Search

The epizootic disease outbreak known as stony coral tissue loss disease (SCTLD) is arguably the most devastating coral disease in recorded history. SCTLD emerged off the coast of South Florida in 2014 and has since moved into the Caribbean, resulting in coral mortality rates that have changed reef structure and function. Currently, the cause of SCTLD is unknown, but there is evidence from 16S rRNA gene sequencing and bacterial culture studies that the microbial community plays a role in the progression of SCTLD lesions. In this study, we applied shotgun metagenomics to characterize the potential function of bacteria, as well as the composition of the micro-eukaryotic community, associated with SCTLD lesions. We re-examined samples that were previously analyzed using 16S rRNA gene high-throughput sequencing from four coral species: Stephanocoenia intersepta, Diploria labyrinthiformis, Dichocoenia stokesii, and Meandrina meandrites. For each species, tissue from apparently healthy (AH) corals, and unaffected tissue (DU) and lesion tissue (DL) on diseased corals, were collected from sites within the epidemic zone of SCTLD in the Florida Keys. Within the micro-eukaryotic community, the taxa most prominently enriched in DL compared to AH and DU tissue were members of Ciliophora. We also found that DL samples were relatively more abundant in less energy-efficient pathways like the pentose phosphate pathways. While less energy-efficient processes were identified, there were also relatively higher abundances of nucleotide biosynthesis and peptidoglycan maturation pathways in diseased corals compared to AH, which suggests there was more bacteria growth in diseased colonies. In addition, we generated 16 metagenome-assembled genomes (MAGs) belonging to the orders Pseudomonadales, Beggiatoales, Rhodobacterales, Rhizobiales, Rs-D84, Flavobacteriales, and Campylobacterales, and all MAGs were enriched in DL samples compared to AH samples. Across all MAGs there were antibiotic resistance genes that may have implications for the treatment of SCTLD with antibiotics. We also identified genes and pathways linked to virulence, such as nucleotide biosynthesis, succinate dehydrogenase, ureases, nickel/iron transporters, Type-1 secretion system, and metalloproteases. Some of these enzymes/pathways have been previously targeted in the treatment of other bacterial diseases and they may be of interest to mitigate SCTLD lesion progression.

Rapid and widespread declines in coral health and abundance have driven increased investments in coral reef restoration interventions to jumpstart population recovery. Microfragmentation, an asexual propagation technique, is used to produce large numbers of corals for research and restoration. As part of resilience-based restoration, coral microfragments of different genotypes and species are exposed to various stressors to identify candidates for propagation. Growth rate is one of several important fitness-related traits commonly used in candidate selection, and being able to rapidly and accurately quantify growth rates of different genotypes is ideal for high-throughput stress tests. Additionally, it is crucial, as coral restoration becomes more commonplace, to establish practical guidelines and standardized methods of data collection that can be used across independent groups. Herein, we developed a streamlined workflow for growth rate quantification of live microfragmented corals using a structured-light 3D scanner to assess surface area (SA) measurements of live tissue over time. We then compared novel 3D and traditional 2D approaches to quantifying microfragment growth rates and assessed factors such as accuracy and speed. Compared to a more conventional 2D approach based on photography and ImageJ analysis, the 3D approach had comparable reliability, greater accuracy regarding absolute SA quantification, high repeatability, and low variability between scans. However, the 2D approach accurately measured growth and proved to be faster and cheaper, factors not trivial when attempting to upscale for restoration efforts. Nevertheless, the 3D approach has greater capacity for standardization across dissimilar studies, making it a better tool for restoration practitioners striving for consistent and comparable data across users, as well as for those conducting networked experiments, meta-analyses, and syntheses. Furthermore, 3D scanning has the capacity to provide more accurate surface area (SA) measurements for rugose, mounding, or complex colony shapes. This is the first protocol developed for using structured-light 3D scanning as a tool to measure growth rates of live microfragments. While each method has its advantages and disadvantages, disadvantages to a 3D approach based on speed and cost may diminish with time as interest and usage increase. As a resource for coral restoration practitioners and researchers, we provide a detailed 3D scanning protocol herein and discuss its potential limitations, applications, and future directions.

The Caribbean spiny lobster Panulirus argus supports important fisheries throughout the greater Caribbean and is also the only known host for the pathogenic virus Panulirus argus virus 1 (PaV1). While discovered nearly 2 decades ago, gaps still exist in our knowledge of PaV1, such as the dose required to establish infection and its viability outside of the host. To help answer such questions and to enhance diagnostic capabilities, we developed a TaqMan real-time quantitative polymerase chain reaction (qPCR) assay for PaV1. Of the advantages offered by qPCR, one of the most important benefits is its ability to accurately quantify viral DNA copies in a clinical sample. The qPCR assay was found to be efficient (mean ± SD: 99.19 ± 4.67%) and sensitive, detecting as few as 10 copies of PaV1 plasmid DNA. Its diagnostic sensitivity and specificity determined using a set of 165 lobster samples (138 from Florida, USA, and 27 from across the Caribbean) were 100 and 84%, respectively. The qPCR assay should thus prove useful as a research tool and for detecting and quantifying PaV1 infection severity in Caribbean spiny lobsters.

Ventless (escape vents blocked) trap surveys are becoming increasingly common and provide data that are useful for making well-informed management decisions. The purpose of this study was to conduct ventless and standard trap surveys, in parallel with SCUBA surveys, to determine how lobster catch in both types of traps relates to the size structure and abundance of lobster populations on the bottom. Because trap saturation may affect catch-per-unit-effort, we also quantified how catch changed over time by pulling traps after a period of 10 distinct soak times, ranging from 2 to 96 h. All surveys were carried out in 2010 and 2011, at a study site along the coast of New Hampshire, USA. Ventless traps collectively captured ∼10 times as many lobsters as standard traps, but the mean size of the lobsters captured did not differ between the trap types. Catch in standard traps changed little over time and thus the time to saturate was difficult to assess. However, ventless traps saturated between 16 and 24 h. Ventless traps saturated at all lobster densities, but had higher final catch values at times when lobsters were most abundant (as determined by SCUBA surveys). These data indicate that ventless traps provide valuable information about natural lobster populations, which can be useful in the assessment of this valuable fishery.