Browsing by Author "Johnson, Zackary I"

Although there are many examples of microbial biogeography, few microbes have been studied at high taxonomic resolution over large spatial scales. As a result, the environmental and ecological processes that drive niche partitioning, diversity, composition, and activity of microbial taxa are often poorly understood. To address this gap, I examine the most abundant phytoplankton in the global ocean, Prochlorococcus sp., a marine cyanobacterium. Using amplicon libraries of the Prochlorococcus internal transcribed spacer (ITS) region and 23S rRNA gene as markers, I demonstrate several key differences between the two major high light (HL) clades of Prochlorococcus. First, by examining ITS amplicon libraries at high taxonomic resolution it is revealed that “sub-ecotype” clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Whereas unique combinations of environmental traits drive the distribution of the HL-I sub-ecotype clades, the HL-II sub-ecotype clades appear ecologically coherent. Second, using 23S rRNA and rDNA libraries I show that activity (rRNA) and abundance (rDNA) are highly correlated for Prochlorococcus across all sites and operational taxonomic units (OTUs) in the surface ocean, demonstrating a tight coupling between activity and abundance. Finally, I investigate the associations between Prochlorococcus and the rest of the microbial community in the North Pacific and find region-specific trends in both strength and sign. Associations with other microbes are strongest for HL-I in the temperate region and strongest for HL-II in the sub-tropical gyre. This dissertation clarifies the relative importance of the environment, geography, community, and taxonomy in terms of their role in creating complex assemblages of Prochlorococcus and helps improve our understanding of how marine microbial communities are assembled in situ.

A cost-saving strategy of large-scale algae cultivation that can lead to more economical production of algal food, feed, and fuels involves reusing the cultivation water after algae harvesting. Few studies have focused on predictors of algae growth success in reused water, or explained these results in terms of algal ecology. Factors such as dissolved organic matter accumulation and interactions with bacteria are also understudied in the context of water reuse, yet could inform cultivation decisions to maximize water reuse without losses in algal productivity. This dissertation investigated trends in previous studies and also used an experimental approach to determine how reusing cultivation water affects algae growth, dissolved organic carbon (DOC) accumulation, DOC release rates, and relative abundances of bacteria. Based on over 80 previous studies testing algae growth in reused water, algae taxon was the only factor significantly associated with algae growth response. A possible explanation for this result could be differences in the amount and composition of DOC excreted by different algae. I therefore experimented with three taxonomically and physiologically distinct algae, two diatoms and a green alga, to test their growth responses, DOC excretion rates, and the extent of DOC accumulation in reused water. Algae growth response in reused water varied by algae, yet was not correlated with DOC concentrations. Additionally, DOC concentrations steadily increased with each water reuse, suggesting a build-up of recalcitrant DOC after bacteria, or possibly algae, degraded more labile DOC. To further explore the extent of strain-specific growth responses, I tested the effect of reused water from a self-inhibitory algae strain on other algae strains. This reused water did not inhibit two other algae strains, suggesting that the inhibitory mechanism was strain-specific and was likely from build-up of a certain DOC compound. Across the three algae cultures, different bacteria taxa became enriched or depleted in reused water, despite all cultures being exposed to the same reused water source. DOC composition and concentration in reused water were therefore likely not driving observed differences in final bacteria communities, and DOC produced from the growing algae may be more influential. Overall, results from this dissertation support strain-specific features of algae growth responses, and suggest that algae screening processes should include tests in reused water. Identifying algae strains with uninhibited growth responses will be important for implementing water reuse for algae cultivation, to ultimately improve the economic feasibility of algae bioproducts.

Marine microalgae are photosynthetic microbes that are a potential source of fuels, animal feed, and other specialized products. Large scale cultivation of microalgae occurs in open, outdoor raceway ponds, which are exposed to the natural environment and these cultures quickly become a complex milieu of microbes. Microalgae interact with attached and free-floating bacteria found in their medium, with both positive and negative outcomes. To investigate the diversity and dynamics of microbes associated with these systems, samples were collected during multiple growth cycles of two biofuel-relevant microalgae strains, Desmodesmus sp. and Oocystis sp. in ~4,500 L outdoor raceway ponds. Microbiome community composition and diversity was dramatically different between ponds from the two algae and from the natural microbiome of the treated seawater used in pond medium. In spite of variable environments, the pond microbiomes were most similar to their inoculum PBR (photobioreactor) communities suggesting the importance of priority effects or environmental conditioning by the host algae. Ponds when both algae strains were grown were dominated by Rhodobacteraceae and Saprospiraceae while unhealthy microbiomes were dominated by Cytophagaceae and Puniceicoccaceae. Microbiome change was variable over time and resulted in different community structures at the time of algae harvest. Variation in the microbiome community structure was driven by the strain of algae grown, time, pond temperature and percent oxygen saturation. These results provide insight into this industrial ecology and are a foundation for future microbiome research to improve microalgae production.

While much is known about the abundance and genetic diversity of environmental microbial communities, little is known about their taxon-specific activity. In this thesis I address this gap using a model marine microbe, the cyanobacterium Prochlorococcus spp., which numerically dominates tropical and subtropical open oceans and encompasses a group of genetically defined clades that are ecologically distinct. Ribosomal RNA is a promising indicator of in situ activity because of its essential role in protein synthesis as well as its phylogenetic information, which could be used to distinguish clades among mixed populations. Here I show that, in a laboratory system the specific growth rate of representative Prochlorococcus strains could be quantitative predicted from cellular rRNA content (assessed by RT-qPCR), cell size (assessed by flow cytometry) and temperature. Applying this approach in the field, I show unique clade-specific activity patterns for Prochlorococcus. For example, vertically within the euphotic zone, eHL-II activity is strongly impacted by light and is consistent with patterns of photosynthesis and on a horizontal transect from Hawaii to San Diego, eHL-I and eHL-II activities exhibit significant transitions and appear to be regulated by temperature, nutrient and vertical mixing gradients. Using ribosomal tag pyrosequencing of DNA and RNA, I have extended our observation to the Eubacterial community and described the biomass distribution (rDNA) and activity (rRNA) patterns from two representative depths (25 and 100 m) at a well-studied oligotrophic ocean station. These results show that for some populations the abundances and activities are significantly uncoupled, which suggests substantial top-down controls or physical transport processes. Further exploring the taxon-specific activity patterns along with abundances and environmental variables across time and space is essential to better understanding the dynamics of a complex microbial system as well as predicting the consequences of environmental change.