Date of Award
8-2025
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Biological Sciences
Committee Chair/Advisor
Dr. Barbara J. Campbell
Committee Member
Dr. Anna M. Seekatz
Committee Member
Dr. Tzuen-Rong Jeremy Tzeng
Committee Member
Dr. Kristi Whitehead
Abstract
In this dissertation, water samples from the Chesapeake and Delaware Bay estuaries were analyzed to see how estuarine environmental gradients drive distributions, functional potential, growth estimates and gene expressions of bacteria. To answer this, the abundant and versatile taxa– Rhodobacterales and Actinobacteriota, along with broader particle-attached (PA) vs. free-living (FL) bacterial assemblages of these Bays were analyzed using a multifaceted ‘omics approach.
The PA fraction, differing from the FL in taxonomy, distribution, functional potential and estimated growth rates across salinities, and bays harbored genes degrading complex aggregates, and surface attachment. The FL counterpart presented genes involved in nutrient uptake succussing the primary invaders. Estimated growth rates of PA was enhanced in the estuarine salinity highlighting nutrient-rich aggregates colonization. However, FL MAGs were estimated as growing rapidly in oligotrophic marine waters.
Rhodobacterales distribution varied between bays and were influenced by temperature, salinity, and silicate and phosphate concentrations. Eleven genera possessed both unique and shared genes for various metabolisms reflecting seasonal differences in abundance and activity. Planktomarina was more ubiquitous, but HIMB11, CPC320, LFER01 and MED-G52 were niche-specialists. Phosphate and silicate concentrations, cell density and light affected estimated growths diversely. Metatranscriptomics of four representative genomospecies revealed genes expressed differently in two conditions like night vs. day or summer vs. spring. For example, in summer, phosphate concentrations and light penetration in the Chesapeake Bay contributed to higher estimated growth rates of genera HIMB11 and LFER01, respectively compared to the Delaware Bay.
Actinobacteriota were abundant in low- to medium-salinity spring and summer samples, influenced by salinity, temperature, and phosphate, nitrate, and silicate concentrations. They exhibited high estimated growth rates under low- and medium salinities in warm seasons. Functional capacities of four major families ranged from generalist to specialist. They encoded and differentially expressed biosynthetic gene clusters (BGCs) for secondary metabolites, particularly terpenes and betalactones across salinity gradients and size fractions. Higher expressions of BGCs generally observed in medium compared to low salinities highlighting estuarine impact.
Our study highlights the spatial and temporal shifts in estuarine bacterioplankton within and between these bays reflected through their composition, abundance, metabolisms, estimated growths and activity changes.
Recommended Citation
Ahmed, Mir Alvee, "Distribution, Roles and Environmental Drivers of Bacterial Communities in the Chesapeake and Delaware Bays" (2025). All Dissertations. 4064.
https://open.clemson.edu/all_dissertations/4064
Author ORCID Identifier
https://orcid.org/0009-0008-8163-7156
Included in
Bioinformatics Commons, Environmental Microbiology and Microbial Ecology Commons, Marine Biology Commons, Terrestrial and Aquatic Ecology Commons