A revision of the genus Muricea Lamouroux, 1821 (Anthozoa,Octocorallia) in the eastern Pacific. Part I: Eumuricea Verrill, 1869 revisited

Muricea is an amphi-American genus. Verrill proposed dividing the species from the Pacific Ocean into three genera and established the genus Eumuricea for five eastern Pacific species with tubular calyces. Eumuricea is basically characterized by colonies with elongate, cylindrical calyces with truncate margins and star-like opercula, and the occurrence of unilateral spinous spindles. According to these characteristics, Eumuricea does not show enough difference from Muricea to be treated as a separate genus. Original type material of Eumuricea was morphologically analysed and illustrated using optical and scanning electron microscopy. We conclude that the eastern Pacific species should be placed in the genus Muricea and form a group characterised by tubular calyces that comprises four species at present, Muricea acervata, Muricea hispida, Muricea squarrosa, and Muricea tubigera and a dubious species Muricea horrida. Lectotypes were designated for Muricea squarrosa and Muricea hispida to establish their taxonomic status. The genus Eumuricea has also been misunderstood by former authors who erroneously assigned species to it. For these species we propose new combinations: Swiftia pusilla, Astrogorgia splendens and Astrogorgia ramosa.     

The Streptomyces leeuwenhoekii genome: de novo sequencing and assembly in single contigs of the chromosome,circular plasmid pSLE1 and linear plasmid pSLE2

Background

Next Generation DNA Sequencing (NGS) and genome mining of actinomycetes and other microorganisms is currently one of the most promising strategies for the discovery of novel bioactive natural products, potentially revealing novel chemistry and enzymology involved in their biosynthesis. This approach also allows rapid insights into the biosynthetic potential of microorganisms isolated from unexploited habitats and ecosystems, which in many cases may prove difficult to culture and manipulate in the laboratory. Streptomyces leeuwenhoekii (formerly Streptomyces sp. strain C34) was isolated from the hyper-arid high-altitude Atacama Desert in Chile and shown to produce novel polyketide antibiotics.

Results

Here we present the de novo sequencing of the S. leeuwenhoekii linear chromosome (8 Mb) and two extrachromosomal replicons, the circular pSLE1 (86 kb) and the linear pSLE2 (132 kb), all in single contigs, obtained by combining Pacific Biosciences SMRT (PacBio) and Illumina MiSeq technologies. We identified the biosynthetic gene clusters for chaxamycin, chaxalactin, hygromycin A and desferrioxamine E, metabolites all previously shown to be produced by this strain (J Nat Prod, 2011, 74:1965) and an additional 31 putative gene clusters for specialised metabolites. As well as gene clusters for polyketides and non-ribosomal peptides, we also identified three gene clusters encoding novel lasso-peptides.

Conclusions

The S. leeuwenhoekii genome contains 35 gene clusters apparently encoding the biosynthesis of specialised metabolites, most of them completely novel and uncharacterised. This project has served to evaluate the current state of NGS for efficient and effective genome mining of high GC actinomycetes. The PacBio technology now permits the assembly of actinomycete replicons into single contigs with >99 % accuracy. The assembled Illumina sequence permitted not only the correction of omissions found in GC homopolymers in the PacBio assembly (exacerbated by the high GC content of actinomycete DNA) but it also allowed us to obtain the sequences of the termini of the chromosome and of a linear plasmid that were not assembled by PacBio. We propose an experimental pipeline that uses the Illumina assembled contigs, in addition to just the reads, to complement the current limitations of the PacBio sequencing technology and assembly software.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1652-8) contains supplementary material, which is available to authorized users.     

Humpback whale abundance in the North Pacific estimated by photographic capture‐recapture with bias correction from simulation studies

We estimated the abundance of humpback whales in the North Pacific by capture‐recapture methods using over 18,000 fluke identification photographs collected in 2004–2006. Our best estimate of abundance was 21,808 (CV = 0.04). We estimated the biases in this value using a simulation model. Births and deaths, which violate the assumption of a closed population, resulted in a bias of +5.2%, exclusion of calves in samples resulted in a bias of ?10.5%, failure to achieve random geographic sampling resulted in a bias of ?0.4%, and missed matches resulted in a bias of +9.3%. Known sex‐biased sampling favoring males in breeding areas did not add significant bias if both sexes are proportionately sampled in the feeding areas. Our best estimate of abundance was 21,063 after accounting for a net bias of +3.5%. This estimate is likely to be lower than the true abundance due to two additional sources of bias: individual heterogeneity in the probability of being sampled (unquantified) and the likely existence of an unknown and unsampled breeding area (?8.7%). Results confirm that the overall humpback whale population in the North Pacific has continued to increase and is now greater than some prior estimates of prewhaling abundance.     

Activity budget of inshore Indo‐Pacific bottlenose dolphins (Tursiops aduncus): A critical evaluation of methods and comparison among other populations

Activity budgets are widely used to compare behavior patterns but sampling methods vary, rendering comparisons difficult. The two main methods used are instantaneous and continuous sampling. Their comparability was examined by applying them to data obtained from bottlenose dolphins in the Port River estuary, South Australia. They gave comparable results for activity budgets, but instantaneous sampling did not detect most of the behavioral events. Individual differences in behavior and/or follow duration influenced results. Variability in activity definitions and categories among studies makes comparative analysis difficult. Comparison of the Port River dolphin's activity budget with other inshore populations indicated the former spent more time feeding and resting, and less time traveling. The greater feeding time seemed to be due to small prey size rather than reduced abundance or unpredictable distribution. The reduced traveling time, possibly the result of low predation pressure and/or evenly distributed prey, gave them more time to rest. They traveled mostly at 2.5 kn or less, consistent with studies from other shallow areas. Most feeding was individual, probably on demersal species. Surface feeding incorporated physical barriers rather than cooperative behavior. Activity durations ranged from 2 s to 2.9 h, with mean durations varying from 7.8 to 22.9 min.     

Insights from life history traits of Risso's dolphins (Grampus griseus) in Taiwanese waters: Shorter body length characterizes northwest Pacific population

Risso's dolphins (Grampus griseus) are widely distributed throughout temperate to tropical pelagic waters of the world and are one of the most frequently encountered cetaceans in eastern Taiwanese coastal waters. Because their life history is poorly known, the goal of this study was to investigate the relationship between age, body length, and sexual maturity of Risso's dolphins in Taiwanese waters. Ninety‐two carcasses of dead‐stranded or fisheries bycaught dolphins (1994–2008) were measured and dissected (total body length, TBL 125–290 cm); sexual maturity was assessed in 33 dolphins; and age was estimated by counting dentinal growth layer groups in routine histologically prepared tooth sections of 28 dolphins. Sexual dimorphism in TBL was not detected. The onset of sexual maturity occurred at 240–255 cm in females and 253–265 cm in males, which was at about 10 yr of age for both sexes. Our stranding, bycatch, and previous boat survey records suggest that Risso's dolphins occur year‐round and likely have a summer‐fall calving season in Taiwanese waters. The similar life history parameters and calving season in dolphins from Taiwanese and Japanese waters suggest a common population in the northwest Pacific, which has a noticeably shorter body length than in other regions.     

First report of the benthic dinoflagellate,Gambierdiscus belizeanus (Gonyaulacales: Dinophyceae) for the east coast of Sabah,Malaysian Borneo

Species of the genus Gambierdiscus Adachi & Fukuyo, in particular G. toxicus Adachi & Fukuyo are known producers of neurotoxins associated with ciguatera fish poisoning (CFP). In this study live samples were collected from seaweed beds of the east coast of Sabah, Malaysian Borneo and a strain of Gambierdiscus was isolated and cultured. Examination of the thecal fine morphology was undertaken using light, epifluorescence, and scanning electron microscopy. Observed morphological features and their associated morphometric information enabled identification to Gambierdiscus belizeanus Faust. This represents the first report for the occurrence of G. belizeanus in the Asia Pacific region.     

Cardicola opisthorchis n. sp. (Trematoda: Aporocotylidae) from the Pacific bluefin tuna, Thunnus orientalis (Temminck & Schlegel, 1844), cultured in Japan

A new aporocotylid blood fluke is described, based on specimens from the ventricle of the Pacific bluefin tuna, Thunnus orientalis (Temminck et Schlegel), cultured in Wakayama and Nagasaki Prefectures, Japan. The new species is morphologically similar to the members of the genus Cardicola Short, 1953, but shows distinct differences in the body form, location of the testis and the orientation of the ootype. The body of the new species is long and slender, whereas other Cardicola species are small and generally lanceolate. The testis is mostly located posterior to the caeca and anterior to the ovary, occupying 31–45% of body length, in contrast to the known Cardicola species, whose testis is typically intercaecal. The ootype is oriented anteriorly, while in most congeners, it is directed posteriorly or horizontally. Phylogenetic analyses of this aporocotylid, together with Cardicola orientalis Ogawa, Tanaka, Sugihara et Takami, 2010 from the same host, were conducted based on DNA sequences of the ITS2 rDNA and the 28S region of ribosomal RNA. The analyses revealed that the new blood fluke belongs to the genus Cardicola despite the marked morphological differences. Thus, this aporocotylid is named Cardicola opisthorchis n. sp. and the generic diagnosis is emended in this paper. In addition, 100% identity among the ITS2 sequences from the present species, Cardicola sp. from T. orientalis in Mexico and Cardicola sp. from the northern bluefin tuna, Thunnus thynnus (Linnaeus) in Spain suggests that C. opisthorchis n. sp. has a broad geographical distribution and that it infects both the Pacific and northern bluefin tuna.     

Spermatogonial transplantation in fish: A novel method for the preservation of genetic resources

Recent progress in genome-based breeding has created various fish strains carrying desirable genetic traits; however, methods for the long-term preservation of their genetic resources have not yet been developed, mainly due to the lack of cryopreservation techniques for fish eggs and embryos. Recently, we established an alternative cryopreservation technique for fish spermatogonia using a slow-freezing method. Furthermore, we developed a transplantation system to produce functional eggs and sperm derived from spermatogonia. Spermatogonia isolated from the testes of vasa-green fluorescent protein (Gfp) transgenic rainbow trout (Oncorhynchus mykiss) were transplanted into the peritoneal cavity of triploid masu salmon (Oncorhynchus masou) hatchlings of both genders. The transplanted trout spermatogonia migrated towards the gonadal anlagen of the recipient salmon, into which they were subsequently incorporated. We confirmed that the donor-derived spermatogonia resumed gametogenesis, and produced sperm and eggs in male and female recipient salmon, respectively. Fertilization of the resultant eggs and sperm produced only rainbow trout in the first filial (F₁) generation, suggesting that the sterile triploid recipient salmon produced functional eggs and sperm derived from the trout donors. A combination of spermatogonial transplantation and cryopreservation could be a powerful tool for preserving valuable fish strains with desirable genetic traits and endangered species.     

Tropical and north Pacific teleconnections influence fire regimes in pine-dominated forests of north-eastern California, USA

Aim To assess the importance of drought and teleconnections from the tropical and north Pacific Ocean on historical fire regimes and vegetation dynamics in north‐eastern California. Location The 700 km² study area was on the leeward slope of the southern Cascade Mountains in north‐eastern California. Open forests of ponderosa pine (Pinus ponderosa var. ponderosa Laws.) and Jeffrey pine (P. jeffreyi Grev. & Balf) surround a network of grass and shrub‐dominated meadows that range in elevation from 1650 to 1750 m. Methods Fire regime characteristics (return interval, season and extent) were determined from crossdated fire scars and were compared with tree‐ring based reconstructions of precipitation and temperature and teleconnections for the period 1700–1849. The effect of drought on fire regimes was determined using a tree‐ring based proxy of climate from five published chronologies. The number of forest‐meadow units that burned was compared with published reconstructions of the El Niño/Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO). Results Landscape scale fires burned every 7–49 years in meadow‐edge forests and were influenced by variation in drought, the PDO and ENSO. These widespread fires burned during years that were dryer and warmer than normal that followed wetter and cooler years. Less widespread fires were not associated with this wet, then dry climate pattern. Widespread fires occurred during El Niño years, but fire extent was mediated by the phase of the PDO. Fires were most widespread when the PDO was in a warm or normal phase. Fire return intervals, season and extent varied at decadal to multi‐decadal time scales. In particular, an anomalously cool, wet period during the early 1800s resulted in widespread fires that occurred earlier in the year than fires before or after. Main conclusions Fire regimes in north‐eastern California were strongly influenced by regional and hemispheric‐scale climate variation. Fire regimes responded to variation that occurred in both the north and tropical Pacific. Near normal modes of the PDO may influence fire regimes more than extreme conditions. The prevalence of widespread teleconnection‐driven fires in the historic record suggests that variation in the Pacific Ocean was a key regulator of fire regimes through its influence on local fuel production and successional dynamics in north‐eastern California.