[Eoas-seminar] Oceanography Dissertation Defense - Lauren Campbell - April 2, 10am - CSL1005

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Mon Mar 25 09:58:03 EDT 2019

Oceanography Seminar
Lauren Gillies Campbell
Ph.D. Biological Oceanography Candidate

Title: Analysis of microbial abundance, transcriptional activity and metabolic potential in the Gulf of Mexico "dead zone" reveals an ammonia-oxidizing hotspot

Major Professor: Dr. Olivia U. Mason
Defense Date: April 2, 2019
Time: 10:00 AM
Location: Chemistry 1005 (CSL1005)

Ocean deooxygenation is accelerating as a result of greenhouse gas-driven atmospheric warming and subsequent increase in global ocean temperature. One of the world's largest coastal hypoxic zones occurs annually in the northern Gulf of Mexico (nGOM). These hypoxic zones are also known as "dead zones" because dissolved oxygen (DO) concentrations of ≤ 2 mg L-1 are inhospitable to economically valuable fisheries. However, microorganisms flourish in "dead zones" because of their ability to utilize diverse metabolic pathways. Decades worth of geochemical data has provided fine-scale resolution on nutrient and oxygen dynamics the nGOM, however little is known about microbial community structure and activity despite the implication that microbial respiration is responsible for forming low DO conditions. To begin to fill this knowledge gap, samples collected across the nGOM shelf for two consecutive hypoxic seasons in July 2013 (Y13) and 2014 (Y14) were analyzed using 16S rRNA gene iTag sequencing, quantification of bacterial and thaumarchaeal 16S rRNA genes and archaeal ammonia-monooxygenase (amoA) genes using quantitative polymerase chain reaction (qPCR) assays, as well as shotgun metagenomic and metatranscriptomic sequencing.
Analysis of the microbial community16S rRNA gene sequence data (iTag) showed that ammonia-oxidizing Thaumarchaeota (100% similar to Nitrosopumilus maritimus) were significantly enriched in hypoxic samples and inversely correlated with DO concentrations. In agreement with the iTag data, subsequent analyses of the absolute abundance (qPCR) of Thaumarchaeota 16S rRNA and amoA gene copy numbers revealed these data to be significantly more abundant in hypoxic samples and inversely correlated with DO concentrations. These results of significantly higher Thaumarchaeota abundances and amoA gene copy numbers in hypoxic samples were confirmed with analyses of Y14 data.
To better understand the ecological significance of the high thaumarchaeal abundances in the hypoxic zone, shotgun metagenomic and metatranscriptomic sequencing was carried out. Annotation of unassembled metatranscriptomic reads revealed that functional genes involved in nitrification and ammonia assimilation were some of the most abundant transcripts in both hypoxic and oxic samples, with urease enzymes being significantly more abundant in hypoxic samples. Next, the physiological and metabolic potential of two novel Thaumarchaeota metagenome assembled genomes (MAGs) was described. Bioinformatic analyses of these MAGs revealed that one contained transcripts coding for urea utilization, consistent with the analysis of unassembled metatranscriptomic sequences. Both MAGs recruited more metatranscriptomic reads derived from hypoxic samples compared to oxic samples, suggesting that archaeal ammonia oxidation (AOA) may be influenced by local changes in DO concentrations.
Collectively, analyses of the datasets in this dissertation that include data from iTag sequencing, qPCR assays, and meta-omics sequencing, found that seasonal hypoxic conditions influenced Thaumarchaeota abundance, activity and diversity, with the annual nGOM "dead zone" emerging as a niche for low DO-adapted, cosmopolitan AOA.  Overall, the findings in this dissertation provided significant new insights into the ecology and biogeochemical contributions of marine Archaea, particularly in regards to the nitrogen cycle during a eutrophic-driven hypoxic event.
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