Underwater Application of Quantitative PCR on an Ocean Mooring

The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as a means to remotely identify and quantify, in situ, marine microorganisms and substances they produce. Here, we added functionality to the ESP through the development and incorporation of a module capable of solid-phase nucleic acid extraction and quantitative PCR (qPCR). Samples collected by the instrument were homogenized in a chaotropic buffer compatible with direct detection of ribosomal RNA (rRNA) and nucleic acid purification. From a single sample, both an rRNA community profile and select gene abundances were ascertained. To illustrate this functionality, we focused on bacterioplankton commonly found along the central coast of California and that are known to vary in accordance with different oceanic conditions. DNA probe arrays targeting rRNA revealed the presence of 16S rRNA indicative of marine crenarchaea, SAR11 and marine cyanobacteria; in parallel, qPCR was used to detect 16S rRNA genes from the former two groups and the large subunit RuBisCo gene (rbcL) from Synecchococcus. The PCR-enabled ESP was deployed on a coastal mooring in Monterey Bay for 28 days during the spring-summer upwelling season. The distributions of the targeted bacterioplankon groups were as expected, with the exception of an increase in abundance of marine crenarchaea in anomalous nitrate-rich, low-salinity waters. The unexpected co-occurrence demonstrated the utility of the ESP in detecting novel events relative to previously described distributions of particular bacterioplankton groups. The ESP can easily be configured to detect and enumerate genes and gene products from a wide range of organisms. This study demonstrated for the first time that gene abundances could be assessed autonomously, underwater in near real-time and referenced against prevailing chemical, physical and bulk biological conditions

Density-dependent mortality in an oceanic copepod population.

Planktonic copepods are primary consumers in the ocean and are perhaps the most numerous metazoans on earth. Secondary production by these zooplankton supports most food webs of the open sea, directly affecting pelagic fish populations and the biological pump of carbon into the deep ocean. Models of marine ecosystems are quite sensitive to the formulation of the term for zooplankton mortality, although there are few data available to constrain mortality rates in such models. Here we present the first evidence for nonlinear, density-dependent mortality rates of open-ocean zooplankton. A high-frequency time series reveals that per capita mortality rates of eggs of Calanus finmarchicus Gunnerus are a function of the abundance of adult females and juveniles. The temporal dynamics of zooplankton populations can be influenced as much by time-dependent mortality rates as by variations in 'bottom up' forcing. The functional form and rates chosen for zooplankton mortality in ecosystem models can alter the balance of pelagic ecosystems, modify elemental fluxes into the ocean's interior, and modulate interannual variability in pelagic ecosystems

Contributions of long-term research and time-series observations to marine ecology and biogeochemistry

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Marine Science 1 (2009): 279-302, doi:10.1146/annurev.marine.010908.163801.Time-series observations form a critical element of oceanography. New interdisciplinary efforts launched in the past two decades complement the few earlier, longer-running time series in building a better, though still poorly-resolved, picture of lower-frequency ocean variability, the climate processes driving it, and its implications for foodweb dynamics, carbon storage and climate feedbacks. Time-series also enlarge our understanding of ecological processes and are integral for improving models of physical-biogeochemical-ecological ocean dynamics. The major time-series observatories go well beyond simple monitoring of core ocean properties, although that important activity forms the critical center of all time-series efforts. Modern ocean time series have major process and experimental components, entrain ancillary programs and have integrated modeling programs for deriving better understanding of the observations and the changing, three-dimensional ocean in which the observatories are embedded.HWD was supported by NSF grant OPP-0217282. SCD was supported by the Center for Microbial Oceanography Research and Education (C-MORE; NSF CCF-424599). DKS was supported by NSF grant OCE-0628444