John R. Hyde

Whole-body endothermy in a mesopelagic fish, the opah, Lampris guttatus

A cold-water fish with a warm heart Mammals and birds warm their entire bodies above the ambient temperature. Generally, this ability is lacking in other vertebrates, although some highly active fish can temporarily warm their swim muscles. Wegner et al. show that the opah, a large deepwater fish, can generate heat with its swim muscles and use this heat to warm both its heart and brain. This ability increases its metabolic function in cold deep waters, which will help the fish compete with other, colder-blooded species. Science, this issue p. 786 Unlike other fish, opah distribute warmed blood throughout their bodies, enhancing physiological performance in the deep ocean. Endothermy (the metabolic production and retention of heat to warm body temperature above ambient) enhances physiological function, and whole-body endothermy generally sets mammals and birds apart from other animals. Here, we describe a whole-body form of endothermy in a fish, the opah (Lampris guttatus), that produces heat through the constant “flapping” of wing-like pectoral fins and minimizes heat loss through a series of counter-current heat exchangers within its gills. Unlike other fish, opah distribute warmed blood throughout the body, including to the heart, enhancing physiological performance and buffering internal organ function while foraging in the cold, nutrient-rich waters below the ocean thermocline.

Population genetic structure in the redefined vermilion rockfish (Sebastes miniatus) indicates limited larval dispersal and reveals natural management units

Recent studies have revealed that the vermilion rockfish Sebastes miniatus is a cryptic species pair. The splitting of this species impacts stock size estimates and draws attention to the unintended consequences of current management policies. Differences in exploitation level between the species necessitated an evaluation of population structure and connectivity among regional management segments of the fishery. Analysis of gene flow and calculations of larval dispersal values were accomplished using 782xa0bp of DNA sequence data from the mitochondrial cytochromexa0b gene of 684 vermilion rockfish sampled from 16 sites between Kyuquot Sound, Canada, and San Quintin, Mexico. Significant genetic heterogeneity was found among sample sites (ΦST = 0.0742, pxa0< 0.001 and FST = 0.0899, pxa0< 0.001). Isolation by distance analysis produced a significant correlation, suggesting low average larval dispersal distance. Analysis of molecular variance showed significant partitioning of genetic variance across the biogeograph...

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

Various indoor, outdoor, and host-associated environments contain small quantities of microbial biomass and represent a niche that is often understudied because of technical constraints. Many studies that attempt to evaluate these low-biomass microbiome samples are riddled with erroneous results that are typically false positive signals obtained during the sampling process. We have investigated various low-biomass kits and methods to determine the limit of detection of these pipelines. Here we present KatharoSeq, a high-throughput protocol combining laboratory and bioinformatic methods that can differentiate a true positive signal in samples with as few as 50 to 500 cells. We demonstrate the application of this method in three unique low-biomass environments, including a SAF, a hospital NICU, and an abalone-rearing facility. ABSTRACT Microbiome analyses of low-biomass samples are challenging because of contamination and inefficiencies, leading many investigators to employ low-throughput methods with minimal controls. We developed a new automated protocol, KatharoSeq (from the Greek katharos [clean]), that outperforms single-tube extractions while processing at least five times as fast. KatharoSeq incorporates positive and negative controls to reveal the whole bacterial community from inputs of as few as 50 cells and correctly identifies 90.6% (standard error, 0.013%) of the reads from 500 cells. To demonstrate the broad utility of KatharoSeq, we performed 16S rRNA amplicon and shotgun metagenome analyses of the Jet Propulsion Laboratory spacecraft assembly facility (SAF; n = 192, 96), 52 rooms of a neonatal intensive care unit (NICU; n = 388, 337), and an endangered-abalone-rearing facility (n = 192, 123), obtaining spatially resolved, unique microbiomes reproducible across hundreds of samples. The SAF, our primary focus, contains 32 sOTUs (sub-OTUs, defined as exact sequence matches) and their inferred variants identified by the deblur algorithm, with four (Acinetobacter lwoffii, Paracoccus marcusii, Mycobacterium sp., and Novosphingobium) being present in >75% of the samples. According to microbial spatial topography, the most abundant cleanroom contaminant, A. lwoffii, is related to human foot traffic exposure. In the NICU, we have been able to discriminate environmental exposure related to patient infectious disease, and in the abalone facility, we show that microbial communities reflect the marine environment rather than human input. Consequently, we demonstrate the feasibility and utility of large-scale, low-biomass metagenomic analyses using the KatharoSeq protocol. IMPORTANCE Various indoor, outdoor, and host-associated environments contain small quantities of microbial biomass and represent a niche that is often understudied because of technical constraints. Many studies that attempt to evaluate these low-biomass microbiome samples are riddled with erroneous results that are typically false positive signals obtained during the sampling process. We have investigated various low-biomass kits and methods to determine the limit of detection of these pipelines. Here we present KatharoSeq, a high-throughput protocol combining laboratory and bioinformatic methods that can differentiate a true positive signal in samples with as few as 50 to 500 cells. We demonstrate the application of this method in three unique low-biomass environments, including a SAF, a hospital NICU, and an abalone-rearing facility.

Defining an ideal temperature range for the northern subpopulation of Pacific sardine, Sardinops sagax caeruleus

The aim of this study was to determine a physiologically “ideal” temperature range of Pacific sardine (Sardinops sagax caeruleus) from the northern stock by assessing the effects of cumulatively increasing or decreasing temperature on their stress physiology. Sardines collected off the coast of Southern California during late spring and late fall were exposed to cumulatively increasing or decreasing temperatures that reached +/− 8xa0°C from their acclimation temperature over a period of approximately one month. Blood plasma and tissue samples were collected at every 2xa0°C temperature change. Measurements included plasma cortisol, expression of heat shock proteins (Hsp70, Hsp90, HOP) in liver tissue, expression of an immune gene (IgM) in liver tissue, and Michaelis-Menton (Km) determinations of lactate dehydrogenase (LDH) and citrate synthase (CS) from white and red muscle tissue, respectively. Critical thermal minimum and maximum temperatures were also measured to identify the outer edges of their thermal tolerance. Feeding behavior ceased and plasma cortisol was elevated at the lowest temperature, while Hsp90 and Kmpyr (LDH) values were elevated at the highest temperatures to which sardines were exposed. An additional finding was that Vmax of LDH increased with increasing condition factor, indicating the occurrence of metabolic scaling in Pacific sardine. Critical thermal minimums and maximums for sardines acclimated to 15xa0°C and 17xa0°C were 3.4xa0°C – 29.1xa0°C and 4.8xa0°C – 29.9xa0°C, respectively. This study indicates Pacific sardine from the northern stock have a physiologic ideal temperature range of 9xa0°C – 19xa0°C for 15xa0°C acclimated sardines and 11xa0°C – 21xa0°C for 17xa0°C acclimated sardines.

A taxonomic review of Lampris guttatus (Brünnich 1788) Lampridiformes; Lampridae) with descriptions of three new species

The genus Lampris (Lampridae) currently comprises two species, Lampris guttatus (Brünnich 1788) and L. immaculatus (Gilchrist 1905) commonly known as Opah and Southern Opah, respectively. Hyde et al. (2014) presented DNA sequence data which revealed the presence of five distinct, monophyletic lineages within L. guttatus. In this paper, we present morphological and meristic data supporting the presence of five species previously subsumed within L. guttatus (Brünnich 1788). We restrict Lampris guttatus (Brünnich 1788), resurrect L. lauta (Lowe 1838), and describe three new species of Lampris. A key to the species of Lampris is provided.

Erratum: KAREN E. UNDERKOFFLER, MEAGAN A. LUERS, JOHN R. HYDE & MATTHEW T. CRAIG (2018) A taxonomic review of Lampris guttatus (Brünnich 1788) (Lampridiformes; Lampridae) with descriptions of three new species. Zootaxa , 4413: 551–565.

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Basking Shark (Cetorhinus maximus) Movements in the Eastern North Pacific Determined Using Satellite Telemetry

To fill data gaps on movements, behaviors and habitat use both near- and offshore, two programs were initiated to deploy satellite tags on basking sharks. Basking sharks are large filter feeding sharks that are second in size only to whale sharks. Similar to many megafauna populations, available data suggest that populations are below historic levels. In the northeast Pacific Ocean, the limited information on basking sharks comes from nearshore habitats where they forage. From 2010-2011, four sharks were tagged with pop-off satellite archival tags with deployments ranging from 9-240 days. The tags provided both transmitted and archived data on habitat use and geographic movement patterns. Nearshore, sharks tended to move north in the summer and prefer shelf and slope habitat around San Diego, Point Conception and Monterey Bay. The two sharks with 180 and 240 day deployments left the coast in the summer and fall. Offshore their paths diverged and by January one shark had moved to near the tip of the Baja Peninsula, Mexico and the other to the waters near Hawaii, USA. Vertical habitat use was variable both within and among individuals and changed as sharks moved offshore. Nearshore, most time was spent in the mixed layer but sharks did spend hours in cold waters below the mixed layer. Offshore vertical movements depended on location. The shark that went to Hawaii had a distinct diel pattern, with days spent at ~450-470 m and nights at ~250-300 m and almost no time in surface waters, corresponding with the diel migration of a specific portion of the deep scattering layer. The shark that moved south along the Baja Peninsula spent progressively more time in deep water but came to the surface daily. Movement patterns and shifts in vertical habitat and use are likely linked to shifts in prey availability. Data collected indicate the potential for large-scale movements and the need for international dialogue in any recovery efforts.