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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.

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.

The study of the early life history of large, open-ocean pelagic fishes such as tunas and billfish, and the identification of spawning and nursery habitats, has been extremely difficult as these animals are intrinsically rare, highly migratory, and difficult to study in captivity. Traditional methods such as the assembling of a developmental series of life stages, or the culturing of unknown eggs and larvae to a point where they can be identified, has not been easy or fruitful for many pelagic species. The discovery of a putative spawning 'hot spot' off the Kona coast of Hawaii, coupled with the development of shipboard approaches to real time identification and adaptive sampling of eggs, may provide new approaches and insights into the spawning ecology and reproductive biology of these highly valuable but poorly known species. Here we report the use of a shipboard PCR based assay to differentiate species of istiophorid billfish larvae and identify eggs of istiophorid and xiphiid billfish, coryphaenid dolphinfish, and wahoo. A species-specific multiplex PCR assay was designed to amplify a single, unique size fragment of the mitochondrial cytochrome b gene for all 6 species of Indo-Pacific billfish, both dolphinfish, and the monospecific wahoo. A boiling technique used to extract DNA from larval eye tissue or an individual egg, combined with a single-step PCR assay and agarose electrophoresis, allowed species identification within 3 h of sample acquisition. This nearly real-time identification method for morphologically indistinguishable eggs and larvae provides an opportunity to employ adaptive sampling methods to increase sampling efficiency and will help in determining the spatial and temporal dimensions of spawning and nursery habitats offshore. This study describes the occurrence of blue marlin, dolphinfish, shortbill spearfish, swordfish and wahoo off the Kona coast by molecular approaches, and it provides the first description of the eggs of blue marlin, shortbill spearfish and wahoo.

A recent phylogenetic review of the genus Sebastes suggested the existence of a cryptic species of vermilion rockfish (Sebastes miniatus). To evaluate the geographical and bathymetric range of the Type 1 and Type 2 forms reported in that study, cytochrome b sequences were examined from 548 fish. Type 1 fish were found primarily south of Point Conception on reefs deeper than 100 m. Type 2 fish were common range-wide at sites shallower than 100 m. Reproductive isolation between the two types was tested using nine microsatellite loci. Estimates of genetic divergence were made using the fixation index (F(ST)) and correspondence between haplotype and genotype was tested by Bayesian population assignment and multivariate plotting of individual genotypes. Microsatellite analyses gave strong support for the presence of two distinct groups of genotypes. All fish with Type 1 haplotypes and fish with Type 2 haplotypes from < 100 m depth had genotypes unique to their haplotype group. However, most (68%) fish with Type 2 haplotypes from > 100 m depth assigned strongly to the Type 1 genotype group. Morphometric comparisons between the two genotypic groups revealed significant differences at three of the six examined measurements. Differences in both genetics, depth of occurrence, and morphology suggest these are separate species. This observation along with evidence of depth segregation in many recent species pairs led us to hypothesize a speciation model for Sebastes spp. by which the loss or truncation of a depth-related ontogenetic migration can lead to the creation of reproductively isolated populations.

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The goliath grouper Epinephelus itajara (Epinephelidae) is an exceptionally large marine fish that inhabits sub-tropical and tropical waters of the Americas and western Africa. Due to a lack of readily observable morphological variation in specimens across its range, the goliath grouper has been regarded as a single species. We tested the hypothesis that Pacific and West Atlantic populations constitute a single species by analyzing nuclear and mitochondrial DNA sequence data. We found numerous fixed genetic differences for mitochondrial loci between Pacific and West Atlantic goliath grouper (genetic distance D ≈ 3.5% at 16S and D ≈ 6% at cytochrome b; ϕ st = 0.98 [p < 0.001] for 16S and ϕ st = 0.98 [p < 0.001] for cytochrome b). The nuclear S7 intron showed 3 fixed nucleotide differences between Pacific and West Atlantic populations. Within the West Atlantic, we found few absolute genetic differences (D < 0.01 at 16S and D < 0.02 at cytochrome b), but statistically significant population structure based on haplotype frequency data (ϕ st = 0.04 [p = 0.05] at 16S; ϕ st = 0.14 [p < 0.001] at cytochrome b). These data indicate that (1) goliath grouper in the West Atlantic are subdivided into discrete populations, (2) goliath grouper populations in the Pacific and western Atlantic represent 2 (or more) distinct species, and (3) these distinct populations/species require separate management and conservation strategies. We resurrect the species Epinephelus quinquefasciatus (Bocourt 1868) for Pacific goliath grouper. KEY WORDS: Epinephelus itajara · Epinephelus quinquefasciatus · Phylogeography · EpinephelidaeResale or republication not permitted without written consent of the publisher OPEN PEN ACCESS CCESS Contribution to the Theme Section 'Range-wide status and conservation of the goliath grouper'Endang Species Res: 7: 167-174, 2009 tinue to be at the forefront of conservation efforts. Surprisingly, this basic information is lacking in many areas, despite its obvious importance for conservation measures.In the marine environment, biodiversity inventories often reflect the fact that marine species tend to be more broadly distributed than their terrestrial counterparts, with some organisms ranging more than 10 000 km (Jablonski & Lutz 1983). With the now widespread use of molecular genetic techniques, it has become clear that cryptic genetic diversity may confound estimates of both species ranges and biodiversity (reviewed in Bickford et al. 2006). Species once thought to be distributed over immense oceanic expanses are now known to be comprised of discreet lineages that may or may not occur in sympatry (reviewed in Rocha et al. 2007). Although this phenomenon was thought to occur most commonly in small or difficult-to-study organisms, recent evidence shows that these cryptic genetic lineages also occur amongst Earth's largest and most well-studied marine animals (e.g. Bass et al. 2005, Quattro et al. 2006, Vianna et al. 2006. In addition, these genetic studies often elucidate genetic patterns that reflect...

Marine protected areas (MPAs) can facilitate recovery of diminished stocks by protecting reproductive adults. To effectively augment fisheries, however, reproductive output must increase within the bounds of MPAs so that larvae can be exported to surrounding areas and seed the region. In response to dramatic declines of rockfishes (Sebastes spp.) in southern California by the late 1990s two large MPAs, the Cowcod Conservation Areas (CCAs), were established in 2001. To evaluate whether the CCAs affected rockfish productivity we evaluated the dynamics of 8 species that were, and 7 that were not, historically targeted by fishing. Abundances of 6/8 targeted and 4/7 non-targeted species increased regionally from 1998 to 2013. These upturns were probably affected by environmental conditions in addition to changes in fishing pressure as the presence of most species correlated negatively with temperature, and temperature was lower than the historic average in 11/15 years. Seventy-five per cent of the targeted, but none of the non-targeted species increased at a greater rate inside than outside the CCAs while controlling for environmental factors. Results indicate that management actions, coupled with favourable environmental conditions, facilitated the resurgence of multiple rockfish species that were targeted by intense fishing effort for decades.