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Planktonic microbial activity and community structure is dynamic, and can change dramatically on time scales of hours to days. Yet for logistical reasons, this temporal scale is typically under-sampled in the marine environment. In order to facilitate higher-resolution, long-term observation of microbial diversity and activity, we developed a protocol for(More)
The ecological patterns of many invertebrate larvae remain an ongoing mystery, in large part owing to the difficult task of detecting them in the water column. The development of nucleic-acid-based technology has the potential to resolve this issue by direct identification and monitoring of embryonic and larval forms in situ. We report herein on the(More)
Planktonic marine microbes live in dynamic habitats that demand rapid sensing and response to periodic as well as stochastic environmental change. The kinetics, regularity, and specificity of microbial responses in situ, however, are not well-described. We report here simultaneous multitaxon genome-wide transcriptome profiling in a naturally occurring(More)
Pseudo-nitzschia austrulis Frenguelli is a marine pennatc diatom associated with the production of domoic acid-a neurocxcitatory amino acid linked to illness and mortality of humans and wildlife, Distinguishing P. austrulis from its co-occurring congeners is labor intensive and time consuming because of a requirement for scanning electron microscopy. Hcrc,(More)
Oscillating diurnal rhythms of gene transcription, metabolic activity, and behavior are found in all three domains of life. However, diel cycles in naturally occurring heterotrophic bacteria and archaea have rarely been observed. Here, we report time-resolved whole-genome transcriptome profiles of multiple, naturally occurring oceanic bacterial populations(More)
Planktonic microbial communities in the ocean are typically dominated by several cosmopolitan clades of Bacteria, Archaea, and Eukarya characterized by their ribosomal RNA gene phylogenies and genomic features. Although the environments these communities inhabit range from coastal to open ocean waters, how the biological dynamics vary between such disparate(More)
A recent shift from using traditional light microscopy to molecular approaches for identifying and quantifying marine harmful algal bloom (HAB) species has been driven by the need to expedite sample processing for both research and monitoring purposes (Anderson 1995; Scholin et al. 2003). In addition, light microscopy does not always afford sufficient(More)
Monterey Bay, CA is an Eastern boundary upwelling system that is nitrogen limited much of the year. In order to resolve population dynamics of microorganisms important for nutrient cycling in this region, we deployed the Environmental Sample Processor with quantitative PCR assays targeting both ribosomal RNA genes and functional genes for subclades of(More)
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(More)
A sandwich hybridization assay (SHA) was developed to detect 16S rRNAs indicative of phylogenetically distinct groups of marine bacterioplankton in a 96-well plate format as well as low-density arrays printed on a membrane support. The arrays were used in a field-deployable instrument, the Environmental Sample Processor (ESP). The SHA employs a chaotropic(More)