Bacterial community analysis in environmental monitoring programs: a useful approach?

Alfred-Wegener-Institute

for Polar- and Marine Research Helmholtz-Association

Biological Station Helgoland Shelf See Systems Ecology D-27489 Helgoland

Rebecca Störmer*, Antje Wichels*, Gunnar Gerdts*

*Alfred-Wegener Institute for Polar- and Marine Research, Helgoland, Germany;

Introduction

From 2005 to 2010 6 mio m³ of dredged material were dumped 15 kilometres south off Helgoland in the German Bight (North Sea). Dumping activities may cause physical disturbance, including burial of benthic organisms and changes in substrate matter, affecting the whole benthic communities. The monitoring programs of dumping sites base on international conventions (London convention) for dredged material handling. These recommend the assessment of defined physical, chemical and biological parameters to examine the impact of the disposal. Benthic bacterial communities are disregarded by these recommendations. In an interdisciplinary project with environmental agencies we investigated benthic bacterial community in response to dumping activity. Our study aims to assess the suitability of bacterial community analysis as a proxy for environmental perturbation and consequently the applicability for mandatory monitoring programs.

We applied ribosomal community analyses (ARISA fingerprints, 16S ribosomal tag-sequencing) and functional gene arrays (GeoChip 4.2) to investigate structure and function of benthic bacterial communities at the dumping site.

Fig. 4 (A) Bar chart showing the percentage of detected functional genes for the subsamples

(B) Differences were tested applying the analysis of variance and post hoc Tukey tests for pair wise comparison (p<0.05)

Results

Dumping centre:

Low alpha-diversity as revealed by automated ribosomal intergenic spacer analysis (ARISA) and ribosomal tag- sequencing

Highest number of sequences affiliated to Desulfuromonadaceae

Significantly lower diversity in functional genes as compared to a reference site, exemplarily shown for functional genes involved in organic remediation

Fig. 2 Spatial distribution of the sum of ARISA-OTUs as calculated by ordinary kriging. Dots represent the 125 sampling stations.

Bacterial community analysis in environmental monitoring programs: a useful approach?

Fine scale investigations at a dumping site

Fig. 1 The dumping site in the German Bight and the dredging zone in the Elbe River

(A) Sampling scheme of monitoring at the dumping site

(B) Red stars represent samples subjected to 16S ribosomal tag- sequencing and functional gene array (GeoChip 4.2)

Conclusion

Perturbation caused by dumping activities affects structure and function of bacterial communities favoring a less diverse but possibly more specialised bacterial community

bacterial community analyses represent a promising tool for the assessment of environmental perturbation

We recommend the inclusion of bacterial community analyses in mandatory monitoring programs

dum ping

cent re

1.5 km

2 km _1

2 km _2

3 km _1

3 km _2

Referenc e_1

Referenc e_2

No. OTUs

0 500 1000 1500 2000 2500

dum ping

cent re

1.5 km

2 km _1

2 km _2

3 km _1

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Referenc e_1

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No. seqs

0 1000 2000 3000 4000 5000

Desulfuromonadaceae unclassified Desulfobulbaceae unclassified Desulfobulbaceae unclassified Flavobacteriaceae unclassified Desulfobulbaceae unclassified Desulfobulbaceae unclassified Desulfobulbaceae unclassified Gammaproteobacteria unclassified Bacteroidetes unclassified

Gammaproteobacteria unclassified Deltaproteobacteria unclassified Gammaproteobacteria unclassified Sulfurovum

Desulfobulbaceae unclassified Syntrophobacterale sunclassified Gammaproteobacteria unclassified Desulfobacteraceae unclassified Desulfobacteraceae unclassified

dum ping

cent re a

dum ping

cent er b

dum ping

cent re c 1.5 km a

1.5 km b 1.5 km

c 2 km_1

a 2 km

_1 b 2 km_1

c 2 km

_2 a 2 km

_2 b 2 km_2

c 3 km

_1 a 3 km

_1 b 3 km_1

c 3 km

_2 a 3 km

_2 b 3 km_2

c

referenc e_1

a

referenc e_1

b

referenc e_1

c

referenc e_2

a

referenc e_2

b

referenc e_2

c

% deteced functional genes

0 2 4 6 8 10 12 14 16

dumping centre 1.5 km 2 km_1 2 km_2 3 km_1 3 km_2 Reference_1 Reference_2

SQ FG MQ F p dumping centre ^{1.000 0.933 0.002 0.000 0.994 0.000 0.000}

1.5 km ^{1.000 0.822 0.001 0.000 0.963 0.000 0.000}

Konstante ^{2.935 1.000 2.935 39639.430 0.000} 2 km_1 ^{0.933 0.822 0.022 0.001 1.000 0.000 0.000}

Sample ^{0.014 7.000 0.002 27.382 0.000} 2 km_2 ^{0.002 0.001 0.022 0.617 0.010 0.304 0.035}

Error ^{0.001 16.000 0.000} 3 km_1 ^{0.000 0.000 0.001 0.617 0.000 0.999 0.611}

3 km_2 ^{0.994 0.963 1.000 0.010 0.000 0.000 0.000}

Reference_1 ^{0.000 0.000 0.000 0.304 0.999 0.000 0.904}

Reference_2 ^{0.000 0.000 0.000 0.035 0.611 0.000 0.904}

A

B

Fig. 3 OTUs (0.97) derived from tag sequencing: Number of OTUs (A) and top 18 OTUs (contributing > 10% to the whole community) at the sampling sites.

A B

ARISA fingerprints

GeoChip 4.2 approach Ribosomal tag-sequencing

A

B