a foundational biodiversity map of the terrestrial...

A foundational biodiversity map of the terrestrial

microbiome of a sub-Antarctic island.

Siddarthan Venkatachalam1, Robert Pienaar1, Gwynneth Matcher1, Nasipi Mtsi1,

Peter le Roux2, Michelle Greve2, Bettine Jansen van Vuuren3, Sudharshan

Sekar3, Rosemary Dorrington1

1Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 2Department of Plant and Soil Sciences, University of Pretoria 3Department of Zoology, University of Johannesburg

Marion Island (46° 54´ S, 37° 45´ E)

Prince Edward Island (46° 38´ S, 37°

Marion Island (290 km2) and Prince Edward (45 km2)1

PEIs are of volcanic origin

Important breeding site for seabirds and mammals2

Gradual increase 0.04°C per year

Decrease in annual precipitation

Fragile ecosystem

Sub-Antarctic Island: Prince Edward Islands

(courtesy of I. Meiklejohn).

Marion Island Vegetation

The vascular flora (N.J.M. Gremmen, pers. comm.)

22 native species,

18 introduced species

3 unknown species

Indigenous plant

Azorella selago Hook. f.

Invasive plant

Sagina procumbens L.

Courtesy of Robert Pienaar

Research Questions

1. Does different habitat complexes in the Marion island contains different

microbial communities?

2. What microbial groups are associated with the root tissues of plants

(rhizosphere), surrounding soils and how do plants benefit from their

microbiome?

3. Do different soils and plants types host different microbial communities?

4. Is there any significant differences among rhizosphere microbial communities

of indigenous Azorella selago and invasive Sagina procumbens plant species?

If so how they are influencing the sub-Antarctic ecosystems.

Over all objective

To map the genetic diversity of microbial communities and plant species

present in the Marion Island under different habitat complexes.

Habitat Soil Azorella Blechnum Sagina Crassula Cotula Agrostis Acaena Rachomytrium

(moss)

Fellfield 8 7 2 1 Nil Nil Nil Nil 1

Polar

desert 3 Nil Nil Nil Nil Nil Nil Nil Nil

Salt spray 2 6 Nil 9 8 6 Nil Nil Nil

Mire-Slope 8 2 6 8 Nil Nil 1 1 Nil

Sample collection under different habitats

Samples were collected during 2016 Marion takeover voyage, (April/May)

Molecular Taxonomy

Highly conserved regions

– Identical in all bacteria

– Single PCR primer pair

can amplify 16S rRNA

genes from diverse

bacteria

Highly variable regions

– Conserved within

species

– Divergent between

species

E517F (5’-CAGCAGCCGCGGTAA-3’) E969-984 (5’-GTAAGGTTCYTCGCGT-3’)

Bacteria : 16S rRNA gene

Eukaryotes : 18S rRNA gene

Plant Barcoding genes

Ribulose biphosphate

carboxylase large (rbcL)

Maturase K (matK)

Vascular indigenous plant species barcoded in Marion Island

Acaena magellanica,

Agrostis castellana,

Agrostis magellanica,

Blechnum penna-marina,

Callitriche,

Cotula plumose,

Crassula moschata,

Elaphaglossum,

Grammitis kerguelensis,

Hymenophyllum peltatum,

Juncus,

Limosella,

Lycopodium magellanicum,

Lycopodium saururus,

Montia fontaum,

Poa cookii,

Polystichum,

Pringlea antiscorbutica,

Ranunculus biternatus,

Uncinia compacta.

Plant Barcoding

https://wikivisually.com/lang-es/wiki/Acaena_magellanica

Microbial community diversity between different habitats

Phylogenetic classification

Phylogenetic classification of bacterial reads represented by heat map. The bacterial 16S rRNA gene sequences

were amplified from gDNA and classification was carried out using the Silva reference database (Version 128) and

the Mothur software (Version 1.39) platform.

Phylogenetic classification

Phylogenetic classification of bacterial reads represented by heat map. The bacterial 16S rRNA gene sequences

were amplified from gDNA and classification was carried out using the Silva reference database (Version 128) and

the Mothur software (Version 1.39) platform.

Non-Metric Multidimensional Scaling Plot

Non-metric multidimensional scaling (nMDS) ordination plots. The 16S rRNA amplicon libraries generated from gDNA.

The 2D-NMDS was standardized by square-root transformation and a Bray–Curtis dissimilarity matrix. The 16S rRNA

bacterial OTUs generated (cut-off 97%)

Microbial community diversity between

indigenous and invasive plant

Azorella selago Hook. f.

One of the primary colonizers3

Most abundant and widely distributed4

High impact on Marion Island ecosystems

Ecosystem engineers involves in soil

formations

Provides microclimates for microbes and

small insects

Sagina Procumbens L.

First found on Marion Island in 19655

Increasing distribution on Marion6

Can colonize new environments (e.g.

Surtsey)7

Greve et al. 2017

Exposed

Soil

Soil

Control

3

12

6

9 Soil Underneath

Cushion

Diagram of sampling

Indigenous and Invasive plant

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

M1

M3

M1

0

M1

2

M1

9

M2

1

M2

7

M2

9

M3

5

M3

7

M4

3

M4

5

M5

2

M5

4

M6

0

M6

2

RR

08

2

RR

08

4r1

RR

08

5

RR

09

2

RR

09

3r2

RR

10

0

RR

10

2

RR

10

9

RR

11

1

RR

11

9

RR

12

1

RR

12

8

RR

13

0

RR

13

7

RR

13

9

RR

14

6

RR

14

8

ROS 1 ROS 2 ROS 3 ROS 4 ROS 5 ROS 6 ROS 7 ROS 8 SAG 1 SAG 2 SAG3 SAG 4 SAG 5 SAG 6 SAG 7 SAG 8

Ab

un

da

nce

Re

lati

ve

to

Sa

mp

le T

ota

l (%

)

Soil Sample Underneath Plant Body

Acidobacteria

Actinobacteria

Bacteroidetes

Chlamydiae

Chloroflexi

Cyanobacteria

Dependentiae

Fibrobacteres

Firmicutes

Gemmatimonadetes

Latescibacteria

Minor Phyla

Nitrospirae

Patescibacteria

Planctomycetes

Proteobacteria

Rokubacteria

Spirochaetes

Unclassified Bacteria

Verrucomicrobia

Phylogenetic classification

Principal Coordinates Analysis

Fast UniFrac based PCoA ordination plots. The 16S rRNA amplicon libraries generated from gDNA and The 16S rRNA

bacterial OTUs generated at the cut-off 97%. The samples were standardized by square-root transformation and a Bray–Curtis dissimilarity matrix.

Summary

Diversity and distribution of bacterial communities across different

habitat complexes in Marion Island were studied.

Saltspray habitats contains distinct bacterial diversity pattern

Bacterial assemblages between indigenous Azorella selago and

invasive Sagina procumbens found to be significantly different.

Future Work

Priority habitat sites-

Functional Genomics: Metabolic profiles of bacterial genomes

Other flagship programs

Marine spatial planning: Algoa Bay R.A. Dorrington and A.T. Lombard

Antarctic Circumnavigation Expedition

Sarah Fawcett and R.A. Dorrington

Other flagship programs

Stromatolites biodiversity survey:

Gordon and Betty Moore foundation - R.A. Dorrington and Kerry L Mcphail

Freshwater Lake : Algal Blooms - Guy Bate and R.A. Dorrington

1 Venkatachalam S. et al., 2017. PloS One. 12 (8), e0183400

2Venkatachalam S. et al., 2018. Limnology and Oceanography online first

3McGeoch, M. A. et al., 2008. Stellenbosch, RSA: Sun Press, pp. 215–276.

4Phiri, E.E., McGeoch, M.A. & Chown, S.L. 2015. Polar Biology. 38(11):1881–

1890

5Gremmen, N. 1975. South African Journal of Antarctic Research. 5:25–30.

6Ramaswiela, T. 2010. MSc thesis. Stellenbosch University.

7Magnússon, B. et al. 2009. Surtsey Research. 12(5):57–76.

References

ACKNOWLEDGEMENTS

Marine Natural Products Lab, 417

NRF SARchi

Any Queries /Collaboration

/Assistance in genomics platform

Dr. Venkat Siddarthan,

Post-Doctoral Researcher,

Department of Biochemistry and Microbiology,

Rhodes University, Grahamstown

Email: v.siddarthan@ru.ac.za

Bacterial Communities – Azorella selago

Azorella 1 - Large Azorella 3 - Large

Azorella 5 - Large Azorella 7 - Large

Bacterial Communities – Azorella selago

Azorella 2 - Small Azorella 4 - Small

Azorella 6 - Small Azorella 8 - Small

Bacterial Communities – Sagina procumbens

Sagina 1 - Large Sagina 3 - Large

Sagina 5 - Large Sagina 7 - Large

Bacterial Communities – Sagina procumbens

Sagina 2 - Medium

Sagina 4 - Small Sagina 6 - Small

Sagina 8 - Medium