GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

• Published in: FEMS microbiology ecology 2014-12, Vol.90 (3), p.832-843
• Main Authors: Bayer, Kristina, Moitinho-Silva, Lucas, Brümmer, Franz, Cannistraci, Carlo V., Ravasi, Timothy, Hentschel, Ute
• Format: Article
• Language: English
• Subjects: Ammonia - metabolism; Ammonification; amplicon sequencing; Animals; Aquatic Organisms - microbiology; Archaea - genetics; Bacteria - genetics; Base Sequence; Carbon fixation; Chemical analysis; Community composition; Denitrification; Ecology; functional gene; GeoChip; Indian Ocean; Marine; marine sponge; Mediterranean Sea; Microbial Consortia - genetics; Microbiology; Nitrogen - metabolism; Oxidoreductases - genetics; Phylogeny; Porifera; Porifera - genetics; Porifera - microbiology; RNA, Ribosomal, 16S - genetics; Seawater; Seawater - microbiology; Sequence Analysis, DNA; Symbiosis; Water analysis
• ISSN: 0168-6496; 1574-6941
• DOI: 10.1111/1574-6941.12441

Abstract The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater. GeoChip analyses of sponge and seawater microbiomes revealed differences in nitrogen-, carbon metabolism, and stress response. The HMA/LMA dichotomy was confirmed on the level of functional genes. GeoChip analyses of sponge and seawater microbiomes revealed differences in nitrogen-, carbon metabolism, and stress response. The HMA/LMA dichotomy was confirmed on the level of functional genes.