Bycatch and strandings programs as ecological indicators for data-limited cetaceans

An integrated approach of using strandings and bycatch data may provide an indicator of long-term trends for data-limited cetaceans. Strandings programs can give a faithful representation of the species composition of cetacean assemblages, while standardised bycatch rates can provide a measure of relative abundance. Comparing the two datasets may also facilitate managing impacts by understanding which species, sex or sizes are the most vulnerable to interactions with fisheries gear. Here we apply this approach to two long-term datasets in East Australia, bycatch in the Queensland Shark Control Program QSCP, 1992–2012) and strandings in the Queensland Marine Wildlife Strandings and Mortality Program StrandNet, 1996–2012). Short-beaked common dolphins, Delphinus delphis, were markedly more frequent in bycatch than in the strandings dataset, suggesting that they are more prone to being incidentally caught than other cetacean species in the region. The reverse was true for humpback whales, Megaptera novaeangliae, bottlenose dolphins, Tursiops spp.; and species predominantly found in offshore waters. QSCP bycatch was strongly skewed towards females for short-beaked common dolphins, and towards smaller sizes for Australian humpback dolphins, Sousa sahulensis. Overall, both datasets demonstrated similar seasonality and a similar long-term increase from 1996 until 2008. Analysis on a species-by-species basis was then used to explore potential explanations for long-term trends, which ranged from a recovering stock (humpback whales) to a shift in habitat use (short-beaked common dolphins).

Bycatch and strandings programs as ecological indicators for data-limited cetaceans

An integrated approach of using strandings and bycatch data may provide an indicator of long-term trends for data-limited cetaceans. Strandings programs can give a faithful representation of the species composition of cetacean assemblages, while standardised bycatch rates can provide a measure of relative abundance. Comparing the two datasets may also facilitate managing impacts by understanding which species, sex or sizes are the most vulnerable to interactions with fisheries gear. Here we apply this approach to two long-term datasets in East Australia, bycatch in the Queensland Shark Control Program (QSCP, 1992–2012) and strandings in the Queensland Marine Wildlife Strandings and Mortality Program (StrandNet, 1996–2012). Short-beaked common dolphins, Delphinus delphis, were markedly more frequent in bycatch than in the strandings dataset, suggesting that they are more prone to being incidentally caught than other cetacean species in the region. The reverse was true for humpback whales, Megaptera novaeangliae, bottlenose dolphins, Tursiops spp.; and species predominantly found in offshore waters. QSCP bycatch was strongly skewed towards females for short-beaked common dolphins, and towards smaller sizes for Australian humpback dolphins, Sousa sahulensis. Overall, both datasets demonstrated similar seasonality and a similar long-term increase from 1996 until 2008. Analysis on a species-by-species basis was then used to explore potential explanations for long-term trends, which ranged from a recovering stock (humpback whales) to a shift in habitat use (short-beaked common dolphins).

Ecological impacts of feral pig diggings in north Queensland rainforests

This two-year study examined the impacts of feral pig diggings on five ecological indicators: seedling survival, surface litter, subsurface plant biomass, earthworm biomass and soil moisture content. Twelve recovery exclosures were established in two habitats (characterised by wet and dry soil moisture) by fencing off areas of previous pig diggings. A total of 0.59 ha was excluded from further pig diggings and compared with 1.18 ha of unfenced control areas. Overall, seedling numbers increased 7% within the protected exclosures and decreased 37% within the unprotected controls over the two-year study period. A significant temporal interaction was found in the dry habitat, with seedling survival increasing with increasing time of protection from diggings. Feral pig diggings had no significant effect on surface litter biomass, subsurface plant biomass, earthworm biomass or soil moisture content.

Light thresholds derived from seagrass loss in the coastal zone of the northern Great Barrier Reef, Australia

There is a world-wide trend for deteriorating water quality and light levels in the coastal zone, and this has been linked to declines in seagrass abundance. Localized management of seagrass meadow health requires that water quality guidelines for meeting seagrass growth requirements are available. Tropical seagrass meadows are diverse and can be highly dynamic and we have used this dynamism to identify light thresholds in multi-specific meadows dominated by Halodule uninervis in the northern Great Barrier Reef, Australia. Seagrass cover was measured at similar to 3 month intervals from 2008 to 2011 at three sites: Magnetic Island (MI) Dunk Island (DI) and Green Island (GI). Photosynthetically active radiation was continuously measured within the seagrass canopy, and three light metrics were derived. Complete seagrass loss occurred at MI and DI and at these sites changes in seagrass cover were correlated with the three light metrics. Mean daily irradiance (I-d) above 5 and 8.4 mol m(-2) d(-1) was associated with gains in seagrass at MI and DI, however a significant correlation (R = 0.649, p < 0.05) only occurred at MI. The second metric, percent of days below 3 mol m(-2) d(-1), correlated the most strongly (MI, R = -0.714, p < 0.01 and DI, R = -0.859, p = <0.001) with change in seagrass cover with 16-18% of days below 3 mol m(-2) d(-1) being associated with more than 50% seagrass loss. The third metric, the number of hours of light saturated irradiance (H-sat) was calculated using literature-derived data on saturating irradiance (E-k). H-sat correlated well (R = 0.686, p <0.01; and DI, R = 0.704, p < 0.05) with change in seagrass abundance, and was very consistent between the two sites as 4 H-sat was associated with increases in seagrass abundance at both sites, and less than 4 H-sat with more than 50% loss. At the third site (GI), small seasonal losses of seagrass quickly recovered during the growth season and the light metrics did not correlate (p > 0.05) with change in percent cover, except for I-d which was always high, but correlated with change in seagrass cover. Although distinct light thresholds were observed, the departure from threshold values was also important. For example, light levels that are well below the thresholds resulted in more severe loss of seagrass than those just below the threshold. Environmental managers aiming to achieve optimal seagrass growth conditions can use these threshold light metrics as guidelines; however, other environmental conditions, including seasonally varying temperature and nutrient availability, will influence seagrass responses above and below these thresholds. (C) 2012 Published by Elsevier Ltd.

Assessing the relationship between patch type and soil mites: A molecular approach

An urgent need exists for indicators of soil health and patch functionality in extensive rangelands that can be measured efficiently and at low cost. Soil mites are candidate indicators, but their identification and handling is so specialised and time-consuming that their inclusion in routine monitoring is unlikely. The aim of this study was to measure the relationship between patch type and mite assemblages using a conventional approach. An additional aim was to determine if a molecular approach traditionally used for soil microbes could be adapted for soil mites to overcome some of the bottlenecks associated with soil fauna diversity assessment. Soil mite species abundance and diversity were measured using conventional ecological methods in soil from patches with perennial grass and litter cover (PGL), and compared to soil from bare patches with annual grasses and/or litter cover (BAL). Soil mite assemblages were also assessed using a molecular method called terminal-restriction fragment length polymorphism (T-RFLP) analysis. The conventional data showed a relationship between patch type and mite assemblage. The Prostigmata and Oribatida were well represented in the PGL sites, particularly the Aphelacaridae (Oribatida). For T-RFLP analysis, the mite community was represented by a series of DNA fragment lengths that reflected mite sequence diversity. The T-RFLP data showed a distinct difference in the mite assemblage between the patch types. Where possible, T-RFLP peaks were matched to mite families using a reference 18S rDNA database, and the Aphelacaridae prevalent in the conventional samples at PGL sites were identified, as were prostigmatids and oribatids. We identified limits to the T-RFLP approach and this included an inability to distinguish some species whose DNA sequences were similar. Despite these limitations, the data still showed a clear difference between sites, and the molecular taxonomic inferences also compared well with the conventional ecological data. The results from this study indicated that the T-RFLP approach was effective in measuring mite assemblages in this system. The power of this technique lies in the fact that species diversity and abundance data can be obtained quickly because of the time taken to process hundreds of samples, from soil DNA extraction to data output on the gene analyser, can be as little as 4 days.

Development of key soil health indicators for the Australian banana industry

To improve the sustainability and environmental accountability of the banana industry there is a need to develop a set of soil health indicators that integrate physical, chemical and biological soil properties. These indicators would allow banana growers, extension and research workers to improve soil health management practices. To determine changes in soil properties due to the cultivation of bananas, a paired site survey was conducted comparing soil properties under conventional banana systems to less intensively managed vegetation systems, such as pastures and forest. Measurements were made on physical, chemical and biological soil properties at seven locations in tropical and sub-tropical banana producing areas. Soil nematode community composition was used as a bioindicator of the biological properties of the soil. Soils under conventional banana production tended to have a greater soil bulk density, with less soil organic carbon (C) (both total C and labile C), greater exchangeable cations, higher extractable P, greater numbers of plant-parasitic nematodes and less nematode diversity, relative to less intensively managed plant systems. The organic banana production systems at two locations had greater labile C, relative to conventional banana systems, but there was no significant change in nematode community composition. There were significant interactions between physical, chemical and nematode community measurements in the soil, particularly with soil C measurements, confirming the need for a holistic set of indicators to aid soil management. There was no single indicator of soil health for the Australian banana industry, but a set of soil health indicators, which would allow the measurement of soil improvements should include: bulk density, soil C, pH, EC, total N, extractable P, ECEC and soil nematode community structure.

Stakeholders' assessment of welfare indicators for sheep and cattle exported by sea from Australia

An adaptive conjoint analysis was use to evaluate stakeholders' opinion of welfare indicators for ship-transported sheep and cattle, both onboard and in pre-export depots. In consultations with two nominees of each identified stakeholder group (government officials, animal welfare representatives, animal scientists, stockpersons, producers/pre-export depot operators, exporters/ship owners and veterinarians), 18 potential indicators were identified Three levels were assigned to each using industry statistics and expert opinion, representing those observed on the best and worst 5% of voyages and an intermediate value. A computer-based questionnaire was completed by 135 stakeholders (48% of those invited). All indicators were ranked by respondents in the assigned order, except fodder intake, in which case providing the amount necessary to maintain bodyweight was rated better than over or underfeeding, and time in the pre-export assembly depot, in which case 5 days was rated better than 0 or 10 days. The respective Importance Values (a relative rating given by the respondent) for each indicator were, in order of declining importance: mortality (8.6%), clinical disease incidence (8.2%), respiration rate (6.8%), space allowance (6.2%), ammonia levels (6.1%), weight change (6.0%), wet bulb temperature (6.0%), time in assembly depot (5.4%), percentage of animals in hospital pen (5.4%), fodder intake (5.2%), stress-related metabolites (5.0%), percentage of feeding trough utilised (5.0%), injuries (4.8%), percentage of animals able to access food troughs at any one time (4.8%), percentage of animals lying down (4.7%), cortisol concentration (4.5Y.), noise (3.9y.), and photoperiod (3.4%). The different stakeholder groups were relatively consistent in their ranking of the indicators, with all groups nominating the some top two and at least five of the top seven indicators. Some of the top indicators, in particular mortality, disease incidence and temperature, are already recorded in the Australian industry, but the study identified potential new welfare indicators for exported livestock, such as space allowance and ammonia concentration, which could be used to improve welfare standards if validated by scientific data. The top indicators would also be useful worldwide for countries engaging in long distance sea transport of livestock.

As clear as mud: A critical review of evidence for the ecological roles of Australian dingoes

Top-predators have been reported to have an important role in structuring food webs and maintaining ecological processes for the benefit of biodiversity at lower trophic levels. This is thought to be achieved through their suppressive effects on sympatric mesopredators and prey. Great scientific and public interest surrounds the potential use of top-predators as biodiversity conservation tools, and it can often be difficult to separate what we think we know and what we really know about their ecological utility. Not all the claims made about the ecological roles of top-predators can be substantiated by current evidence. We review the methodology underpinning empirical data on the ecological roles of Australian dingoes (Canis lupus dingo and hybrids) to provide a comprehensive and objective benchmark for knowledge of the ecological roles of Australia's largest terrestrial predator. From a wide variety of methodological flaws, sampling bias, and experimental design constraints inherent to 38 of the 40 field studies we assessed, we demonstrate that there is presently unreliable and inconclusive evidence for dingoes role as a biodiversity regulator. We also discuss the widespread (both taxonomically and geographically) and direct negative effects of dingoes to native fauna, and the few robust studies investigating their positive roles. In light of the highly variable and context-specific impacts of dingoes on faunal biodiversity and the inconclusive state of the literature, we strongly caution against the positive management of dingoes in the absence of a supporting evidence-base for such action.

Ecological risk assessment of the East Coast Otter Trawl Fishery in the Great Barrier Reef Marine Park: Data report

An ecological risk assessment of the East Coast Otter Trawl Fishery in the Great Barrier Reef Region was undertaken in 2010 and 2011. It assessed the risks posed by this fishery to achieving fishery-related and broader ecological objectives of both the Queensland and Australian governments, including risks to the values and integrity of the Great Barrier Reef World Heritage Area. The risks assessed included direct and indirect effects on the species caught in the fishery as well as on the structure and functioning of the ecosystem. This ecosystem-based approach included an assessment of the impacts on harvested species, by-catch, species of conservation concern, marine habitats, species assemblages and ecosystem processes. The assessment took into account current management arrangements and fishing practices at the time of the assessment. The main findings of the assessment were: Current risk levels from trawling activities are generally low. Some risks from trawling remain. Risks from trawling have reduced in the Great Barrier Reef Region. Trawl fishing effort is a key driver of ecological risk. Zoning has been important in reducing risks. Reducing identified unacceptable risks requires a range of management responses. The commercial fishing industry is supportive and being proactive. Further reductions in trawl by-catch, high compliance with rules and accurate information from ongoing risk monitoring are important. Trawl fishing is just one of the sources of risk to the Great Barrier Reef.

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.

Microbial indicators related to yield and disease and changes in soil microbial community structure with ginger farm management practices

TRFLP (terminal restriction fragment length polymorphism) was used to assess whether management practices that improved disease suppression and/or yield in a 4-year ginger field trial were related to changes in soil microbial community structure. Bacterial and fungal community profiles were defined by presence and abundance of terminal restriction fragments (TRFs), where each TRF represents one or more species. Results indicated inclusion of an organic amendment and minimum tillage increased the relative diversity of dominant fungal populations in a system dependant way. Inclusion of an organic amendment increased bacterial species richness in the pasture treatment. Redundancy analysis showed shifts in microbial community structure associated with different management practices and treatments grouped according to TRF abundance in relation to yield and disease incidence. ANOVA also indicated the abundance of certain TRFs was significantly affected by farming system management practices, and a number of these TRFs were also correlated with yield or disease suppression. Further analyses are required to determine whether identified TRFs can be used as general or soil-type specific bio-indicators of productivity (increased and decreased) and Pythium myriotylum suppressiveness.

Linking spatial stock dynamics and economics: Evaluation of indicators and fishery management for the travelling eastern king prawn (Melicertus plebejus)

Reduced economic circumstances have moved management goals towards higher profit, rather than maximum sustainable yields in several Australian fisheries. The eastern king prawn is one such fishery, for which we have developed new methodology for stock dynamics, calculation of model-based and data-based reference points and management strategy evaluation. The fishery is notable for the northward movement of prawns in eastern Australian waters, from the State jurisdiction of New South Wales to that of Queensland, as they grow to spawning size, so that vessels fishing in the northern deeper waters harvest more large prawns. Bio-economic fishing data were standardized for calibrating a length-structured spatial operating model. Model simulations identified that reduced boat numbers and fishing effort could improve profitability while retaining viable fishing in each jurisdiction. Simulations also identified catch-rate levels that were effective for monitoring in simple within-year effort-control rules. However, favourable performance of catch-rate indicators was achieved only when a meaningful upper limit was placed on total allowed fishing effort. The methods and findings will allow improved measures for monitoring fisheries and inform decision makers on the uncertainty and assumptions affecting economic indicators.