Coral reefs in transition: Temporal photoquadrat analyses and validation of underwater hyperspectral imaging for resource-efficient monitoring in Guam.

The island of Guam in the west Pacific has seen a significant decrease in coral cover since 2013. Lafac Bay, a marine protected area in northeast Guam, served as a reference site for benthic communities typical of forereefs on the windward side of the island. The staghorn coral Acropora abrotanoides is a dominant and characteristic ecosystem engineer of forereef communities on exposed shorelines. Photoquadrat surveys were conducted in 2015, 2017, and 2019, and a diver-operated hyperspectral imager (i.e., DiveRay) was used to survey the same transects in 2019. Machine learning algorithms were used to develop an automated pipeline to assess the benthic cover of 10 biotic and abiotic categories in 2019 based on hyperspectral imagery. The cover of scleractinian corals did not differ between 2015 and 2017 despite being subjected to a series of environmental disturbances in these years. Surveys in 2019 documented the almost complete decline of the habitat-defining staghorn coral Acropora abrotanoides (a practically complete disappearance from about 10% cover), a significant decrease (~75%) in the cover of other scleractinian corals, and a significant increase (~55%) in the combined cover of bare substrate, turf algae, and cyanobacteria. The drastic change in community composition suggests that the reef at Lafac Bay is transitioning to a turf algae-dominated community. However, the capacity of this reef to recover from previous disturbances suggests that this transition could be reversed, making Lafac Bay an excellent candidate for long-term monitoring. Community analyses showed no significant difference between automatically classified benthic cover estimates derived from the hyperspectral scans in 2019 and those derived from photoquadrats. These findings suggest that underwater hyperspectral imagers can be efficient and effective tools for fast, frequent, and accurate monitoring of dynamic reef communities.

Assessment of the utility of underwater hyperspectral imaging for surveying and monitoring coral reef ecosystems.

Technological innovations that improve the speed, scale, reproducibility, and accuracy of monitoring surveys will allow for a better understanding of the global decline in tropical reef health. The DiveRay, a diver-operated hyperspectral imager, and a complementary machine learning pipeline to automate the analysis of hyperspectral imagery were developed for this purpose. To evaluate the use of a hyperspectral imager underwater, the automated classification of benthic taxa in reef communities was tested. Eight reefs in Guam were surveyed and two approaches for benthic classification were employed: high taxonomic resolution categories and broad benthic categories. The results from the DiveRay surveys were validated against data from concurrently conducted photoquadrat surveys to determine their accuracy and utility as a proxy for reef surveys. The high taxonomic resolution classifications did not reliably predict benthic communities when compared to those obtained by standard photoquadrat analysis. At the level of broad benthic categories, however, the hyperspectral results were comparable to those of the photoquadrat analysis. This was particularly true when estimating scleractinian coral cover, which was accurately predicted for six out of the eight sites. The annotation libraries generated for this study were insufficient to train the model to fully account for the high biodiversity on Guam's reefs. As such, prediction accuracy is expected to improve with additional surveying and image annotation. This study is the first to directly compare the results from underwater hyperspectral scanning with those from traditional photoquadrat survey techniques across multiple sites with two levels of identification resolution and different degrees of certainty. Our findings show that dependent on a well-annotated library, underwater hyperspectral imaging can be used to quickly, repeatedly, and accurately monitor and map dynamic benthic communities on tropical reefs using broad benthic categories.

Community assessment of crustose calcifying red algae as coral recruitment substrates.

Successful recruitment of invertebrate larvae to reef substrates is essential to the health of tropical coral reef ecosystems and to their capacity to recover from disturbances. Crustose calcifying red algae (CCRA) are a species rich group of seaweeds that have been identified as important recruitment substrates for scleractinian corals. Most studies on the settlement preference of coral larvae on CCRA use morphological species identifications that can lead to unreliable species identification and do not allow for examining species-specific interactions between coral larvae and CCRA. Accurate identifications of CCRA species is important for coral reef restoration and management to assess CCRA community composition and to detect CCRA species that are favored as coral recruitment substrates. In this study, DNA sequence analysis, was used to identify CCRA species to (1) investigate the species richness and community composition of CCRA on experimental coral recruitment tiles and (2) assess if the coral Acropora surculosa preferred any of these CCRA species as recruitment substrates. The CCRA community assemblages on the coral recruitment tiles was species-rich, comprising 27 distinct CCRA species of the orders Corallinales and Peyssonneliales which constitute new species records for Guam. Lithophylloideae sp. 1 (Corallinales) was the CCRA species that was significantly favored by coral larvae as a recruitment substrate. Lithophylloideae sp. 1 showed to hold a valuable ecological role for coral larval recruitment preference. Lithophylloideae sp. 1 had the highest benthic cover on the recruitment tiles and contained most A. surculosa recruits. DNA barcoding revealed a high taxonomic diversity of CCRA species on a microhabitat scale and provided detailed insight into the species-specific ecological interactions between CCRA and corals. With a steady decline in coral cover, detailed information on species interactions that drive reef recovery is valuable for the planning of marine management actions and restoration efforts.

Diffractive deep neural network adjoint assist or (DNA)2: a fast and efficient nonlinear diffractive neural network implementation.

The recent advent of diffractive deep neural networks or D2NNs has opened new avenues for the design and optimization of multi-functional optical materials; despite the effectiveness of the D2NN approach, there is a need for making these networks as well as the design algorithms more general and computationally efficient. The work demonstrated in this paper brings significant improvements to both these areas by introducing an algorithm that performs inverse design on fully nonlinear diffractive deep neural network - assisted by an adjoint sensitivity analysis which we term (DNA)2. As implied by the name, the procedure optimizes the parameters associated with the diffractive elements including both linear and nonlinear amplitude and phase contributions as well as the spacing between planes via adjoint sensitivity analysis. The computation of all gradients can be obtained in a single GPU compatible step. We demonstrate the capability of this approach by designing several types of three layered D2NN to classify 8800 handwritten digits taken from the MNIST database. In all cases, the D2NN was able to achieve a minimum 94.64% classification accuracy with 192 minutes or less of training.

The habitat-modifying red alga Ramicrusta on Pacific reefs: A new generic record for the Tropical Northwestern Pacific and the description of four new species from Guam.

The genus Ramicrusta (order Peyssonneliales) is a new record for Micronesia, with range expansions of Ramicrusta fujiiana and R. lateralis to Guam. In addition, four species (Ramicrusta adjoulanensis, R. asanitensis, R. labtasiensis, and R. taogamensis) are newly described from Guam using molecular and anatomical characters. Ramicrusta lateralis specimens from Guam share most anatomical features with the holotype description from Vanuatu, but the plants from Guam are more tightly adherent, rigid, and robust than those of Vanuatu. Ramicrusta adjoulanensis possesses a well-developed epithallus with frequent cell fusions, secondary pit connections, and lacking hair bases or trichocytes, similar to Ramicrusta bonairensis. Ramicrusta adjoulanensis differs from other Ramicrusta species in having occasionally free margins and being attached by frequently produced, relatively long rhizoids (75-100 µm long). Ramicrusta asanitensis shares features with many other species, but the thickness of the crust (upwards of 2 mm thick), heavy calcification in the epithallus, and the extent of secondary, tertiary, and quaternary growth, differentiate it from other Ramicrusta species. Ramicrusta labtasiensis shares features with its close relative Ramicrusta lateralis but possesses frequent, robust, and relatively long rhizoids (75-95 µm long) throughout its entire undersurface. Ramicrusta taogamensis resembles its close relative Ramicrusta appressa but is primarily distinguished by its generally well-developed epithallus with occasional secondary pit connections and cell fusions. The six species reported here make Guam equal to Vanuatu in currently having the highest known species richness of Ramicrusta in the world.

A Different Perspective on Cholesteric Liquid Crystals Reveals Unique Color and Polarization Changes.

Planar cholesteric liquid crystals (CLCs) are well known for having vibrant reflective coloration that is associated with the handedness and the pitch length of the helicoidal twist of the liquid crystalline molecules. If one observes these films at oblique angles, the reflected colors blue-shift with increasing angles from normal. On the other hand, uniform lying helix (ULH) CLCs, where the helicoidal axis lies in the plane of the substrate, are well-known but are not typically associated with vibrant colors. Here, we examine the unique optical properties of CLCs at oblique incidence angles, specifically the spectral and polarization changes associated with switching between planar and ULH CLCs for various incidence angles. At small angles of incidence (0° < ψ < 45°, where ψ is the angle of incidence relative to the surface normal at the substrate-CLC interface), the electrically driven helical reorientation from planar to ULH results in a blue-shifting of the color and circularly polarized to unpolarized switching behavior. At large angles (45° < ψ < 90°), the behavior is reversed, with a red-shifting color change occurring and the polarization switching from unpolarized to circularly polarized. Modeling of the light propagation through ULH CLCs is used to confirm the change in position and polarization characteristic of the reflection band with incidence angle observed experimentally. This study provides a new perspective on ULH CLCs and reveals a unique reconfigurable angular chromaticity.

Interactions between self-channeled optical beams in soft-matter systems with artificial nonlinearities.

We demonstrate optical interactions between stable self-trapped optical beams in soft-matter systems with pre-engineered saturable self-focusing optical nonlinearities. Our experiments, carried out in dilute suspensions of particles with negative polarizabilities, show that optical beam interactions can vary from attractive to repulsive, or can display an energy exchange depending on the initial relative phases. The corresponding observations are in good agreement with theoretical predictions.

Fully vectorial accelerating diffraction-free Helmholtz beams.

We show that new families of diffraction-free nonparaxial accelerating optical beams can be generated by considering the symmetries of the underlying vectorial Helmholtz equation. Both two-dimensional transverse electric and magnetic accelerating wave fronts are possible, capable of moving along elliptic trajectories. Experimental results corroborate these predictions when these waves are launched from either the major or minor axis of the ellipse. In addition, three-dimensional spherical nondiffracting field configurations are presented along with their evolution dynamics. Finally, fully vectorial self-similar accelerating optical wave solutions are obtained via oblate-prolate spheroidal wave functions. In all occasions, these effects are illustrated via pertinent examples.

Trapping and guiding microparticles with morphing autofocusing Airy beams.

We observe optical trapping and manipulation of dielectric microparticles using autofocusing radially symmetric Airy beams. This is accomplished by exploiting either the inward or outward transverse acceleration associated with their chirped wavefronts. We experimentally demonstrate, for the first time to our knowledge, that such Airy beams morph into nondiffracting Bessel beams in their far-field. Furthermore, the ability of guiding and transporting microparticles along the primary rings of this class of beams is explored.