16S rRNA gene analysis of prokaryotic communities among three different marine hosts Authors: Andrea Aldas-Vargas1,2, Detmer Sipkema1, Hauke Smidt1, Georg Steinert1 1Laboratory of Microbiology, Wageningen University, The Netherlands 2Subdepartment of Environmental Technology, Wageningen University, The Netherlands
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Background
Results
Microbial communities are often dense and diverse in many marine invertebrates. Macroinvertebrates are one of the most important hosts for bacteria and
Anthozoa
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archaea and those associations have potentially shaped the evolutionary paths Porifera
of both host and symbiont alike. The marine invertebrates selected for the study were: Ascidiacea, Anthozoa, Porifera.
Ascidiacea 74 0
Porifera
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200
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Figure 5. The number of samples before quality filtering evaluated for this project. Samples were analysed from 42 studies, collected as part of the meta-data collection phase.
High and low microbial abundance Solitary Colonial Gut and tunic tissue
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Seawater
Surface mucus layer Coral tissue Calcium carbonate skeleton
Ascidiaceae
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HMA - 108 – 109 LMA - 105– 106 (microbial cells/g sponge)
Anthozoa
Figure 1. Factors which showed influence the microbial distribution per host
Those three marine invertebrates already showed some patterns of microbial distribution, which depend on factors represented on the Figure 1. Ascidian Coral Sponge Seawater
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Objective The symbiotic relationships between the microorganisms and macroinvertebrates are quite complex. The two working hypothesis are represented in the Figure 2.
Figure 6. nMDS ordination plot (Bray-Curtis distance) of marine invertebrates and seawater samples at A) phylum and B) genus level.
The microbial distribution is influenced by the host type: Ascidiaceae, Anthozoa or Porifera
Alphaproteobacteria Ruegeria
There are congruent patterns of microbial distribution at five taxonomic ranks (from phylum to genus level) in those three hosts.
Prevent larval and algal settlement
Gammaproteobacteria Produce quorum sensing signalling molecules
Endozoicomonas
Figure 2. General hypothesis of the present research project
Cyanobacteria
Methods
Synechococcus
Provide both: energy and carbon
The identification of the different microorganisms in marine hosts can now be achieved by 16S rRNA gene amplicon sequencing. Figure 3 shows a descriptive scheme of the methodology.
Figure 7. Potential function of the most abundant taxa per host at low taxonomic ranks A
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Studies
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Mothur • Sequence information (raw data or demultiplexed)
• OTU tables • Taxonomy classification
• Concatenation • Diversity and community analysis
Databases
Figure 3. General methodology overview.
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Collapsed Genus (A to L)
Collapsed Family (A to L)
Collapsed Order (A to L)
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C
Abundance tables (OTUs)
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G
D E
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The microbial community of the marine hosts is composed by generalists at high taxonomic levels and specialist microbes at low taxonomic levels. Collapsed Class (A to L)
Collapsed Phylum (A to L)
Figure 4. Integration from different datasets to collapsed abundance tables.
Overcoming Methodological Challenges v The studies used different amplicons of the 16S rRNA. v Individual abundance tables were obtained after processing. v Different taxonomic levels were evaluated on the collapsed files. A scheme on how the wide variety of studies were treated in order to evaluate a relevant number of datasets is presented in Figure 4.
Take home messages
The most abundant microbes at low taxonomic ranks have potentially specific ecological roles for the host.
The host type influences the microbial community but not as much as the host identity (i.e. host species) at all microbial taxonomic ranks.
Sponge’s microbial community clustered in accordance with the dichotomy between LMA and HMA sponges.
