A stratified transect approach captures reef complexity with canopy-forming organisms

On the Great Barrier Reef (GBR), persistent changes to reef communities have begun to be documented, and on inshore reefs these shifts may favour the proliferation of macroalgae. Critical to understanding changes to reef community structure in response to anthropogenic impacts is developing effective methods to accurately document the abundance of different reef organisms. Effective monitoring must be time and cost efficient, replicable, and able to sufficiently and accurately detect disturbances to allow development of strategies to mitigate their impacts. Traditional techniques to document coral reef communities (i.e. photo-quadrats, benthic intercept transects) rely on planar views, which tend to either over- or under-represent canopy-forming organisms. As canopy-forming organisms are likely to be affected by anthropogenic influences (corals negatively, algae positively), it is essential for monitoring programs to implement methods sufficient to document changes to the vertical dimension of coral reefs. Here we build on previous work to document the canopy effect in coral-dominated ecosystems and propose a new survey approach suitable for implementation in algal-dominated systems. A vertically stratified transect, modified from a traditional point intercept transect, captures benthic and canopy-forming members of reef communities and provides information on three-dimensional complexity. To test the capability of the new method to detect changes in vertical reef structure, seaweed was removed from experimental quadrats and monitoring techniques were applied before and after four months of regrowth. A stratified method more accurately captured the three-dimensional change resulting from algal canopy growth, while resolving the over- and under-representation of algal biomass in two traditional techniques. We propose that a stratified transect method improves abundance estimates of canopy-forming organisms whilst maintaining data compatibility with traditional methods

MCViNE -- An object oriented Monte Carlo neutron ray tracing simulation package

MCViNE (Monte-Carlo VIrtual Neutron Experiment) is a versatile Monte Carlo (MC) neutron ray-tracing program that provides researchers with tools for performing computer modeling and simulations that mirror real neutron scattering experiments. By adopting modern software engineering practices such as using composite and visitor design patterns for representing and accessing neutron scatterers, and using recursive algorithms for multiple scattering, MCViNE is flexible enough to handle sophisticated neutron scattering problems including, for example, neutron detection by complex detector systems, and single and multiple scattering events in a variety of samples and sample environments. In addition, MCViNE can take advantage of simulation components in linear-chain-based MC ray tracing packages widely used in instrument design and optimization, as well as NumPy-based components that make prototypes useful and easy to develop. These developments have enabled us to carry out detailed simulations of neutron scattering experiments with non-trivial samples in time-of-flight inelastic instruments at the Spallation Neutron Source. Examples of such simulations for powder and single-crystal samples with various scattering kernels, including kernels for phonon and magnon scattering, are presented. With simulations that closely reproduce experimental results, scattering mechanisms can be turned on and off to determine how they contribute to the measured scattering intensities, improving our understanding of the underlying physics.Comment: 34 pages, 14 figure

Sea-weeding: Manual removal of macroalgae facilitates rapid coral recovery

Coral reef ecosystems globally are under threat, leading to declining coral cover and macroalgal proliferation. Manually removing macroalgae (i.e. ‘sea-weeding’) may promote local-scale coral recovery by reducing a biological barrier, though the impact of removal on community composition of benthic reef organisms has not been quantified. In this three-year study (2018–2021), fleshy macroalgae (predominantly Sargassum spp.) were periodically removed from 25 m2 experimental plots on two inshore fringing reefs of Yunbenun (Magnetic Island) in the central Great Barrier Reef. By the end of the study, coral cover in removal plots (n = 12 plots) assessed through in-field transects increased by at least 47% (2019 mean: 25.5%, 2021 mean: 37.4%), and macroalgal cover decreased by more than half. In contrast, in control plots (n = 12 plots), there was no change in macroalgal cover while coral cover remained stable (2019 mean: 16.4%, 2021 mean: 13.6%). Changes in benthic cover were supported by photoquadrat data, with Bayesian probability modelling indicating a 100% likelihood that coral cover more than doubled in removal plots over the study period, compared to only a 29% chance of increased coral cover in control plots. Synthesis and applications. Manual macroalgal removal can provide rapid benefits and enhance inshore coral reef recovery. Through involvement of community groups and citizen scientists, larger scale removal of macroalgae is a low-tech, high-impact, and achievable method for local reef management

Observations of simultaneous sperm release and larval planulation suggest reproductive assurance in the coral Pocillopora acuta

Despite being an extensively studied group of corals, the reproductive biology of the scleractinian genus Pocillopora remains a mystery. Pocillopora acuta has been proposed to exhibit a mixed reproductive mode, sexually producing gametes (sperm and eggs) and asexually brooding larvae simultaneously within a single colony. Here, we report observations of night-time spawning of sperm during the peak monthly larval release period. We offer a new hypothesis for the regulation of sexual and asexual reproduction in the species and posit that sexual reproduction may occur more often than previously suggested. However, the success of internal oocyte fertilization and subsequent zygote development is dependent on sperm making contact with a fertile colony. We hypothesize that asexual development of larvae occurs when sperm is absent, but more extensive genetic, genomic, and histological data are required to determine the pathway by which unfertilized oocytes may develop. We also propose that this mixed mode of reproduction is an adaptation to mating failure, common in sessile marine invertebrates. The reproductive assurance enjoyed by the species may therefore be the key to its ecological and evolutionary persistence

Generalized Stoichiometry and Biogeochemistry for Astrobiological Applications

A central need in the field of astrobiology is generalized perspectives on life that make it possible to differentiate abiotic and biotic chemical systems. A key component of many past and future astrobiological measurements is the elemental ratio of various samples. Classic work on Earth's oceans has shown that life displays a striking regularity in the ratio of elements as originally characterized by Redfield. The body of work since the original observations has connected this ratio with basic ecological dynamics and cell physiology, while also documenting the range of elemental ratios found in a variety of environments. Several key questions remain in considering how to best apply this knowledge to astrobiological contexts: How can the observed variation of the elemental ratios be more formally systematized using basic biological physiology and ecological or environmental dynamics? How can these elemental ratios be generalized beyond the life that we have observed on our own planet? Here we expand recently developed generalized physiological models to create a simple framework for predicting the variation of elemental ratios found in various environments. We then discuss further generalizing the physiology for astrobiological applications. Much of our theoretical treatment is designed for in situ measurements applicable to future planetary missions. We imagine scenarios where three measurements can be made - particle/cell sizes, particle/cell stoichiometry, and fluid or environmental stoichiometry - and develop our theory in connection with these often deployed measurements.Comment: 18 pages, 5 figure

Green algal infection of American horseshoe crab (Limulus polyphemus) exoskeletal structures

Author Posting. © The Author(s), 2012. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Journal of Invertebrate Pathology 111 (2012): 90-93, doi:10.1016/j.jip.2012.06.002.Degenerative lesions in the dorsum of the horseshoe crab (Limulus polyphemus) exoskeleton, eyes, arthrodial membrane, and base of the telson were documented in a population of wild caught laboratory animals. The disease can lead to loss of tissue structure and function, deformed shells, abnormal molting, loss of ocular structures, erosion of interskeletal membranes, and cardiac hemorrhage. Microscopy, histopathology, and in vitro culture confirmed the causative agent to be a green algae of the family Ulvaceae. Further research may explain how green algae overcome horseshoe crab innate immunity leading to external and internal damage.This study was supported in part by the Frederick B. Bang Fellowship and a grant from the Division of Research Resources, National Institutes of Health (P-40-RR1333-07)

Spin-State Effects on the Thermal Dihydrogen Release from Solid-State [MH(η^2‑H_2)dppe_2]^+ (M = Fe, Ru, Os) Organometallic Complexes for Hydrogen Storage Applications

Mössbauer spectroscopy, experimental thermodynamic measurements, and computational studies were performed to investigate the properties of molecular hydrogen binding to the organometallic fragments [MHdppe_2]^+ (M = Fe, Ru, Os; dppe =1,2-bis(diphenylphosphino)ethane) to form the dihydrogen complex fragments [MH(η^2-H_2)dppe_2]^+. Mössbauer spectroscopy showed that the dehydrogenated complex [FeHdppe_2]^+ adopts a geometry consistent with the triplet spin state, transitioning to a singlet state complex upon addition of the dihydrogen molecule in a manner similar to the previously studied dinitrogen complexes. From simulations, this spin transition behavior was found to be responsible for the strong binding behavior experimentally observed in the iron complex. Spin-singlet to spin-singlet transitions were found to exhibit thermodynamics consistent with the 5d > 3d > 4d binding trend observed for other transition metal dihydrogen complexes. Finally, the method for distinguishing between dihydrogen and dihydride complexes based on partial quadrupole splittings observed in Mössbauer spectra was confirmed, providing a tool for further characterization of these unique species for Mössbauer active compounds

Temporal variation in the microbiome of Acropora coral species does not reflect seasonality

The coral microbiome is known to fluctuate in response to environmental variation and has been suggested to vary seasonally. However, most studies to date, particularly studies on bacterial communities, have examined temporal variation over a time frame of less than 1 year, which is insufficient to establish if microbiome variations are indeed seasonal in nature. The present study focused on expanding our understanding of long-term variability in microbial community composition using two common coral species, Acropora hyacinthus, and Acropora spathulata, at two mid-shelf reefs on the Great Barrier Reef. By sampling over a 2-year time period, this study aimed to determine whether temporal variations reflect seasonal cycles. Community composition of both bacteria and Symbiodiniaceae was characterized through 16S rRNA gene and ITS2 rDNA metabarcoding. We observed significant variations in community composition of both bacteria and Symbiodiniaceae among time points for A. hyacinthus and A. spathulata. However, there was no evidence to suggest that temporal variations were cyclical in nature and represented seasonal variation. Clear evidence for differences in the microbial communities found between reefs suggests that reef location and coral species play a larger role than season in driving microbial community composition in corals. In order to identify the basis of temporal patterns in coral microbial community composition, future studies should employ longer time series of sampling at sufficient temporal resolution to identify the environmental correlates of microbiome variation

Energy depletion and opportunistic microbial colonisation in white syndrome lesions from corals across the Indo-Pacific

Corals are dependent upon lipids as energy reserves to mount a metabolic response to biotic and abiotic challenges. This study profiled lipids, fatty acids, and microbial communities of healthy and white syndrome (WS) diseased colonies of Acropora hyacinthus sampled from reefs in Western Australia, the Great Barrier Reef, and Palmyra Atoll. Total lipid levels varied significantly among locations, though a consistent stepwise decrease from healthy tissues from healthy colonies (HH) to healthy tissue on WS-diseased colonies (HD; i.e. preceding the lesion boundary) to diseased tissue on diseased colonies (DD; i.e. lesion front) was observed, demonstrating a reduction in energy reserves. Lipids in HH tissues were comprised of high energy lipid classes, while HD and DD tissues contained greater proportions of structural lipids. Bacterial profiling through 16S rRNA gene sequencing and histology showed no bacterial taxa linked to WS causation. However, the relative abundance of Rhodobacteraceae-affiliated sequences increased in DD tissues, suggesting opportunistic proliferation of these taxa. While the cause of WS remains inconclusive, this study demonstrates that the lipid profiles of HD tissues was more similar to DD tissues than to HH tissues, reflecting a colony-wide systemic effect and provides insight into the metabolic immune response of WS-infected Indo-Pacific corals