Three-dimensional modeling of acoustic backscattering from fluid-like zooplankton

Author Posting. © Acoustical Society of America, 2002. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 111 (2002): 1197-1210, doi:10.1121/1.1433813.Scattering models that correctly incorporate organism size and shape are a critical component for the remote detection and classification of many marine organisms. In this work, an acoustic scattering model has been developed for fluid-like zooplankton that is based on the distorted wave Born approximation (DWBA) and that makes use of high-resolution three-dimensional measurements of the animal's outer boundary shape. High-resolution computerized tomography (CT) was used to determine the three-dimensional digitizations of animal shape. This study focuses on developing the methodology for incorporating high-resolution CT scans into a scattering model that is generally valid for any body with fluid-like material properties. The model predictions are compared to controlled laboratory measurements of the acoustic backscattering from live individual decapod shrimp. The frequency range used was 50 kHz to 1 MHz and the angular characteristics of the backscattering were investigated with up to a 1° angular resolution. The practical conditions under which it is necessary to make use of high-resolution digitizations of shape are assessed.This work was supported in part by the Woods Hole Oceanographic Institution Education Office

Going Deeper: Metagenome of a Hadopelagic Microbial Community

The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above

Genes Required for Growth at High Hydrostatic Pressure in Escherichia coli K-12 Identified by Genome-Wide Screening

Despite the fact that much of the global microbial biosphere is believed to exist in high pressure environments, the effects of hydrostatic pressure on microbial physiology remain poorly understood. We use a genome-wide screening approach, combined with a novel high-throughput high-pressure cell culture method, to investigate the effects of hydrostatic pressure on microbial physiology in vivo. The Keio collection of single-gene deletion mutants in Escherichia coli K-12 was screened for growth at a range of pressures from 0.1 MPa to 60 MPa. This led to the identification of 6 genes, rodZ, holC, priA, dnaT, dedD and tatC, whose products were required for growth at 30 MPa and a further 3 genes, tolB, rffT and iscS, whose products were required for growth at 40 MPa. Our results support the view that the effects of pressure on cell physiology are pleiotropic, with DNA replication, cell division, the cytoskeleton and cell envelope physiology all being potential failure points for cell physiology during growth at elevated pressure

A Study of the Effects of Hydrostatic Pressure on Macromolecular Synthesis in Escherichia coli

In cultures of Escherichia coli 15 (thymine(-), leucine(-)) which were incubated at high hydrostatic pressures, cell division occurred only at pressures below 430 atm but in a somewhat synchronous fashion at around 250 atm. The rate of leucine-(14)C incorporation into a macromolecular fraction of the cells diminished to a zero value at about 580 atm and that of uracil-(14)C incorporation to a zero value at about 770 atm. The rate of thymine-(14)C incorporation at pressures around 330 atm was that to be expected with a culture in which DNA synthesis is somewhat synchronous. At pressures above 500 atm, thymine-(14)C was incorporated only over the initial part of the pressure incubation and further incorporation under pressure was not observed no matter how long the duration of the incubation. We present evidence along several lines that the thymine incorporation kinetics reflect an effect of pressure on a locus at the origin (or termination) of a replication of the bacterial chromosome. The recovery of cell division and of the incorporation rates upon release of pressure were found to depend on the magnitude of the pressure and the duration of the pressure incubation

The influence of nutrition on the physiology of piezophilic bacteria

ABSTRACT The adaptation known as piezophily is a hallmark of the true bacterial inhabitants of the cold deep sea below a threshold depth of about 2,000m. Because of advection of water masses and particle transport, there is mixing of bacterial populations of different depths. There is also a variability in nutrient supply. An understanding of bacterial processes in the oceans thus requires studies of how bacteria respond to changes in temperature, pressure, nutrition and community structure. A first step towards understanding this complexity was to employ pressure and temperature as coordinate variables in experiments. This led to the definition of piezophily. The next step is to add the variable of nutrition. The pressure response of cells of isolate PE36 was found to be a function of the carbon compound they were utilizing. The piezopsychrophile PE36 was grown in a minimal salts medium with glycerol, glucose, glutamate or citrate as a carbon source. Growth on each of these carbon sources also resulted in a distinct membrane protein profile (results to be published elsewhere) that was also a function of the pressure during growth