1. Status and next steps
The Australian Marine Microbial Biodiversity Initiative: Establishing a continental scale, long term oceanography observatory
Brown, M.V., Van de Kamp, J., Ostrowski, M., Seymour, J.R., Bissett, A., Goossen, K., Ingleton, T., Messer, L., Laverock., B, Siboni., N, Jeffries T., Bibiloni Isaakson, J., Nelson, T., Coman, F., Davies, C., Frampton D., Robert S., Holmes, B., Abell, G., Craw, P., Kahlke T., Sow, S.L-S., Mcallister, K., Windsor, J., Skuza, M., Crossing, R., Patten, N., Malthouse, P., Paulsen, I., Steinberg, C., Richardson, A., VanRuth, P., Koval, J., Fuhrman, J.A., Fitzgerald, A., Moltmann, T., Bodrossy, L.
Levente Bodrossy

2. AMMBI – Status and next steps
BPA
Coastal/estuarine opportunities
Autonomous sampling devices
Next steps

3. AMMBI – Status and next steps
BPA
Coastal/estuarine opportunities
Autonomous sampling devices
Next steps

4. Multihead peristaltic pump
What’s involved
2L seawater
Sterivex filter
-80 °C
Multihead peristaltic pump
$ 16
$ 5000
$ 60
$180 - $800
ng DNA
Genomic analyses
Aliquot 1 – for first genomic analyses
Aliquots 2-6 – freeze dried, at -80C, for a range of projects
Aliquot 7 – QIAsafe 96 well plate, -80C, long term storage

5. Community composition for: Bacteria Archaea
Rottnest Island
Since July 2015
6 depths
12x per year
Port Hacking
Since July 2010
Maria Island
Since July 2012
Darwin
Since July 2015
3 depths
4x per year*
2L water
Community composition for:
Bacteria
Archaea
Eukaryotes (~phytoplankton)
Functional composition (recent addition)
Sequenced until May/June 2016
Yongala
Since July 2015
4 depths
12x per year
North Stradbroke Island
Since July 2012
6 depths
12x per year
Kangaroo Island
Since July 2015
6 depths
6x per year

6. 7 Stations, 48/12 months, 5 voyages
Bacteria, rchaea and eukaryotes > OTUs
AMMBI represents the first methodologically standardized, continental scale, microbial ocean-observing network.
The data provide a critical baseline against which to measure, and from which to predict, changes in microbial assemblages under future scenarios.

8. Martin Ostrowski, Macquarie University

9. Martin Ostrowski, Macquarie University

10. Conditionally abundant bacteria
(<0.01% overall, but >10% in at least 1 sample)
MAI PHB NSI
30% % %
Conditionally abundant ones
Kirianne’s poster!

11. Conditionally abundant bacteria
(<0.01% overall, but >10% in at least 1 sample)
MAI PHB NSI
10% % %
Conditionally abundant ones
Kirianne’s poster!

12. Bacteria-phytoplankton interactions
Darwin (12.4° S)
Port Hacking (34.1° S)
Maria Island (42.6° S)
Yongala (19.3° S)
North Stradbroke Island (27.4° S)
Rottnest Island (34.8° S)
Kangaroo Island (34.8° S)
SAR11Oligo 12567
SAR11Oligo 12503
Mamiellaceae Chloroplast OTU
Mark Brown, UNSW

13. Bacteria-phytoplankton interactions
Port Hacking (34.1° S)
Maria Island (42.6° S)
SAR11Oligo 12567
SAR11Oligo 12503
Mamiellaceae Chloroplast OTU
Δ: SAR11Oligo – SAR11Oligo 12503
Mamiellaceae Chloroplast OTU
Mark Brown, UNSW

14. AMMBI – Status and next steps
BPA
Coastal/estuarine opportunities
Autonomous sampling devices
Next steps

15. BPA Marine Microbial project – pelagic component
Rottnest Island
Yongala
Kangaroo Island
Darwin
North Stradbroke Island
Port Hacking
Maria Island
Inv2014-e03
CSC_Trip5913
SAIMOS2014_RC48/51
SS2013_t03+t07
SS2010_c09
Pelagic component = AMMBI (IMOS) samples + oceanic voyages extending spatial coverage
2 years, 7 stations + voyage samples, ~1000 samples
Amplicon sequencing, ~1000
Bacterial 16S
Archaeal 16S
Eukaryote 18S
Shotgun metagenome sequencing, ~500
Genome sequencing of bacterial isolates, ~20
Transcriptome sequencing of eukaryote isolates, ~10
Total sequencing costs ~$400k

17. Australian Microbiome Database

18. AMMBI – Status and next steps
BPA
Coastal/estuarine opportunities
Autonomous sampling devices
Next steps

19. Genomics tools for estuarine status assessment
10 g sediment contains tens of millions of microbes and micro-invertebrates – thousands of different species These organisms live in intimate relationship with the environment and are sensitive indicators of its status (of many different aspects of it) Using genomics we can tell their stories Read their community structure as a fingerprint In order to be able to read this fingerprint we need to establish a baseline database Australia-wide baseline project: Microbial community structure fingerprint vs. estuarine status
around 10 g of sediment that can tell the story of thousands of bacteria, phytoplankton and microinvertebrates (amongst others) living in it. these are living in an intimate relationship with the environment and their community structure is a fingerprint of the status and health of the environment. we are not yet able to read this fingerprint in detail, to a large extent because we don't have the baseline dataset to interpret it. to this end, we are working on an Australia-wide baseline of estuarine genomics – BGC – environmental status dataset.

20. Fragmented efforts
Report
Report
Survey
Management
decision
Publication
Publication
Management
decision
Report
Report
Publication
PhD thesis
a second one that visually tells the story of the fragmented efforts into estuarine observations and how these could be glued together by support for sequencing (BPA likely to provide it), for bioinformatics (BPA/CSIRO) and for BGC (missing). maybe add modelling plans there, leading to improved advice to estuarine management.
Management decision
= Agencies, GMOs, research groups, etc. running separate projects, collecting samples, running various analyses (chemical, physical, sometimes genomics observations). In vastly different ways to allow for direct comparison, minimizing any chance for leverage.

21. Fragmented efforts – can we leverage?
Chemistry
Sequencing
Bio-informatics
a second one that visually tells the story of the fragmented efforts into estuarine observations and how these could be glued together by support for sequencing (BPA likely to provide it), for bioinformatics (BPA/CSIRO) and for BGC (missing). maybe add modelling plans there, leading to improved advice to estuarine management.
Publications, PhD theses
Reports, surveys
Best practice, cost efficiency
Continent-wide baseline database, leading to:
Better understanding of estuarine health and status
Modeling of estuarine BGC processes, leading to:
Improved support for estuarine management decisions

22. CSIRO Environomics Future Science Platform
Environmental genomics of coastal environments – proposal
2 years initially; 4 FTE; BPA support
Relationship between microbial community phenotype and process rates  incorporating microbial data into process models
Biodiversity assessment and baseline data establishment at a range of coastal/estuarine sites within Australia (seek partnerships)
Define indicators of ecosystem health within these environments
Apply modelling (at 1 or 2 sites?)

23. AMMBI – Status and next steps
BPA
Coastal/estuarine opportunities
Autonomous sampling devices
Next steps

24. SAFA Sample Filtration & Archival unit
Function:
In-situ microbial sampling and preservation for subsequent laboratory analysis. Collects up to 24 samples.
Cost:
~$25-30,000
Status:
Second generation; field test successful (30 m)
First customers will take delivery in March 2017

25. STAN Standalone unit for Low cost, high flexibility monitoring
Function:
Collection, filtration and preservation of a single 2L water sample for lab based analysis.
Can be triggered manually, by time or remotely
Very low cost allows high spatial and temporal coverage
Sampling location flexibility.
Cost:
~$200 per unit
Status:
First field tests done – leak at 30 m, being fixed

26. MOBI Microbial Oceanography Biosensing Instrument
Function :
Near real-time, in-situ microbial sampling and analysis.
ddPCR with telemetry
Cost:
~30k for core instrument
Status:
Prototype development. Assay validation

27. AMMBI – Status and next steps
BPA
Coastal/estuarine opportunities
Autonomous sampling devices
Next steps

28. Next steps
Merge with other Australian environmental microbiome sequencing projects (AMD)
Enter data into Atlas of Living Australia database (-> release data, initiate broad community involvement)
Extend into coastal and estuarine environments
Quantification – B16S, A16S, E18S qPCRs? Flow cytometry including SYBR Green?
Remotely deployable samplers – event based sampling and higher frequency sampling
Linking genomics observations of phytoplankton to microscopy and satellite observations
HABs: understanding events and underlying microbial community dynamics leading to blooms
Phytoplankton productivity – cyanobacterial community dynamics; biogeochemical cycling supporting phytoplankton

29. Thank you
© Malou Zuidema