Spatial variability of oceanic phycoerythrin spectral types derived from airborne laser-induced fluorescence emissions

Multiple scattering effects on the return spectrum of oceanic high-spectral-resolution lidar

The return spectrum of the oceanic high-spectral-resolution lidar (HSRL) is simulated with a semianalytic spectral Monte Carlo (MC) method. The results show that the spectrum is similar to the single scattering spectrum at the water surface but broadens with the depth due to multiple scattering. Therefore, if the non-spectral MC method that ignores the spectrum broadening is used, deviations will be introduced into the HSRL retrieval, e.g., the effective particulate 180° volume scattering function (backscatter) and lidar attenuation coefficient (attenuation). The simulation indicates that the backscatter and attenuation deviations are within 10% and 2%, respectively, when the HSRL discriminator is the iodine absorption cell, and are within 3% and 1%, respectively, when the discriminator is changed to the field-widened Michelson interferometer.

Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria

Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined due to the lack of a single-genetic marker resolving all pigment types (PTs). Here, we developed and employed a robust method based on three distinct marker genes (cpcBA, mpeBA, and mpeW) to estimate the relative abundance of all known Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to reveal the global distribution of Synechococcus PTs and to define their environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified populations in which CA4 might be nonfunctional due to the lack of specific CA4 genes, notably in warm high-nutrient low-chlorophyll areas. Major ecotypes within clades I-IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study provides important insights into the ecology of Synechococcus and highlights the complex interactions between vertical phylogeny, pigmentation, and environmental parameters that shape Synechococcus community structure and evolution.

Retrieving the seawater volume scattering function at the 180° scattering angle with a high-spectral-resolution lidar

A high-spectral-resolution lidar (HSRL) is proposed to retrieve the seawater volume scattering function at the 180° scattering angle βπ without the assumption of the lidar extinction-to-backscatter ratio. A field-widened Michelson interferometer is employed as the ultra-narrow spectral discriminator to reject particulate scattering and molecular Rayleigh scattering but transmit molecular Mandelshtam-Brillouin scattering. The theoretical framework to retrieve βπ is presented in detail based on a dual-channel HSRL configuration. Simulation on the retrieval and error estimation shows that, the proposed oceanographic HSRL based on the ship or aircraft can perform well to extract the profile of βπ and has a real potential in the oceanographic remote sensing.

Diversity of Synechococcus at the Martha's Vineyard Coastal Observatory: Insights from Culture Isolations, Clone Libraries, and Flow Cytometry

The cyanobacterium Synechococcus is a ubiquitous, important phytoplankter across the world's oceans. A high degree of genetic diversity exists within the marine group, which likely contributes to its global success. Over 20 clades with different distribution patterns have been identified. However, we do not fully understand the environmental factors that control clade distributions. These factors are likely to change seasonally, especially in dynamic coastal systems. To investigate how coastal Synechococcus assemblages change temporally, we assessed the diversity of Synechococcus at the Martha's Vineyard Coastal Observatory (MVCO) over three annual cycles with culture-dependent and independent approaches. We further investigated the abundance of both phycoerythrin (PE)-containing and phycocyanin (PC)-only Synechococcus with a flow cytometric setup that distinguishes PC-only Synechococcus from picoeukaryotes. We found that the Synechococcus assemblage at MVCO is diverse (13 different clades identified), but dominated by clade I representatives. Many clades were only isolated during late summer and fall, suggesting more favorable conditions for isolation at this time. PC-only strains from four different clades were isolated, but these cells were only detected by flow cytometry in a few samples over the time series, suggesting they are rare at this site. Within clade I, we identified four distinct subclades. The relative abundances of each subclade varied over the seasonal cycle, and the high Synechococcus cell concentration at MVCO may be maintained by the diversity found within this clade. This study highlights the need to understand how temporal aspects of the environment affect Synechococcus community structure and cell abundance.

An instrument design for non-contact detection of biomolecules and minerals on Mars using fluorescence

We discuss fluorescence as a method to detect polycyclic aromatic hydrocarbons and other organic molecules, as well as minerals on the surface of Mars. We present an instrument design that is adapted from the ChemCam instrument which is currently on the Mars Science Lander Rover Curiosity and thus most of the primary components are currently flight qualified for Mars surface operations, significantly reducing development costs. The major change compared to ChemCam is the frequency multipliers of the 1064 nm laser to wavelengths suitable for fluorescence excitation (266 nm, 355 nm, and 532 nm). We present fluorescence spectrum for a variety of organics and minerals relevant to the surface of Mars. Preliminary results show minerals already known on Mars, such as perchlorate, fluoresce strongest when excited by 355 nm. Also we demonstrate that polycyclic aromatic hydrocarbons, such as those present in Martian meteorites, are highly fluorescent at wavelengths in the ultraviolet (266 nm, 355 nm), but not as much in the visible (532 nm). We conclude that fluorescence can be an important method for Mars applications and standoff detection of organics and minerals. The instrument approach described in this paper builds on existing hardware and offers high scientific return for minimal cost for future missions.

Field trial of a dual-wavelength fluorescent emission (L.I.F.E.) instrument and the Magma White rover during the MARS2013 Mars analog mission

Abstract We have developed a portable dual-wavelength laser fluorescence spectrometer as part of a multi-instrument optical probe to characterize mineral, organic, and microbial species in extreme environments. Operating at 405 and 532 nm, the instrument was originally designed for use by human explorers to produce a laser-induced fluorescence emission (L.I.F.E.) spectral database of the mineral and organic molecules found in the microbial communities of Earth's cryosphere. Recently, our team had the opportunity to explore the strengths and limitations of the instrument when it was deployed on a remote-controlled Mars analog rover. In February 2013, the instrument was deployed on board the Magma White rover platform during the MARS2013 Mars analog field mission in the Kess Kess formation near Erfoud, Morocco. During these tests, we followed tele-science work flows pertinent to Mars surface missions in a simulated spaceflight environment. We report on the L.I.F.E. instrument setup, data processing, and performance during field trials. A pilot postmission laboratory analysis determined that rock samples acquired during the field mission exhibited a fluorescence signal from the Sun-exposed side characteristic of chlorophyll a following excitation at 405 nm. A weak fluorescence response to excitation at 532 nm may have originated from another microbial photosynthetic pigment, phycoerythrin, but final assignment awaits development of a comprehensive database of mineral and organic fluorescence spectra. No chlorophyll fluorescence signal was detected from the shaded underside of the samples.

Assessing phytoplankton using a two-rank database based on excitation-emission fluorescence spectra

The feasibility of using a two-rank database of reference spectra based on in vivo fluorescence excitation-emission matrix (EEMs) spectra to assess dominant groups of phytoplankton was explored. Twenty-six species belonging to 20 genera of seven divisions were studied. First, fluorescent characteristics of these EEMs were extracted using Daubechies-7 wavelet analysis. Second, the optimal characteristic spectra of scale vectors (SOCS) and time-series vectors (TOCS) were selected; phytoplankton of different genera were classified using Fisher linear discriminant analysis. Third, SOCS and TOCS reference spectra databases were obtained by hierarchical cluster analysis. Using non-negative least squares as the method to assess the phytoplankton, a two-rank reference spectra database was established according to their respective ability to identify the 2818 single-species samples. Using this fluorimetric technique, the correct identification rates (CIRs) for single-species samples were 88.8-100% at the genus level and 98.8-100% at the division level. Dominant species in the 465 laboratory mixtures had corresponding CIRs of 85.6% and 96.1%. Moreover, 15 of the 19 species used as dominants were correctly identified at the genus level. In 27 natural seawater samples, Prorocentrum donghaiense, Thalassiosira nordenskioldi, and Chaetoceros socialis (bloom-forming species with a density of about 10(7) cell L(-1)), and Alexandrium sp. (dominant species with abundance of about 10(6) cell L(-1)) were qualitatively identified at the genus level; other dominant species, with densities of 10(5) to 10(6) cell L(-1), were identified at the division level. The quantitative identification was relatively poor in the natural water samples, and several potential resolutions, including trying both new measuring methods and calculating methods, for future study are given.

Discrimination of phytoplankton classes using characteristic spectra of 3D fluorescence spectra

The discrimination of phytoplankton classes using the characteristic fluorescence spectra extracted from three-dimensional fluorescence spectra was investigated. Single species cultures of 11 phytoplankton species, representing 5 major phytoplankton divisions, were used. The 3D fluorescence spectra of the cultures grown at different temperatures (20 and 15 degrees C) and illumination intensities (140, 80 and 30 microM m(-2) s(-1)) were measured and their feature extraction methods were explored. Ordering Rayleigh and Raman scattering data as zero, the obtained excitation-emission matrices were processed by both singular value decomposition (SVD) and trilinear decomposition methods. The resulting first principal component can be regarded as the characteristic spectrum of the original 3D fluorescence spectrum. The analysis shows that such characteristic spectra have a discriminatory capability. At different temperatures, the characteristic spectra of Isochrysis galbana, Platymonas helgolanidica and Skeletonema costatuma have high degrees of similarity to their own species samples, while the spectra similarities of Alexandrium tamarense, Prorocentrum dentatum, Pseudo-nitzschia pungens, Chaetoceros curvisetus, Ch. Debilis, Ch. Didymus and Synechococcus sp. are not as significant as the other three species. C. curvisetus, Ch. Debilis and Ch. Didymus, belonging to genus Chaetoceros, have identical spectra and cannot be discriminated at all. Regarding all six diatom species as one class, the average discriminant error rate is below 9%. It is worth mentioning that the diatom class can be distinguished from A. tamarense and P. dentatum, which belong to Dinophyta.

A Multistate Model for the Fluorescence Response of R-Phycoerythrin

Although strong fluorescence makes the R-phycoerythrin (R-PE) proteins increasingly useful in biological and clinical assays, they are subject to nonlinear effects including transitions to collective dark states and photodegradation, which complicate quantitative applications. We report measurements of R-PE fluorescence intensity as a function of incident power, duration of illumination and temperature. Emission intensity in the band at 570 nm is proportional to incident power for low power levels. At higher incident power, the emission at 570 nm is smaller than expected from a linear dependence on power. We propose that R-PE undergoes both reversible emission cessation on a millisecond time scale attributed to transitions to a collective dark state, and irreversible photodegradation on a time scale of minutes. Singlet oxygen scavengers such as dithiothreitol and n-propyl gallate have protective effects against the latter effect but not the former. Electrophoretic analysis of irradiated solutions of R-PE indicates that significant noncovalent aggregation is correlated with photodegradation. A multistate model based on fluorescence measurements and geometric analysis is proposed for the fluorophores in R-PE. The phycobilin fluorophores are partitioned into three groups: the phycourobilins (PUB) absorbing at 490 nm, one group of phycoerythobilins (PEB) absorbing at 530 nm (PEB-530) and another group of PEB absorbing at 560 nm (PEB-560). The two processes that result in the loss of fluorescence intensity are most likely associated with the PEB-560 group.

Validation of Terra-MODIS phytoplankton chlorophyll fluorescence line height. I. Initial airborne lidar results

The Moderate Resolution Imaging Spectroradiometer (MODIS) aboard the Terra spacecraft contains spectral bands that allow retrieval of solar-induced phytoplankton chlorophyll fluorescence emission radiance. Concurrent airborne laser-induced (and water-Raman normalized) phytoplankton chlorophyll fluorescence data is used to successfully validate the MODIS chlorophyll fluorescence line height (FLH) retrievals within Gulf Stream, continental slope, shelf, and coastal waters of the Middle Atlantic Bight portion of the western North Atlantic Ocean for 11 March 2002. Over the entire approximately 480-km flight line a correlation coefficient of r2 = 0.85 results from regression of the airborne laser data against the MODIS FLH. It is also shown that the MODIS FLH product is not influenced by blue-absorbing chromophoric dissolved organic matter absorption. These regional results strongly suggest that the FLH methodology is equally valid within similar oceanic provinces of global oceans.

Physiological diversity and niche adaptation in marine Synechococcus

During the twenty years or so since the discovery of tiny photosynthetic cells of the genus Synechococcus in marine oceanic systems, a tremendous expansion of interest has been seen in the literature pertaining to these organisms. The fact that they are ubiquitous and abundant in major oceanic regimes underlies their ecological importance as significant contributors to marine C fixation. Recent advances in the physiology and biochemistry of these organisms are presented here, focusing on strains of the MC-A and MC-B clusters; it is stressed that the data contained herein should be put into the context of the ecological niche occupied by particular genotypes in situ. This system is ripe for joining the often separate disciplines of molecular ecology and microbial physiology and provides a great opportunity to tease out the underlying processes that both mediate organism evolution and also the environmental factors that dictate this.

Helicopter-based lidar system for monitoring the upper ocean and terrain surface

A compact helicopter-based lidar system is developed and tested under laboratory and field conditions. It is shown that the lidar can measure concentrations of chlorophyll a and dissolved organic matter at the surface of water bodies, detect fluorescence spectra of ground vegetation at a distance of up to 530 m, and determine the vertical profile of light-scattering particle concentration in the upper ocean. The possibilities of the lidar system are demonstrated by detection of polluted areas at the ocean surface, by online monitoring of three-dimensional distribution of light-scattering layers, and by recognition of plant types and physiological states.

Remote Mapping of Vegetation and Geological Features by Lidar in the 9-11-mum Region

We report examples of the use of a scanning tunable CO(2) laser lidar system in the 9-11-mum region to construct images of vegetation and rocks at ranges as far as 5 km from the instrument. Range information is combined with horizontal and vertical distances to yield an image with three spatial dimensions simultaneous with the classification of target type. Object classification is based on reflectance spectra, which are sufficiently distinct to allow discrimination between several tree species, between trees and scrub vegetation, and between natural and artificial targets. Limitations imposed by laser speckle noise are discussed.

Next-Generation NASA Airborne Oceanographic Lidar System

The complete design and flight test of the next-generation Airborne Oceanographic Lidar (AOL-3) is detailed. The application of new technology has allowed major reductions in weight, volume, and power requirements compared with the earlier AOL sensor. Subsystem designs for the new AOL sensor include new technology in fiber optics, spectrometer detector optical train, miniature photomultiplier modules, dual-laser wavelength excitation from a single small laser source, and new receiver optical configuration. The new design reduced telescope size and maintained the same principal fluorescence and water Raman bands but essentially retained a comparable measurement accuracy. A major advancement is the implementation of single-laser simultaneous excitation of two physically separate oceanic target areas: one stimulated by 532 nm and the other by 355 nm. Backscattered fluorescence and Raman signals from both targets are acquired simultaneously by use of the same telescope and spectrometer-detector system. Two digital oscilloscopes provide temporal- and depth-resolved data from each of seven spectral emission bands.

Satellite retrieval of the absorption coefficient of phytoplankton phycoerythrin pigment: theory and feasibility status

Oceanic radiance model inversion methods are used to develop a comprehensive algorithm for retrieval of the absorption coefficients of phycourobilin (PUB) pigment, type I phycoerythrobilin (PEB) pigment rich in PUB, and type II PEB deficient in PUB pigment (together with the usual "big three" inherent optical properties: the total backscattering coefficient and the absorption coefficients of chromophoric dissolved organic matter (CDOM)-detritus and phytoplankton). This fully modeled inversion algorithm is then simplified to yield a hybrid modeled-unmodeled inversion algorithm in which the phycoerythrin (PE) absorption coefficient is retrieved as unmodeled 488-nm absorption (which exceeds the modeled phytoplankton and the CDOM-detritus absorption coefficients). Each algorithm was applied to water-leaving radiances, but only hybrid modeled-unmodeled inversions yielded viable retrievals of the PE absorption coefficient. Validation of the PE absorption coefficient retrieval was achieved by relative comparison with airborne laser-induced PEB fluorescence. The modeled-unmodeled retrieval of four inherent optical properties by direct matrix inversion is rapid and well conditioned, but the accuracy is strongly limited by the accuracy of the three principal inherent optical property models across all four spectral bands. Several research areas are identified to enhance the radiance-model-based retrievals: (a) improved PEB and PUB absorption coefficient models, (b) PE spectral shifts induced by PUB chromophore substitution at chromophore binding sites, (c) specific absorption-sensitive phytoplankton absorption modeling, (d) total constituent backscattering modeling, (e) unmodeled carotinoid and phycocyanin absorption that are not now accounted for in the chlorophyll-dominated phytoplankton absorption coefficient model, and (f) iterative inversion techniques to solve for six constituents with only five radiances. Although considerable progress has been made toward the satellite recovery of PE absorption, the maturity of the retrieval is presently insufficient for routine global application. Instead it must currently be used on a regional basis where localized ship and aircraft validation can be made available. The algorithm was developed for the MODIS (Moderate-Resolution Imaging Spectroradiometer) sensor but is applicable to any sensor having comparable band locations.