integrating genomics, biogeochemistry, and modelling to...
TRANSCRIPT
-
ENVIRONOMICS FUTURE SCIENCE PLATFORM
Integrating genomics, biogeochemistry, and modelling to inform management of Australian estuariesKristen Karsh, Jennifer Skerratt, Eric Raes, Andrew Bissett, Levente Bodrossy, Jodie van de Kamp, Bronwyn HolmesACOMO 2018
-
Goals for today
• More explicitly modelling microbial processes is worthwhile
• Doing so is feasible within existing model frameworks
• Show approaches and early data that support this
Presentation title | Presenter name2 |
Water
-
Marine nitrogen cycle
3 |
WaterSediment
metres
mm - cm
Microbial Community = Filter
1) Predict2) Identify intervention points3) Focus further research
-
How does the CSIRO Environmental Modelling Suite (EMS) currently represent microbial processes?
Presentation title | Presenter name4 |
-
Dissolved inorganic nitrogen = currency
Presentation title | Presenter name5 |
N2 NO3- NH4+
livingPON
detritalPON
denitrification
nitrification
remineralisation
mortality and sinkingN2 fixation
NO3-assimilation
NH4+ assimilation
-
Identify worthwhile microbial processes to add
Presentation title | Presenter name6 |
N2 NO3- NH4+DNRAdenitrification
nitrification
anammox
OrgC : NO3- supply
-
Presentation title | Presenter name7 |
CSIRO Environmental Modelling SuiteNitrogen
𝑽𝑽𝒅𝒅𝒅𝒅𝒅𝒅 = 𝑽𝑽𝒎𝒎𝒎𝒎𝒎𝒎−𝒅𝒅𝒅𝒅𝒅𝒅 ×[𝑵𝑵𝑵𝑵𝟑𝟑−]
𝑲𝑲𝑴𝑴𝑵𝑵𝑵𝑵𝟑𝟑
−+ [𝑵𝑵𝑵𝑵𝟑𝟑−]
×[𝑵𝑵𝟐𝟐]
𝑲𝑲𝑴𝑴𝑵𝑵𝟐𝟐 + [𝑵𝑵𝟐𝟐]
×[𝑪𝑪𝒐𝒐𝒐𝒐𝒐𝒐]
𝑲𝑲𝑴𝑴𝑵𝑵𝑵𝑵𝟑𝟑
−+ [𝑪𝑪𝒐𝒐𝒐𝒐𝒐𝒐]
-
𝑉𝑉𝑑𝑑𝑑𝑑𝑑𝑑 = 𝑉𝑉𝑚𝑚𝑚𝑚𝑚𝑚−𝑑𝑑𝑑𝑑𝑑𝑑 ×[𝑁𝑁𝑁𝑁3−]
𝐾𝐾𝑀𝑀𝑁𝑁𝑁𝑁3− + [𝑁𝑁𝑁𝑁3−]
×[𝑁𝑁2]
𝐾𝐾𝑀𝑀𝑁𝑁2 + [𝑁𝑁2]
×[𝐶𝐶𝑜𝑜𝑜𝑜𝑜𝑜]
𝐾𝐾𝑀𝑀𝑁𝑁𝑁𝑁3− + [𝐶𝐶𝑜𝑜𝑜𝑜𝑜𝑜]
Rate Maximum rate Affinity for the substrate
Substrateconcentration
V Vmax KM [S]
Explicitly including microbial community properties in existing model frameworks
Rate Maximum rate Affinity for the substrate
Substrateconcentration
V Vmax KM [S]
𝑉𝑉𝑑𝑑𝑑𝑑𝑑𝑑 = 𝑉𝑉𝑚𝑚𝑚𝑚𝑚𝑚−𝑑𝑑𝑑𝑑𝑑𝑑 ×[𝑁𝑁𝑁𝑁3−]
𝐾𝐾𝑀𝑀𝑁𝑁𝑁𝑁3− + [𝑁𝑁𝑁𝑁3−]
×[𝑁𝑁2]
𝐾𝐾𝑀𝑀𝑁𝑁2 + [𝑁𝑁2]
×[𝐶𝐶𝑜𝑜𝑜𝑜𝑜𝑜]
𝐾𝐾𝑀𝑀𝑁𝑁𝑁𝑁3− + [𝐶𝐶𝑜𝑜𝑜𝑜𝑜𝑜]
-
9 |
𝑉𝑉𝑑𝑑𝑑𝑑𝑑𝑑 = 𝑉𝑉𝑚𝑚𝑚𝑚𝑚𝑚−𝑑𝑑𝑑𝑑𝑑𝑑 ×[𝑁𝑁𝑁𝑁3−]
𝐾𝐾𝑀𝑀𝑁𝑁𝑁𝑁3− + [𝑁𝑁𝑁𝑁3−]
×[𝑁𝑁2]
𝐾𝐾𝑀𝑀𝑁𝑁2 + [𝑁𝑁2]
×[𝐶𝐶𝑜𝑜𝑜𝑜𝑜𝑜]
𝐾𝐾𝑀𝑀𝑁𝑁𝑁𝑁3− + [𝐶𝐶𝑜𝑜𝑜𝑜𝑜𝑜]
Rate Maximum rate Affinity for the substrate
Substrateconcentration
V Vmax KM [S]
• Microbial biomass = source of enzymatic activity that underlies the rate• Microbial turnover = mortality• Microbial growth efficiency = microbial biomass produced per unit of substrate
consumed• Microbial functional community (?)• These are parameters underlying much of the sensitivity of rate to temperature,
source of organic matter, pH, etc
-
More meaningful measure of resilience
Presentation title | Presenter name10 |
Vigor is the system’s function – the activity, metabolism, or primary productivity.
Resilience, is the system's capacity to maintain the above two, structure and function, in the presence of stress. When resilience is exceeded, the system can `flip'
to an alternate state.
Organization is the system’s structure - the diversity and number of interactions between system components.
Ecosystem health defined in terms of organisation, vigor, and resilience:
-
Revised model
Presentation title | Presenter name11 |
N2 NO3- NH4+
livingPON
detritalPON
DNRAdenitrification
nitrification
remineralisation
mortality and sinkingN2 fixation
NO3-assimilation
NH4+ assimilation
anammox
-
Proxy developmentCase study 1: Coastal nitrogen removal vs retention
12 |
Process
Enzyme kinetics
(Enzyme)
N2 NO3- NH4+DNRAdenitrification
nitrification
anammox
nrfAnirK, nirShzsA, hzsB, hzo
Nitrogen RetentionNitrogen Removal
-
Presentation title | Presenter name
Proxy developmentCase study 1: Coastal nitrogen removal vs retention
13 |
y = ax4 + bx3+ cx2 + dx + e
Rdenitrification : RDNRA nirK,nirS : nrfA
0
1
2
3
4
5
6
7
0 2 4 6
nrfA
: ni
rKrate of DNRA : rate of denitrification
Functional Gene DNA
-
Proxy development
Presentation title | Presenter name14 |
-
Presentation title | Presenter name15 |
N2 NO3- NH4+
livingPON
detritalPON
DNRAdenitrification
nitrification
remineralisation
mortality and sinkingN2 fixation
NO3-assimilation
NH4+ assimilation
-
Presentation title | Presenter name
Proxy developmentCase study 2: Open ocean nitrification
16 |
N2 NO3- NH4+DNRAdenitrification
nitrification
anammox
nrfA
-
Presentation title | Presenter name
Proxy developmentCase study 2: Open ocean nitrification
17 |
-
What processes hold most promise for genomics-based proxies?
Presentation title | Presenter name18 |
Most successful proxies (?):• Obligate metabolism• Processes narrowly
distributed within phylogenies
-
19 |
Biogeography through The Australian Microbiome Database
-
Review
• Worthwhile• Majority of nitrogen cycling carried out by microorganisms• Biomass feedbacks may provide way to model resilience/system
capacity• Proxy development may lead to increase in spatial and temporal
sources of model validation
• Feasible• Progressively speaking the same language, • Can validly build parameters characterising microbial community
identity, condition, and function into existing Michaelis-Menten-type model framework
Presentation title | Presenter name20 |
-
ENVIRONOMICS FUTURE SCIENCE PLATFORM
Thank you - ACOMO
Contact with questions, comments, and ideas:
This project Kristen [email protected]
Jenny SkerrattBiogeochemical [email protected]
Eric Raes,Molecular [email protected]
Environmental genomicsat CSIRO
Lev BodrossyEnvironmental Genomics Team [email protected]
Australian Microbiome database
Andrew Bissett Project [email protected]
Jodie Van de KampMolecular Ecologist and Bioinformatics
Nitrate isotopes Kristen Karsh Andy [email protected]
Sample collection and DNA extraction
Bronwyn HolmesMost Important Person = Research Technician
mailto:[email protected]:[email protected]:[email protected]:[email protected]:[email protected]:[email protected]
-
Presentation title | Presenter name22 |
-
• Text level one (24pt)• Text level two (20pt)
– Text level three (20pt)– Text level four (20pt)
• Text level five (18pt)
• These font sizes are recommended, font must be Calibri • You can increase font sizes providing the hierarchy of information
is maintained (ie. slide heading is largest, followed by Level 1, then Level 2 and so on)
• Font size must be consistent across all slides• Do not use font sizes smaller than 16pt; if you do not have enough
room to fit your text, spread your content over multiple slides
Presentation title | Presenter name
One column layoutSecond level
23 |
-
Two column layout
• To remove the bullets and indent on the text level one• right-click and select Bullets |
None, or select the Bullets button and select None
• right-click select Paragraph | Indentation – set Before text to 0cm and change Special: Hangingto (none)
Example of Text level one without bullets
• Text level two (to make this a bullet select all the text and click tab or increase indent button, and then click the bullet button)– Text level three
– Text level four
Presentation title | Presenter name24 |
-
Approved colour palette
Presentation title | Presenter name25 |
Midday BlueR0 G169 B206
Midnight BlueR0 G49 B60
LavenderR159 G174 B229
BlueberryR30 G34 B170
CORE PRIMARY
ACCENT (charts only)
Light TealR45 G204 B211
Dark TealR0 G115 B119
Light ForestR120 G190 B32
Dark ForestR68 G105 B61
Sky BlueR65 G182 B230
Ocean BlueR0 G75 B135
Light MintR113 G204 B152
Dark MintR0 G122 B83
Plum VermilionFuschia Orange Gold
-
Section 1:Level 2Level 3
Section divider slide with 3 text levels
-
Example of table
TITLE TITLE TITLE
Text • Bullet• Bullet
• Bullet• Bullet
Presentation title | Presenter name27 |
-
Example of figure
• Introductory text
Presentation title | Presenter name28 |
PlatformTechnology
Applications Pharmaceutical applicationsVeterinary
applicationsProbiotics/
storage PrebioticsNutrient delivery in vitro
Immunofood
Microencapsulation Incorporation of resistant starch
Successful
Successful Successful Successful
-
Example of figure
Presentation title | Presenter name29 |
00%00%00%00%00%00%00%00%00%
Chart1
category name
category name
category name
category name
category name
category name
category name
category name
category name
Column1
45
15
12
8
6
5
5
2
2
Sheet1
Column1
category name45
category name15
category name12
category name8
category name6
category name5
category name5
category name2
category name2
-
Make content easier to see
• text should be no smaller than 16 pt for content and 12 pt for graphical objects
• avoid use of slide transitions and text animations• as these can be problematic for many users, best practice is to avoid slide
transitions and text animations unless necessary to communicate information• use the approved colour palette (see slide 9) as these colours have
sufficient contrast• do not use images of text
Presentation title | Presenter name30 |
-
Make the content easy to understand
• when possible write clear and short sentences• avoid making your presentation too cluttered
• use lots of white space• stick to the slide template fonts and colours
• provide context for hyperlinks• give each slide a title
Presentation title | Presenter name31 |
-
Troubleshooting
• The background image disappears when I print• Make sure your presentation has not turned off the background
– Go to the Office button (top left hand corner) select PowerPoint options– Under the Advanced tab ensure Print in background is checked– If the background still disappears select all slides, go to Design menu –
uncheck Hide Background Graphics• The file size of my presentation is very large
• If your presentation has multiple images the file size will be large. You can compress your images to help the final size
• Compress images by using the Picture toolbar• Either change the resolution of your images (which can affect image quality
so make sure to check your images if you select this option) or compress pictures which works with colour without affecting the quality of your image
• Deleting cropped areas of images will also reduce the file size
Presentation title | Presenter name32 |
Integrating genomics, biogeochemistry, and modelling to inform management of Australian estuariesGoals for todayMarine nitrogen cycleHow does the CSIRO Environmental Modelling Suite (EMS) currently represent microbial processes?Dissolved inorganic nitrogen = currencyIdentify worthwhile microbial processes to addSlide Number 7Explicitly including microbial community properties in existing model frameworksSlide Number 9More meaningful measure of resilienceRevised modelSlide Number 12Slide Number 13Proxy developmentSlide Number 15Slide Number 16Slide Number 17What processes hold most promise for genomics-based proxies?Slide Number 19ReviewThank you - ACOMOSlide Number 22Slide Number 23Two column layoutApproved colour paletteSlide Number 26Example of tableExample of figureExample of figureMake content easier to seeMake the content easy to understandTroubleshooting