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Open Access Publications from the University of California

Scholarly Works (5 results)

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Research Theses and Dissertations (1998)

Many marine sponges possess dense microbial populations, but little is known regarding specific members or interactions of the microbial community within sponges. This study utilized molecular phylogenetic techniques, including quantitative ribosomal RNA (rRNA) hybridization with domain­ specific oligonucleotide probes and phylogenetic analysis of isolated l6S rRNA gene sequences, to assay the diversity of prokaryotes within marine sponges (Xestospongia sp, Cliona celata, and Axinella mexicana). All the sponges harbored diverse prokaryotic assemblages. The majority of rRNA phylotypes were similar to those commonly found in the marine environment. However, the dominance of Prochlorococcus-like rRNA gene clones within Xestospongia sp., and the presence of archaeal rRNA and rDNA within A. mexicana might suggest that these prokaryotes represent sponge-specific microflora.

The association between the marine archaea and A. mexicana was further investigated to determine if the relationship was specific and persistent. rRNA hybridization studies showed that archaea inhabited all specimens of A. mexicana from the Santa Barbara Channel and Monterey, CA, and that the association could be maintained over 4 years in laboratory aquaria. Phylogenetic analysis of the 16S rDNA showed that the archaeal population of a single individual consisted of highly-related strains of an archaeon named Cenarchaeum symbiosum that were affiliated with, but distinct from uncultivated marine planktonic crenarchaeotes. The presence of the strains in natural populations of A. mexicana was investigated using strain-specific 23S rRNA oligonucleotide probes and 16S rRNA signature sequence analysis. Several highly related rRNA phylotypes (>99.2% sequence similarity) were detected in single specimens of A. mexicana. Sequence analysis of the 165 rRNA gene also indicated minor differences in the Monterey and Santa Barbara Channel strains of C. symbiosum. Using in situ hybridization with fluorescently­ labeled 165 rRNA oligonucleotide and 16S/23S ribosomal polynucleotide probes that target marine crenarchaea, the sponge-associated archaea were identified and found to inhabit extracellular regions of the sponge matrix. The results of the above study indicated that the association between A. mexicana and Cenarchaeum symbiosum. is a symbiosis. The association represents the first description of Archaea inhabiting a sponge. and the first specific association between crenarchaea and a metazoan.

    Cover page: Prokaryotic Diversity in Marine Sponges: A Description of a Specific Association Between the Marine Archaeon, Cenarchaeum symbiosum, and the Marine Sponge, Axinella mexicana
    • Article
    • Peer Reviewed
    UC Santa Cruz Previously Published Works (2012)
    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 cyanobacteria (Synechococcus) and ammonia-oxidizing Archaea (Thaumarchaeota) populations. Results showed a strong correlation between Thaumarchaea abundances and nitrate during the spring upwelling but not the fall sampling period. In relatively stratified fall waters, the Thaumarchaeota community reached higher numbers than in the spring, and an unexpected positive correlation with chlorophyll concentration was observed. Further, we detected drops in Synechococcus abundance that occurred on short (that is, daily) time scales. Upwelling intensity and blooms of eukaryotic phytoplankton strongly influenced Synechococcus distributions in the spring and fall, revealing what appear to be the environmental limitations of Synechococcus populations in this region. Each of these findings has implications for Monterey Bay biogeochemistry. High-resolution sampling provides a better-resolved framework within which to observe changes in the plankton community. We conclude that controls on these ecosystems change on smaller scales than are routinely assessed, and that more predictable trends will be uncovered if they are evaluated within seasonal (monthly), rather than on annual or interannual scales.
      Cover page: Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation
      • Article
      • Peer Reviewed
      UC Santa Cruz Previously Published Works (2015)
        Cover page: Erratum: Single-taxon field measurements of bacterial gene regulation controlling DMSP fate
        • Article
        • Peer Reviewed
        UC Santa Cruz Previously Published Works (2015)
        The 'bacterial switch' is a proposed regulatory point in the global sulfur cycle that routes dimethylsulfoniopropionate (DMSP) to two fundamentally different fates in seawater through genes encoding either the cleavage or demethylation pathway, and affects the flux of volatile sulfur from ocean surface waters to the atmosphere. Yet which ecological or physiological factors might control the bacterial switch remains a topic of considerable debate. Here we report the first field observations of dynamic changes in expression of DMSP pathway genes by a single marine bacterial species in its natural environment. Detection of taxon-specific gene expression in Roseobacter species HTCC2255 during a month-long deployment of an autonomous ocean sensor in Monterey Bay, CA captured in situ regulation of the first gene in each DMSP pathway (dddP and dmdA) that corresponded with shifts in the taxonomy of the phytoplankton community. Expression of the demethylation pathway was relatively greater during a high-DMSP-producing dinoflagellate bloom, and expression of the cleavage pathway was greater in the presence of a mixed diatom and dinoflagellate community [corrected].These field data fit the prevailing hypothesis for bacterial DMSP gene regulation based on bacterial sulfur demand, but also suggest a modification involving oxidative stress response, evidenced as upregulation of catalase via katG, when DMSP is demethylated.
          Cover page: Single-taxon field measurements of bacterial gene regulation controlling DMSP fate
          • Article
          • Peer Reviewed
          LBL Publications (2019)
          Metagenomic and metatranscriptomic time-series data covering a 52-day period in the fall of 2016 provide an inventory of bacterial and archaeal community genes, transcripts, and taxonomy during an intense dinoflagellate bloom in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes (0.8 terabases), 82 metatranscriptomes (1.1 terabases), and 88 16S rRNA amplicon libraries from samples collected on 41 dates. The dataset also includes 88 18S rRNA amplicon libraries, characterizing the taxonomy of the eukaryotic community during the bloom. Accompanying the sequence data are chemical and biological measurements associated with each sample. These datasets will facilitate studies of the structure and function of marine bacterial communities during episodic phytoplankton blooms.
            Cover page: Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom
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