The research activities of the consortium are listed below to encourage and enhance collaboration and avoid duplication of research.

Bodrossy L et al. – IMOS NRS Marine microbial observatories
January 2019

Affiliation – Integrated Marine Observing System (IMOS), CSIRO

Summary – Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) was created to provide methodologically standardised, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria, Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. AMMBI was further expanded into the IMOS National Reference Station Marine microbial observatories (NRS). Samples are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30° of latitude and ~38° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion.

Keywords: pelagic, marine, microbial observatories, reference station, bacteria, archaea, eukaryotes, amplicon, metagenome

Harding J et al. – BushBlitz
January 2019

Affiliation – Parks Australia

Summary – BushBlitz is Australia’s largest nature discovery project – a unique multi-million dollar partnership between the Australian Government through Parks Australia and the Australian Biological Resources Study, BHP and Earthwatch Australia to document plants and animals across Australia. The activities associated with the Australian Microbiome Initiative, will work alongside the BushBlitz expeditions to collect samples for the microbial diversity at the sites. This will allow to provide a holistic view of the natural ecosystem from macro to micro organisms.

Keywords: national parks, monitoring, management, soil, lakes and rivers, marine parks, amplicon, metagenome, discovery

Berg S – Soil and root microbiomes of crop probiotic treated field grown sugar cane
January 2019

Affiliation – School of Agriculture and Food Sciences, University of Queensland

Summary – Sustainable cropping: Field-grown sugarcane was treated with putative crop beneficial microbes (commercial products). The analysis of soil and root microbiomes from the treated plants showed that soil and root bacterial communities were not affected by microbial product application. However, three OUT assigned to fungi were altered (initiated as part of BASE).
Commercial products were also applied to vegetable seedlings in the nursery to investigate the potential improvement of growth and performance. Ongoing research will explore whether commercial crop ‘probiotics’ are of benefit for crop industries.

Keywords: crop, soil, root, sugarcane, bacteria, fungi, probiotic

Schmidt S, Anderson J – Biocontrol microbes for cucurbits crop disease
January 2019

Affiliation – School of Agriculture and Food Sciences, University of Queensland

Summary – Investigation of microbiome to identify potential biocontrol microbes for ‘Gummy stem disease’ in cucurbits.

Keywords: crop, cucurbit, biocontrol, disease

Schmidt S, Williams W – Investigation of Nitrogen fixation microbial hotspot to assist rangeland management and support a sustainable grazing industry
January 2019

Affiliation – School of Agriculture and Food Sciences, University of Queensland

Summary – Sustainable grazing lands: Microbial communities of northern Rangelands (Kidman Springs Research Station, NT) are being examined to identify nitrogen fixation hotspots. Soil surface and deeper soil communities have been analysed are part of the BASE initiative. The findings will inform further research to quantify N fixation and assist strategic decisions on rangeland management to maximise biological N fixation, minimise land degradation, and support a sustainable grazing industry. The study is planned to expand to the Wombiana Research Station (North-Central QLD).

Keywords: nitrogen fixation, grazing, soil, management

Webster N, Thomas T, Murray S, Sherman C and Seymour J – Australian Coastal Microbial Observatory Network
January 2020

Affiliation – IMOS, AIMS, UTS, UNSW, Deakin Uni

Summary – This project will establish a new network of coastal microbial observatories that will operationally mirror the IMOS National Reference Stations, but provide a new capacity to understand the microbiology of the Australian coastline. Coastal environments have fundamental economic, environmental and cultural importance to Australia, and also represent a key interface for human interactions with natural communities of microorganisms. These environments are highly dynamic due to both natural perturbations and anthropogenic impacts and represent both excellent model systems for studying microbial ecology and sites where environmental microbial assemblages can have substantial human health and economic impacts. Our aim is to characterise the dynamics of planktonic microbial assemblages within 3 key coastal locations that have significance due to their environmental, economic and human health importance. This initial phase will be the catalyst for the establishment of a sustained and expanded network of coastal microbial observatories around the Australian continent.

Keywords: Coastal microbial observatory, bacteria, archaea, eukaryotes, marine, amplicon

Breed M, Spindler R, Bradby K, Kennedy S – Recovery of microbial communities during post-agricultural land restoration
January 2020

Affiliation – Flinders Uni, Bush Heritage Australia, Gondwana Link Inc., SA Water

Summary – This project aims to improve how soil microbiota are considered in ecosystem restoration, with a particular focus of post-agricultural land. It has potential to not only improve our understanding of soil microbial responses to restoration, but also help inform and hopefully improve the decisions made to restore ecosystems in Australia. Furthermore, it has potential to improve specific outcomes of ecosystem restoration – including benefits to human health.

Keywords: Soil, microbial diversity, restoration, human health, agricultural land, amplicon

Vadakattu G, Osana Y, Knox O – Cotton soil microbiome
January 2020

Affiliation – CSIRO, UNE

Summary – This project will build a baseline data based on soil microbiomes in Australian cotton fields that would help in the development of new management options required to cope with changing climate and facilitate monitoring both temporal and agronomic changes over coming years. A comparison with nearby or associated native and undisturbed vegetation is proposed to be included as a guide to potential deviation over the time since clearing and land development, due to agricultural practice, to provide an indication of the time needed prior to future monitor sampling, the microbial groups that are most likely to be informative of change and for comparison with other undisturbed systems.

Keywords: cotton, soil, microbiome, agricultural practice, land management, amplicon, metagenome

Ostrowski M, Seymour J, Doblin M, Raes E, Paulsen I, Beckley L, Focardi A and international PIs – IN19_v03: A coupled bio-physical, ecosystem-scale, examination of Australia’s International Indian Ocean Expedition line
January 2020

Affiliation – UTS, Macquarie Uni, Murdoch Uni

Summary – This voyage in the Indian Ocean will provide a set of samples that are highly complementary with the GO-Ships voyage (IN16_v03) which sampled the Pacific Ocean in 2016. The sampling effort will traverse 40˚of Latitude, 5,000 m in depth, and provide reference material from numerous Marine Parks. Priority for a targeted set of amplicon and metagenome observations will enhance our capacity for species-, function- and BGC-modelling across the entire marine estate, providing essential boundary conditions for higher resolution coastal modelling efforts.

Keywords: marine, ocean transect, Indian Ocean, metagenomes, amplicons

Rinke C – Brisbane River estuary
January 2020

Affiliation – UQ

Summary – this project will assess the microbial and viral community succession along the Brisbane River estuary via metagenomics and single-cell genomics, and track seasonal changes. By integrating all data from this project (metagenomics, viromics, single-cell genomics, meta data) the investigators will characterise the microbial and viral community in the economically important Brisbane River estuary and will assess the role of MGII Archaea and their viral predators.

Keywords: Brisbane river estuary, amplicon, metagenome, archaea

IndigoAg, Bissett A – Crop-associated Soil Microbiome: Wheat and Barley
January 2020

Affiliation – IndigoAg, CSIRO

Summary – Wheat and Barley are two major cereal crops in Australia. Soil and plant microbiome has been linked to plant performance, and improvements in Agricultural efficiency may be made with increased knowledge of microbiome. Furthermore, knowledge of current soil and crop microbiomes will allow improved management of microbiome interventions, particularly where they concern biological agents developed outside the proposed application area. The objective of this work is to add to the underrepresented agricultural data on soil microbiomes in the Australian Microbiome database by investigating Wheat and Barley fields to enable development of new management options to improve plant performance with changing climate, facilitate improved biosecurity management of opportunities for agricultural improvement opportunities and, facilitate monitoring of future temporal and agronomic changes. In addition to the proposed soil sampling, a parallel study is being conducted that will sample and sequence plant and rhizosphere associated microbiomes from the same sites, thereby adding to the knowledge around crop symbionts and plant health.

Keywords: soil microbiome, wheat, barley, agricultural practices, management, amplicon

Thomas T, Ostrowski M, Webster N, Seymour J – Australian MAG database
January 2020

Affiliation – UNSW, AIMS, UTS

Summary – This project will generate a central database of metagenome-assembled genomes (MAG) for key microbial habitats that will significantly add value to the Australian Microbiome Initiative (AMI) rRNA database. Functional information contained within Australian MAG database (AMD) will be used as taxon-resolved scaffolds for existing and future metagenome and metatranscriptome studies. MAGs will also enhance the value of the existing rRNA gene data by increasing the accuracy of predicting functional gene profiles, which may provide a richer insight into environmental indicators.

Keywords: metagenome-assembled genomes, deep shotgun sequencing, functional gene profile

Schmidt S, Dennis P, Williams W, Robinson N, Cowley R, O’Reagain P, Knicker H – Metagenomic profiling of biocrusts in northern grazing lands
January 2020

Affiliation – UQ, NT Gov, QLD DAF, U Seville IRNAS-CSIC – Spain

Summary – Biocrusts – the ‘living skin’ of soils – are made up of consortia of cyanobacteria, bacteria, fungi, lichen, and others organisms. Biocrusts fix carbon and nitrogen, but their activities (and organisms) are compromised in degraded systems, and fundamental knowledge about biocrusts is limited in Australian savannas and grasslands. In northern Australian, 2 million km2 of native pastures are grazed by cattle. Declining soil fertility, reduced pasture productivity, erosion and dust storms demand better land management strategies for extensive grazing systems. This MLA-collaboration will generate fundamental knowledge on how to harness the natural N regeneration potential of biocrusts. We are quantifying biocrust function along gradients of fire interval, spelling regimes (taking cattle off the land for certain periods), and cattle stocking densities, to inform sustainable grazing management.

Keywords: soil, biocrust, grazing land, land management, amplicon, metagenome, biodiversity and function

Hahs A, Aponte C, Mavoa S – Pilot study: how does the soil microbiome vary between types of urban green space where children spend time
January 2020

Affiliation – University of Melbourne

Summary – Exposure to micro-organisms has been linked to immunity levels in children and adolescents, yet much of this research has been conducted overseas. This project proposes to conduct a pilot sampling to determine the variation in the soil microbiome of the different types of green space children visit, and the level of human activity within those green spaces.

Keywords: Urban Green Space, microbiome, amplicon, human health

Flies E, Jones P – Can urban green spaces provide microbially biodiverse health refuges for city residents? A study of soil and aerial microbiomes across the greater Hobart region
January 2020

Affiliation – University of Tasmania

Summary – Over the last few decades, the rate of allergic and autoimmune disorders has been increasing. Several hypotheses (Hygiene, Old Friends and Biodiversity Hypotheses) suggest that this trend is related to urbanization and humans’ reduced exposure to biodiverse microbial communities. However, few studies have tested the underlying assumption that people living in cities are exposed to microbial communities of lower diversity by comparing the diversity of microbial communities along urbanisation gradients. This study will contribute to Australian and international microbiome science by testing differences in microbial composition and diversity in residential and public green spaces along an urbanisation gradient in Hobart, Tasmania: ranging from the rural fringe to highly built up zones. The study will complement a parallel study of public green spaces in Melbourne. 

Keywords: Urban Green Space, microbiome, amplicon, human health

Munoz-Rojas M, Erickson T, Merritt D, Chilton A – Harnessing native soil microbes for dryland restoration in Western Australia
January 2020

Affiliation – UNSW, UWA, Kings Park Science DBCA – WA

Summary – This project aims to explore and develop new technologies to increase plant recruitment and soil function through effective targeted delivery of native soil microorganisms in degraded arid soils. Soil inoculation can be a powerful tool to both restore disturbed terrestrial ecosystems and steer plant community development. Most evidence for microbially-mediated plant responses comes from inoculation studies using specific soil microorganisms previously cultured (such as our current work using cyanobacteria from biocrust), or even commercially available non-native microbial consortium. However, the effects of whole microbial communities adapted to different environmental conditions on the recruitment and growth of native plant species in restoration settings, remain largely unknown. The expected outcome of the sampling plan is to provide baseline information on the soil microbial taxa in key ecosystems of Australian drylands, with a focus on the Pilbara region, and elucidate the roles and benefits of native soil microbial species for the re-establishment of plant-soil feedbacks and ecosystem functions in degraded soils.

Keywords: soil, amplicon, restoration, arid, Pilbara

Dafforn K, Johnston E, Mayer Pinto M, Bracewell S, Bodrossy L – East coast of Australia / Mapping estuarine health from the sediment microbiome
January 2020

Affiliation – MQ, UNSW, CSIRO

Summary – Traditionally, coastal biomonitoring has focused on macroinvertebrate communities and studies of microbial communities in estuarine systems have largely employed fingerprinting techniques or targeted the abundance and expression of specific genes. These techniques do not capture the true diversity of sediment communities. Next generation sequencing (NGS) tools, which can extract information rapidly and cost-effectively from environmental samples offer a promising solution to these problems. Further they provide a wealth of additional data from microorganisms that would not be detected with other sampling methodologies and so are posited to be more sensitive to environmental change. However, this needs to be tested across a broad spectrum of environmental conditions and therefore we propose sampling along the length of the east coast of Australia. Soft sedimentary environments have recreational, aesthetic and intrinsic value, but they also provide direct and indirect benefits to society as sources of food and medicine, stabilizers of inshore environments and regulators of atmospheric processes through nutrient cycling. For example, sediment microbes are vital to the denitrification of excessive nutrients, remediation of contaminants and overall water quality in estuaries. They can also act as a long-term integrated measure of environmental change since sediments are a sink for many contaminants and act as a source to water column communities if resuspended. Creating a baseline of microbial diversity in Australia’s estuaries is therefore vital for future management of these systems and can provide information about their health. This project will provide a map of sediment microbial biodiversity from multiple estuaries along the east coast of Australia. We will investigate links between the sediment microbiome and potential environmental drivers and identify species from the sediment microbiome that could be used as potential indicators of estuarine health.

Keywords: sediment microbiome, amplicon, environmental health, estuary, indicator species

Huggett M, Seymour J, Dafforn K, Stat M, Leggat B, Potts J – Indicators of water quality health in coastal lakes
January 2020

Affiliation – University of Newcastle, UTS, MQ, DPIE

Summary – Coastal lakes and estuaries represent valuable resources. These areas provide nursery grounds and habitat for species of recreational and commercial importance including fish, bivalves and crustaceans; support aquaculture efforts; act as natural filters of nutrient and sediment inputs from terrestrial systems and are valuable for aquatic and land-based recreational activities. Despite their importance, coastal ecosystems are being increasingly threatened and disturbed by growing urbanisation resulting in overfishing and intensification of nutrient, sediment and pathogen loads from stormwater, agriculture and sewage. Impacts of these multiple stressors include outbreaks of aquatic and human diseases, loss of biodiversity and large-scale fish mortality. The early detection of signs of stress within aquatic ecosystems is crucial in maximising the effectiveness of management strategies. Microorganisms is now being increasingly used to understand the health of aquatic ecosystems. Sources of microbial contamination have been a contentious issue in both the Northern Beaches of Sydney as well as in a number of coastal water bodies on the Central Coast of NSW. The investigators have been working closely with local councils and State government (DPIE) to apply genomics techniques to understand the drivers of microbial contamination and the responsive organisms. The project will be undertaken alongside work from DPIE aimed at understanding the source of poor water quality in these environments. Water and sediment quality analysis will be conducted across storm events and during dry weather and we will conduct microbial diversity and functional analyses to link the microbial community diversity and function with observed impacts to these ecosystems and provide DPIE and local councils with a recommendation regarding the utility of genomics applications to water quality assessment programs such as BeachWatch.

Keywords: water quality, ecosystem health, coastal lakes, amplicon, metagenome, assessment program, management, storm event, dry weather

Van de Kamp J – Derwent Estuary Program
January 2020

Affiliation – CSIRO

Summary – This project will continue the establishment of a high resolution coastal/estuarine microbial observatory in the Derwent estuary. This aligns with recent efforts to contribute to a greater understanding of the Derwent ecosystem while investigating microbial community patterns in an impacted system subject to heavy metal loads, high nutrient concentrations and a variety of pollutants. In addition, the CSIRO Environmental Modelling Suite includes 3D hydrodynamic, sediment and biogeochemical models which were implemented for the Derwent Estuary in 2005. This provides an opportunity to couple genomics observations with model outputs in an effort to inform model processes and improve predictions.

Keywords: estuary, amplicon, microbiome, ecosystem health

Krauss S, Tibbett M, Breed M, Bullock P, Dobrowolski M, Sarah Jones S – Post-mining restoration of soil microbiota
January 2020

Affiliation – DBCA, University of Reading (UK), Flinders Uni, South32, Iluka, Tronox

Summary – Large areas of land in Australia are now subject to strip mining, with a single mine able to clear and restore as much as 500 ha of forest or heathland annually. Considerable efforts have been made to restore post-mining bauxite and mineral sand sector in particular. Little is known about the below-ground microbiology of restored sites as well as the native undisturbed ecosystems. Recent analysis of vegetation communities at some sites have shown that soil chemistry and vegetation community are developing in a trajectory that is distinct from the native target vegetation community. Our aim is to assess the temporal and spatial changes in soil microbial communities in these developing soil systems to ascertain whether developmental changes occurring in soil microbial communities are following trajectories away from or toward native undisturbed reference ecosystem soil communities. Our proposal harnesses a uniquely replicated experimental opportunity through our multiple mining partner sites to assess temporal changes in soil biota post disturbance at the regional scale. Our study addresses a priority issue (soil quality post-mining) for our industry partners, and the ecological restoration sector more broadly.

Keywords: soil microbial communities, amplicon, mine, ecological restoration

Messer L, Tyson G, webster N, Bourne D – Spatial and temporal sampling of the model coral species, Acropora tenuis and Porites lutea, at inner and outer reef sites
January 2020

Affiliation – UQ, AIMS, JCU

Summary – Our understanding of coral resilience to thermal stress is hindered by a limited understanding of the functional roles of coral-associated microbial communities. Our goal is to generate a comprehensive genomic database of taxonomic and functional information for coral-associated bacteria, archaea, and viruses. We aim to identify “core” microbial symbionts of A. tenuis and P. lutea, by tracking their prevalence and abundance through time and space, and through in situ visualisation. Comparative genomics will be used to determine the functional contributions of the microbiome, and the expression of metabolic functions will be validated through metatranscriptomics. The data generated through this project will provide insight into how the microbiome contributes to coral health. This knowledge is vital for our understanding of coral resilience in the face of climate change, and is necessary to inform microbiome manipulation efforts currently being explored in the context of reef restoration.

Keywords: coral-associated microbial communities, diversity and function, amplicon, metagenome, health and resilience, restoration

Watkin E, Santini T, Boase K – Some like it acidic: leveraging the unique acidic saline lakes of Western Australia to interrogate the origins of haloacidophily
January 2020

Affiliation – Curtin Uni, UWA

Summary – Acidic saline environments are rare ecological niches on Earth, found in only a few known locations hence, there have been a relatively small number of haloacidophilic microorganisms identified. Additionally, these microorganisms and the mechanisms that they employ to deal with both osmotic stress and acidic conditions have not been extensively characterised. The proposed study will examine the microbial ecology of Western Australian acidic saline lakes. Amplicon and metagenomic sequencing coupled with analysis of geochemical and physical metadata will enable insights into controls on the distribution and abundance of haloacidophiles (and their biotechnological applications) as well as the origins of this unusual poly-extremophily. The characterisation of microbial communities found in the acidic, saline waters and soils of the Western Australian Yilgarn region has potential to reveal novel microbial species and functional capacities and inform our understanding of evolutionary lineages and relationships, and result in the isolation of novel haloacidiphilic Fe- and S-oxidising microbial species for bioleaching applications.

Keywords: acid saline lakes, biocrust, soil and sediment, amplicon, metagenome, bioleaching, biodiscovery

Brown M, Ostrowski M, Seymour J, Doblin M, Bodrossy L, Raes E, Waite – Pacific Ocean P15S – GO-Ships Line: A decadally repeated 7,000km transect from 66 °S to 0 ° along ~-170 Longitude
January 2020

Affiliation – University of Newcastle, UTS, CSIRO, Dalhousie University (US)

Summary – GO-SHIPS, the Global Ocean Ship-based Hydrographic Investigations Program, is a systematic, interdisciplinary program combining physical, chemical and biological oceanography to investigate marine biogeochemistry and in particular carbon cycling in the interior of the global ocean to inform climate observing systems. Currently 62 lines crossing entire oceans or seas (coast to coast) have been surveyed by this initiative. The P15S line occurred in 2016 (RV Investigator IN16_v03) and sampled from the surface to the sediment (down to ~6000 m) every 0.5° latitude from the sea-ice at 66 °S to the equator (0 )° along Longitude 170 E. This transect incorporated globally relevant oceanographic provinces including and representative of Australian Marine Reserves. A total of 1050 samples have already been sequenced using 16S/18S approaches to census for microbial biodiversity and this data is already incorporated in the AMI database. From this approach we can now describe distinct microbial provinces that change both latitudinally and with depth (along the transect and in epi, meso and bathypelagic zones). This project seeks to undertake metagenomic sampling of multiple representative assemblages from each of these biologically distinct provinces. The dataset will include samples from the highly underrepresent meso and bathypelagia, along with samples from the south pacific which currently constitutes < 4% of publicly available marine metagenomes.

Keywords: metagenomes, GO-SHIPS, Pacific Ocean, Southern Ocean, microbial provinces, pelagic zones, functional repository, MAGs, genomic hypervariable regions, environmental genomic adaptation

Brace A, Fontaine J, Ruthroff K, Miller B, Froend R, Hopkins A – Effect of fuel age and prescribed burns on soil microbial community
January 2020

Affiliation – ECU

Summary – The aim of this project is to examine the impact of differing fire intervals on the soil microbial community of selected Banksia Woodland species. Very little is known about the biotic interactions that underpin Banksia woodland (a community recently classified as endangered), much of the bacterial and fungal diversity has not been described, nor of the functional roles they play within the system and how this affects the rest of the community. This project aims to fill that gap in the knowledge. It will also examine how changes in fire frequency and management interact to affect soil microbial community composition. Changes to soil microbial communities could have profound impacts on regeneration, recruitment and ecosystem stability in these fragile woodlands. The ‘time since fire’ range from over 40 years to around 10, this would allow for a large post fire successional chronosequence of the microbial community to be quantified, thus informing when the microbial community not only returns to it pre fire state, but also when it is at its most fragile. Comparing this to recently burnt sites of differing fuel ages will also allow to see how fires at different intervals can cause divergence in the successional stages.

Keywords: : National parks, nature reserve, fire impact, soil microbiome, Banksia woodland, chronosequence, amplicon

Paungfoo C, di Bella L, Wright N, Schmidt S – Evaluating green technologies for wide production of a sustainable eco-friendly biofertiliser
January 2020

Affiliation – UQ, SOSBio

Summary – This project aligns with the investigators current Cooperative Research Centre Project that aims to evaluate green technologies for wide production of a sustainable eco-friendly biofertiliser. The project involves the comparison of the effects of conventional vs green technologies (organic fertiliser and microbial inoculant) on the plant development, nutrient acquisition and runoff, the soil microbial biomass and diversity, and the soil physico-chemical properties. Rhizosphere soil samples of sugarcane/Macadamia/avocado will be collected from the field trials established with the industry partners in the Childers, Bundaberg Ingham and Cairns regions of Queensland. The effect on crop growth, nutrient acquisition, nutrient runoff, soil physico-chemical properties, and soil biology will be assessed at the early, mid, and late stages of the crop growth cycle. This sampling procedure allows evaluating the effects of the fertilisers on different crop growth stage.

Keywords: biofertilisers, amplicon, soil, green technologies, rhizosphere, crop and growth, field trials