Microscale Quantification of the Absorption by Dissolved and Particulate Material in Coastal Waters with an ac-9

Measuring coastal and oceanic absorption coefficients of dissolved and particulate matter in the visible domain usually requires a methodology for amplifying the natural signal because conventional spectrophotometers lack the necessary sensitivity. The WET Labs ac-9 is a recently developed in situ absorption and attenuation meter with a precision better than ±0.001 m−1 in the raw signal, which is sufficient to make these measurements in pristine samples. Whereas the superior sensitivity of the ac-9 has been well documented, the accuracy of in situ measurements for bio-optical applications has not been rigorously evaluated. Obtaining accurate results with an ac-9 requires careful attention to calibration procedures because baselines drift as a result of the changing optical properties of several ac-9 components. To correct in situ measurements for instrument drift, a pressurized flow procedure was developed for calibrating an ac-9 with optically clean water. In situ, micro- (cm) to fine- (m) scale vertical profiles of spectral total absorption, at(λ), and spectral absorption of dissolved materials, ag(λ), were then measured concurrently using multiple meters, corrected for drift, temperature, salinity, and scattering errors and subsequently compared. Particulate absorption, ap(λ), was obtained from at(λ) − ag(λ). CTD microstructure was simultaneously recorded. Vertical profiles of ag(λ), at(λ), and ap(λ) were replicated with different meters within ±0.005 m−1, and spectral relationships compared well with laboratory measurements and hydrographic structure

Hidden state prediction: a modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses

Complex symbioses between animal or plant hosts and their associated microbiotas can involve thousands of species and millions of genes. Because of the number of interacting partners, it is often impractical to study all organisms or genes in these host-microbe symbioses individually. Yet new phylogenetic predictive methods can use the wealth of accumulated data on diverse model organisms to make inferences into the properties of less well-studied species and gene families. Predictive functional profiling methods use evolutionary models based on the properties of studied relatives to put bounds on the likely characteristics of an organism or gene that has not yet been studied in detail. These techniques have been applied to predict diverse features of host-associated microbial communities ranging from the enzymatic function of uncharacterized genes to the gene content of uncultured microorganisms. We consider these phylogenetically informed predictive techniques from disparate fields as examples of a general class of algorithms for Hidden State Prediction (HSP), and argue that HSP methods have broad value in predicting organismal traits in a variety of contexts, including the study of complex host-microbe symbioses.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Frontiers Research Foundation. The published article can be found at: http://www.frontiersin.org/Microbiology.Keywords: phylogenetic prediction, “virtual” metagenomes, systems biology, predictive metagenomics, ecotoxicology, 16S rRNA gene copy numbe

Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny

Scleractinian corals' microbial symbionts influence host health, yet how coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. We show that coral microbiomes are anatomically compartmentalized in both modern microbial ecology and evolutionary assembly. Coral mucus, tissue, and skeleton microbiomes differ in microbial community composition, richness, and response to host vs. environmental drivers. We also find evidence of coral-microbe phylosymbiosis, in which coral microbiome composition and richness reflect coral phylogeny. Surprisingly, the coral skeleton represents the most biodiverse coral microbiome, and also shows the strongest evidence of phylosymbiosis. Interactions between bacterial and coral phylogeny significantly influence the abundance of four groups of bacteria-including Endozoicomonas-like bacteria, which divide into host-generalist and host-specific subclades. Together these results trace microbial symbiosis across anatomy during the evolution of a basal animal lineage

Occurrence and mechanisms of formation of a dramatic thin layer of marine snow in a shallow Pacific fjord

Huge accumulations of diatom-dominated marine snow (aggregates \u3e0.5 mm in diameter) were observed in a layer approximately 50 cm thick persisting over a 24 h period in a shallow fjord in the San Juan Islands, Washington, USA. The layer was associated with the 22.4 σt density surface. A second thin layer of elevated phytoplankton concentration located at a density discontinuity 1.5 to 2 m above the marine snow layer occurred within a dense diatom bloom near the surface. At the end of the study period, isopycnals shoaled and the 2 layers merged. More than 80% of the diatom bloom consisted of Thalassiosira spp. (50 to 59%), Odontella longicruris (5 to 14%), Asterionellopsis glacialis, and Thalassionema nitzschioides. A much higher proportion of O. longicruris occurred in marine snow (about 53%) than among suspended cells suggesting that this species differentially aggregated. Most zooplankton avoided the mucus-rich aggregate layer. The layer of marine snow was formed when sinking aggregated diatoms reached neutral buoyancy at the 22.4 isopycnal, probably due to the presence of low salinity mucus resistant to salt exchange in the interstices of the aggregates. Rates of turbulent kinetic energy dissipation throughout the water column rarely exceeded 10-8 m2 s-3 and aggregates below the thin layer were largely detrital in composition indicating that small-scale shears due to turbulence did not erode the layer of marine snow. The accumulation of marine snow and phytoplankton in persistent, discrete layers at density discontinuities results in habitat partitioning of the pelagic zone, impacts the distribution and interactions of planktonic organisms as well as the intensity and location of biological processes in the water column, and helps maintain species diversity

Microscale Quantification of the Absorption by Dissolved and Particulate Material in Coastal Waters with an ac-9

Measuring coastal and oceanic absorption coefficients of dissolved and particulate matter in the visible domain usually requires a methodology for amplifying the natural signal because conventional spectrophotometers lack the necessary sensitivity. The WET Labs ac-9 is a recently developed in situ absorption and attenuation meter with a precision better than ±0.001 m⁻¹ in the raw signal, which is sufficient to make these measurements in pristine samples. Whereas the superior sensitivity of the ac-9 has been well documented, the accuracy of in situ measurements for bio-optical applications has not been rigorously evaluated. Obtaining accurate results with an ac-9 requires careful attention to calibration procedures because baselines drift as a result of the changing optical properties of several ac-9 components. To correct in situ measurements for instrument drift, a pressurized flow procedure was developed for calibrating an ac-9 with optically clean water. In situ, micro- (cm) to fine- (m) scale vertical profiles of spectral total absorption, a[subscript]t(λ), and spectral absorption of dissolved materials, a[subscript]g(λ), were then measured concurrently using multiple meters, corrected for drift, temperature, salinity, and scattering errors and subsequently compared. Particulate absorption, a[subscript]p(λ), was obtained from a[subscript]t(λ) − a[subscript]g(λ). CTD microstructure was simultaneously recorded. Vertical profiles of a[subscript]g(λ), a[subscript]t(λ), and a[subscript]p(λ) were replicated with different meters within ±0.005 m⁻¹, and spectral relationships compared well with laboratory measurements and hydrographic structur

Direct sequencing of the human microbiome readily reveals community differences

Future sequencing of the human microbiota will require greater breadth rather than depth