A molecular analysis of subsurface microbial communities across a hydrothermal gradient in Okinawa Trough sediments

Open Access
Brandt, Leah Danielle
Graduate Program:
Doctor of Philosophy
Document Type:
Date of Defense:
June 03, 2016
Committee Members:
  • Christopher Howard House, Dissertation Advisor
  • subsurface
  • hydrothermal
  • diversity
  • sequencing
  • microbial
Decades ago, life in the deep subseafloor was assumed to be non-existent. At thousands of meters under the surface and decoupled from the photic zone, the deep marine world is a hostile environment. However, the discovery of life thriving around deep-sea hydrothermal vent systems revolutionized our perception of the extent and tenacity of life on Earth and set in motion a movement to understand life at the seafloor and its significant in global biogeochemical and nutrient cycling. Seafloor sediments host an incredible diversity of microbial life, and much interest has sought to understand the spatial and stratigraphic extent of the biosphere, and also taxonomic and functional capacities of such resilient organisms. This dissertation represents a series of studies centered around these concepts – I analyze samples from a sediment profile exposed to a hydrothermal gradient as a scaled-down proxy for how microbial life may exist and/or adapt to conditions as they become buried deeper into the subsurface. I have focused on the application of culture-independent, molecular methods to understand whether the taxonomic and functional data reflect changes through this temperature gradient in support of a more temperature-adapted microbial community. In chapter 2, I examined the microbial community composition at approximately meter intervals by analyzing the taxonomically specific 16S rRNA marker gene. We presumed the biosphere to be restricted to only the upper 15 m, based on phylotype vetting and decreased sequencing recovery below. However, we observed a significant proportion of archaeal sequences throughout the 15 m, with a particularly high abundance in the deepest 15 m horizon. An in-depth look at the taxa at 15 m indicates an appearance of an uncultured, high-temperature taxon here, and an abundance of a thermophilic, methane-oxidizing archaeon, which suggests thermophilic niche at this particular temperature/depth regime. The exciting results from Chapter 2 were the motivation for a continued metagenomics analysis of select samples in the same sediment profile for Chapter 3. Probing through total genomic DNA from six samples, I found evidence for temperature-dependent trends through the detection of genes of specific proteins involved in thermal processes, and attempted to correlate these genes with a taxonomic identity. I found that the deepest, hottest sample encompassed organisms from both thermophilic and hyperthermophilic temperature regimes. The dichotomy reflected between the existence of two temperature-specific niches implies that, due to the dynamic nature of the hydrothermal vent system, the deepest horizon may be undergoing a transition in temperature, thus, microbial community. Lastly, Chapter 4 was intended to provide a dataset from extractable RNA in order to distinguish representatives of the active microbial population from those represented from extant DNA; however, many challenges encountered in extraction and sequencing yield have restricted the dataset and ability to make reliable interpretations. Considering the current state of knowledge in the marine subsurface due to its challenges in sampling, low biomass yield, and diversity distantly related to what is known from surface life, this work herein contributes greatly to our understanding of microbial biogeography in terms of temperature constraints in marine subsurface sediments. The challenges in phylotype vetting and need for quality controls speak to the degree of complexities in performing and interpreting molecular analyses from subseafloor sediments. Moreover, I have also produced significant datasets, both 16S rRNA gene and metagenomics, that can continue to be used for future investigations and comparisons of microbial life in the marine seafloor.