Quantifying responses of ecological communities to bioclimatic gradients

The biotic change along environmental gradients has been the subject of study for well over a century, forming one of the first tools to understand how environment shapes the species and ecosystems that occur. However, gradient studies have historically relied on limited observations on a single transect, limiting their inductive power. Here, I investigate how this limitation can be addressed. I present case studies to illustrate how next-generation transect studies can integrate observations from a wider range of observations of phenotypes, species and communities; together with observations from multiple taxa and gradients. Leaf carbon isotope data from bioclimatic gradients in China, South Australia and Western Australia are integrated to demonstrate a variety of species- and community-level responses to water availability, providing evidence against the previously asserted claim of a simple and universal response. Vegetation data from the same gradient is surveyed with two separate survey methodologies are co-analysed to demonstrate climate is the primary regional determinant of vegetation structure and composition in South Australia, while topographic and edaphic variables are important at a local scale. I find no evidence of ecological disjunctions that may indicate a threshold of vegetation change associated with climate shifts. Comparison of plant and ant species turnover on a spatial gradient suggested that ant communities are ca. 7.5 times more sensitive than plant assemblages to spatial change, providing evidence that future climate change may force community reorganisation and a decoupling of these two taxa, potentially disrupting important interactions and ecosystem function. Well-designed transect studies have the potential to help resolve long-standing questions around the modes of species adaptation to change, as well as improving our understanding of how climate change will shape ecosystems in to the futureThesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Biological Sciences, 201

Advancing DNA barcoding and metabarcoding applications for plants requires systematic analysis of herbarium collections-an Australian perspective

Building DNA barcode databases for plants has historically been ad hoc, and often with a relatively narrow taxonomic focus. To realize the full potential of DNA barcoding for plants, and particularly its application to metabarcoding for mixed-species environmental samples, systematic sequencing of reference collections is required using an augmented set of DNA barcode loci, applied according to agreed data generation and analysis standards. The largest and most complete reference collections of plants are held in herbaria. Australia has a globally significant flora that is well sampled and expertly curated by its herbaria, coordinated through the Council of Heads of Australasian Herbaria. There exists a tremendous opportunity to provide a comprehensive and taxonomically robust reference database for plant DNA barcoding applications by undertaking coordinated and systematic sequencing of the entire flora of Australia utilizing existing herbarium material. In this paper, we review the development of DNA barcoding and metabarcoding and consider the requirements for a robust and comprehensive system. We analyzed the current availability of DNA barcode reference data for Australian plants, recommend priority taxa for database inclusion, and highlight future applications of a comprehensive metabarcoding system. We urge that large-scale and coordinated analysis of herbarium collections be undertaken to realize the promise of DNA barcoding and metabarcoding, and propose that the generation and curation of reference data should become a national investment priority

Designing environmental research for impact

Transdisciplinary research, involving close collaboration between researchers and the users of research, has been a feature of environmental problem solving for several decades, often spurred by the need to find negotiated outcomes to intractable problems. In 2005, the Australian government allocated funding to its environment portfolio for public good research, which resulted in consecutive four-year programmes (Commonwealth Environmental Research Facilities, National Environmental Research Program). In April 2014, representatives of the funders, researchers and research users associated with these programmes met to reflect on eight years of experience with these collaborative research models.This structured reflection concluded that successful multi-institutional transdisciplinary research is necessarily a joint enterprise between funding agencies, researchers and the end users of research. The design and governance of research programmes need to explicitly recognise shared accountabilities among the participants, while respecting the different perspectives of each group. Experience shows that traditional incentive systems for academic researchers, current trends in public sector management, and loose organisation of many end users, work against sustained transdisciplinary research on intractable problems, which require continuity and adaptive learning by all three parties. The likelihood of research influencing and improving environmental policy and management is maximised when researchers, funders and research users have shared goals; there is sufficient continuity of personnel to build trust and sustain dialogue throughout the research process from issue scoping to application of findings; and there is sufficient flexibility in the funding, structure and operation of transdisciplinary research initiatives to enable the enterprise to assimilate and respond to new knowledge and situations

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Corrected by: Erratum: Introducing BASE: The Biomes of Australian Soil Environments soil microbial diversity database [GigaScience. 5, 1, (2016) (1-11)] DOI: 10.1186/s13742-016-0126-5. In GigaScience 6(5):1, the authorship list should have included Leon Court, who was responsible for sample collection and preparation, sampling design and sequencing method design. The authors regret this omission.BACKGROUND Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function. FINDINGS BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project’s data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the ‘Atlas of Living Australia’. CONCLUSIONS Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.Andrew Bissett, Anna Fitzgerald, Thys Meintjes, Pauline M. Mele, Frank Reith, Paul G. Dennis, Martin F. Breed, Belinda Brown, Mark V. Brown, Joel Brugger, Margaret Byrne, Stefan Caddy-Retalic, Bernie Carmody, David J. Coates, Carolina Correa, Belinda C. Ferrari, Vadakattu V. S. R. Gupta, Kelly Hamonts, Asha Haslem, Philip Hugenholtz, Mirko Karan, Jason Koval, Andrew J. Lowe, Stuart Macdonald, Leanne McGrath, David Martin, Matt Morgan, Kristin I. North, Chanyarat Paungfoo-Lonhienne, Elise Pendall, Lori Phillips, Rebecca Pirzl, Jeff R. Powell, Mark A. Ragan, Susanne Schmidt, Nicole Seymour, Ian Snape, John R. Stephen, Matthew Stevens, Matt Tinning, Kristen Williams, Yun Kit Yeoh, Carla M. Zammit, and Andrew Youn

Bioclimatic transect networks: Powerful observatories of ecological change

Transects that traverse substantial climate gradients are important tools for climate change research and allow questions on the extent to which phenotypic variation associates with climate, the link between climate and species distributions, and variation in sensitivity to climate change among biomes to be addressed. However, the potential limitations of individual transect studies have recently been highlighted. Here, we argue that replicating and networking transects, along with the introduction of experimental treatments, addresses these concerns. Transect networks provide cost-effective and robust insights into ecological and evolutionary adaptation and improve forecasting of ecosystem change. We draw on the experience and research facilitated by the Australian Transect Network to demonstrate our case, with examples, to clarify how population- and community-level studies can be integrated with observations from multiple transects, manipulative experiments, genomics, and ecological modeling to gain novel insights into how species and systems respond to climate change. This integration can provide a spatiotemporal understanding of past and future climate-induced changes, which will inform effective management actions for promoting biodiversity resilience

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Background: Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The 'Biomes of Australian Soil Environments' (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function. Findings: BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project's data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the 'Atlas of Living Australia'. Conclusions: Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services

Floristic and structural assessment of Australian rangeland vegetation with standardized plot-based surveys.

We describe and correlate environmental, floristic and structural vegetation traits of a large portion of Australian rangelands. We analysed 351 one hectare vegetation plots surveyed by Australia's Terrestrial Ecosystem Research Network (TERN) using the AusPlots Rangelands standardized method. The AusPlots Rangelands method involves surveying 1010 one meter-spaced point-intercepts (IPs) per plot. At each IP, species were scored, categorised by growth-form, converted to percentage cover as the input for the plot x species matrix. Vegetation structure is depicted by growth-form configuration and relative importance. The floristic and structural distance matrices were correlated with the Mantel test. Canonical correspondence analysis (CCA) related floristic composition to environmental variables sourced from WorldClim, the Atlas of Living Australia and TERN's Soil and Landscape Grid. Differences between clusters were tested with ANOVA while principal component analysis (PCA) ordered the plots within the environmental space. Our plot x species matrix required segmentation due to sparsity and high β-diversity. Based on the ordination of plots latitude within environmental space, the matrix was segmented into three "superclusters": the winter rain and temperate Mediterranean, the monsoonal rain savannas and the arid deserts. Further classification, with the UPGMA linkage method, generated two, four and five clusters, respectively. All groupings are described by species richness, diversity indices and growth form conformation. Several floristic disjunctions were apparent and their possible causes are discussed. For all superclusters, the correspondence between the floristic and the structural or growth form matrices was statistically significant. CCA ordination clearly demarcated all groupings. Aridity, rainfall, temperature, seasonality, soil nitrogen and pH are significant correlates to the ordination of superclusters and clusters. At present, our results are influenced by incomplete sampling. As more sites are surveyed, this pioneer analysis will be updated and refined providing tools for the effective management of Australian rangelands

Components of leaf-trait variation along environmental gradients

•Leaf area (LA), mass per area (LMA), nitrogen per unit area (Narea) and the leaf-internal to ambient CO2 ratio (χ) are fundamental traits for plant functional ecology and vegetation modelling. Here we aimed to assess how their variation, within and between species, tracks environmental gradients. •Measurements were made on 705 species from 116 sites within a broad north–south transect from tropical to temperate Australia. Trait responses to environment were quantified using multiple regression; within- and between-species responses were compared using analysis of covariance and trait-gradient analysis. •Leaf area, the leaf economics spectrum (indexed by LMA and Narea) and χ (from stable carbon isotope ratios) varied almost independently among species. Across sites, however, χ and LA increased with mean growing-season temperature (mGDD0) and decreased with vapour pressure deficit (mVPD0) and soil pH. LMA and Narea showed the reverse pattern. Climate responses agreed with expectations based on optimality principles. Within-species variability contributed 90% for χ, with LMA and Narea intermediate. •These findings support the hypothesis that acclimation within individuals, adaptation within species and selection among species combine to create predictable relationships between traits and environment. However, the contribution of acclimation/adaptation vs species selection differs among traits