Dominant drivers of seedling establishment in a fire-dependent obligate seeder: climate or fire regimes?

Climate change is causing fire regime shifts in ecosystems worldwide. Plant species with regeneration strategies strongly linked to a fire regime, such as obligate seeders, may be particularly threatened by these changes. It is unclear whether changes in fire regimes or the direct effects of climate change will be the dominant threats to obligate seeders in future. We investigated the relative importance of fire-related variables (fire return interval andfire severity) and environmental factors (climate and topography) on seedling establishment in the world's tallest angiosperm, an obligate seeder, Eucalyptus regnans. Throughout its range, this species dominates the wet montane forests of south-eastern Australia and plays a keystone role in forest structure. Following major wildfires, we investigated seedling establishment in E. regnanswithin 1 year of fire as this is a critical stage in the regeneration niche of obligate seeders. Seedling presence and abundance were strongly related to the occurrence of fire but not to variation in fire severity (moderate vs. high severity). Seedling abundance increased with increasing fire return interval (range 26-300 years). First-year seedling establishment was also strongly associated with low temperatures and with high elevations, high precipitation and persistent soil water availability. Our results show that both climate and fire regimes are strong drivers of E. regnans seedling establishment. The predicted warming and drying of the climate might reduce the regeneration potential for some obligate seeders in future and these threats are likely to be compounded by changes in fire regimes, particularly increases in fire frequency.

The dynamic regeneration niche of a forest following a rare disturbance event

Aim: Knowledge of how climate and fire regimes affect regeneration in foundation species is critical to the conservation of entire ecosystems. Different stages of regeneration often require different ecological conditions, but dynamic constraints on regeneration are poorly known for species that regenerate only after infrequent wildfires. Focussing on a long-lived, foundation tree species (Eucalyptus regnans), we tested the hypothesis that the relative importance of fire regime variables (fire severity and time since previous fire) and environmental gradients on post-fire regeneration would shift as seedlings developed. Location: South-eastern Australia. Methods: Following a large (> 59,000 ha) summer wildfire in 2009, we sampled 131 sites (61 burnt) annually for four years (2009-2012), representing the range of environmental conditions in which E. regnans occurs. We analysed the effect of fire severity, time since fire and environmental variables on early regeneration processes critical for post-fire species distributions: seedling establishment, seedling density and growth through different height stages (10 cm, 25 cm, 50 cm and 200 cm). Results: The regeneration niche of E. regnans was defined by different factors at different stages of development. Initially, seedlings established prolifically on burnt sites, regardless of severity. Three years into the regeneration process, high-severity fire became the dominant driver of seedling persistence and growth over 25 cm. Growth over 50 cm was dependent on environmental conditions relating to elevation and precipitation. Main conclusions: Our results describe how fire occurrence, fire severity and environmental gradients affected seedling establishment, persistence and growth. The dynamic constraints on regeneration likely reflect temporal changes in the biotic and abiotic environment and variation in resource requirements during the early post-fire years. Our findings will enable more accurate forecasts of species distributions to assist forest conservation in the face of global changes in climate and fire regimes.

Interacting amino acid preferences of 3D pattern pairs at the binding sites of transient and obligate protein complexes

To assess the physico-chemical characteristics of protein-protein interactions, protein sequences and overall structural folds have been analyzed previously. To highlight this, discovery and examination of amino acid patterns at the binding sites defined by structural proximity in 3-dimensional (3D) space are essential. In this paper, we investigate the interacting preferences of 3D pattern pairs discovered separately in transient and obligate protein complexes. These 3D pattern pairs are not necessarily sequence-consecutive, but each residue in two groups of amino acids from two proteins in a complex is within certain °A threshold to most residues in the other group. We develop an algorithm called AA-pairs by which every pair of interacting proteins is represented as a bipartite graph, and it discovers all maximal quasi-bicliques from every bipartite graph to form our 3D pattern pairs. From 112 and 2533 highly conserved 3D pattern pairs discovered in the transient and obligate complexes respectively, we observe that Ala and Leu is the highest occuring amino acid in interacting 3D patterns of transient (20.91%) and obligate (33.82%) complexes respectively. From the study on the dipeptide composition on each side of interacting 3D pattern pairs, dipeptides Ala-Ala and Ala-Leu are popular in 3D patterns of both transient and obligate complexes. The interactions between amino acids with large hydrophobicity difference are present more in the transient than in the obligate complexes. On contrary, in obligate complexes, interactions between hydrophobic residues account for the top 5 most occuring amino acid pairings.

Kin selection, not group augmentation, predicts helping in an obligate cooperatively breeding bird

Kin selection theory has been the central model for understanding the evolution of cooperative breeding, where non-breeders help bear the cost of rearing young. Recently, the dominance of this idea has been questioned; particularly in obligate cooperative breeders where breeding without help is uncommon and seldom successful. In such systems, the direct benefits gained through augmenting current group size have been hypothesized to provide a tractable alternative (or addition) to kin selection. However, clear empirical tests of the opposing predictions are lacking. Here, we provide convincing evidence to suggest that kin selection and not group augmentation accounts for decisions of whether, where and how often to help in an obligate cooperative breeder, the chestnut-crowned babbler (Pomatostomus ruficeps). We found no evidence that group members base helping decisions on the size of breeding units available in their social group, despite both correlational and experimental data showing substantial variation in the degree to which helpers affect productivity in units of different size. By contrast, 98 per cent of group members with kin present helped, 100 per cent directed their care towards the most related brood in the social group, and those rearing half/full-sibs helped approximately three times harder than those rearing less/non-related broods. We conclude that kin selection plays a central role in the maintenance of cooperative breeding in this species, despite the apparent importance of living in large groups.

Salicylic acid suppression of clubroot in broccoli (Brassicae oleracea var. italica) caused by the obligate biotroph Plasmodiophora brassicae

The obligate soil-borne biotroph Plasmodiophora brassicae has a significant economic impact on Brassicaceae crops. The pathogen severely disrupts the roots by inducing the production of galls which leads to malformation and reduced growth of the roots and a reduced ability to take up water and nutrients. Control of P. brassicae is difficult because it has a number of survival and dissemination strategies that involve both motile and resting stages that need to be targeted by any control agent. We investigated, under controlled conditions and in glasshouse and field experiments, the potential of salicylic acid (SA), a key phytohormone, that is required for defence against certain biotic and abiotic stresses, to reduce infection by P. brassicae in broccoli (Brassicae oleracea var. italica). Under controlled conditions in a growth cabinet exogenous application of SA to roots resulted in its transport systemically to the leaves where it promoted the up-regulation of the pathogenesis related genes PR-1 and PR-2 in an SAR-like response as early as 24 h post-treatment. Concentrations of SA >20 mM reduced significantly both shoot and root weights when applied exogenously but lower concentrations had little measureable effect on plant growth. When SA was applied to plants above 5 mM there was a significant reduction (25-65 %) in gall formation 6 weeks post-inoculation with P. brassicae, indicating that the pathogen was being controlled by the addition of SA. A combination of SA and JA was also shown to reduce severity (25-35 %) of disease associated with P. brassicae. These findings indicate that there may be SA inducible mechanisms in B. oleracea that if fine-tuned could provide enhanced resistance to clubroot disease.

Urban to forest gradients: suitability for hollow bearing trees and implications for obligate hollow nesters

 Resource availability is a limiting factor influencing the distribution and composition of faunal communities. Globally, hollow bearing trees are a resource required by wildlife at all trophic levels, and are used for a diverse range of ecological functions. In the northern hemisphere avian species act as primary hollow excavators, whereas the southern hemisphere must rely on complex interactions between stochastic events, and eventual decay. Hollow formation is therefore a slow process in the southern hemisphere. In contrast, hollow loss is quite rapid and influenced greatly by anthropogenic impacts.To identify the ecological characteristics driving hollows over an urban to forest gradient as a resource for the powerful owl (Ninox strenua) and its prey we used presence-only modelling. The potential for an area to support tree hollows suitable for powerful owls and their prey was linked to the density of ephemeral rivers, land cover, tree cover and distance from riparian vegetation. The potential for large hollows throughout the landscape, suitable for the powerful owl, was also influenced by density of permanent rivers. Potential habitat for tree hollows, capable of supporting powerful owls and their prey was greatest in forested environments, declining with increased urbanization. However the urban region still supported some smaller tree hollows suitable for arboreal marsupials. Managing for urban dwelling species, is not as simple as retaining old hollow producing trees or providing alternate nesting structures. We also need to mitigate increased mortality associated with built environments (e.g. electrocution, collisions).

Breeding habitat selection in an obligate beach bird: a test of the food resource hypothesis

The food resource hypothesis of breeding habitat selection in beach-nesting birds suggests that birds breed at sites with more prey to meet the increased energetic requirements associated with breeding. We compare prey resources using pitfall traps and core samples at breeding sites and absence sites of the eastern population of hooded plover, Thinornis rubricollis rubricollis, which, in this part of its range, is a threatened obligate beach bird. Breeding sites had higher abundances, equivalent species richness, and different assemblages of invertebrate prey compared with absence sites. Assemblages at breeding sites were characterised by more isopods, and fewer beetles of the family Phycosecidae. Breeding habitat selection by plovers appears to be associated with selection for sites with more food, and any process that degrades food resources at a site (e.g. kelp harvesting or marine pollution events) may reduce the likelihood of occupancy of that site by breeding birds.

An obligate beach bird selects sub-, inter- and supra-tidal habitat elements

Few habitat models are available for widespread, obligate, high-energy sandy shore vertebrates, such as the Eastern Hooded Plover Thinornis cucullatus cucullatus. We examined habitat attributes which determined the difference between sites where plovers breed and randomly-selected absence sites (determined from long-term systematic monitoring). A variety of habitat variables were derived from aerial photography and bathymetric and terrestrial Light Detection And Ranging (LiDAR) data. Logistic regression against eight candidate variables, in a model selection framework, revealed considerable support for four variables with respect to explaining the presence of breeding territories. In particular, the amount of unvegetated dune and foredune which was unvegetated, and the amount of intertidal and sub-tidal reef were positively associated with the presence of breeding territories. Thus, plovers apparently select certain habitat in which to breed, involving sub-tidal, intertidal and supra-tidal habitat elements. The model also helps explain the virtual absence of breeding plovers from long sections of superficially suitable habitat, such as the fourth longest continuous beach in the world.

Reproductive cycle of Urolophus cruciatus in south-eastern Australia: does the species exhibit obligate or facultative diapause?

Observations of synchronous rapid growth of embryos and ovarian follicles in pregnant females during the half-year December–May leading to parturition, ovulation, mating, and fertilization suggest Urolophus cruciatus has the capacity for an annual reproductive cycle. Conversely, the higher proportion of the pregnant females in the population carrying eggs than carrying embryos in utero during December–May and all pregnant females in the population only carrying eggs in utero during June–November indicate a longer reproductive cycle. Analysis based on the usual assumptions implies that the species most likely exhibits a biennial cycle with ~18-month period of diapause following ovulation prior to ~6-month period of rapid embryogenesis. However, it is feasible that the period of the cycle is triennial with ~30-month period of diapause or alternatively diapause varies among individuals and varies from year to year. Rather than exhibiting a fixed-term reproductive cycle where obligatory diapause leads to parturition timed every year to provide favourable conditions for neonates, as suggested for several other chondrichthyan species, U. cruciatus may exhibit facultative diapause where the period of diapause and hence the reproductive cycle varies depending on the prevailing environmental conditions or density-dependent factors as described for many terrestrial species. U. cruciatus is highly matrotrophic (>4000 % wet mass gain from ovum to full-term embryo), litter size (1–4) increases with maternal length, sex ratio among embryos is 1:1, and male breeding condition varies seasonally with peak sperm production coinciding with female ovulation.

DDT and metabolites residues in the southern bent-wing bat (Miniopterus schreibersii bassanii) of south-eastern Australia

The southern bent-wing bat (Miniopterus schreibersii bassanii) is an insectivorous, obligate cave dwelling species found in south-eastern South Australia and western Victoria, Australia. In recent times, the finger of blame for an apparent population decline at Bat Cave, Naracoorte (one of only two known maternity roosts for this species, the other being Starlight Cave, Warrnambool) has been pointed at pesticide use in the region, following the finding of organochlorine and organophosphate insecticide residues in bat guano. This study sampled juvenile southern bent-wing bats from Bat Cave and Starlight Cave, and determined DDT, DDD and DDE concentrations in liver, pectoral muscle, brain and back-depot fat tissues.

CIDB: Chlamydia Interactive Database for cross-querying genomics, transcriptomics and proteomics data

Chlamydiae are important pathogens of humans, birds and a wide range of animals. They are a unique group of bacteria, characterized by their developmental cycle. Chlamydia has been difficult to study because of their obligate intracellular growth habit and lack of a genetic transformation system. However, the past 5 years has seen the full genome sequencing of seven strains of Chlamydia and a rapid expansion of genomic, transcriptomic (RT-PCR, microarray) and proteomic analysis of these pathogens. The Chlamydia Interactive Database (CIDB) described here is the first database of its type that holds genomic, RT-PCR, microarray and proteomics data sets that can be cross-queried by researchers for patterns in the data. Combining the data of many research groups into a single database and cross-querying from different perspectives should enhance our understanding of the complex cell biology of these pathogens. The database is available at: http://www3.it.deakin.edu.au:8080/CIDB/.

Investigation of plasmodiophora brassicae (clubroot disease) in vegetable brassica using arabidopsis thaliana as a model system

Clubroot, caused by Plasmodiophora brassicae, is the most devastating soil-borne disease of vegetable brassicas. It occurs all over the world and is responsible for crop losses of up to 10% every year. In Australia, the disease is being managed effectively with chemicals and cultural practices, but ideally control can be improved in the long term by the introduction of resistant cultivars. The life cycle ofP. brassicae and mode of action of plant resistance has not been fully elucidated because of the technical difficulties of working with an obligate, soil-borne plant pathogen. However, Arabidopsis thaliana, which is a host ofP. brassicae, has great potential as a model system for studying the life cycle, the infection process and development of resistance. We have developed a sand-liquid-culture system for growing Arabidopsis that allows easy observation of all life stages and, most importantly, the primary plasmodial stages within the root hair. The method was first optimised for observations of the lifecycle of the pathogen in a susceptible Arabidopsis ecotype (Col-3) where all stages of the lifecycle have now been observed and characterised. Further screening of Arabidopsis ecotypes for disease resistance has utilised one of the most virulent Australian pathotypes of brassica (ECD number 16/19/31). To date, Arabidopsis ecotype Ta-0 has shown a level of tolerance to the disease even though the roots get infected. It has been reported earlier that resistance toP. brassicae in Arabidopsis is due to one or a small number of genes. To examine changes in gene expression during the early, critical stages of infection, RNA was extracted from the susceptible and resistant ecotypes at two time points, 4 days and 17 days after inoculation. Microarray analysis will be used to investigate genome wide changes in gene expression during infection but also to identify candidate genes that may confer resistance to Australian isolates of the pathogen.

Comparison of life-history characteristics of island and mainland populations of the swamp antechinus

The reproductive ecology of the swamp antechinus Antechinus minimus, a small dasyurid (Dasyuridae) marsupial with obligate male semelparity, was investigated in populations inhabiting the mainland coast and on a nearby offshore island in south-eastern Australia. The size and sex ratios of litters, individual body mass and size, timing of births and female longevity were determined from live-trapped animals. The island population had significantly smaller litter sizes and greater adult body mass in comparison with the mainland population. This is consistent with features of the ‘island syndrome’, which predicts directional selection for these traits in high-density populations with reduced extrinsic mortality. However, inter-annual variability in litter sizes in the island population suggests that litter size is more responsive to fluctuating local conditions, such as population density, which is likely to affect food availability, rather than directional genetic changes. In contrast with other antechinus species, biased sex ratios were not evident. In addition, large variations of the timing of births were estimated at both sites and these appear to be related to seasonal conditions such as autumn rainfall and female body mass before mating.

Jellyfish aggregations and leatherback turtle foraging patterns in a temperate coastal environment

Leatherback turtles (Dermochelys coriacea) are obligate predators of gelatinous zooplankton. However, the spatial relationship between predator and prey remains poorly understood beyond sporadic and localized reports. To examine how jellyfish (Phylum Cnidaria: Orders Semaeostomeae and Rhizostomeae) might drive the broad-scale distribution of this wide ranging species, we employed aerial surveys to map jellyfish throughout a temperate coastal shelf area bordering the northeast Atlantic. Previously unknown, consistent aggregations of Rhizostoma octopus extending over tens of square kilometers were identified in distinct coastal “hotspots” during consecutive years (2003–2005). Examination of retrospective sightings data (>50 yr) suggested that 22.5% of leatherback distribution could be explained by these hotspots, with the inference that these coastal features may be sufficiently consistent in space and time to drive long-term foraging associations.

Climate-driven impacts of prey abundance on the population structure of a tropical aquatic predator

In the present study we explore how annual variation in climate (late wet-season rainfall) affects population demography in a gape-limited obligate piscivorous predator, the Arafura filesnake Acrochordus arafurae in the Australian tropics. These aquatic snakes display extreme sexual dimorphism, with body sizes and relative head sizes of females much larger than those of males. Two consecutive years with low rainfall during the late wet season reduced the abundance of small but not large sized fish. Although snake residual body mass (RBM, calculated from a general linear regression of ln-transformed mass to ln-SVL) decreased after the first year with low prey availability, it was not until the second year that reduced prey abundance caused a dramatic decline in filesnake survival, and hence in population numbers. Thus, our results suggest that most snakes survived the first year of reduced prey abundance, but a successive year with low prey availability proved fatal for many animals. However, the effects of prey scarcity on RBM and survival fell disproportionately on some size classes of snakes. Medium-sized animals (large males and intermediate-sized females) were affected more dramatically than were small or large snakes. We attribute the higher survival of small snakes to their lower energy needs compared to medium-sized individuals, and the higher survival of large snakes to the continued abundance of large prey (mainly large catfish). Two successive years with low abundance of smaller sized prey thus massively modified the size-structure of the filesnake population, virtually eliminating large males and intermediate-sized females. Our field data provide a clear demonstration of the ways in which stochastic variation in climatic conditions can have dramatic effects on predator population demography, mediated via effects on prey availability.