Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris
Open Access
- 13 April 2023
- journal article
- research article
- Published by American Society for Microbiology in Microbiology Spectrum
- Vol. 11 (2), e0435322
- https://doi.org/10.1128/spectrum.04353-22
Abstract
Marine and freshwater sponges harbor diverse communities of bacteria with vast potential to produce secondary metabolites that may play an important role in protecting the host from predators and infections. In this work, we initially used cultivation and metagenomics to investigate the microbial community of the freshwater sponge Spongilla lacustris collected in an Austrian lake. Representatives of 41 bacterial genera were isolated from the sponge sample and classified according to their 16S rRNA gene sequences. The genomes of 33 representative isolates and the 20 recovered metagenome-assembled genomes (MAGs) contained in total 306 secondary metabolite biosynthesis gene clusters (BGCs). Comparative 16S rRNA gene and genome analyses showed very little taxon overlap between the recovered isolates and the sponge community as revealed by cultivation-independent methods. Both culture-independent and -dependent analyses suggested high biosynthetic potential of the S. lacustris microbiome, which was confirmed experimentally even at the subspecies level for two Streptomyces isolates. To our knowledge, this is the most thorough description of the secondary metabolite production potential of a freshwater sponge microbiome to date.IMPORTANCE A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received so far much less attention with respect to their microbiomes, members of which may produce bioactive secondary metabolites with potential to be developed into drugs to treat a variety of diseases. In this work, we investigated the potential of bacteria associated with the freshwater sponge Spongilla lacustris to biosynthesize diverse secondary metabolites. Using culture-dependent and -independent methods, we discovered over 300 biosynthetic gene clusters in sponge-associated bacteria and proved production of several compounds by selected isolates using genome mining. Our results illustrate the importance of a complex approach when dealing with microbiomes of multicellular organisms that may contain producers of medically important secondary metabolites. A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received so far much less attention with respect to their microbiomes, members of which may produce bioactive secondary metabolites with potential to be developed into drugs to treat a variety of diseases.Keywords
Funding Information
- Universität Wien (MetaBac)
This publication has 79 references indexed in Scilit:
- Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine spongesThe ISME Journal, 2013
- SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genesBioinformatics, 2012
- Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine spongesThe ISME Journal, 2011
- MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile dataBMC Bioinformatics, 2010
- Metabolomic Characterization of the Salt Stress Response in Streptomyces coelicolorApplied and Environmental Microbiology, 2010
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Microbial community of freshwater sponges in Lake BaikalBiology Bulletin, 2008
- Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern ChinaApplied and Environmental Microbiology, 2006
- Photosynthesis by symbiotic algae in the freshwater sponge, Spongilla lacustrisLimnology and Oceanography, 1994
- Population Dynamics and Standing Biomass of the Freshwater Sponge Spongilla LacustrisEcology, 1982