Project: Pattern and Process in Marine Bacterial, Archaeal, and Protistan Biodiversity, and Effects of Human Impacts

Description from NSF award abstract:
Bacteria, Archaea, and Protists dominate global elemental cycling and are immensely diverse genetically, taxonomically, and functionally. Yet the extent of marine microbial diversity, its patterns, and relationships among genetic, taxonomic, and functional diversity are very poorly characterized, even though the ocean covers 70% of the planet's surface. Among the least well known variables is the effect of human impacts on native marine microbial systems, although it is recognized that impacted systems are more prone to events like harmful algal blooms. Knowledge of these relationships and impacts are necessary to anticipate the responses of biota to global changes and feedback mechanisms that may alter the extents, rates, and even pathways of such changes. This project will expand upon an existing NSF-funded 10+-year monthly ocean time series (Microbial Observatory) that has focused on a single site midway between Los Angeles and Santa Catalina Island, to also include quarterly sampling adjacent to the impacted LA Harbor region to the barely-impacted Catalina coast. USC already runs facilities in LA Harbor and Catalina, with daily boats between (no cost). Measurements include (1) Genetic diversity: high throughput DNA sequences of "housekeeping" and functional genes. (2) Taxonomic diversity: high throughput tag sequences of small subunit ribosomal RNA genes, flow cytometry, automated image analysis (3) Functional Diversity: (a) Functional measurements (carbon fixation and respiration rates, microbial growth and grazing rates, cell size, morphology, and biomass variations), (b) distribution and expression of particular target functional genes involved with processes central to the cycles of carbon, nitrogen, and sulfur, (c) exploratory metatranscriptomics to explore functionalities that were not anticipated. (4) Integrating these: Multivariate statistical and network approaches including newly developed techniques (e.g. Bayesian networks to examine cause-effect relationships), and high speed computational approaches to assess the relationships among the genetic, taxonomic, and functional aspects of biodiversity observed. The PIs will also examine the collected data for signatures and specific effects (on organism identity and functions) associated with human impacted harbor site vs. the relatively pristine one.

The PIs will use network and time series analysis, along with other statistical tools to integrate "classical" microbial and oceanographic rate process measurements, flow cytometric and microscopic characterizations of communities, along with targeted as well as untargeted metagenomics and metatranscriptomics to relate genetic and taxonomic diversity with specific functions (at organismal, food web, and system levels). For example, they should be able to determine how different variants of particular taxa (e.g. at resolution levels ranging from what might be considered near the subspecies to genus levels) would differ in their association with particular measured functions, functional genes, or particular other taxa - or they might see how particular clusters of related organisms behave similarly or differently in their associations. This project offers an unprecedented and potentially transformative opportunity to combine and integrate measurements of genetic, taxonomic, and functional diversity along with direct measurements of system function in a well studied marine system that includes a gradient from one of the world's busiest harbors to a largely pristine ocean habitat. Far beyond just describing the distributions of organisms and functions (itself a necessary first step), they will specifically link spatial and temporal variations in a variety of functions with variations in genetic and taxonomic community composition.