School of Botany - Research Publications
Now showing items 1-12 of 67
Empirically validating a dense woody regrowth 'problem' and thinning 'solution' for understory vegetation
In landscapes with a short history of intensive land use, woody plant regrowth on cleared land is often favorably received as a shift back to a more natural state. However, it is common for these regrowth stands to be much denser than undisturbed forest. High stem density can adversely affect stand structure, understory composition, and habitat for dependent fauna. Thinning to reduce stem density is one common silvicultural method used to manage dense stands for ecological or restoration objectives. The effect of thinning on the stand structure is well understood but those on the understory vegetation are not. We address this knowledge gap in anticipation of an increasing call for public investment in ‘ecological’ thinning across public and private land. Our case study is from the eucalypt woodlands and forests of central Victoria, Australia, an ecosystem in which dense woody regrowth is common. From a broad survey of 98 sites, spanning a range of stem densities, we explored the effect of density on understory vegetation. High densities of small trees (<20cm DBH) caused the greatest suppression of native and exotic cover and species richness. We compared our observations with benchmarks and found that sites with stem densities exceeding their benchmark had median values approximately one-seventh of the benchmark native understory cover, which was also less than a quarter of the cover of those sites with benchmark or lower stem density. We conducted an additional targeted survey of 11 thinned sites paired with non-thinned sites to evaluate the effects of thinning. We built models combining broad and targeted survey data relating understory response to stem density, thinning, land tenure and environmental covariates. These models predicted that thinning is likely to elicit positive responses from the understory plant community in the short term. This is the desired response from native species, but we caution that thinning can equally favor exotic plant species.
Asparagus Spears as a Model to Study Heteroxylan Biosynthesis during Secondary Wall Development
(PUBLIC LIBRARY SCIENCE, 2015-04-20)
Garden asparagus (Asparagus officinalis L.) is a commercially important crop species utilized for its excellent source of vitamins, minerals and dietary fiber. However, after harvest the tissue hardens and its quality rapidly deteriorates because spear cell walls become rigidified due to lignification and substantial increases in heteroxylan content. This latter observation prompted us to investigate the in vitro xylan xylosyltransferase (XylT) activity in asparagus. The current model system for studying heteroxylan biosynthesis, Arabidopsis, whilst a powerful genetic system, displays relatively low xylan XylT activity in in vitro microsomal preparations compared with garden asparagus therefore hampering our ability to study the molecular mechanism(s) of heteroxylan assembly. Here, we analyzed physiological and biochemical changes of garden asparagus spears stored at 4 °C after harvest and detected a high level of xylan XylT activity that accounts for this increased heteroxylan. The xylan XylT catalytic activity is at least thirteen-fold higher than that reported for previously published species, including Arabidopsis and grasses. A biochemical assay was optimized and up to seven successive Xyl residues were incorporated to extend the xylotetraose (Xyl4) acceptor backbone. To further elucidate the xylan biosynthesis mechanism, we used RNA-seq to generate an Asparagus reference transcriptome and identified five putative xylan biosynthetic genes (AoIRX9, AoIRX9-L, AoIRX10, AoIRX14_A, AoIRX14_B) with AoIRX9 having an expression profile that is distinct from the other genes. We propose that Asparagus provides an ideal biochemical system to investigate the biochemical aspects of heteroxylan biosynthesis and also offers the additional benefit of being able to study the lignification process during plant stem maturation.
The Apical Complex Provides a Regulated Gateway for Secretion of Invasion Factors in Toxoplasma
(PUBLIC LIBRARY SCIENCE, 2014-04-01)
The apical complex is the definitive cell structure of phylum Apicomplexa, and is the focus of the events of host cell penetration and the establishment of intracellular parasitism. Despite the importance of this structure, its molecular composition is relatively poorly known and few studies have experimentally tested its functions. We have characterized a novel Toxoplasma gondii protein, RNG2, that is located at the apical polar ring--the common structural element of apical complexes. During cell division, RNG2 is first recruited to centrosomes immediately after their duplication, confirming that assembly of the new apical complex commences as one of the earliest events of cell replication. RNG2 subsequently forms a ring, with the carboxy- and amino-termini anchored to the apical polar ring and mobile conoid, respectively, linking these two structures. Super-resolution microscopy resolves these two termini, and reveals that RNG2 orientation flips during invasion when the conoid is extruded. Inducible knockdown of RNG2 strongly inhibits host cell invasion. Consistent with this, secretion of micronemes is prevented in the absence of RNG2. This block, however, can be fully or partially overcome by exogenous stimulation of calcium or cGMP signaling pathways, respectively, implicating the apical complex directly in these signaling events. RNG2 demonstrates for the first time a role for the apical complex in controlling secretion of invasion factors in this important group of parasites.
Interspecific variation in the phenology of advertisement calling in a temperate Australian frog community
Spatial and temporal partitioning of resources underlies the coexistence of species with similar niches. In communities of frogs and toads, the phenology of advertisement calling provides insights into temporal partitioning of reproductive effort and its implications for community dynamics. This study assessed the phenology of advertisement calling in an anuran community from Melbourne, in southern Australia. We collated data from 1432 surveys of 253 sites and used logistic regression to quantify seasonality in the nightly probability of calling and the influence of meteorological variables on this probability for six species of frogs. We found limited overlap in the predicted seasonal peaks of calling among these species. Those shown to have overlapping calling peaks are unlikely to be in direct competition, due to differences in larval ecology (Crinia signifera and Litoria ewingii) or differences in calling behavior and acoustics (Limnodynastes dumerilii and Litoria raniformis). In contrast, closely related and ecologically similar species (Crinia signfera and Crinia parinsignifera;Litoria ewingii and Litoria verreauxii) appear to have staggered seasonal peaks of calling. In combination with interspecific variation in the meteorological correlates of calling, these results may be indicative of temporal partitioning of reproductive activity to facilitate coexistence, as has been reported for tropical and temperate anurans from other parts of the globe.
Detecting Extinction Risk from Climate Change by IUCN Red List Criteria
Anthropogenic climate change is a key threat to global biodiversity. To inform strategic actions aimed at conserving biodiversity as climate changes, conservation planners need early warning of the risks faced by different species. The IUCN Red List criteria for threatened species are widely acknowledged as useful risk assessment tools for informing conservation under constraints imposed by limited data. However, doubts have been expressed about the ability of the criteria to detect risks imposed by potentially slow-acting threats such as climate change, particularly because criteria addressing rates of population decline are assessed over time scales as short as 10 years. We used spatially explicit stochastic population models and dynamic species distribution models projected to future climates to determine how long before extinction a species would become eligible for listing as threatened based on the IUCN Red List criteria. We focused on a short-lived frog species (Assa darlingtoni) chosen specifically to represent potential weaknesses in the criteria to allow detailed consideration of the analytical issues and to develop an approach for wider application. The criteria were more sensitive to climate change than previously anticipated; lead times between initial listing in a threatened category and predicted extinction varied from 40 to 80 years, depending on data availability. We attributed this sensitivity primarily to the ensemble properties of the criteria that assess contrasting symptoms of extinction risk. Nevertheless, we recommend the robustness of the criteria warrants further investigation across species with contrasting life histories and patterns of decline. The adequacy of these lead times for early warning depends on practicalities of environmental policy and management, bureaucratic or political inertia, and the anticipated species response times to management actions.
Localization of iron in rice grain using synchrotron X-ray fluorescence microscopy and high resolution secondary ion mass spectrometry
(ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 2014-03-01)
Cereal crops accumulate low levels of iron (Fe) of which only a small fraction (5–10%) is bioavailable in human diets. Extensive co-localization of Fe in outer grain tissues with phytic acid, a strong chelator of metal ions, results in the formation of insoluble complexes that cannot be digested by humans. Here we describe the use of synchrotron X-ray fluorescence microscopy (XFM) and high resolution secondary ion mass spectrometry (NanoSIMS) to map the distribution of Fe, zinc (Zn), phosphorus (P) and other elements in the aleurone and subaleurone layers of mature grain from wild-type and an Fe-enriched line of rice (Oryza sativa L.). The results obtained from both XFM and NanoSIMS indicated that most Fe was co-localized with P (indicative of phytic acid) in the aleurone layer but that a small amount of Fe, often present as “hotspots”, extended further into the subaleurone and outer endosperm in a pattern that was not co-localized with P. We hypothesize that Fe in subaleurone and outer endosperm layers of rice grain could be bound to low molecular weight chelators such as nicotianamine and/or deoxymugineic acid.
Evidence for land plant cell wall biosynthetic mechanisms in charophyte green algae
(OXFORD UNIV PRESS, 2014-10-01)
BACKGROUND AND AIMS: The charophyte green algae (CGA) are thought to be the closest living relatives to the land plants, and ancestral CGA were unique in giving rise to the land plant lineage. The cell wall has been suggested to be a defining structure that enabled the green algal ancestor to colonize land. These cell walls provide support and protection, are a source of signalling molecules, and provide developmental cues for cell differentiation and elongation. The cell wall of land plants is a highly complex fibre composite, characterized by cellulose cross-linked by non-cellulosic polysaccharides, such as xyloglucan, embedded in a matrix of pectic polysaccharides. How the land plant cell wall evolved is currently unknown: early-divergent chlorophyte and prasinophyte algae genomes contain a low number of glycosyl transferases (GTs), while land plants contain hundreds. The number of GTs in CGA is currently unknown, as no genomes are available, so this study sought to give insight into the evolution of the biosynthetic machinery of CGA through an analysis of available transcriptomes. METHODS: Available CGA transcriptomes were mined for cell wall biosynthesis GTs and compared with GTs characterized in land plants. In addition, gene cloning was employed in two cases to answer important evolutionary questions. KEY RESULTS: Genetic evidence was obtained indicating that many of the most important core cell wall polysaccharides have their evolutionary origins in the CGA, including cellulose, mannan, xyloglucan, xylan and pectin, as well as arabino-galactan protein. Moreover, two putative cellulose synthase-like D family genes (CSLDs) from the CGA species Coleochaete orbicularis and a fragment of a putative CSLA/K-like sequence from a CGA Spirogyra species were cloned, providing the first evidence that all the cellulose synthase/-like genes present in early-divergent land plants were already present in CGA. CONCLUSIONS: The results provide new insights into the evolution of cell walls and support the notion that the CGA were pre-adapted to life on land by virtue of the their cell wall biosynthetic capacity. These findings are highly significant for understanding plant cell wall evolution as they imply that some features of land plant cell walls evolved prior to the transition to land, rather than having evolved as a result of selection pressures inherent in this transition.
Estimating population size in the presence of temporary migration using a joint analysis of telemetry and capture-recapture data
1. Temporary migration - where individuals can leave and re-enter a sampled population - is a feature of many capture-mark-recapture (CMR) studies of mobile populations which, if unaccounted for, can lead to biased estimates of population capture probabilities and consequently biased estimates of population abundance.2. We present a method for incorporating radiotelemetry data within a CMR study to eliminate bias due to temporary migration using a Bayesian state-space model.3. Our results indicate that using a relatively small number of telemetry tags, it is possible to greatly reduce bias in estimates of capture probabilities using telemetry data to model transition probabilities in and out of the sampling area. In a capture-recapture data set for trout Cod in the Murray river, Australia, accounting for temporary migration led to overall higher estimates of capture probabilities than models assuming permanent or zero migration. Also, individual heterogeneity in detectability can be managed through explicit modelling. We show how accounting for temporary migration when estimating capture probabilities can be used to estimate the abundance and size distribution of a population as though it were closed.4. Our model provides a basis for more complex models that might integrate telemetry data into other CMR scenarios, thus allowing for greater precision in estimates of vital rates that might otherwise be biased by temporary migration. Our results highlight the importance of accounting for migration in survey design and parameter estimation, and the potential scope for supplementing large-scale CMR data sets with a subset of auxiliary data that provide information on processes that are hidden to primary sampling processes.