Global analysis of mRNA half-lives and de novo transcription in a dinoflagellate, Karenia brevis

Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into the roles of differential mRNA stability and de novo transcription in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed and pre-existing RNA pools in Karenia brevis. These isolated fractions were then used for analysis of global mRNA stability and de novo transcription by hybridization to a K. brevis microarray. Global K. brevis mRNA half-lives were calculated from the ratio of newly transcribed to pre-existing RNA for 7086 array features using the online software HALO (Half-life Organizer). Overall, mRNA half-lives were substantially longer than reported in other organisms studied at the global level, ranging from 42 minutes to greater than 144 h, with a median of 33 hours. Consistent with well-documented trends observed in other organisms, housekeeping processes, including energy metabolism and transport, were significantly enriched in the most highly stable messages. Shorter-lived transcripts included a higher proportion of transcriptional regulation, stress response, and other response/regulatory processes. One such family of proteins involved in post-transcriptional regulation in chloroplasts and mitochondria, the pentatricopeptide repeat (PPR) proteins, had dramatically shorter half-lives when compared to the arrayed transcriptome. As transcript abundances for PPR proteins were previously observed to rapidly increase in response to nutrient addition, we queried the newly synthesized RNA pools at 1 and 4 h following nitrate addition to N-depleted cultures. Transcriptome-wide there was little evidence of increases in the rate of de novo transcription during the first 4 h, relative to that in N-depleted cells, and no evidence for increased PPR protein transcription. These results lend support to the growing consensus of post-transcriptional control of gene expression in dinoflagellates.

Severe droughts reduce estuarine primary productivity with cascading effects on higher trophic levels

Using a 10-yr time-series data set, we analyzed the effects of two severe droughts on water-quality and ecosystem processes in a temperate, eutrophic estuary (Neuse River Estuary, North Carolina). During the droughts, dissolved inorganic nitrogen concentrations were on average 46–68% lower than the long-term mean due to reduced riverine input. Phytoplankton productivity and biomass were slightly below average for most of the estuary during a spring–autumn drought in 2002, but were dramatically lower than average throughout the estuary during an autumn–winter drought in 2007–2008. Droughts affected upper trophic levels through alteration of both habitat condition (i.e., bottom-water dissolved oxygen levels) and food availability. Bottomwater dissolved oxygen levels were near or slightly above average during the 2002 drought and during summer 2007. Concomitant with these modest improvements in bottom-water oxygen condition, fish kills were greatly reduced relative to the long-term average. Low-oxygen bottom-water conditions were more pronounced during summer 2008 in the latter stages of the 2007–2008 drought, and mesozooplankton abundances were eight-fold lower in summer 2008 than during nondrought years. Below-average mesozooplankton abundances persisted for well over 1 yr beyond cessation of the drought. Significant fish kills were observed in summer 2008 and 2009, perhaps due to the synergistic effects of hypoxia and reduced food availability. These results indicate that droughts can exert both ephemeral and prolonged multiyear influence on estuarine ecosystem processes and provide a glimpse into the future, when many regions of the world are predicted to face increased drought frequency and severity due to climate change.

Integration of fisheries acoustics surveys and bathymetric mapping to characterize midwater-seafloor habitats of US Virgin Islands and Puerto Rico (2008-2010)

NOAA’s Coral Reef Conservation program (CRCP) develops coral reef management priorities by bringing together various partners to better understand threats to coral reef ecosystems with the goal of conserving, protecting and restoring these resources. Place-based and ecosystem-based management approaches employed by CRCP require that spatially explicit information about benthic habitats and fish utilization are available to characterize coral reef ecosystems and set conservation priorities. To accomplish this, seafloor habitat mapping of coral reefs around the U.S. Virgin Islands (USVI) and Puerto Rico has been ongoing since 2004. In 2008, fishery acoustics surveys were added to NOAA survey missions in the USVI and Puerto Rico to assess fish distribution and abundance in relation to benthic habitats in high priority conservation areas. NOAA’s National Centers for Coastal Ocean Science (NCCOS) have developed fisheries acoustics survey capabilities onboard the NOAA ship Nancy Foster to complement the CRCP seafloor habitat mapping effort spearheaded by the Center for Coastal Monitoring and Assessment Biogeography Branch (CCMA-BB). The integration of these activities has evolved on the Nancy Foster over the three years summarized in this report. A strategy for improved operations and products has emerged over that time. Not only has the concurrent operation of multibeam and fisheries acoustics surveys been beneficial in terms of optimizing ship time and resources, this joint effort has advanced an integrated approach to characterizing bottom and mid-water habitats and the fishes associated with them. CCMA conducts multibeam surveys to systematically map and characterize coral reef ecosystems, resulting in products such as high resolution bathymetric maps, backscatter information, and benthic habitat classification maps. These products focus on benthic features and live bottom habitats associated with them. NCCOS Centers (the Center for Coastal Fisheries and Habitat Research and the Center for Coastal Environmental Health and Biomolecular Research) characterize coral reef ecosystems by using fisheries acoustics methods to capture biological information through the entire water column. Spatially-explicit information on marine resources derived from fisheries acoustics surveys, such as maps of fish density, supports marine spatial planning strategies and decision making by providing a biological metric for evaluating coral reef ecosystems and assessing impacts from pollution, fishing pressure, and climate change. Data from fisheries acoustics surveys address management needs by providing a measure of biomass in management areas, detecting spatial and temporal responses in distribution relative to natural and anthropogenic impacts, and identifying hotspots that support high fish abundance or fish aggregations. Fisheries acoustics surveys conducted alongside multibeam mapping efforts inherently couple water column data with information on benthic habitats and provide information on the heterogeneity of both benthic habitats and biota in the water column. Building on this information serves to inform resource managers regarding how fishes are organized around habitat structure and the scale at which these relationships are important. Where resource managers require place-based assessments regarding the location of critical habitats along with high abundances of fish, concurrent multibeam and fisheries acoustics surveys serve as an important tool for characterizing and prioritizing coral reef ecosystems. This report summarizes the evolution of fisheries acoustics surveys onboard the NOAA ship Nancy Foster from 2008 to 2010, in conjunction with multibeam data collection, aimed at characterizing benthic and mid-water habitats in high priority conservation areas around the USVI and Puerto Rico. It also serves as a resource for the continued development of consistent data products derived from acoustic surveys. By focusing on the activities of 2010, this report highlights the progress made to date and illustrates the potential application of fisheries data derived from acoustic surveys to the management of coral reef ecosystems.

Sediment Quality Triad assessment in Kachemak Bay: characterization of soft bottom benthic habitats and contaminant bioeffects assessment

A baseline environmental characterization of the inner Kachemak Bay, Alaska was conducted using the sediment quality triad approach based on sediment chemistry, sediment toxicity, and benthic invertebrate community structure. The study area was subdivided into 5 strata based on geophysical and hydrodynamic patterns in the bay (eastern and western intertidal mud flats, eastern and western subtidal, and Homer Harbor). Three to seven locations were synoptically sampled within each stratum using a stratified random statistical design approach. Three sites near the village of Port Graham and two sites in the footprint of a proposed Homer Harbor expansion were also collected for comparison. Concentrations of over 120 organic and metallic contaminants were analyzed. Ambient toxicity was assessed using two amphipod bioassays. A detailed benthic community condition assessment was performed. Habitat parameters (depth, salinity, temperature, dissolved oxygen, sediment grain size, and organic carbon content) that influence species and contaminant distribution were also measured at each sampling site. Sediments were mostly mixed silt and sand; characteristic of high energy habitats, with pockets of muddy zones. Organic compounds (PAHs, DDTs, PCBs, cyclodienes, cyclohexanes) were detected throughout the bay but at relatively low concentrations. Tributyltin was elevated in Homer Harbor relative to the other strata. With a few exceptions, metals concentrations were relatively low and probably reflect the input of glacial runoff. Relative to other sites, Homer Harbor sites were shown to have elevated concentrations of metallic and organic contaminants. The Homer Harbor stratum however, is a deep, low energy depositional environment with fine grained sediment. Concentrations of organic contaminants measured were five to ten times higher in the harbor sites than in the open bay sites. Concentration of PAHs is of a particular interest because of the legacy of oil spills in the region. There was no evidence of residual PAHs attributable to oil spills, outside of local input, beyond the confines of the harbor. Concentrations were one to ten times below NOAA sediment quality guidelines. Selected metal concentrations were found to be relatively elevated compared to other data collected in the region. However, levels are still very low in the scale of NOAA’s sediment quality guidelines, and therefore appear to pose little or no ecotoxicity threat to biota. Infaunal assessment showed a diverse assemblage with more than 240 taxa recorded and abundances greater than 3,000 animals m-22 in all but a few locations. Annelid worms, crustaceans, snails, and clams were the dominant taxa accounting for 63 %, 19%, 5%, and 7 % respectively of total individuals. Specific benthic community assemblages were identified that were distributed based on depth and water clarity. Species richness and diversity was lower in the eastern end of the bay in the vicinity of the Fox River input. Abundance was also generally lower in the eastern portion of the study area, and in the intertidal areas near Homer. The eastern portions of the bay are stressed by the sediment load from glacial meltwater. Significant toxicity was virtually absent. Conditions at the sites immediately outside the existing Homer Harbor facility did not differ significantly from other subtidal locations in the open Kachemak Bay. The benthic fauna at Port Graham contained a significant number of species not found in Kachemak Bay. Contaminant conditions were variable depending on specific location. Selected metal concentrations were elevated at Port Graham and some were lower relative to Kachemak Bay, probably due to local geology. Some organic contaminants were accumulating at a depositional site.

Abundance of cetaceans in the oceanic northern Gulf of Mexico from 2003 and 2004 ship surveys

The Gulf of Mexico (GMx) is a subtropical marginal sea of the western North Atlantic Ocean with a diverse cetacean community. Ship-based, line-transect abundance surveys were conducted in oceanic waters (>200 m deep) of the northern GMx within U.S. waters (380,432 square km) during summer 2003 and spring 2004. Data from these surveys were pooled and minimum abundance estimates were based on 10,933 km of effort and 433 sightings of at least 17 species.The most commonly sighted species (number of groups) were pantropical spotted dolphin, Stenella attenuata (115); sperm whale, Physeter macrocephalus (85); dwarf/pygmy sperm whale, Kogia sima/breviceps (27); Risso’s dolphin, Grampus griseus (26); and bottlenose dolphin, Tursiops truncatus (26). The most abundant species (number of individuals; coefficient of variation) were S. attenuata (34,067; 0.18); Clymene dolphin, S. clymene (6,575; 0.36); T. truncatus (3,708; 0.42); and striped dolphin, S. coeruleoalba (3,325; 0.48). The only large whales sighted were P. macrocephalus (1,665; 0.20) and Bryde’s whale, Balaenoptera edeni (15; 1.98). Abundances for other species or genera ranged from 57 to 2,283 animals. Cetaceanswere sighted throughout the oceanic northern GMx, and whereas many species were widely distributed, some had more regional distributions. Compared to abundance estimates for this area based on 1996-2001 surveys, the estimate for S. attenuata was significantly smaller (P <0.05) and that for the spinner dolphin, S. longirostris, appeared much smaller. Also, P. macrocephalus estimates were based on less negatively biased estimates of group-size using 90-minute counts during 2003 and 2004.

Abundance of cetatceans in the southern U.S. North Atlantic Ocean during summer 1998

The U.S. Marine Mammal Protection Act requires that the abundance of marine mammals in U.S. waters be assessed. Because this requirement had not been met for a large portion of the North Atlantic Ocean (U.S. waters south of Maryland), a ship-based, line-transect survey was conducted with a 68 m research ship between Maryland (38.00°N) and central Florida (28.00°N) from the 10-m isobath to the boundary of the U.S. Exclusive Economic Zone. The study area (573,000 km2) was surveyed between 8 July and 17 August 1998. Minimum abundance estimates were based on 4163 km of effort and 217 sightings of at least 13 cetacean species and other taxonomic categories. The most commonly sighted species (number of groups) were bottlenose dolphins, Tursiops truncatus (38); sperm whales, Physeter macrocephalus (29); Atlantic spotted dolphins, Stenella frontalis (28); and Risso’s dolphins, Grampus griseus (22). The most abundant species (abundance; coeffi cient of variation) were Atlantic spotted dolphins (14,438; 0.63); bottlenose dolphins (13,085; 0.40); pantropical spotted dolphins, S. attenuate (12,747; 0.56); striped dolphins, S. coeruleoalba (10,225; 0.91); and Risso’s dolphins (9533; 0.50). The abundance estimate for the Clymene dolphin, S. clymene (6086; 0.93), is the first for the U.S. Atlantic Ocean. Sperm whales were the most abundant large whale (1181; 0.51). Abundances for other species or taxonomic categories ranged from 20 to 5109. There were an estimated 77,139 (0.23) cetaceans in the study area. Bottlenose dolphins and Atlantic spotted dolphins were encountered primarily in continental shelf (<200 m) and continental slope waters (200−2000 m). All other species were generally sighted in oceanic waters (>200 m). The distribution of some species varied north to south. Striped dolphins, Clymene dolphins, and sperm whales were sighted primarily in the northern part of the study area; whereas pantropical spotted dolphins were sighted primarily in the southern portion.

Genetic analysis of juvenile coho salmon (Oncorhynchus kisutch) off Oregon and Washington reveals few Columbia River wild fish

Little is known about the ocean distributions of wild juvenile coho salmon off the Oregon-Washington coast. In this study we report tag recoveries and genetic mixed-stock estimates of juvenile fish caught in coastal waters near the Columbia River plume. To support the genetic estimates, we report an allozyme-frequency baseline for 89 wild and hatchery-reared coho salmon spawning populations, extending from northern California to southern British Columbia. The products of 59 allozyme-encoding loci were examined with starch-gel electrophoresis. Of these, 56 loci were polymorphic, and 29 loci had P0.95 levels of polymorphism. Average heterozygosities within populations ranged from 0.021 to 0.046 and averaged 0.033. Multidimensional scaling of chord genetic distances between samples resolved nine regional groups that were sufficiently distinct for genetic mixed-stock analysis. About 2.9% of the total gene diversity was due to differences among populations within these regions, and 2.6% was due to differences among the nine regions. This allele-frequency data base was used to estimate the stock proportions of 730 juvenile coho salmon in offshore samples collected from central Oregon to northern Washington in June and September-October 1998−2000. Genetic mixed-stock analysis, together with recoveries of tagged or fin-clipped fish, indicates that about one half of the juveniles came from Columbia River hatcheries. Only 22% of the ocean-caught juveniles were wild fish, originating largely from coastal Oregon and Washington rivers (about 20%). Unlike previous studies of tagged juveniles, both tag recoveries and genetic estimates indicate the presence of fish from British Columbia and Puget Sound in southern waters. The most salient feature of genetic mixed stock estimates was the paucity of wild juveniles from natural populations in the Columbia River Basin. This result reflects the large decrease in the abundances of these populations in the last few decades.

Local distribution and abundance of swimming crabs (Callinectes spp. and Arenaeus cribrarius) on a tropical arid beach

Distribution, abundance, and several population features were studied in Ensenada de La Vela (Venezuela) between 1993 and 1998 as a first step in the assessment of local fisheries of swimming crabs. Arenaeus cribrarius was the most abundant species at the marine foreshore. Callinectes danae prevailed at the estuarine location. Callinectes bocourti was the most abundant species at the offshore. Abundances of A. cribrarius and C. danae fluctuated widely and randomly. Ovigerous females were almost absent. Adults of several species were smaller than previously reported. This study suggests that fisheries based on these swimming crabs probably will be restricted to an artisanal level because abundances appear too low to support industrial exploitation.

Shortspine thornyhead (Sebastolobus alascanus) abundance and habitat associations in the Gulf of Alaska

Shortspine thornyhead (Sebastolobus alascanus) abundance was estimated from 107 video transects at 27 stations recorded from a research submersible in 1991 off southeast Alaska at depths ranging from 165 to 355 m. Numbers of invertebrates in seven major taxa were estimated, as was substrate type. Thornyhead abundance ranged from 0 to 7.5/100 m2, with a mean of 1.22/100 m2, and was positively correlated with depth and amount of hard substrate. Invertebrate abundances were not significantly correlated with numbers of thornyheads. Shortspine thornyhead abundance estimates from this study were several times higher than estimates produced by bottom trawl surveys off southeast Alaska in 1990 and 1993, the two years of survey that encompassed the submersible transects; however, the trend of increasing abundance with depth was similar in the trawl surveys and in the submersible transects, suggesting that trawl surveys systematically underestimate abundance of shortspine thornyheads

Fish species diversity in the Victoria and Kyoga lake basins: their conservation and sustainable use

Introduction of exotic fish species especially the Nile perch Lates niloticus, is believed to be responsible for the decline of fish species diversity in lakes Victoria, Kyoga and Nabugabo.About 60% of the haplochromine cichlids are thought to have become extinct from L. Victoria due to predation by the Nile perch. However there are many lakes satelite to the lakes Victoria and Kyoga basins which still have fish fauna similar to that of the main lakes. many of the satellite lakes are separated from the main lakes in, which Nile perch was introduced by extensive swamps that provide a barrier to Nile perch .A survey was carried out in a number of these satelite lakes and an inventory made of existing fish species. Their distribution and relative abundances were also determined. The lakes studied included Nawampasa, Nakuwa,Kawi Lamwa Gigate, Nyaguo, Agu, Nabugabo. Kayanja, Kaytigi, Mburo, Kachera and Wamala.Some habitats within the main lakes Victoria and Kyoga, especially those with rocky outcrops· and macrophyte cover that provide refugia for endangered species from Nile perch,were also surveyed) Various stations along the River Nile were also sampled to quantify the fish species that are still resent. Kyoga minor lakes were found to have the highest number of fish species especially of haplochromine cichlids. Many haplochromine trophic groups that were thought to be extinct from 1. Victoria still occur in these lakes.!Some of the satellite lakes, especially lakes Kayugi, Mburo and Kachera still contain .healili populations of oreochromis. I esculentus that could be used as brood stock in fish farming. Many of these lakes should .I ( I therefore be protected for conservation offish species diversity