Rapid isolation of high-quality RNA from symbiotic dinoflagellates

This report details a reliable and efficient RNA extraction protocol for the symbiotic dinoflagellate Symbiodinium microadriaticum Freudenthal (Gymnodiniales, Dinophyceae). The method typically gives yields of 500 mu g total RNA from 0.4 g wet weight of algae, and, in comparison to current protocols, it is technically simple and less time consuming. This method isolates high-quality, intact RNA from in vine cultured as well as host-isolated cells, as demonstrated by spectrophotometry, gel electrophoresis, and northern analysis. The total RNA obtained was suitable for reverse transcription and PCR amplification of Symbiodinium cDNAs. We have successfully applied our method to isolate total RNA from a different dinoflagellate, Amphidinium carterae Hulburt (Gymnodiniales, Dinophyceae), found in symbiotic association with marine invertebrates.

Retinal and lenticular ultrastructure in the aestivating salamanderfish, Lepidogalaxias salamandroides (Galaxiidae, Teleostei) with special reference to a new type of photoreceptor mosaic

The salamanderfish, Lepidogalaxias salamandroides (Galaxiidae, Teleostei) is endemic to southwestern Australia and inhabits shallow, freshwater pools which evaporate during the hot summer months. Burrowing into the substrate in response to falling water levels allows these fish to aestivate for extended periods of time while encapsulated in a mucous cocoon even when the pools contain no water. Only a few minutes after a major rainfall, these fish emerge into relatively clear water which subsequently becomes laden with tannin, turning the water black and reducing the pH to approximately 4.3. As part of a large study of the visual adaptations of this unique species, the retinal and lenticular morphology of the aestivating salamanderfish is examined at the level of the light and electron microscopes. The inner retina is highly vascularised by a complex system of vitreal blood vessels, while the outer retina receives a blood supply by diffusion from a choriocapillaris. This increased retinal blood supply may be an adaptation for reducing the oxygen tension during critical periods of aestivation. Large numbers of Muller cells traverse the thickness of the retina from the inner to the outer limiting membranes. The ganglion cells are arranged in two ill-defined layers, separated from a thick inner nuclear layer containing two layers of horizontal cells by a soma-free inner plexiform layer. The photoreceptors can be divided into three types typical of many early actinopterygian representatives; equal double cones, small single cones and large rods (2:1:1). These photoreceptors are arranged into a unique regular square mosaic comprising a large rod bordered by four equal double cones with a small single cone located at the corner of each repeating unit. The double cones may optimise perception of mobile prey which it tracks by flexion of its head and neck and the large rods may increase sensitivity in the dark tannin-rich waters in which it lives. Each single cone also possesses a dense collection of polysomes and glycogen (a paraboloid) beneath its ellipsoid, the first such finding in teleosts. The retinal pigment epithelium possesses melanosomes, pha,oocytes and a large number of mitochondria. The anatomy of the retina and the photoreceptor mosaic is discussed in relation to the primitive phylogeny of this species and its unique life history.

Infection of the epaulette shark, Hemiscyllium ocellatum (Bonnaterre), by the nematode parasite Proleptus australis Bayliss (Spirurida : Physalopteridae)

Seventy-two epaulette sharks, Hemiscyllium ocellatum (Bonnaterre), were infected with the nematode parasite Proleptus australis Bayliss, 1933. The parasite population was overdispersed. Infection intensity ranged from 3 to 1002 worms per fish stomach, and there was a positive correlation between shark length and number of parasites present. The majority of worms were attached to the stomach wall, and scanning electron microscopy and histological examination showed that worms penetrated the stomach lining. Worms were observed within the lamina propria of the stomach and occasionally penetrated the muscularis mucosa. Little to no inflammatory or cellular immune reaction to the presence of the parasites was observed, except in one case where a worm was being degraded by a host tissue response. There was a large amount of connective tissue proliferation as a result of nematode attachment,, but no obvious effects on the overall health of the sharks were seen. Three sharks were also found to be infected by the cestode Callitetrarhynchus sp.

Evidence of multiple transcription initiation and termination sites within the rDNA intergenic spacer and rRNA readthrough transcription in the urochordate Herdmania curvata

Analysis of the structure of the urochordate Herdmania curvata ribosomal DNA intergenic spacer (IGS) and its role in transcription initiation and termination suggests that rRNA gene regulation in this chordate differs from that in vertebrates. A cloned H, curvata IGS is 1881 bp and composed predominantly of two classes of similar repeat sequences that largely alternate in a tandem array. Southern blot hybridization demonstrates that the IGS length variation within an individual and population is largely the result of changes in internal repeat number. Nuclease S1 mapping and primer extension analyses suggest that there are two transcription initiation sites at the 3' end of the most 3' repetitive element; these sites are 6 nucleotides apart. Unlike mouse, Xenopus, and Drosophila, there is no evidence of transcription starting elsewhere in the IGS. Most sequence differences between the promoter repeat and the other internal repeats are in the vicinity of the putative initiation sites. As in Drosophila, nuclease S1 mapping of transcription termination sites suggest that there is not a definitive stop site and a majority of the pre-rRNAs read through a substantial portion of the IGS. Some transcription appears to proceed completely through the promoter repeat into the adjacent rDNA unit. Analysis of oocyte RNA by reverse transcription-polymerase chain reaction (RT-PCR) confirms that readthrough transcription into the adjacent rDNA unit is occurring in some small IGS length variants; there is no evidence of complete readthrough of IGSs larger than 1.0 kb.

Observations on the diet and feeding habits of the epaulette shark, Hemiscyllium ocellatum (Bonnaterre), on Heron Island Reef, Great Barrier Reef, Australia

The diet and feeding habits of the epaulette shark, Hemiscyllium ocellatum, were investigated through stomach content analysis. Five groups of prey items were found. The index of relative importance showed worms and crabs,to be of greatest value at 51.3% and 40.1% respectively. The three minor prey groups were shrimps (7.7%), small fishes (0.7%) and amphipods (0.3%). Epaulette sharks tend to be crepuscular, although feeding bouts may occur at any time. They appear to be opportunistic predators, using olfaction and electroreception in prey capture. This species appears to be an important benthic predator in the reef flat environment on Heron Island Reef.

Effects of cyanide on coral photosynthesis: implications for identifying the cause of coral bleaching and for assessing the environmental effects of cyanide fishing

Modulated chlorophyll fluorescence techniques were used to examine the effects of cyanide (NaCN) from cyanide fishing on photosynthesis of the symbiotic algae (zooxanthellae) located within the tissues of the zooxanthellate hard coral Plesiastrea versipora. Incubating corals for 3 h in a cyanide concentration of >10(-5) M NaCN under a saturating light intensity (photosynthetically active radiation [PAR] intensity of 250 mu mol quanta m(-2) s(-1)) caused a long-term decrease in the ratio of variable to maximal fluorescence (dark-adapted F-v/F-m). The effect of cyanide on dark-adapted F-v/F-m was Light dependent; thus F-v/F-m only decreased in corals exposed to 10(-4) M NaCN for 3 h under PAR of 250 mu mol quanta m(-2) s(-1). In corals where dark-adapted F-v/F-m was significantly lowered by cyanide exposure, we observed significant loss of zooxanthellae from the tissues. causing the corals to discolour (bleach). To further examine the light-dependent effect of cyanide and its relation to loss of zooxanthellae, corals were exposed to 10-4 M NaCN or seawater only (control), either in darkness or under 250 mu mol quanta m(-2) s(-1). ill significant decrease in dark-adapted F-v/F-m and loss of zooxanthellae only occurred in corals exposed to cyanide in the light. These results suggest cyanide causes the dissociation of the symbiosis (bleaching) by affecting photosynthesis of the zooxanthellae. Quenching analysis using the saturation-pulse technique revealed the development of high levels of non-photochemical quenching in cyanide-exposed coral. This result is consistent with the known property of cyanide as an inhibitor of the dark reactions of the Calvin cycle, specifically as an inhibitor of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Therefore, chronic photoinhibition and an impairment of photosynthesis of zooxanthellae provides an important 'signal' to examine the environmental effects of cyanide fishing during controlled releases in situ.

Availability of two forms of dissolved nitrogen to the coral Pocillopora damicornis and its symbiotic zooxanthellae

The relative contribution of dissolved nitrogen (ammonium and dissolved free amino acids DFAAs) to the nitrogen budget of the reef-building coral Pocillopora damicornis was assessed for colonies growing on control and ammonium-enriched reefs at One Tree Island (southern Great Barrier Reef) during the ENCORE (Enrichment of Nutrient on Coral Reef; 1993 to 1996) project. P. damicornis acquired ammonium at rates of between 5.1 and 91.8 nmol N cm(-2) h(-1) which were not affected by nutrient treatment except in the case of one morph. In this case, uptake rates decreased from 80.5 to 42.8 nmol cm(-2) h(-1) (P < 0.05) on exposure to elevated ammonium over 12 mo. The presence or absence of light during measurement did not influence the uptake of ammonium ions. Nitrogen budgets revealed that the uptake of ammonium from concentrations of 0.11 to 0.13 mu M could completely satisfy the demand of growing P. damicornis for new nitrogen. P. damicornis also took up DFAAs at rates ranging from 4.9 to 9.8 nmol N cm(-2) h(-1). These rates were higher in the dark than in the light (9.0 vs 5.1 nmol m(-2) h(-1), P < 0.001). Uptake rates were highest for the amino acids serine, arginine and alanine, and lowest for tyrosine. DFAA concentrations within the ENCORE microatolls that received ammonium were undetectable, whereas they ranged up to 100 nM within the control microatolls. The contribution of DFAAs to the nitrogen budget of P. damicornis constituted only a small fraction of the nitrogen potentially contributed by ammonium under field conditions. Even at the highest field concentrations measured during this study, DFAAs could contribute only similar or equal to 11.3% of the nitrogen demand of P. damicornis. This contribution, however, may be an important source of nitrogen when other sources such as ammonium are scarce or during periods when high concentrations of DFAAs become sporadically available (e.g. cell breakage during fish-grazing).

The phylogenetic relationships of Caulobacter, Asticcacaulis and Brevundimonas species and their taxonomic implications

The phylogenetic relationships among the species of Caulobacter, Asticcacaulis and Brevundimonas were studied by comparison of their 16S rDNA sequences. The analysis of almost complete sequences confirmed the early evolutionary divergence of the freshwater and marine species of Caulobacter reported previously [Stahl, D. A., Key, R,, Flesher, B, & Smit, J. (1992), J Bacteriol 174, 2193-2198]. The freshwater species formed two distinct clusters. One cluster contained the species Caulobacter bacteroides, Caulobacter crescentus, Caulobacter fusiformis and Caulobacter henricii. C, bacteroides and C, fusiformis are very closely related (sequence identity 99.8%). The second cluster was not exclusive and contained the species Caulobacter intermedius, Caulobacter subvibrioides and Caulobacter variabilis, as well as Brevundimonas diminuta and Brevundimonas vesicularis, The marine species Caulobacter halobacteroides and Caulobacter maris were very closely related, with a sequence identity of 99.7%, These two species were most closely but distantly related to the marine hyphal/budding bacteria Hyphomonas jannaschiana and Hirschia baltica, which formed a deep phylogenetic line with Rhodobacter sphaeroides and Rhodobacter capsulatus, Caulobacter leidyia is unrelated to the other species of Caulobacter and belongs to the alpha-4 subclass of the Proteobacteria, forming a distinct cluster with Asticcacaulis excentricus and Asticcacaulis biprosthecium, The taxonomic implications of the polyphyletic nature of the genus Caulobacter and the absence of a type culture for the type species of the genus, Caulobacter vibrioides, are discussed.

Net uptake of dissolved free amino acids by the giant clam, Tridacna maxima: alternative sources of energy and nitrogen?

The role of dissolved free amino acids (DFAA) in nitrogen and energy budgets was investigated for the giant clam, Tridacna maxima, growing under field conditions at One Tree Island, at the southern end of the Great Barrier Reef, Australia. Giant clams (121.5-143.7 mm in shell length) took up neutral, acidic and basic amino acids. The rates of net uptake of DFAA did not differ between light and dark, nor for clams growing under normal or slightly enriched ammonium concentrations. Calculations based on the net uptake concentrations typical of the maximum concentrations of DFAA found in coral reef waters (similar to 0.1 mu M)revealed that DFAA could only contribute 0.1% and 1% of the energy and nitrogen demands of giant clams, respectively. These results suggest that DFAA does not supply significant amounts of energy or nitrogen for giant clams or their symbionts.

Influence of field-based nutrient enrichment on the photobiology of the giant clam Tridacna maxima

Nutrients were added to 12 microatolls in One Tree Island lagoon every low tide for 13 mo to an initial concentration of 10 mu M (ammonium, N) and 2 mu M (phosphate, P). These concentrations remained above background for 2 to 3 h after addition. The addition of ammonium (N and NI-P but not P alone) significantly increased P, (gross photosynthesis) P,, (net photosynthesis) and R (respiration) per unit wet-tissue weight and cc (photosynthetic efficiency) in Tridacna maxima after 3 mo nutrient enrichment. These responses to small and transient changes in ammonium concentrations suggest that symbiotic clams are not nutrient-replete, and that even subtle changes in nutrients can have a measurable effect on photosynthesis. The same clams did not show significant differences in photosynthetic parameters 6 mo after the beginning of nutrient enrichment, suggesting that their previous responses had either been seasonal or that symbiotic clams such as T. maxima are able to adjust their photophysiology following external changes in nutrient concentrations.

Strong genetic structuring in a habitat specialist, the Oxleyan Pygmy Perch Nannoperca oxleyana

This study used allozyme and mitochondrial DNA variation to examine genetic structure in the Oxleyan Pygmy Perch Nannoperca oxleyana. This small-bodied freshwater fish has a very restricted distribution occurring only in some small coastal streams in south-east Queensland and northern New South Wales. It was expected that subpopulations may contain little genetic variation and be highly differentiated from one another. The results, based on allozyme and mitochondrial DNA control region variation were in agreement with these expectations. Allozyme variation was very low overall, with only one locus showing variation at most sites. The high differentiation was because a different locus tended to be polymorphic at each site. Mitochondrial variation within sites was also low, but some sites had unique haplotypes. The patterns of similarity among mitochondrial DNA haplotypes were not as expected from geographical proximity alone. In particular, although some northern sites had unique haplotypes, four sites spread along 200 km of coastline were remarkably similar, sharing the same common haplotype at similar frequencies. We suggest that these four streams may have had a confluence relatively recently, possibly when sea levels were lower, 8000-10 000 BP.

Photoinhibition and photoprotection in symbiotic dinoflagellates from reef-building corals

Pulse-amplitude-modulation fluorometry and oxygen respirometry were used to investigate diel photosynthetic responses by symbiotic dinoflagellates to light levels in summer and winter on a high latitude coral reef. The symbiotic dinoflagellates from 2 species of reef-building coral (Porites cylindrica and Stylophora pistillata) showed photoinhibitory decreases in the ratio of variable (F-v) to maximal (F-m) fluorescence (F-v/F-m) as early as 09:00 h on both summer and winter days on the reefs associated with One Tree Island (23 degrees 30' S, 152 degrees 06' E; Great Barrier Reef, Australia). This was due to decreases in maximum, F-m, and to a smaller extent minimum, F-0, chlorophyll fluorescence. Complete recovery took 4 to 6 h and began to occur as soon as light levels fell each day. Chlorophyll fluorescence quenching analysis of corals measured during the early afternoon revealed classic regulation of photosystem II (PSII) efficiency through non-photochemical quenching (NPQ). These results appear to be similar to data collected for other algae and higher plants, suggesting involvement of the xanthophyll cycle of symbiotic dinoflagellates in regulating the quantum efficiency of PSII. The ability of symbiotic dinoflagellates to develop significant NPQ, however, depended strongly on when the symbiotic dinoflagellates were studied. Whereas symbiotic dinoflagellates from corals in the early afternoon showed a significant capacity to regulate the efficiency of PSII using NPQ, those sampled before sunrise had a slower and much reduced capacity, suggesting that elements of the xanthophyll cycle are suppressed prior to sunrise. A second major finding of this study is that the quantum efficiency of PSII in symbiotic dinoflagellates is strongly diurnal, and is as much as 50% lower just prior to sunrise than later in the day. When combined with oxygen flux data, these results indicate that a greater portion of the electron transport occurring later in the day is likely to be due to the increases in the rate of carbon fixation by Rubisco or to higher flutes through the Mehler-Ascorbate-Peroxidase (MAP) cycle.

Ontological changes in the crystallin composition of the eye lenses of the territorial damselfish Parma microlepis and their possible effects on trace-metal accumulation

The eye lenses of Parma microlepis from the rocky barrens of Sydney (New South Wales, Australia) were found to contain Ba, Hg, Rb, and Sr at concentrations above the quantitative detection limits of solution-based inductively-coupled plasma-mass spectrometry (ICP-MS). Lenses were separated into the hard central nucleus and the softer surrounding cortex. Nuclei contained lower (equal for Ba) concentrations of these metals. Biochemical analysis of the protein composition of these lenses revealed differences in the ratio of gamma-crystallin to beta-crystallin in the lens nucleus and cortex. These changes were shown to be attributable both to protein degradation and changes in protein synthesis as fish age. Such changes may lead to the loss of sequestered metals from older cell layers, or change the affinity of new layers for particular trace metals. Differential binding affinities of these crystallins may, therefore, partially account for trace-metal differences observed in the lens nucleus and cortex.

Pyruvated carrageenans from Solieria robusta and its adelphoparasite Tikvahiella candida

Solieria, the type genus of the commercially important red algal family Solieriaceae (Gigartinales), contains seven or eight species, three of which are represented in Australia. The cell-wall galactans of the most common Australian Solieria species, S. robusta (Greville) Kylin, were analysed by a combination of compositional assays, linkage analysis, and Fourier transform infrared (FTIR) and C-13 nuclear magnetic resonance (NMR) spectroscopy. They are shown to be composed predominantly of carrabiose 2,4'-disulphate units (the repeating unit of iota-carrageenan) and a significant proportion of 4',6'-pyruvated carrabiose 2-sulphate units. The constituent sugars, pyruvate content, FTIR spectrum, and linkage and substitution patterns of the galactans from Tikvahiella candida Kraft et Gabrielson, an adelphoparasite of Solieria robusta, closely resemble those of its host and furnish evidence in support of a close phylogenetic relationship between the two species.