Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment.

Carboxyl-rich alicyclic molecules (CRAMs) widely exist in the ocean and constitute the central part of the refractory dissolved organic matter (RDOM) pool. Although a consensus has been reached that microbial activity forms CRAMs, the detailed molecular mechanisms remain largely unexplored. To better understand the underlying genetic mechanisms driving the microbial transformation of CRAM, a long-term macrocosm experiment spanning 220 days was conducted in the Aquatron Tower Tank at Dalhousie University, Halifax, Canada, with the supply of diatom-derived DOM as a carbon source. The DOM composition, community structure, and metabolic pathways were characterised using multi-omics approaches. The addition of diatom lysate introduced a mass of labile DOM into the incubation seawater, which led to a low degradation index (IDEG) and refractory molecular lability boundary (RMLB) on days 1 and 18. The molecular compositions of the DOM molecules in the later incubation period (from day 120 to day 220) were more similar in composition to those on day 0, suggesting a rapid turnover of phytoplankton debris by microbial communities. Taxonomically, while Alpha proteobacteria dominated during the entire incubation period, Gamma proteobacteria became more sensitive and abundant than the other bacterial groups on days 1 and 18. Recalcitrant measurements such as IDEG and RMLB were closely related to the DOM molecules, bacterial community, and Kyoto encyclopaedia of Genes and Genomes (KEGG) modules, suggesting close associations between RDOM accumulation and microbial metabolism. KEGG modules that showed strong positive correlation with CRAMs were identified using a microbial ecological network approach. The identified KEGG modules produced the substrates, such as the acetyl-CoA or 3­hydroxy-3-methylglutaryl-CoA, which could participate in the mevalonate pathway to generate the precursor of CRAM analogues, isopentenyl-PP, suggesting a potential generation pathway of CRAM analogues in bacteria and archaea. This study revealed the potential genetic and molecular processes involved in the microbial origin of CRAM analogues, and thus indicated a vital ecological role of bacteria and archaea in RDOM production. This study also offered new perspectives on the carbon sequestration in the ocean.

Correcting a major error in assessing organic carbon pollution in natural waters.

Microbial degradation of dissolved organic carbon (DOC) in aquatic environments can cause oxygen depletion, water acidification, and CO2 emissions. These problems are caused by labile DOC (LDOC) and not refractory DOC (RDOC) that resists degradation and is thus a carbon sink. For nearly a century, chemical oxygen demand (COD) has been widely used for assessment of organic pollution in aquatic systems. Here, we show through a multicountry survey and experimental studies that COD is not an appropriate proxy of microbial degradability of organic matter because it oxidizes both LDOC and RDOC, and the latter contributes up to 90% of DOC in high-latitude forested areas. Hence, COD measurements do not provide appropriate scientific information on organic pollution in natural waters and can mislead environmental policies. We propose the replacement of the COD method with an optode-based biological oxygen demand method to accurately and efficiently assess organic pollution in natural aquatic environments.

A global compilation of in situ aquatic high spectral resolution inherent and apparent optical property data for remote sensing applications.

Light emerging from natural water bodies and measured by radiometers contains information about the local type and concentrations of phytoplankton, non-algal particles and colored dissolved organic matter in the underlying waters. An increase in spectral resolution in forthcoming satellite and airborne remote sensing missions is expected to lead to new or improved capabilities for characterizing aquatic ecosystems. Such upcoming missions include NASA's Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission; the NASA Surface Biology and Geology designated observable mission; and NASA Airborne Visible/Infrared Imaging Spectrometer - Next Generation (AVIRIS-NG) airborne missions. In anticipation of these missions, we present an organized dataset of geographically diverse, quality-controlled, high spectral resolution inherent and apparent optical property (IOP-AOP) aquatic data. The data are intended to be of use to increase our understanding of aquatic optical properties, to develop aquatic remote sensing data product algorithms, and to perform calibration and validation activities for forthcoming aquatic-focused imaging spectrometry missions. The dataset is comprised of contributions from several investigators and investigating teams collected over a range of geographic areas and water types, including inland waters, estuaries, and oceans. Specific in situ measurements include remote-sensing reflectance, irradiance reflectance, and coefficients describing particulate absorption, particulate attenuation, non-algal particulate absorption, colored dissolved organic matter absorption, phytoplankton absorption, total absorption, total attenuation, particulate backscattering, and total backscattering. The dataset can be downloaded from https://doi.org/10.1594/PANGAEA.902230 (Casey et al., 2019).

Radiance transmittance measured at the ocean surface.

The radiance transmittance (Tr) is the ratio of the water-leaving radiance (Lw(0+)) to the sub-surface upwelling radiance (Lu(0-)), which is an important optical parameter for ocean optics and ocean color remote sensing. Historically, a constant value (~0.54) based on theoretical presumptions has been adopted for Tr and is widely used. This optical parameter, however, has never been measured in the aquatic environments. With a robust setup to measure both Lu(0-) and Lw(0+) simultaneously in the field, this study presents Tr in the zenith direction between 350 and 700 nm measured in a wide range of oceanic waters. It is found that the measured Tr values are generally consistent with the long-standing theoretical value of 0.54, with mean relative difference less than 10%. In particular, the agreement within the spectral domain of 400-600 nm is found to be the best (with the averaged difference less than 5%). The largest difference is observed for wavelengths longer than 600 nm with the average difference less than 15%, which is related to the generally very small values in both Lu(0-) and Lw(0+) and rough environmental conditions. These results provide a validation of the setup for simultaneous measurements of upwelling radiance and water-leaving radiance and confidence in the theoretical Tr value used in ocean optics studies at least for oceanic waters.

Submersible optical sensors exposed to chemically dispersed crude oil: wave tank simulations for improved oil spill monitoring.

In situ fluorometers were deployed during the Deepwater Horizon (DWH) Gulf of Mexico oil spill to track the subsea oil plume. Uncertainties regarding instrument specifications and capabilities necessitated performance testing of sensors exposed to simulated, dispersed oil plumes. Dynamic ranges of the Chelsea Technologies Group AQUAtracka, Turner Designs Cyclops, Satlantic SUNA and WET Labs, Inc. ECO, exposed to fresh and artificially weathered crude oil, were determined. Sensors were standardized against known oil volumes and total petroleum hydrocarbons and benzene-toluene-ethylbenzene-xylene measurements-both collected during spills, providing oil estimates during wave tank dilution experiments. All sensors estimated oil concentrations down to 300 ppb oil, refuting previous reports. Sensor performance results assist interpretation of DWH oil spill data and formulating future protocols.

A new instrument for measuring the high dynamic range radiance distribution in near-surface sea water.

A new instrument for measuring the full radiance distribution in the ocean interior is introduced. The system is based on CMOS technology to achieve intra-scene dynamic range of 6 decades and system dynamic range of more than 9 decades. The spatial resolution is nominally 0.5 degrees with a temporal frame rate between 1 and 15 frames per second. The general instrumentation, detailed calibration, and a characterization of the system are described. Validity of the camera systems is demonstrated by comparison of the radiance measurements with other classical oceanographic radiometers.

Retrieving composition and sizes of oceanic particle subpopulations from the volume scattering function.

For a particle population with known size, composition, structure, and shape distributions, its volume scattering function (VSF) can be estimated from first principles through a governing relationship, the Fredholm linear integral equation of the first kind. Inverting the Fredholm equation to derive the composition and size distribution of particles from measured VSFs remains challenging because 1) the solution depends on the kernel function, and 2) the kernel function needs to be constructed to avoid singularity. In this study, a thorough review of the earlier and current inversion techniques is provided. An inversion method based on nonnegative least squares is presented and evaluated using the VSFs measured by a prototype volume scattering meter at the LEO-15 site off the New Jersey coast. The kernel function was built by a compilation of individual subpopulations, each of which follows a lognormal size distribution and whose characteristic size and refractive index altogether cover the entire ranges of natural variability of potential marine particles of the region. Sensitivity analyses were conducted to ensure the kernel function being constructed is neither singular nor pathological. A total of 126 potential subpopulations were identified, among which 11 are common in more than half of the inversions and only five consistently present (>90% of measurements). These five subpopulations can be interpreted as small colloidal type particles of sizes around 0.02 µm, submicrometer detritus-type particles (n(r)=1.02, r(mode)=0.2 µm), two micrometer-sized subpopulations with one relatively soft (n(r)=1.04 and r(mode)=1.6 µm) and the other relatively refringent (n(r)=1.10 and r(mode)=3.2 µm), and bubbles of relatively large sizes (n(r)=0.75 and r(mode)=10 µm). Reconstructed PSDs feature a bimodal shape, with the smaller peak dominated by the colloidal subpopulations and the larger particles closely approximated by a power-law function. The Junge-type slope averages -4.0±0.2, in close agreement with the well-known mean value of -4.0 over the global ocean. The distribution of the refractive index suggested a dominance of particles of higher water content, also in agreement with earlier results based on the backscattering ratio and attenuation coefficients at the same area. Surprisingly, the colloidal-type subpopulations, which have often been operationally classified as "dissolved" and neglected for their scattering, exhibit significant backscattering with contributions of up to 40% over the entire backward angles.

Global phytoplankton decline over the past century.

In the oceans, ubiquitous microscopic phototrophs (phytoplankton) account for approximately half the production of organic matter on Earth. Analyses of satellite-derived phytoplankton concentration (available since 1979) have suggested decadal-scale fluctuations linked to climate forcing, but the length of this record is insufficient to resolve longer-term trends. Here we combine available ocean transparency measurements and in situ chlorophyll observations to estimate the time dependence of phytoplankton biomass at local, regional and global scales since 1899. We observe declines in eight out of ten ocean regions, and estimate a global rate of decline of approximately 1% of the global median per year. Our analyses further reveal interannual to decadal phytoplankton fluctuations superimposed on long-term trends. These fluctuations are strongly correlated with basin-scale climate indices, whereas long-term declining trends are related to increasing sea surface temperatures. We conclude that global phytoplankton concentration has declined over the past century; this decline will need to be considered in future studies of marine ecosystems, geochemical cycling, ocean circulation and fisheries.

Spectra of particulate backscattering in natural waters.

Hyperspectral profiles of downwelling irradiance and upwelling radiance in natural waters (oligotrophic and mesotrophic) are combined with inverse radiative transfer to obtain high resolution spectra of the absorption coefficient (a) and the backscattering coefficient (b(b)) of the water and its constituents. The absorption coefficient at the mesotrophic station clearly shows spectral absorption features attributable to several phytoplankton pigments (Chlorophyll a, b, c, and Carotenoids). The backscattering shows only weak spectral features and can be well represented by a power-law variation with wavelength (lambda): b(b) approximately lambda(-n), where n is a constant between 0.4 and 1.0. However, the weak spectral features in b(b)b suggest that it is depressed in spectral regions of strong particle absorption. The applicability of the present inverse radiative transfer algorithm, which omits the influence of Raman scattering, is limited to lambda < 490 nm in oligotrophic waters and lambda < 575 nm in mesotrophic waters.

Optical influence of ship wakes.

The optical variations observed within ship wakes are largely due to the generation of copious amounts of air bubbles in the upper ocean, a fraction of which accumulate as foam at the surface, where they release scavenged surfactants. Field experiments were conducted to test previous theoretical predictions of the variations in optical properties that result from bubble injection in the surface ocean. Variations in remote-sensing reflectance and size distribution of bubbles within the ship-wake zone were determined in three different optical water types: the clear equatorial Pacific Ocean, moderately turbid coastal waters, and very turbid coastal waters, the latter two of which were offshore of New Jersey. Bubbles introduced by moving vessels increased the backscattering in all cases, which in turn enhanced the reflectance over the entire visible and infrared wave bands. The elevated reflectance had different spectral characteristics in the three locations. The color of ship wakes appears greener in the open ocean, whereas little change in color was observed in near-coastal turbid waters, consistent with predictions. Colorless themselves, bubbles increase the reflected radiance and change the color of the ocean in a way that depends on the spectral backscattering and absorption of the undisturbed background waters. For remote observation from aircraft or satellite, the foam and added surfactants further enhance the reflectance to a degree dependent on the illumination and the viewing geometry.