Heavy metals in the sediments of Northern Moreton Bay, Queensland, Australia

This project was the first comprehensive assessment of heavy metals to be conducted in the sediments of Northern Moreton Bay since the 1970s and found that shipping and shipping related activities contributed significantly to the level of sediment contamination in the area. The study was also used to develop and test new methods of assessing heavy metal sediment quality.

Flood related loss and recovery of intertidal seagrass meadows in southern Queensland, Australia

The loss and recovery of intertidal seagrass meadows were assessed following the flood related catastrophic loss of seagrass meadows in February 1999 in the Sandy Strait, Queensland. Region wide recovery rates of intertidal meadows following the catastrophic disturbance were assessed by mapping seagrass abundance in the northern Great Sandy Strait region prior to and on 3 occasions after widespread loss of seagrass. Meadow-scale assessments of seagrass loss and recovery focussed on two existing Zostera capricorni monitoring meadows in the region. Mapping surveys showed that approximately 90% of intertidal seagrasses in the northern Great Sandy Strait disappeared after the February 1999 flooding of the Mary River. Full recovery of all seagrass meadows took 3 years. At the two study sites (Urangan and Wanggoolba Creek) the onset of Z. capricorni germination following the loss of seagrass occurred 14 months post-flood at Wanggoolba Creek, and at Urangan it took 20 months for germination to occur. By February 2001 (24 months post-flood) seagrass abundance at Wanggoolba Creek sites was comparable to pre-flood abundance levels and full recovery at Urangan sites was complete in August 2001 (31 months post-flood). Reduced water quality characterised by 2–3 fold increases in turbidity and nutrient concentrations during the 6 months following the flood was followed by a 95% loss of seagrass meadows in the region. Reductions in available light due to increased flood associated turbidity in February 1999 were the likely cause of seagrass loss in the Great Sandy Strait region, southern Queensland. Although seasonal cues influence the germination of Z. capricorni, the temporal variation in the onset of seed germination between sites suggests that germination following seagrass loss may be dependent on other factors (eg. physical and chemical characteristics of sediments and water). Elevated dissolved nitrogen concentrations during 1999 at Wanggoolba Creek suggest that this site received higher loads of sediments and nutrients from flood waters than Urangan. The germination of seeds at Wanggoolba Creek one year prior to Urangan coincides with relatively low suspended sediment concentrations in Wanggoolba Creek waters. The absence of organic rich sediments at Urangan for many months following their removal during the 1999 flood may also have inhibited seed germination. Data from population cohort analyses and population growth rates showed that rhizome weight and rhizome elongation rates increased over time, consistent with rapid growth during increases in temperature and light availability from May to October

Developments in controlled green-water larval culture technologies for estuarine fishes in Queensland, Australia and elsewhere

Since 1989, researchers with the Department of Primary Industries and Fisheries (DPI&F) in Queensland, Australia, have successfully used controlled low-water exchange green-water cultures to rear the larvae of estuarine fishes and crustaceans through to metamorphosis. High survivals and excellent fry condition have been achieved for several commercially important endemic species produced for various projects. They include barramundi or sea bass, Lates calcarifer, Australian bass, Macquaria novemaculeata, dusky flathead, Platycephalus fuscus, sand whiting, Sillago ciliata, red sea bream or snapper, Pagrus auratus, banana prawn, Fenneropenaeus merguiensis, and others. The consistent success of our standardised and relatively simple approach at different localities has led to it being incorporated into general fingerling production practices at several establishments in Australia. Although post-metamorphosis rearing methods have differed for each species investigated, due to various biological and behavioural traits and project requirements, these larval rearing methods have been successful with few species-specific modifications. Initially modelled on the Taiwanese approach to rearing Penaeids in aerated low-water exchange cultures, the approach similarly appears to rely on a beneficial assemblage of micro-organisms. Conceptually, these micro-organisms may include a mixture of the air-borne primary invaders of pure phytoplankton cultures when exposed to outdoor conditions. Whilst this would vary with different sites, our experiences with these methods have consistently been favourable. Mass microalgal cultures with eco-physiological youth are used to regularly augment larval fish cultures so that rearing conditions simulate an exponential growth-phase microalgal bloom. Moderate to heavy aeration prevents settlement of particulate matter and encourages aerobic bacterial decomposition of wastes. The green-water larval rearing approach described herein has demonstrated high practical utility in research and commercial applications, and has greatly simplified marine finfish hatchery operations whilst generally lifting production capacities for metamorphosed fry in Australia. Its potential uses in areas of aquaculture other than larviculture are also discussed.

Variable growth rates of the tropical estuarine fish barramundi Lates calcarifer (Bloch) under different freshwater flow conditions

Relationships between freshwater flows and growth rates of the opportunistic predatory finfish barramundi Lates calcarifer in a dry tropical estuary were examined using data from a long-term tag-recapture programme. Lagged effects were not investigated. After accounting for length at release, time at liberty and seasonal variation (e.g. winter, spring, summer and autumn), growth rates were significantly and positively related to fresh water flowing to the estuary. Effects were present at relatively low levels of freshwater flow (i.e. 2.15 m3 s-1, the 5th percentile of the mean flow rate experienced by fish in the study during time at liberty). The analysis, although correlative, provides quantitative evidence to support the hypothesis that freshwater flows are important in driving the productivity of estuaries and can improve growth of species high in the trophic chain.

The effect of habitat and environmental history on otolith chemistry of barramundi Lates calcarifer in estuarine populations of a regulated tropical river

We examine the microchemistry of otoliths of cohorts of a fished shed population of the large catadromous fish, barramundi Lates calcarifer from the estuary of a large tropical river. Barramundi from the estuary of the large, heavily regulated Fitzroy River, north eastern Australia were analysed by making transects of 87Sr/86Sr isotope and trace metal/Ca ratios from the core to the outer edge. Firstly, we examined the Sr/Ca, Ba/Ca, Mg/Ca and Mn/Ca and 87Sr/86Sr isotope ratios in otoliths of barramundi tagged in either freshwater or estuarine habitats that were caught by the commercial fishery in the estuary. We used 87Sr/86Sr isotope ratios to identify periods of freshwater residency and assess whether trace metal/Ca ratios varied between habitats. Only Sr/Ca consistently varied between known periods of estuarine or freshwater residency. The relationships between trace metal/Ca and river flow, salinity, temperature were examined in fish tagged and recaptured in the estuary. We found weak and inconsistent patterns in relationships between these variables in the majority of fish. These results suggest that both individual movement history within the estuary and the scale of environmental monitoring were reducing our ability to detect any patterns. Finally, we examined fish in the estuary from two dominant age cohorts (4 and 7 yr old) before and after a large flood in 2003 to ascertain if the flood had enabled fish from freshwater habitats to migrate to the estuary. There was no difference in the proportion of fish in the estuary that had accessed freshwater after the flood. Instead, we found that larger individuals with each age cohort were more likely to have spent a period in freshwater. This highlights the need to maintain freshwater flows in rivers. About half the fish examined had accessed freshwater habitats before capture. Of these, all had spent at least their first two months in marine salinity waters before entering freshwater and some did not enter freshwater until four years of age. This contrasts with the results of several previous studies in other parts of the range that found that access to freshwater swamps by larval barramundi was important for enhanced population productivity and recruitment.

Habitat dynamics in the bed sediments of an intermittent upland stream

The effects of the hydrological regime on temporal changes to physical characteristics of substratum habitat, sediment texture of surface sediments (<10 cm), were investigated in a sub-tropical headwater stream over four years. Surface discharge was measured together with vertical hydraulic gradient and groundwater depth in order to explore features of sediment habitat that extend beyond the streambed surface. Whilst the typical discharge pattern was one of intermittent base flows and infrequent flow events associated with monsoonal rain patterns, the study period also encompassed a drought and a one-in-a-hundred-year flood. Rainfall and discharge did not necessarily reflect the actual conditions in the stream. Although surface waters were persistent long after discharge ceased, the streambed was completely dry on several occasions. Shallow groundwater was present at variable depths throughout the study period, being absent only at the height of the drought. The streambed sediments were mainly gravels, sand and clay. Finer sediment fractions showed a marked change in grain size over time, although bedload movement was limited to a single high discharge event. In response to a low discharge regimen (drought), sediments characteristically showed non-normal distributions and were dominated by finer materials. A high-energy discharge event produced a coarsening of sands and a diminished clay fraction in the streambed. Particulate organic matter from sediments showed trends of build-up and decline with the high and low discharge regimes, respectively. Within the surface sediment intersticies three potential categories of invertebrate habitat were recognised, each with dynamic spatial and temporal boundaries.

Recovery of fish and crustacean communities during remediation of tidal wetlands affected by leachate from acid sulfate soils in north-eastern Australia.

In the 1970s, acid sulfate soils (ASS) distributed within about 720 ha of predominantly mangrove and salt pan wetlands at East Trinity in north Queensland were developed after the area was isolated from tidal flooding by a surrounding seawall and the installation of tidal gates on major drainage creeks. Following drainage and oxidation of these estuarine acidic sediments, resultant acid leachate caused considerable, ongoing environmental problems including regular fish kills. A rehabilitation program covering much of these former tidal wetlands commenced in 2000 using a lime-assisted tidal exchange management regime. Changes in the established populations of estuarine fish and crustaceans were monitored in the two creeks (Firewood and Hills Creeks) where tidal flows were reinstated. In Firewood Creek between 2001 and 2005, there was a progressive increase in fish species richness, diversity and abundance. The penaeid prawn Fenneropenaeus merguiensis was a major component of the cast net catches in the lower sections of both Firewood and Hills Creeks but its relative abundance decreased upstream of the tidal gates on the seawall. Well established stocks of predominantly juvenile, male Scylla serrata resident upstream of the tidal gates indicated suitable habitats with acceptable water and sediment quality and adequate availability of food. The regular fish kills that occurred prior to the management regime abated and, overall, the implementation of the rehabilitation program is yielding positive benefits for the local fisheries.

Flow impacts on estuarine finfish fisheries of the Gulf of Carpentaria

The estuaries of Australia s tropical rivers support commercial fisheries for finfish and shellfish valued at over $220 million per annum. There are also significant tourism-related and local recreational and indigenous fisheries for icon species such as barramundi. Development of water resources in Australia's Tropical Rivers region is being considered for the Flinders, Mitchell, McArthur, Roper, Daly and Victoria catchments. Greater knowledge of the freshwater requirements of tropical aquatic ecosystems, including estuaries is crucial, so that the communities of catchments where water resource development occurs can be assured that the downstream effects of such development are considered and managed based on the best available knowledge.

A multi-faceted approach for quantifying the estuarine-nearshore transition in the life cycle of the bull shark, Carcharhinus leucas.

Understanding the ontogenetic habitat linkages of sharks is important for conservation and managing human interactions. We used acoustic telemetry, catch data, elemental and stable isotope signatures and dietary analyses to investigate ontogenetic habitat use in south-east Queensland, Australia, by the bull shark Carcharhinus leucas, a IUCN 'near-threatened' species that is implicated in many shark attacks on humans in urban estuaries. Sequential analyses for delta(15)N and delta(13)C of vertebrae from five adult C. leucas and laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) for elemental composition from 23 C. leucas, including a pregnant female, were also used to trace ontogenetic habitat dependence. Acoustic telemetry indicated large juvenile and subadult C. leucas remained in estuarine habitats. delta(15)N values across shark vertebrae showed an ontogenetic shift in diet with total length (TL), confirmed by stomach contents. LA-ICPMS data reflected the ontogenetic movements of C. leucas from natal habitats. Differences among adults were gender related. Shifts in habitat use by subadults were correlated with a sigmoidal delta(13)C relationship with TL. C. leucas have a multipartite, stage-specific dependency in their transition between habitats along the freshwater-estuarine-marine continuum, making them particularly susceptible to the habitat alteration that is occurring globally.

Spatial variation in life history reveals insight into connectivity and geographic population structure of a tropical estuarine teleost: king threadfin, Polydactylus macrochir

Understanding the life history of exploited fish species is not only critical in developing stock assessments and productivity models, but has a dual function in the delineation of connectivity and geographical population structure. In this study, patterns in growth and length and age at sex change of Polydactylus macrochir, an ecologically and economically important protandrous estuarine teleost, were examined to provide preliminary information on the species' connectivity and geographic structure across northern Australia. Considerable variation in life history parameters was observed among the 18 locations sampled. Both unconstrained and constrained (t(0) = 0) estimates of von Bertalanffy growth function parameters differed significantly among all neighbouring locations with the exception of two locations in Queensland's east coast and two in Queensland's Gulf of Carpentaria waters, respectively. Comparisons of back-calculated length-at-age 2 provided additional evidence for growth differences among some locations, but were not significantly different among locations in the south-eastern Gulf of Carpentaria or on Queensland's east coast. The length and age at sex change differed markedly among locations, with fish from the east coast of Australia changing sex from males to females at significantly greater lengths and ages than elsewhere. Sex change occurred earliest at locations within Queensland's Gulf of Carpentaria, where a large proportion of small, young females were recorded. The observed differences suggest that P. macrochir likely form a number of geographically and/or reproductively distinct groups in Australian waters and suggest that future studies examining connectivity and geographic population structure of estuarine fishes will likely benefit from the inclusion of comparisons of life history parameters. (C) 2012 Elsevier B.V. All rights reserved.

Parasites as indicators of movement and population connectivity of a non-diadromous, tropical estuarine teleost: king threadfin Polydactylus macrochir

Temporal and spatial patterns in parasite assemblages were examined to evaluate the degree of movement and connectivity of post-recruitment life-history stages of a large, non-diadromous tropical estuarine teleost, king threadfin Polydactylus macrochir, collected from 18 locations across northern Australia. Ten parasites types (juvenile stages of two nematodes and seven cestodes, and adults of an acanthocephalan) were deemed to be suitable for use as biological tags, in that they were considered to have a long residence time in the fish, were relatively easy to find and were morphologically very different to each other which aided discrimination. Univariate and discriminant function analysis of these parasites revealed little difference in temporal replicates collected from five locations, suggesting that the parasite communities were stable over the timeframes explored. Univariate, discriminant function, and BrayCurtis similarity analyses indicated significant spatial heterogeneity, with BrayCurtis classification accuracies ranging from 55 to 100% for locations in north-western and northern Australia, 24 to 88% in the Gulf of Carpentaria, and 39 to 88% on the east coast of Queensland. Few differences were observed among locations separated by <200 km. The observed patterns of parasite infection are in agreement with concurrent studies of movement and connectivity of P. macrochir in that they indicate a complex population structure across northern Australia. These results should be considered when reviewing the management arrangements for this species.

Quantifying the effects of climate change and water abstraction on a population of barramundi (Lates calcarifer), a diadromous estuarine finfish

Many aquatic species are linked to environmental drivers such as temperature and salinity through processes such as spawning, recruitment and growth. Information is needed on how fished species may respond to altered environmental drivers under climate change so that adaptive management strategies can be developed. Barramundi (Lates calcarifer) is a highly prized species of the Indo-West Pacific, whose recruitment and growth is driven by river discharge. We developed a monthly age- and length-structured population model for barramundi. Monte Carlo Markov Chain simulations were used to explore the population's response to altered river discharges under modelled total licenced water abstraction and projected climate change, derived and downscaled from Global Climate Model A1FI. Mean values of exploitable biomass, annual catch, maximum sustainable yield and spawning stock size were significantly reduced under scenarios where river discharge was reduced; despite including uncertainty. These results suggest that the upstream use of water resources and climate change have potential to significantly reduce downstream barramundi stock sizes and harvests and may undermine the inherent resilience of estuarine-dependent fisheries. © 2012 CSIRO.

Molecular phylogeny of Archaea in boreal forest soil, freshwater and temperate estuarine sediment

Suurin osa luonnossa havaitsemistamme mikrobeista on sellaisia, joita emme edelleenkään osaa kasvattaa laboratorio-oloissa, vaikka tietomme mikrobien monimuotoisuudesta paranevat koko ajan. Luonnontilaisen mikrobieliöstön kokoonpano eri ympäristöissä on paljolti epäselvä ja ymmärrämme vielä hyvin puutteellisesti mikrobien ekologiaa ja niiden rooleja eliöyhteisöissä. Nykyaikaiset molekulaariset tutkimusmenetelmät auttavat selvittämään mikrobien monimuotoisuutta kokonaisvaltaisesti ja nopeasti. Ympäristöstä kemiallisesti puhdistetut ribosomaalista RNA:ta koodaavat geenit edustavat periaatteessa kaikkia eliöyhteisön geneettisesti toisistaan poikkeavia eliöitä. Niistä voidaan valikoida halutut genomit jatkotutkimuksia varten. Uusien menetelmien käyttö on tuonut esiin sen merkittävän seikan, että "tavanomaisten" elinympäristöjen eliöyhteisöihin kuuluu suuri joukko entuudestaan tuntemattomia arkkieliöitä. Aiemmin kuviteltiin, että arkkieliöt asuttavat vain sellaisia "epätavallisia" tai "äärimmäisiä" elinympäristöjä, joita luonnehtii joku seuraavista ominaisuuksista: hyvin korkea lämpötila, korkea suolapitoisuus, korkea happamuus tai emäksisyys, hapettomuus. Tutkijat ovat viimeisen noin kymmenen vuoden aikana osoittaneet, että arkkieliöt asuttavat hyvin monenlaisia kylmän ja lauhkean vyöhykkeen ympäristöjä, yhtä hyvin maaperää kuin suolaisen ja makean veden pohjaa tai pintakerroksia. Nämä löydöt ovat avanneet uuden alun arkkieliöiden tutkimukselle, erityisesti sen selvittämiselle, mitkä ovat niiden fysiologiset ja ekologiset roolit monimuotoisissa mikrobiyhteisöissä. Tämä väitöskirja kuvaa entuudestaan tuntemattomien arkkieliöiden löytymistä havumetsävyöhykkeen metsämaasta. Arkkieliöitä löytyi myös lauhkean vyöhykkeen vuorovesialueelta, murtoveden huuhtelemasta pohjasta. Nämä löydöt ovat perustavalaatuisia vuorovesialueen eliöyhteisöjen ymmärtämiseksi. Suomalaisen metsäjärven vedestä määritettiin molempien arkkieliöiden pääryhmien - tieteellisiltä nimiltään Crenarchaeota ja Euryarchaeota - edustajia. Euryarchaeota-ryhmän edustajia voitiin havainnoida myös fluoresenssi-mikroskopoinnilla. Löydöt viittaavat siihen, että arkkieliöillä on oma biogeokemiallinen roolinsa makeanveden ravintoketjujen hiilen käytössä. Tässä työssä määritetyt uudet arkkieliöiden genomien nukleotidisekvenssit on toimitettu ARB-tietokantaan, jonka kasvava vertailuaineisto edelleen parantaa uusien arkkieliösekvenssien analyysiä ja auttaa hybridisaatiokoetinten ja polymeraasiketjureaktioalukkeiden suunnittelussa ja arvioinnissa. Tässä väitöskirjassa esitellyt tulokset yhdessä lukuisien vesi-, maaperä- ja muiden ympäristöjen arkkieliöitä käsittelevien julkaisujen kanssa osoittavat, että arkkieliöt asuttavat monia erilaisia elinympäristöjä ja että ne ovat ekologisesti paljon menestyneempiä, kuin tieteenalalla on kuviteltu. Voimme olettaa, että heti kun joitain näistä eliöistä onnistutaan kasvattamaan ja ylläpitämään laboratorio-oloissa, niiden joukosta löydetään aivan uusia, entuudestaan tuntemattomia fysiologisia fenotyyppejä, jotka avaavat mielenkiintoisia näkymiä aineenvaihdunnan ja perinnöllisten ominaisuuksien tutkimukselle.