Author ORCID Identifier


Defense Date


Document Type


Degree Name

Doctor of Philosophy


Integrative Life Sciences

First Advisor

Rima Franklin


Microbial communities are critical biological components of the world’s ecosystems, and their respiratory pathways are directly involved in the biogeochemical cycling of essential nutrients. As genomic technologies advance, allowing for more detailed profiling of microbial communities, efforts have successfully linked microbial community composition to ecosystem-level functions and have shown microbial communities are susceptible and resistant to disturbance events. The goal of this dissertation is to address the temporal scales in which microbial communities respond to the disturbance of salinization, and the repercussions this has on microbially-meditated carbon and nitrogen cycling. Coastal freshwater wetlands are an excellent study system to investigate salinization effects, as their soils harbor functionally- and taxonomically-diverse communities that provide critical ecosystem services, which appear sensitive to changes in salinity.

For this dissertation, I performed three experiments to advance our understanding of how prokaryotic communities respond in both structure and function to salinization in coastal freshwater wetlands. I utilized in-situ salinity manipulations over relatively long temporal scales (2-3 years) as well as shorter-term laboratory incubations. I paired DNA-based assessments of the prokaryotic communities with functional measurements (NO3-reduction, CH4 production, and CO2 production) for a more complete understanding of the temporal scales in which freshwater communities change due to salinization.

The response of prokaryotic communities to salinization was predicated on salinity level and exposure length. Mesohaline levels of salinity resulted in the rapid formation of transitional communities, which took approximately two years to match native mesohaline communities. However, freshwater prokaryotic communities appear structurally resistant to salinization when allowing for and excluding the immigration of more saline-adapted prokaryotic taxa. The differential response of freshwater prokaryotes to different salinity levels suggests that freshwater prokaryotes are somewhat capable of competing with oligohaline taxa for resources, but are less competitive under mesohaline conditions, a pattern that was also observed in the response of putative nitrate-reducing taxa. The effects of salinization on nitrate reduction pathways agreed well with past efforts that found rates of dissimilatory nitrate reduction to ammonium (DNRA) are higher under increased salinities, which I observed under mesohaline levels of salinity. However, the effects of salinization on denitrification were more difficult to interpret, as no consistent response to salinization was observed, highlighting the importance of studying changes to this pathway over longer (years) time scales and multiple salinity levels.

I observed changes in the terminal end products of soil organic matter mineralization, wherein oligohaline levels of salinization consistently suppressed methane production, without decreasing the abundance of the archaea responsible for methanogenesis, suggesting these prokaryotes either switch to alternative respiratory pathways or, more likely, become dormant under moderate salinity levels. Unlike methane production, carbon dioxide production did not show a response to oligohaline levels of salinity. This could be a result of the freshwater community structure being relatively resistant to oligohaline salinity levels, the exclusion of immigration of more saline-tolerant community members, or it could be due to functional redundancy as multiple respiratory pathways produce carbon dioxide as an end product. I observed that freshwater soil enzyme activities were not suppressed by salinization, but rather were unchanged or stimulated when exposed to salinization ranging from freshwater to mesohaline salinities. This suggests that the enzymes produced by freshwater prokaryotes are functional under more saline conditions, at least when considering short time scales.

This work underscores the importance of considering multiple disturbance levels and exposure lengths when profiling the prokaryotic community response, and that these two effects can interact to dictate changes to community structure. Novel communities that form during a salinity disturbance are transitional when viewed over multi-year temporal scales. Findings of this dissertation also suggest that the prokaryotes of coastal freshwater wetland soils can tolerate oligohaline levels of salinity without drastic changes to taxonomic profiles, but functional changes may manifest without observed treatment effects on metrics of prokaryotic community structure. The findings of this dissertation highlight the value of profiling the prokaryotic communities responsible for the biogeochemical cycling of carbon and nitrogen. Furthermore, my results suggest that coastal freshwater wetland soils, from both tidal and non-tidal wetlands, are relatively resistant to oligohaline levels of salinity, suggesting that mechanisms of salinization resulting in oligohaline levels of salinity will likely not result in the restructuring of these communities.


© Joseph C. Morina II

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