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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?


Dissolved inorganic nitrogen = currency


N2 NO3- NH4+

livingPON

detritalPON

denitrification

nitrification

remineralisation

mortality and sinkingN2 fixation

NO3-assimilation

NH4+ assimilation

Identify worthwhile microbial processes to add


N2 NO3- NH4+DNRAdenitrification

nitrification

anammox

OrgC : NO3- supply


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



V Vmax KM [S]



×[𝑁𝑁2]




9 |



×[𝑁𝑁2]






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


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


N2 NO3- NH4+

livingPON

detritalPON

DNRAdenitrification

nitrification

remineralisation


NO3-assimilation

NH4+ assimilation

anammox

Proxy developmentCase study 1: Coastal nitrogen removal vs retention

12 |

Process

Enzyme kinetics

(Enzyme)


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



N2 NO3- NH4+

livingPON

detritalPON

DNRAdenitrification

nitrification

remineralisation


NO3-assimilation

NH4+ assimilation


Proxy developmentCase study 2: Open ocean nitrification

16 |


nitrification

anammox

nrfA


Proxy developmentCase study 2: Open ocean nitrification

17 |

What processes hold most promise for genomics-based proxies?


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


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]

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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

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