Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach

Abstract

Relatively little is known about the role of sponge microbiomes in the Antarctic marine environment, where sponges may dominate the benthic landscape. Specifically, we understand little about how taxonomic and functional diversity contributes to the symbiotic lifestyle and aids in nutrient cycling. Here we use functional metagenomics to investigate the community composition and metabolic potential of microbiomes from two abundant Antarctic sponges, Leucetta antarctica and Myxilla sp. Genomic and taxonomic analyses show that both sponges harbor a distinct microbial community with high fungal abundance, which differs from the surrounding seawater. Functional analyses reveal both sponge-associated microbial communities are enriched in functions related to the symbiotic lifestyle (e.g., CRISPR system, Eukaryotic-like proteins, and transposases), and in functions important for nutrient cycling. Both sponge microbiomes possessed genes necessary to perform processes important to nitrogen cycling (i.e., ammonia oxidation, nitrite oxidation, and denitrification), and carbon fixation. The latter indicates that Antarctic sponge microorganisms prefer light-independent pathways for CO2 fixation mediated by chemoautotrophic microorganisms. Together, these results show how the unique metabolic potential of two Antarctic sponge microbiomes help these sponge holobionts survive in these inhospitable environments, and contribute to major nutrient cycles of these ecosystems.

Host species determine symbiotic community composition in Antarctic sponges (Porifera: Demospongiae)

“…Contrastingly, these phyla represent a much lower percentage in Antarctic sponges (0.0005-0.4%). Our results are in agreement with previous studies carried out in Antarctica (Rodríguez-Marconi et al 2015; Cárdenas et al 2018; Steinert et al 2019; Moreno-Pino et al 2020). Other widely described but less abundant phyla associated with sponges from other geographical areas are Poribacteria and PAUC34f (Moitinho-Silva et al 2017b).…”

“…Other widely described but less abundant phyla associated with sponges from other geographical areas are Poribacteria and PAUC34f (Moitinho-Silva et al 2017b). These bacterial groups were not detected neither in the Antarctic sponges from the present study nor in other species previously studied in Antarctica (Rodríguez-Marconi et al 2015; Cárdenas et al 2018; Steinert et al 2019; Cárdenas et al 2019; Moreno-Pino et al 2020). These phyla have been found overrepresented in HMA over LMA sponges and can be used as “HMA/LMA indicators” (Moitinho-Silva et al 2017b; Glasl et al 2018).…”

“…To date, published data support the combination of host identity, geography, and environment as the main forces determining the structure of sponge microbiomes (Webster et al 2010; Schmitt et al 2012; Easson et al 2020). In Antarctica in particular, the microbial signature of sponges might be also related to a biogeographic partitioning of Southern Ocean microorganisms caused by the Polar Front, such as the deficit of Cyanobacteria in Antarctica (Wilkins et al 2013), as evidenced in the present and previous studies (Rodríguez-Marconi et al 2015; Cárdenas et al 2018; Moreno-Pino et al 2020). Since most collection efforts of sponges have so far explored tropical and temperate environments, this study contributes to expand our knowledge on sponge microbiome structure in polar waters.…”

“…This work describes the bacterial and archaeal diversity and the community composition of four Antarctic sponge species, revealing that the sponges had a microbial signature different from the richer and diverse seawater community. In Antarctica, due to the difficult access to this region, only few studies have made comprehensive descriptions of microbial symbionts of marine sponges (Webster et al 2004; Rodríguez-Marconi et al 2015; Cárdenas et al 2018; Steinert et al 2019; Cárdenas et al 2019; Moreno-Pino et al 2020). However, this is the first study that assesses the microbial communities associated to Antarctic sponges using high throughput sequencing, considering biological replications and covering a spatial scale over 650 km.…”

“…However, the most comprehensive studies describing microbial communities associated to Antarctic sponges using classic and high throughput sequencing described a total prokaryotic composition of 26 bacterial and 3 archaeal phyla and the presence of 8 eukaryotic groups (Webster et al 2004; Rodríguez-Marconi et al 2015; Cárdenas et al 2018; Steinert et al 2019; Cárdenas et al 2019). Recently, functional metagenomics has been used to characterize the community composition and metabolic potential of microbiomes of two Antarctic sponges (Moreno-Pino et al 2020). In the Bacteria domain those assemblages primarily clustered within the Gamma and Alphaproteobacteria followed by the Bacteroidetes phylum.…”