Bacterial and fungal community composition over time in chicken litter with high or low moisture content

1. Changes in bacterial and fungal communities in chicken litter with high and low moisture content over a five week period during a single chicken grow out cycle in a poultry shed in subtropical Australia were investigated to study the association between specific microbes and odour production. 2. Microbial biomass, as indicated by DNA yields, was higher and community composition was more dynamic over time in moist compared with dry chicken litter. 3. Bacillus, Atopostipes and Aspergillus species increased in relative abundance in moist chicken litter samples over time reflecting the relatively high fitness and hence activity of these specific bacteria and this specific fungus in this environment.

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.

Environmental and fishing effects on the dynamics of brown tiger prawn (Penaeus esculentus) in Moreton Bay (Australia)

This analysis of the variations of brown tiger prawn (Penaeus esculentus) catch in Moreton Bay multispecies trawl fishery estimated catchability using a delay difference model. It integrated several factors responsible for variations in catchability: targeting of fishing effort, increasing fishing power and changing availability. An analysis of covariance was used to define fishing events targeted at brown tiger prawns. A general linear model estimated inter-annual variations of fishing power. Temperature-induced changes in prawn behaviour played an important role on the dynamics of this fishery. Maximum likelihood estimates of targeted catchability (4.09 ± 0.42 × 10−4 boat-day−1) were twice as large as non-targeted catchability (1.86 ± 0.25 × 10−4 boat-day−1). The causes of recent declines in fishing effort in this fishery were discussed.

Can soil nematode community structure be used to indicate soil carbon dynamics in horticultural systems?

There is a need to develop indicators that relate the dynamics of soil organic carbon (SOC) with changes in land management of horticultural production systems. Soil nematode communities have been shown to be sensitive to land management changes, but often do not include plant-parasites in the calculation of soil nematode community indices. The concept of nematode functional guilds was used to estimate the proportion of carbon entering the soil ecosystem through different channels, such as through decomposition of organic material, the detrital channel, through the roots of plants, the root channel or recycled through the activity of predators, a predation channel. Calculations of the indices were developed and validated using case studies in the north Queensland banana industry. Firstly, a survey of organic and conventional banana farms found a greater proportion of C entering the soil ecosystem through the detrital channel and a reduced proportion of C originating through the root channel at the organic sites relative to conventional sites. Secondly, a field experiment comparing compost amendments, found application of fresh compost significantly increased the proportion of C entering the soil ecosystem through the detrital channel and decreased proportion of C originating from the root channel. Thirdly, a field experiment comparing 'conventional' banana production to an 'alternative' system which incorporated organic matter, found the proportion of C entering the soil ecosystem through the root channel was significantly greater in the conventional systems relative to the alternative system. This research demonstrates that nematode indices can be used to assess horticultural systems, by indicating the origins of SOC.

Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing

Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria , Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression. © 2014 Penton et al.

Deriving optimal fishing effort for managing Australia's Moreton Bay multispecies trawl fishery with aggregated effort data

Deriving an estimate of optimal fishing effort or even an approximate estimate is very valuable for managing fisheries with multiple target species. The most challenging task associated with this is allocating effort to individual species when only the total effort is recorded. Spatial information on the distribution of each species within a fishery can be used to justify the allocations, but often such information is not available. To determine the long-term overall effort required to achieve maximum sustainable yield (MSY) and maximum economic yield (MEY), we consider three methods for allocating effort: (i) optimal allocation, which optimally allocates effort among target species; (ii) fixed proportions, which chooses proportions based on past catch data; and (iii) economic allocation, which splits effort based on the expected catch value of each species. Determining the overall fishing effort required to achieve these management objectives is a maximizing problem subject to constraints due to economic and social considerations. We illustrated the approaches using a case study of the Moreton Bay Prawn Trawl Fishery in Queensland (Australia). The results were consistent across the three methods. Importantly, our analysis demonstrated the optimal total effort was very sensitive to daily fishing costs—the effort ranged from 9500–11 500 to 6000–7000, 4000 and 2500 boat-days, using daily cost estimates of $0, $500, $750, and $950, respectively. The zero daily cost corresponds to the MSY, while a daily cost of $750 most closely represents the actual present fishing cost. Given the recent debate on which costs should be factored into the analyses for deriving MEY, our findings highlight the importance of including an appropriate cost function for practical management advice. The approaches developed here could be applied to other multispecies fisheries where only aggregated fishing effort data are recorded, as the literature on this type of modelling is sparse.

Satisfaction with fishing and the desire to leave

Predicting who may leave a fishery is an important consideration when designing capacity reduction programs to enhance both ecological and economic sustainability. In this paper, the relationship between satisfaction and the desire to exit a fishery is examined for the Queensland East Coast Trawl fishery. Income from fishing, and changes in income over the last 5 years, were key factors affecting overall satisfaction. Relative income per se was not a significant factor, counter to most satisfaction studies. Continuing a family tradition of fishing and, for one group, pride in being a fisher was found to be significant. Satisfaction with fishing overall and the challenge of fishing were found to be the primary drivers of the desire to stay or leave the fishery. Surprisingly, public perceptions of fishing, trust in management and perceptions of equity in resource allocation did not significantly affect overall satisfaction or the desire to exit the fishery.

Selecting and assessing social objectives for Australian fisheries management

This paper details Australian research that developed tools to assist fisheries managers and government agencies in engaging with the social dimension of industry and community welfare in fisheries management. These tools are in the form of objectives and indicators. These highlight the social dimensions and the effects of management plans and policy implementation on fishing industries and associated communities, while also taking into account the primacy of ecological imperatives. The deployment of these objectives and indicators initially provides a benchmark and, over the life of a management plan, can subsequently be used to identify trends in effects on a variety of social and economic elements that may be objectives in the management of a fishery. It is acknowledged that the degree to which factors can be monitored will be dependent upon resources of management agencies, however these frameworks provide a method for effectively monitoring and measuring change in the social dimension of fisheries management.Essentially, the work discussed in this paper provides fisheries management with the means to both track and begin to understand the effects of government policy and management plans on the social dimension of the fishing industry and its associated communities. Such tools allow the consideration of these elements, within an evidence base, into policy arrangements, and consequently provide an invaluable contribution to the ability to address resilience and sustainability of fishing industries and associated communities.

Flying-foxes in the Australian urban environment - community attitudes and opinions

The urban presence of flying-foxes (pteropid bats) in eastern Australia has increased in the last 20 years, putatively reflecting broader landscape change. The influx of large numbers often precipitates community angst, typically stemming from concerns about loss of social amenity, economic loss or negative health impacts from recently emerged bat-mediated zoonotic diseases such as Hendra virus and Australian bat lyssavirus. Local authorities and state wildlife authorities are increasingly asked to approve the dispersal or modification of flying-fox roosts to address expressed concerns, yet the scale of this concern within the community, and the veracity of the basis for concern are often unclear. We conducted an on-line survey to capture community attitudes and opinions on flying-foxes in the urban environment to inform management policy and decision-making. Analysis focused on awareness, concerns, and management options, and primarily compared responses from communities where flying-fox management was and was not topical at the time of the survey. While a majority of respondents indicated a moderate to high level of knowledge of both flying-foxes and Hendra virus, a substantial minority mistakenly believed that flying-foxes pose a direct infection risk to humans, suggesting miscommunication or misinformation, and the need for additional risk communication strategies. Secondly, a minority of community members indicated they were directly impacted by urban roosts, most plausibly those living in close proximity to the roost, suggesting that targeted management options are warranted. Thirdly, neither dispersal nor culling was seen as an appropriate management strategy by the majority of respondents, including those from postcodes where flying-fox management was topical. These findings usefully inform community debate and policy development and demonstrate the value of social analysis in defining the issues and options in this complex human - wildlife interaction. The mobile nature of flying-foxes underlines the need for a management strategy at a regional or larger scale, and independent of state borders.

Fauna community trends during early restoration of alluvial open forest/woodland ecosystems on former agricultural land

Vertebrate fauna was studied over 10 years following revegetation of a Eucalyptus tereticornis ecosystem on former agricultural land. We compared four vegetation types: remnant forest, plantings of a mix of native tree species on cleared land, natural regeneration of partially cleared land after livestock removal, and cleared pasture land with scattered paddock trees managed for livestock production. Pasture differed significantly from remnant in both bird and nonbird fauna. Although 10 years of ecosystem restoration is relatively short term in the restoration process, in this time bird assemblages in plantings and natural regeneration had diverged significantly from pasture, but still differed significantly from remnant. After 10 years, 70 and 66% of the total vertebrate species found in remnant had been recorded in plantings and natural regeneration, respectively. Although the fauna assemblages within plantings and natural regeneration were tracking toward those of remnant, significant differences in fauna between plantings and natural regeneration indicated community development along different restoration pathways. Because natural regeneration contained more mature trees (dbh > 30 cm), native shrub species, and coarse woody debris than plantings from the beginning of the study, these features possibly encouraged different fauna to the revegetation areas from the outset. The ability of plantings and natural regeneration to transition to the remnant state will be governed by a number of factors that were significant in the analyses, including shrub cover, herbaceous biomass, tree hollows, time since fire, and landscape condition. Both active and passive restoration produced significant change from the cleared state in the short term.

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific. © 2015 Macmillan Publishers Limited.

Developing Jungle Perch Fingerling Production to Improve Fishing Opportunities

This project has for the first time demonstrated the feasibility of hatchery production of jungle perch fingerlings. The research on jungle perch production has enabled a hatchery production manual with accompanying videos to be produced. This has given private commercial hatcheries the information needed to produce jungle perch fingerlings. Several hatcheries have already indicated an interest in producing jungle perch and will be assisted to do so in 2016. Currently jungle perch are not a permitted stocking species, so cannot be sold to fish stocking groups. However, hatcheries will be able to sell fingerlings to the aquarium trade or supply grow out facilities that could produce jungle perch for human consumption. Should jungle perch become a permitted species for stocking, this will provide hatcheries with a major new product option to sell to fish stocking groups. It would also benefit anglers by providing another iconic species for impoundment stocking programs. This could have flow-on benefits to regional economies through angler tourism. Should the pilot reintroductions of jungle perch into streams result in self-sustaining jungle perch populations, then there will be three restored jungle perch populations close to major population centres. This will create a new opportunity for anglers not normally able to target jungle perch. Since the majority of anglers who target jungle perch are catch and release fishers, angling is expected to have minimal impact on recovery of the populations. This project led to the development of a hatchery manual for jungle perch production and to a summary brochure. In late 2014 and in 2015 researchers were able to make the first ever releases of jungle perch fingerlings back into rivers and streams within their historical range.