SpongeNOB SquarePants: Microbial Nitrification in a Marine Sponge

Microbes are essential to the cycling of nitrogenous compounds in ocean systems. The process of nitrification involves the oxidation of ammonia to bioavailable nitrate via a nitrite intermediary. Ammonia can exist in marine environments as a fixation product of diazotrophic cyanobacteria, however a large source is attributable to the nitrogenous waste of various organisms. Sponges excrete ammonia as a waste product however there is evidence to suggest that this waste is detoxified by the metabolic activity of the sponge microbiome. Previous metagenomic studies (such as Bayer et al, 2008) identified 16S rRNA genetic signatures of nitrifying microbiota in marine sponges. This implies that the filtration activities of sponges may play a key biochemical role in the nitrification of regional waters. However, transcriptional data for such species is lacking and therefore the functional nitrifying activity of these microbes is poorly understood.

To rectify this, Feng et al, 2016 applied gene-sequencing and transcriptional profiling to the nitrifying microbiome of the widely distributed sponge Theonella swinhoei (Porifera: Demospongiae) collected from the South China Sea. The authors characterised the community identity by PCR amplification of 16S rRNA and microbial nitrification gene sequences using targeted primers. Subsequent phylogenetic analyses revealed that archaeal 16S rRNA and amoA amplicons (the latter coding for a subunit of ammonia monooxygenase) were closely related to Nitrosopumilus-like ammonia-oxidising Archaea (AOA) while bacterial 16S rRNA and nxrB amplicons (the latter coding for a subunit of nitrite oxidoreductase) were closely related to Nitrospira-like nitrite-oxidising Bacteria (NOB). Interestingly, the authors went on to quantify the relative abundance of these taxa and found AOA’s to be significantly more prevalent than NOB’s, which correlated to the increased relative abundance of AOA amoA to NOB nxrB mRNA as measured using qPCR. The authors hypothesise that the abundance of AOA is attributable to the importance of ammonia detoxification in maintaining the health of the sponge. Overall, this study provides a key insight into nitrification within a model sponge holobiont. Previous studies have exemplified the importance of marine microbes in global nitrification (such as Karner et al, 2001), however it appears that similar processes govern regional and intra-organismal nitrification.

However, there should be caution in extrapolating these findings too broadly. Even at an intraspecific scale, the AOA and NOB community structure identified in this study is incongruent with that characterised from an allopatric Palau population of the same species. This suggests that idiosyncrasies are rife in the sponge holobiont, attributable to either biogeographically differential abiotic factors or host selection of microbiota.

In the future, I would like to see this study embellished with mesocosmic studies, perhaps using the nitrification inhibitor nitrapyrin to gain a greater understanding of sponge nitrification as a phenotype.  I would also be excited to see these findings augmented with further research into the diversity and genetic repertoire of denitrifying sponge-associated Bacteria. As sponges possess the ability to filter vast volumes of water, a comprehensive understanding of such Bacteria may enable researchers to exploit this ability in the bioremediation of eutrophicated waters.

In conclusion, this research should be appreciated as a fascinating case study into microbial nitrification within a sponge holobiont but cannot at this stage represent a generalisation. Its significance should not be exaggerated until further research is conducted.  

Reviewed Paper: Feng, G., Sun, W., Zhang, F., Karthik, L., & Li, Z. (2016). Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei. Scientific reports, 6. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844951/

Further Reading: Bayer, K., Schmitt, S., & Hentschel, U. (2008). Physiology, phylogeny and in situ evidence for bacterial and archaeal nitrifiers in the marine sponge Aplysina aerophoba. Environmental Microbiology, 10(11), 2942-2955. http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2008.01582.x/full