a foundational biodiversity map of the terrestrial...
TRANSCRIPT
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: [email protected]
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