and Diversity on the New England Shelf



The marine cyanobacterium Synechococcus is an important primary producer in coastalsystems. It can account for up to 20% of primary production (Li 1994) and is often the numerically dominant picoplankter in these waters. Despite many investigations, a complete picture of what controls Synechococcus population abundance at specific times during the year, as well as variation in year-to-year cycles, is still lacking in coastal systems. It is critical that we understand the bottom-up as well as the top-down factors that govern their abundance.

The environmental controls of coastal Synechococcus populations are likely to change throughout the year, especially given the complexity and frequently shifting conditions of coastal systems. How populations respond to these changes, however, is also likely to be a function of the physiological diversity present within the Synechococcus genus. Synechococcus is a diverse group. The genus has been partitioned into at least 14 clades, (Palenik 1994, Ahlgren & Rocap 2006, Penno et al. 2006), and natural Synechococcus populations are believed to be a composite of different clades. One hypothesis for this apparent diversity is that each clade has an ecologically distinct role, representing an ecotype with physiological adaptations that match prevalent environmental conditions (Rocap et al. 2002). Different ecotypes may differ in their contribution to primary production, nutrient cycling and food web interactions, which could have implications for ecosystem functioning.

The goal of my thesis research is to understand how environmental factors control Synechococcus population abundance and how the response of the population as a whole is determined by the diversity present. This project explores the Synechococcus population present at Martha’s Vineyard Coastal Observatory (MVCO) from an interdisciplinary approach. The first part of my thesis is a quantitative investigation into the relationship between environmental parameters (light, temperature and nutrients) and population metrics (abundance, growth rate, loss rate and productivity) using high resolution data from the automated submerged flow cytometer, FlowCytobot (Olson et al. 2003), that has been deployed at MVCO since 2003.

At this coastal site, a general seasonal pattern is observed from year to year, where a distinct spring bloom is characterized by a population increase of several orders of magnitude from roughly 100 cells per mL in winter to over 100,000 cells per mL in summer. However, data from FlowCytobot has revealed that there is significant variability at shorter timescales (days to weeks) that is much less predictable than the larger seasonal cycle. These small-scale variations can result in a 10-fold change in population abundance, which seem more prevalent during summer and autumn when cell concentrations are highest. It is not known whether these fluctuations are related to shifts in diversity, such as the decline of one ecotype. We do not fully understand what environmental and community factors shape an ecotype niche or which factors favor coexistence or complete dominance in a system. The second part of my thesis research investigates the Synechococcus population diversity at this site and how this diversity changes over different timescales.

To do this, I am currently undertaking the following thesis research objectives:

1) Characterize Synechococcus diversity patterns over annual cycles at MVCO using a targeted qPCR approach.

2) Isolate and characterize strains of Synechococcus from MVCO and determine whether any physiological differences are able to explain diversity patterns and larger population dynamics.

My data so far indicates that the population at MVCO is diverse as determined from sequencing environmental ntcA amplicons (the ntcA gene is our chosen diversity marker). I have found that two different clades are present at this site with a total of six distinct sublades present between them. I have been developing specific primer and probes sets that target each clade and subclade present for a qPCR procedure to quantify the abundance of each. Once these primer and probe sets have been optimized and checked for specificity to amplify only the desired clade/subclade, the abundance of each target for a 3-year time series of bimonthly to monthly samples from MVCO will be determined.

I have also cultured many isolates from MVCO over the past two years with the goal of obtaining a representative strain of each subclade/clade into culture.  To identify each strain, the ntcA gene is amplified and sequenced. I have determined the identity of 70 isolates, and at present I have representatives of two out of the six desired subclades. In my culture collection, I have at least 100 more isolates to be sequenced, and these may contain the representatives of the remaining desired subclades. Once isolates have been identified, I will characterize the growth rate response of each representative to different environmental conditions (light, temperature, etc). Growth response differences between the representative strains will provide information on the range of physiological diversity present. This information coupled with the information on diversity patterns (from the qPCR implementation) will help explain any observed diversity patterns.

I am requesting support from the Coastal Ocean Institute specifically to sequence the diversity marker gene (ntcA) of the remaining isolates in the culture collection to determine which clade/sublcade each belongs to. Without this information, the project cannot go forward as the choice of strains to characterize hinges on their identification. Funds are also requested for continued development and implementation of the qPCR procedure to quantify the abundance of each clade/subclade present. This data will provide insight into the relationship between the change in overall population abundance to the change in clade abundance and is key to be able to link the physiological data from the cultures to the larger population dynamic data.

At present, my advisors do not have funds to carry out these two research activities. Their expertise is not in molecular biology, and I have been collaborating with Anton Post at MBL to complete this aspect of my thesis. While Dr. Post has let me use his laboratory space and general lab reagents and supplies, additional funds are needed to carry out both the qPCR implementation and identification of isolates in my culture collection. This work has so far been supported from small grants from the MIT Student Assistance Fund and private donations. Biology Education Coordinator, Rebecca Gast, has also agreed to contribute $500 towards this project.

This project is unique in that it incorporates approaches from different fields to investigate Synechococcus population dynamics. Each avenue of research provides important knowledge and insight, but combined together, allows for a more detailed and complete picture of how Synechococcus populations respond to their often changing environments. As an important primary producer, it is critical that we understand how the diversity of the population can impact overall population dynamics. Thank you for your time and consideration of this proposal.


Li, WKW. 1994. Primary production of prochlorophytes, cyanobacteria, and eukaryotic ultraphytoplnakton: measurements from flow cytometric sorting. Limnology and Oceanography 39: 169-175.

Olson, R.J., Shalapyonol, A.A. and H.M. Sosik. 2003. An automated submersible flow cytometer for pico­ and nanophytoplankton: FlowCytobot. Deep-Sea Research I 50:301-315.

Palenik, B. 1994. Cyanobacterial community structure as seen from RNA polymerase gene sequence analysis.Applied Environmental Microbiology 60: 3212-3219.

Penno, S. Lindell, D. and A.F. Post. 2006. Diversity of Synechococcus and Prochlorococus populations determinedfrom DNA sequences of the N-regulatory gene ntcA. Environmental Microbiology 8(7): 1200-1211.

Rocap, G., Distel, D., Waterbury, J.B., and S.W. Chisholm. 2002. Resolution of Prochlorococcus andSynechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Applied Environmental Microbiology 68: 1180-1191