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Bacterial community structure and composition does it correlate with pond productivity? Sandra Infante-Villamil , Roger Huerlimann, Kelly Condon, Gregory Maes and Dean Jerry Centre for Sustainable Tropical Fisheries and Aquaculture, James

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Bacterial community structure and composition – does it correlate with pond productivity?

Sandra Infante-Villamil, Roger Huerlimann, Kelly Condon, Gregory Maes and Dean Jerry

Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University

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Challenges to shrimp farming

Global shrimp industry Diseases International market prices Feed costs Trade barriers

Wang et al., 2000 Tran et al., 2013

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Introduction

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Diseases

Bacteria

  • Traditionally

Causative agents of disease

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Production losses Non- biological agents

  • Recently

Bacteria Host = Well-being

Introduction

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Gut microbiome plays an important role in maintaining a host’s health

(Fernandez et al., 2014).

Gut microbiome

Development

  • f the immune

system Protection against pathogens Synthesis of aa and vitamins Modulation of metabolism Caloric extraction from indigestible comp of diet

?

Introduction 4

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Bacterial community

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Bacterial community Culture methods Metagenomics 99% Introduction

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Next generation Sequencing technology (NGS)

Introduction 6

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Bacterial community

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Aquaculture sector

Environment Host Bacterial community Introduction

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From single species detection to whole communities

Introduction 8

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NGS in prawn culture

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Bali bay (non-polluted) 7 295 Bali aquaculture 10 269 Jakarta (polluted) 7 122 OTU Faecal Sample Location Number of samples

Introduction

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Pond productivity

Differences in pond productivity

  • Pond size
  • Stocking date (genetic

stock)

  • Density of PL
  • PL from same hatchery

Introduction10

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Research question

  • Are bacterial communities in the prawn (GUT and Gastric

mill) and the environment (sediments and water) different in ponds with different productivity?

Introduction11

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Methods

Sampling design

Sediment Intestine (GUT) and Gastric mill (GM) Water P1(HP1) P2(HP2) P3(LP1) P4(LP2) Ponds High productive (HP) Low productive (LP) Sample Replicate 4 4 4 n = 12 n = 3 P1(HP1) P2(HP2) P3(LP1) P4(LP2) Ponds Replicate n = 9 n = 9 n = 3 n = 3 3 3 3 1 1 1 1 1 1 3 3 3 1 1 1

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Pond productivity (HP)

  • Standardized to most

productive pond as determined by yield.

  • Pond size
  • Genetic stock
  • Density of PL
  • PL from same

hatchery

Pond Yield (%) HP1 98 HP2 100 LP1 42 LP2 43

Results13

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Bacterial richness (OTU)

Sediment and water GM and GUT LP 147 137 116 79 146 152 102 77 Results14

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Bacterial community

Gut and GM Water Sediment LP HP Results15

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GUT GM

HP HP LP LP

Bacterial community

Results16

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Relative abundance

GM GUT Sed Wat GM GUT Sed Wat X X X X X X X X X X X X X X X X X X X X X X X X X X X X Low Productive Propionigenium Vibrio Salinihabitans Thioalkalispira Candidatus bacilloplasma Candidatus aquiluna Ferrimonas Fusibacter Photobacterium Genus Prochlorococcus Thiohalophilus Desulfococcus High Productive Desulfobulbus

Results17

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Relative abundance

Results18

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Relative abundance

GM GUT Sed Wat GM GUT Sed Wat X X X X X X X X X X X X X X X X X X X X X X X X X X X X Low Productive Propionigenium Vibrio Salinihabitans Thioalkalispira Candidatus bacilloplasma Candidatus aquiluna Ferrimonas Fusibacter Photobacterium Genus Prochlorococcus Thiohalophilus Desulfococcus High Productive Desulfobulbus

Results19

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Relative abundance

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GM GUT Sed Wat GM GUT Sed Wat X X X X X X X X X X X X X X X X X X X X X X X X X X X X Desulfococcus High Productive Desulfobulbus Low Productive Propionigenium Vibrio Salinihabitans Thioalkalispira Candidatus bacilloplasma Candidatus aquiluna Ferrimonas Fusibacter Photobacterium Genus Prochlorococcus Thiohalophilus

Results

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Relative abundance

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GM GUT Sed Wat GM GUT Sed Wat X X X X X X X X X X X X X X X X X X X X X X X X X X X X Desulfococcus High Productive Desulfobulbus Low Productive Propionigenium Vibrio Salinihabitans Thioalkalispira Candidatus bacilloplasma Candidatus aquiluna Ferrimonas Fusibacter Photobacterium Genus Prochlorococcus Thiohalophilus

Results

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Pearson’s correlation

Abundance of Vibrio associated with prawn weight Prawn weight Results22

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Insights

High productive

  • Gut and GM

Photobacterium and Candidatus bacilloplasma Vibrio

  • Sediment

Desulfococcus

Low productive

  • Gut and GM

OTU richness Vibrio , Fusibacter and Propionigenium

  • GUT

Ferrimonas

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$ $

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Insights

  • Bacterial communities

Water ≠ Sediment ≠ GUT and GM (selective pressure)

Chaiyapechara et al. (2012), and by Cardona et al. (2016) in water and GUT.

  • Vibrio

– ˃ 50% bacterial community in GUT and GM in LP. AND – Abundance prawn weight

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Insights and future

  • NGS technology + bioinformatics

✓Enable the understanding of the microbial diversity thriving in aquaculture ponds. ✓Associations among microbial communities and prawn genotype or phenotype + environmental factors? ✓Selection of potential probiotic candidates? (e.g. Candidatus bacilloplasma). Effect in survival, growth, water quality.

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Microbiome

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Acknowledgements

  • Commercial partner
  • JCU – Aquaculture Genetics Group

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Questions?