Monterey Bay Aquarium Research Institute

About: Monterey Bay Aquarium Research Institute is a nonprofit organization based out in Castroville, California, United States. It is known for research contribution in the topics: Upwelling & Population. The organization has 630 authors who have published 2068 publications receiving 119899 citations. The organization is also known as: Monterey Bay Aquarium and Research Institute & MBARI.

In situ enrichment of ocean crust microbes on igneous minerals and glasses using an osmotic flow‐through device

Abstract: The Integrated Ocean Drilling Program (IODP) Hole 1301A on the eastern flank of Juan de Fuca Ridge was used in the first long-term deployment of microbial enrichment flow cells using osmotically driven pumps in a subseafloor borehole Three novel osmotically driven colonization systems with unidirectional flow were deployed in the borehole and incubated for 4 years to determine the microbial colonization preferences for 12 minerals and glasses present in igneous rocks Following recovery of the colonization systems, we measured cell density on the minerals and glasses by fluorescent staining and direct counting and found some significant differences between mineral samples We also determined the abundance of mesophilic and thermophilic culturable organotrophs grown on marine R2A medium and identified isolates by partial 16S or 18S rDNA sequencing We found that nine distinct phylotypes of culturable mesophilic oligotrophs were present on the minerals and glasses and that eight of the nine can reduce nitrate and oxidize iron Fe(II)-rich olivine minerals had the highest density of total countable cells and culturable organotrophic mesophiles, as well as the only culturable organotrophic thermophiles These results suggest that olivine (a common igneous mineral) in seawater-recharged ocean crust is capable of supporting microbial communities, that iron oxidation and nitrate reduction may be important physiological characteristics of ocean crust microbes, and that heterogeneously distributed minerals in marine igneous rocks likely influence the distribution of microbial communities in the ocean crust

New technology reveals the role of giant larvaceans in oceanic carbon cycling

Abstract: To accurately assess the impacts of climate change on our planet, modeling of oceanic systems and understanding how atmospheric carbon is transported from surface waters to the deep benthos are required. The biological pump drives the transport of carbon through the ocean’s depths, and the rates at which carbon is removed and sequestered are often dependent on the grazing abilities of surface and midwater organisms. Some of the most effective and abundant midwater grazers are filter-feeding invertebrates. Although the impact of smaller, near-surface filter feeders is generally known, efforts to quantify the impact of deeper filter feeders, such as giant larvaceans, have been unsuccessful. Giant larvaceans occupy the upper 400 m of the water column, where they build complex mucus filtering structures that reach diameters greater than 1 m. Because of the fragility of these structures, direct measurements of filtration rates require in situ methods. Hence, we developed DeepPIV, an instrument deployed from a remotely operated vehicle that enables the direct measurement of in situ filtration rates. The rates measured for giant larvaceans exceed those of any other zooplankton filter feeder. Given these filtration rates and abundance data from a 22-year time series, the grazing impact of giant larvaceans far exceeds previous estimates, with the potential for processing their 200-m principal depth range in Monterey Bay in as little as 13 days. Technologies such as DeepPIV will enable more accurate assessments of the long-term removal of atmospheric carbon by deep-water biota.

A Review of Advances in Deep-Ocean Raman Spectroscopy

Abstract: We review the rapid progress made in the applications of Raman spectroscopy to deep-ocean science. This is made possible by deployment of instrumentation on remotely operated vehicles used for providing power and data flow and for precise positioning on targets of interest. Early prototype systems have now been replaced by compact and robust units that have been deployed well over 100 times on an expeditionary basis over a very wide range of ocean depths without failure. Real-time access to the spectra obtained in the vehicle control room allows for expedition decision making. Quantification of some of the solutes in seawater or pore waters observed in the spectra is made possible by self-referencing to the ubiquitous v(2) water bending peak. The applications include detection of the structure and composition of complex thermogenic gas hydrates both occurring naturally on the sea floor and in controlled sea floor experiments designed to simulate the growth of such natural systems. New developments in the ability to probe the chemistry of sediment pore waters in situ, long thought impossible candidates for Raman study due to fluorescence observed in recovered samples, have occurred. This permits accurate measurement of the abundance of dissolved methane and sulfide in sediment pore waters. In areas where a high gas flux is observed coming out of the sediments a difference of about X30 between in situ Raman measurement and the quantity observed in recovered cores has been found. New applications under development include the ability to address deep-sea biological processes and the ability to survey the sea floor chemical conditions associated with potential sub-sea geologic CO2 disposal in abandoned oil and gas fields.

In situ observations of giant appendicularians in Monterey Bay

Abstract: Giant appendicularians (Bathochordaeus sp., Urochordata, Appendicularia) were observed in midwater in Monterey Canyon, Monterey Bay, California, from manned submersibles, Deep Rover, Alvin and MIR I, and with video from a ROV. Bathochordaeus utilizes secreted mucus structures to feed, but these structures and the orientation of the animal to the feeding-filter differ significantly from those of other genera in the Family Oikopleuridae. A continuously secreted sheet of mucus (unlike the episodically produced structured houses of other appendicularians) envelops both the body and the feeding-filter, protecting the animal from predators and scavenging large particles from the water feeding-filter, protecting the animal from sheet is occasionally up to 2 m in diameter, and large amounts of particulate material accumulate on this surface over time. We calculate that an individual can maintain the mucus sheet at specific depth horizons for as long as 30 days, collecting and impeding the downward flux of particulates. Eventually the sheet is disturbed or separates from the animal and feeding-filter due to its sediment burden, and collapses into a compacted mass which sinks rapidly (±800 m day− to the sea bed to depths of at least 3500 m. The obvious importance of these often common, large, filter-feeding appendicularians in water column ecology and vertical flux will require further investigation.

Fish identification from videos captured in uncontrolled underwater environments

Abstract: There is an urgent need for the development of sampling techniques which can provide accurate and precise count, size, and biomass data for fish. This information is essential to support the decision-making processes of fisheries and marine conservation managers and scientists. Digital video technology is rapidly improving, and it is now possible to record long periods of high resolution digital imagery cost effectively, making single or stereo-video systems one of the primary sampling tools. However, manual species identification, counting, and measuring of fish in stereo-video images is labour intensive and is the major disincentive against the uptake of this technology. Automating species identification using technologies developed by researchers in computer vision and machine learning would transform marine science. In this article, a new paradigm of image set classification is presented that can be used to achieve improved recognition rates for a number of fish species. State-of-the-art image set construction, modelling, and matching algorithms from computer vision literature are discussed with an analysis of their application for automatic fish species identification. It is demonstrated that these algorithms have the potential of solving the automatic fish species identification problem in underwater videos captured within unconstrained environments.