Depth matters: (anti) microbial diversity of marine sponges

Anak Agung Gede Indraningrat

Research output: Thesisinternal PhD, WU


This thesis aims to investigate the impact of depth on prokaryotic community composition and metabolite profiles, including antimicrobial activities, in marine sponges. Understanding both the prokaryotic community and metabolite profiles of sponges in relation to depth will provide important insights for marine ecology and future bioprospecting efforts of bioactive compounds from the sponge holobiont. A brief overview of prokaryotic community composition in sponges from shallow water to the deep sea and motivation of this research is described in chapter 1. Chapter 2 is a comprehensive literature review on antimicrobial activities (antiviral, antibacterial, antifungal and antiprotozoal) of microbial isolates from marine sponges. The most potent antimicrobial compounds against microbial targets documented to date based on in vitro tests are: 2-undecyl-4-quinolone (human immunodeficiency virus 1 (HIV-1), truncateol M (influenza A virus), thiopeptide YM-266183 (nosocomial Gram positive bacteria), sydonic acid (Escherichia coli), naphthacene glycoside SF2446A2 (Chlamydia trachomatis), manzamine A (Plasmodium spp. and Leishmania donovani), valinomycin and staurosporine (Trypanosoma brucei), and saadamycin (Candida albicans and dermatophytic fungi). Furthermore, we identified Streptomyces, Pseudovibrio, Bacillus, Aspergillus and Penicillium as the leading producers of currently known antimicrobial compounds.

In chapter 3, the impact of depth on prokaryotic community composition and antimicrobial activities of two demosponges, Xestospongia muta and Agelas sventres, was investigated. Sponges were sampled from three depth categories: shallow (< 30 m), medium (30 – 60m) and deep (> 60 m) from the Curaçao Sea. Our findings showed that specific OTUs assigned to Cyanobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Proteobacteria and Thaumarchaeota contributed to the significant variance in prokaryotic community composition observed along the depth gradient. Shallow sponge specimens generally yielded higher antibacterial activities compared to deep specimens. Based on this study, we hypothesized that the observed differences in prokaryotic community composition and antimicrobial activities may be caused by different physicochemical conditions (light and nutrient availability) along the depth gradient.

In chapter 4, cultivability of sponge-associated bacteria of X. muta and A. sventres collected from different depths in the Curaçao Sea was investigated. We observed that the source of inoculum (sponge species) and the cultivation medium had more pronounced impact on the prokaryotic community recovered than the depth from which the sample was collected. Subsequently, antimicrobial screening of 41 and 20 bacterial isolates from X. muta and A. sventres, respectively, led to identification of ten isolates from X. muta and eight isolates from A. sventres with biological activity against at least one of the bacterial indicator strains: Escherichia coli, Aeromonas salmonicida, Bacillus subtilis, and Staphylococcus simulans, whereas no inhibition of the oomycete Saprolegnia parasitica or the yeast Candida oleophila was observed.

It is intriguing how depth impacts prokaryotic community composition and metabolite profiles of deep-sea sponges. In chapter 5, we studied the microbiome and metabolome of the three deep-sea sponges Weberella bursa, Stryphnus fortis and Geodia baretti collected along a depth range of 200 – 1400 m in Davis Strait. The most pre-dominant OTUs that varied with depth (increased, decreased or stable) in S. fortis and G. barretti could be assigned to Acidobacteria, Chloroflexi, Thaumarchaeota and Proteobacteria. In contrast, in W. bursa, the most pre-dominant OTUs that varied with depth were affiliated with Gammaproteobacteria and Planctomycetes. Furthermore, we found that secondary metabolite concentrations associated with these deep-sea sponges also varied with depth. As depth increased we observed that concentrations of anti-biofouling compounds known to be produced by G. barretti (barettin, 8,9-dihydrobarettin and soelterin) decreased significantly, whereas concentrations of known compounds in S. fortis (ianthelline and stryphnusin) substantially increased in deep specimens.

Finally, chapter 6 elaborates and integrates findings obtained from the different research chapters. At two different geographic locations and across different depth ranges, we observed that depth significantly affected prokaryotic community composition at OTU level and at the same time also influenced metabolite profiles and antimicrobial activities in shallow as well as deep-sea sponges. In contrast, depth did not consistently affect cultivability of sponge-associated bacteria as opposed to the source of inocula and the growth media. Future research direction should be focused on metagenomics in order to obtain a clearer insight on how prokaryotic community composition and diversity of biosynthesis secondary metabolite gene clusters of sponges is different across a depth gradient.

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
  • Smidt, Hauke, Promotor
  • Sipkema, Detmer, Co-promotor
  • Becking, Lisa, Co-promotor
Award date29 May 2019
Place of PublicationWageningen
Print ISBNs9789463439442
Publication statusPublished - 29 May 2019


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