Environomics

Natural history collections are vast biodiversity reference libraries, used for hundreds of years to help identify, understand and manage biodiversity.

Rapid assessment of environmental stress will provide information that is important for managing and conserving Australian plants in rapidly changing environments.

Environmental changes cause stress to our biodiversity, increasing the chances of disease outbreaks, extinctions, waves of invasive species and other environmental problems that can occur in stressed ecosystems.

Biodiversity and food security both depend on pollination of native plants and crops. But pollinators are in decline due to threats such as land clearing, habitat fragmentation, pesticides and climate change.

Environmental DNA (eDNA) analysis is an emerging molecular technique for DNA-based identification of organisms.

We are investigating the relationship between microbial diversity and ecosystem health in marine environments.

Our bioinformatics team is developing ways to solve the unique data analysis challenges created by high throughput sequencing of environmental samples and biological collections.

The Environomics Future Science Platform has teamed with the Atlas of Living Australia to build a new online system to make cutting-edge biological records accessible.

This project aims to advance technical developments and foster a deeper theoretical understanding of the epigenetic changes associated with age.

This project will work with and develop a combination of fluorescent DNA tags and PCR-based methodologies that can be used to separate cells of species of interest from environmental cells, and use these to generate genotypes of the animals present in an area.

This project, led by FSP postdoctoral researcher Flavia Tarquinio, is testing whether seagrass restoration can be improved by manipulating the bacterial communities that naturally coexist in their seeds, leaves and roots.

Identifying animals, plants and microbes is important for many industries and activities, including agriculture, forestry and fisheries, human disease, biosecurity, water management, and biodiversity conservation.

Unfortunately, the ability of metabarcoding to provide quantitative information is currently limited due to a number of technical constraints leading to differential amplification between DNA fragments.

We are developing tools that will allow users to combine and analyse standard data types in biodiversity informatics, in this case large-scale information about the evolutionary history of species, traits for individuals or species, and ecological data.

This project is focused on developing new bioinformatic methods for obtaining quantitative information on animal abundance and biomass from eDNA datasets.

Our project will develop and apply ecological and genomic methods to help untangle complex plant-pollinator webs within a range of Australian habitats.

In this project we are using metagenomic sequencing combined with experiments in the laboratory and in the field to unlock the relationships between microbial identity (i.e., who is there) and the ecosystem functions they perform (i.e., what are they doing).

This project will verify whether subsurface microbes can be cultivated in the lab by providing electrons directly as the energy source opening up new possibilities to utilise subsurface microbial life.

In this project, we will quantify the response of plants to temperature stress by sequencing the transcriptome and combine this information with trait data to develop a platform that can predict if a species are near their thermal limits.

Our project aims to test the potential of environomics to provide qualitative and quantitative indicators of bacterial nitrogen cycling at the spatial and temporal scales required by ecosystem managers and modellers. With better model accuracy, we aim to provide industry, government, and communities with the tools they need to manage nutrient pollution.

Working on new and exciting methods of cultivating sub surface microbes, one of our early career researchers, Dr Xiao Deng has contributed to the recently published findings of gold-coated fungal strands in the soil near Boddington in Western Australia.

Environomics, short for environmental genomics, is a new CSIRO science program exploring the limits of what is possible at the interface between genomics and environmental science.

Should I tell you that a bunch of Environomics postdocs met on Rottnest and reveal exactly what they got up to? Or can I just say this….

A Curtin University and CSIRO Environomics FSP collaboration has resulted in the publication of the first long-term environmental analysis based on eDNA in PLOS Genetics.

Phytoplankton are tiny algae that live in the ocean. They can occur in vast numbers and are at the bottom of the food chain that supports all life in the ocean. When conditions are just right, including supply of nutrients and temperature, phytoplankton numbers can explode, causing a bloom. This in turn can set off […]

Simon Jarman, Oliver Berry (Environomics FSP Leader) and Michael Bunce recently penned an article about the need for an environmental DNA (eDNA) biobank. With the advancement of DNA sequencing technology, biomonitoring with environmental DNA (“eDNA”) is revolutionizing biodiversity assessments. Conventionally, characterizing biodiversity requires time-consuming surveys and expert knowledge. However, researchers can now identify organisms without […]

Andreas Zwick, molecular scientist and project leader of ‘Mobilising collections through genomics’ last year installed a $500 000 robotic liquid handler for conducting DNA analyses on historical specimens preserved in Australia’s national biological collections. Biological collections are vast biodiversity reference libraries, used for hundreds of years to help identify, understand and manage biodiversity. Andreas’ team […]

In a recent issue of Science magazine, Clare Holleley (FSP Project Leader) and colleague Arthur Georges (University of Canberra) share exciting new science shedding light on the mechanisms of temperature-dependent sex determination (TSD) in reptiles. Sex determination in reptiles is a complex affair because in many species incubation temperature and genes interact to regulate sexual […]

FSP leader Olly Berry collaborated with colleagues at the University of Canberra to develop a new R software package “dartR” designed to make it easier for researchers to analyse large population genomic datasets. In the past few years researchers have gone from analysing tens of genomic markers to tens of thousands. A pre-print is available […]