In the surface waters of subtropical ocean gyres, resources often severely limit microbial growth. To access nutrients, bacteria may associate with small, widely distributed and abundant planktonic crustaceans known as copepods. In this research, I hypothesized that copepods in the North Atlantic Subtropical Gyre are hotspots of microbial activity and acquire specific bacterial communities on their surfaces(epibionts), guts (endobionts), and surroundings. As such, copepods would provide unique niches in the oligotrophic ocean for microbially-driven food webs and biogeochemical cycles. The first part of this study characterized seasonal variability in the copepod gut microbiome over two years. High throughput amplicon sequencing targeting the universal bacterial 16S rRNA gene revealed major seasonal shifts attributed to changing food sources, suggesting a large part of the copepod gut microbiome is driven by bacteria associated with their prey particles − a path that would be a shortcut in the classical microbial food web. Anaerobic or potentially anaerobic Clostridiales and Bacillales were consistently detected; thus, copepod guts appear to be anaerobic environments that also maintain stable bacterial associations. Comparison of four DNA extraction methods used in past copepod microbiome studies resulted in broadly similar conclusions about bacterial community composition; yet, some biases were identified, highlighting the need to standardize methods for more robust comparisons across studies. Results from at-sea bottle incubations lead us to coin the term “zoosphere” to refer to the nutrient-enriched microzone immediately surrounding a zooplankton individual, supporting specific communities of bacteria not necessarily physically attached to the animal. The copepod zoosphere appears to support certain bacterial groups including Vibrionaceae and Rhodobacteraceae through general nutrient enrichment, but also appears to be selectively “farming” some groups including Flavobacteriaceae and Pseudoalteromonadaceae, by supporting their growth on the animal itself and then releasing them to the surrounding seawater at high abundances. Metatranscriptomic sequencing showed complete bacterial pathways expressed in the copepod association, including chemotaxis, cell signaling, and bacterial alkaline phosphatase utilization. Consistent presence and expression of alkaline phosphatase genes, primarily by Vibrio spp., indicate that bacteria growing in the nitrogen-enriched copepod environment are limited by inorganic phosphorus, demonstrating the basin-wide tendency for phosphorus limitation in the North Atlantic Ocean occurring at microscales. The results suggest that bacteria in copepod association alleviate their phosphorus limitation by breaking down organophosphoesters that are presumably originating from the copepods. The bacterial communities and their fitness strategies supported by copepod association are distinct from the surrounding seawater, and could have global implications for biogeochemical cycling, marine food web structuring, and copepod and ecosystem health.
- Composition and activity of bacterial communities associated with copepods in the oligotrophic North Atlantic Ocean
- Katyanne Marie Shoemaker
- 0000-0002-5129-2387
- Pia H. Moisander (Advisor) - University of Massachusetts Dartmouth, Department of BiologyMark Winston Silby (Committee Member) - University of Massachusetts Dartmouth, Department of BiologyVanni Bucci (Committee Member) - University of Massachusetts DartmouthAnn M. Tarrant (Committee Member) - Associated Scientists at Woods Hole
- xii, 133 pages
- illustrations (chiefly color)
- List of figures -- List of tables -- Chapter 1. Introduction -- The study site -- Bacterial association with copepods -- Chapter 2. Seasonal variation in the copepod gut microbiome in subtropical North Atlantic Ocean -- Abstract -- Introduction -- Methods -- Results -- Discussion -- Statement of publication -- Chapter 3. Influence of sample preservation and DNA extraction methods for determination the copepods microbiome -- Abstract -- Introduction -- Methods -- Results -- Discussion -- Conclusion -- Statement of publication -- Copepods promote bacterial community changes in surrounding seawater through farming and nutrient enrichment -- Abstract -- Introduction -- Methods -- Results -- Discussion -- Statement of publication -- chapter 5. Copepod association bacteria are phosphorous limited in the North Atlantic Subtropical Gyre -- Introduction -- Methods -- Results and Discussion -- Statement of publication -- References -- Appendix A Supplementary methods -- DNA extraction method 1 protocol -- DNA extraction method 2 protocol -- DNA extraction method 3 protocol -- DNA extraction method 4 protocol -- Appendix A. Supplementary methods -- A.1. DNA extraction method 1 protocol -- A.2. DNA extraction method 2 protocol -- A.3. DNA extraction Method 3 protocol -- A.4. DNA extraction method 4 protocol -- Appendix B. Supplementary tables -- Appendix C. Supplementary figures.
- Includes bibliographical references (pages 104-118).
- University of Massachusetts Dartmouth
- Doctor of Philosophy (PHD)
- Marine Science and Technology
- Department of Fisheries Oceanography
- English
- Dissertation
- Copyright 2019 Katyanne Marie Shoemaker
- https://doi.org/10.62791/19841
- 9914424775801301