Research infrastructure challenges in preparing essential biodiversity variables data products for alien invasive species

Essential Biodiversity Variables (EBV) are information products for assessing biodiversity change. Species populations EBVs are one class of EBVs that can be used to monitor the spread of invasive species. However, systematic, reliable, repeatable procedures to process primary data into EBVs do not yet exist, and environmental research infrastructures still must improve their capabilities to deliver EBV data products. Here, we tested the ability of two mature biodiversity data infrastructures, the Global Biodiversity Information Facility and the Atlas of Living Australia to cooperatively produce EBV data products for three alien invasive species. We detailed workflow steps to discover, filter, retrieve and prepare the primary data before evaluating species’ distributional changes. The two data infrastructures were able to execute several workflow steps, but external tools, third-party sources and expert judgement were required, and a repeatable workflow was difficult to establish. Nevertheless, the resulting data products revealed strong range expansions for the invasive species, demonstrating the policy-relevant information about global environmental change that can be provided by EBV data products. Our results show that more coordination between infrastructure providers is needed to efficiently produce EBV-ready data products for invasion monitoring in a repeatable fashion. Addressing these issues will allow improved tracking of invasive species range dynamics and hence monitoring of ongoing global biodiversity change

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

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

Spatial ecology of E. australis : habitat selection at multiple scales

This research investigated links between the occurrence of endangered southern right whales and characteristics of their habitat. Habitat selection is based on physical environmental features, with important roles for social cues and site fidelity. This complex interaction of factors affects spatial recovery capacity and presents challenges for conservation management

Southern right whale (Eubalaena australis) mortalities and human interaction in Australia, 1950-2006

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Blue whale habitat selection and within-season distribution in a regional upwelling system off southern Australia

Blue whales Balaenoptera musculus aggregate to feed in a regional upwelling system during November–May between the Great Australian Bight (GAB) and Bass Strait. We analysed sightings from aerial surveys over 6 upwelling seasons (2001–02 to 2006–07) to assess within-season patterns of blue whale habitat selection, distribution, and relative abundance. Habitat variables were modelled using a general linear model (GLM) that ranked sea surface temperature (SST) and sea surface chlorophyll (SSC) of equal importance, followed by depth, distance to shore, SSC gradient, distance to shelf break, and SST gradient. Further discrimination by hierarchical partitioning indicated that SST accounted for 84.4% of variation in blue whale presence explained by the model, and that probability of sightings increased with increasing SST. The large study area was resolved into 3 zones showing diversity of habitat from the shallow narrow shelf and associated surface upwelling of the central zone, to the relatively deep upper slope waters, broad shelf and variable upwelling of the western zone, and the intermediate features of the eastern zone. Density kernel estimation showed a trend in distribution from the west during November–December, spreading south-eastward along the shelf throughout the central and eastern zones during January–April, with the central zone most consistently utilised. Encounter rates in central and eastern zones peaked in February, coinciding with peak upwelling intensity and primary productivity. Blue whales avoided inshore upwelling centres, selecting SST ~1°C cooler than remotely sensed ambient SST. Whales selected significantly higher SSC in the central and eastern zones than the western zone, where relative abundance was extremely variable. Most animals departed from the feeding ground by late April

Climate and Biodiversity Credentials for Australian Grass-Fed Beef: A Review of Standards, Certification and Assurance Schemes

Extensive livestock production occupies 25% of the ice-free terrestrial surface of the Earth, and Australian beef production contributes about 10% of this total land footprint. Therefore, the management of cattle has major implications for natural vegetation, soils, biodiversity, and atmospheric greenhouse gases in Australia and globally. To meet global sustainability targets and consumer expectations, a variety of environmental Standards, Certification and Assurance (SCA) schemes are being developed and implemented to enable producers to verify claims relating to their products. Improved standardization and coordination are now needed to address the rapid proliferation of credentialing systems that use different frameworks, methods and levels of scientific verification. Using the Australian grass-fed beef industry as a case study, we identified the measures, metrics and methods that are currently used by SCA schemes for climate and biodiversity credentialing. From here, a co-design process with industry representatives was applied to develop recommendations for credentialing in extensive beef production, feedlots and meat processing. It was clear that the successful adoption of credentialing by beef producers will require flexible and user-friendly support tools that use scalable data sources such as existing producer records, agtech databases and remote sensing information. Substantive rewards and incentives will be required to support producer engagement with the SCA schemes. Overall, ’more needs to be done to ensure the transparency of schemes and to meet benchmarks for integrity such as determining uncertainty and support though peer-reviewed science

Towards global data products of essential biodiversity variables on species traits

Essential Biodiversity Variables (EBVs) allow observation and reporting of global biodiversity change, but a detailed framework for the empirical derivation of specific EBVs has yet to be developed. Here, we re-examine and refine the previous candidate set of species traits EBVs and show how traits related to phenology, morphology, reproduction, physiology and movement can contribute to EBV operationalization. The selected EBVs express intra-specific trait variation and allow monitoring of how organisms respond to global change. We evaluate the societal relevance of species traits EBVs for policy targets and demonstrate how open, interoperable and machine-readable trait data enable the building of EBV data products. We outline collection methods, meta(data) standardization, reproducible workflows, semantic tools and licence requirements for producing species traits EBVs. An operationalization is critical for assessing progress towards biodiversity conservation and sustainable development goals and has wide implications for data-intensive science in ecology, biogeography, conservation and Earth observation