Asymptotic light field in the presence of a bubble-layer

We report that the submerged microbubbles are an efficient source of diffuse radiance and may contribute to a rapid transition to the diffuse asymptotic regime. In this asymptotic regime an average cosine is easily predictable and measurable.Comment: 4 pages, 3 Postscript figures, opex2.sty (enclosed), also available from the Optical Society of America htpp://epubs.osa.org/oearchive/pdf/11948.pd

The influence of bottom morphology on reflectance: Theory and two-dimensional geometry model

The reflectance of the bottom is of importance when interpreting optical data in shallow water. Closure studies of radiative transfer, interpretation of laser line scanner data, lidar, and remote sensing in shallow waters require understanding of the bottom reflectance. In the Coastal Benthic Optical Properties experiment (CoBOP), extensive measurements of the material reflectance (reflectance very close to the bottom) were made. Far field reflectance will be needed in carrying out closure of the radiative transfer model and observed radiometric and inherent optical properties. The far field reflectance is the bottom reflectance that includes the effect of bottom morphology (such as sand ripples) as well as the material reflectance. We present here a first-order analytical model to derive the relationship between the material and far field reflectances. We show that the effective reflectance of the bottom is proportional to the average cosine of the bottom slope. Using a simple two-dimensional geometry without scattering and absorption, we show that errors in ignoring the bottom morphology can lead to overestimations of the far field reflectance on the order of 30%

The effect of bottom substrate on inherent optical properties: Evidence of biogeochemical processes

Measurements of inherent optical properties (IOP) were conducted over bottoms with different substrates by use of a sampling package mounted on and operated by a SCUBA diver. It was found that in areas of low ambient currents the distribution of IOP varies with bottom type in (1) its value relative to a nearby bottom of different type, (2) its vertical gradient, and (3) its variability. This implies that radiative transfer modeling in shallow environments may need to include, besides the bottom characteristics, the bottom effect on in-water IOP. In tidally flushed shallow banks, vertical and horizontal gradients over scales of O(1, 10 m), respectively, are as large as temporal gradients over scales of minutes and cannot be separated in our measurements. However, bottom-substrate-related processes over the banks result in gradients over large horizontal spatial scales and tidal timescales. The distribution of IOP is consistent with several biogeochemical processes that may be active at a given bottom substrate and suggest that optical measurements may provide a useful tool to infer and quantify bulk rates of biogeochemical processes

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives

The mammalian gut is an attractive model for exploring the general question of how habitat impacts the evolution of gene content. Therefore, we have characterized the relationship between 16 S rRNA gene sequence similarity and overall levels of gene conservation in four groups of species: gut specialists and cosmopolitans, each of which can be divided into pathogens and non-pathogens. At short phylogenetic distances, specialist or cosmopolitan bacteria found in the gut share fewer genes than is typical for genomes that come from non-gut environments, but at longer phylogenetic distances gut bacteria are more similar to each other than are genomes at equivalent evolutionary distances from non-gut environments, suggesting a pattern of short-term specialization but long-term convergence. Moreover, this pattern is observed in both pathogens and non-pathogens, and can even be seen in the plasmids carried by gut bacteria. This observation is consistent with the finding that, despite considerable interpersonal variation in species content, there is surprising functional convergence in the microbiome of different humans. Finally, we observe that even within bacterial species or genera 16S rRNA divergence provides useful information about average conservation of gene content. The results described here should be useful for guiding strain selection to maximize novel gene discovery in large-scale genome sequencing projects, while the approach could be applied in studies seeking to understand the effects of habitat adaptation on genome evolution across other body habitats or environment types

Human-Associated Microbial Signatures: Examining Their Predictive Value

SummaryHost-associated microbial communities are unique to individuals, affect host health, and correlate with disease states. Although advanced technologies capture detailed snapshots of microbial communities, high within- and between-subject variation hampers discovery of microbial signatures in diagnostic or forensic settings. We suggest turning to machine learning and discuss key directions toward harnessing human-associated microbial signatures