Bacterial aerobic methane cycling by the marine sponge-associated microbiome

BACKGROUND

Methanotrophy by the sponge-hosted microbiome has been mainly reported in the ecological context of deep-sea hydrocarbon seep niches where methane is either produced geothermically or via anaerobic methanogenic archaea inhabiting the sulfate-depleted sediments. However, methane-oxidizing bacteria from the candidate phylum Binatota have recently been described and shown to be present in oxic shallow-water marine sponges, where sources of methane remain undescribed.

RESULTS

Here, using an integrative -omics approach, we provide evidence for sponge-hosted bacterial methane synthesis occurring in fully oxygenated shallow-water habitats. Specifically, we suggest methane generation occurs via at least two independent pathways involving methylamine and methylphosphonate transformations that, concomitantly to aerobic methane production, generate bioavailable nitrogen and phosphate, respectively. Methylphosphonate may be sourced from seawater continuously filtered by the sponge host. Methylamines may also be externally sourced or, alternatively, generated by a multi-step metabolic process where carnitine, derived from sponge cell debris, is transformed to methylamine by different sponge-hosted microbial lineages. Finally, methanotrophs specialized in pigment production, affiliated to the phylum Binatota, may provide a photoprotective function, closing a previously undescribed C1-metabolic loop that involves both the sponge host and specific members of the associated microbial community.

CONCLUSION

Given the global distribution of this ancient animal lineage and their remarkable water filtration activity, sponge-hosted methane cycling may affect methane supersaturation in oxic coastal environments. Depending on the net balance between methane production and consumption, sponges may serve as marine sources or sinks of this potent greenhouse gas. Video Abstract.

Comparative Genomics of Thaumarchaeota From Deep-Sea Sponges Reveal Their Niche Adaptation

Thaumarchaeota account for a large portion of microbial symbionts in deep-sea sponges and are even dominant in some cases. In this study, we investigated three new sponge-associated Thaumarchaeota from the deep West Pacific Ocean. Thaumarchaeota were found to be the most dominant phylum in this sponge by both prokaryotic 16S rRNA amplicons and metagenomic sequencing. Fifty-seven published Thaumarchaeota genomes from sponges and other habitats were included for genomic comparison. Similar to shallow sponge-associated Thaumarchaeota, those Thaumarchaeota in deep-sea sponges have extended genome sizes and lower coding density compared with their free-living lineages. Thaumarchaeota in deep-sea sponges were specifically enriched in genes related to stress adapting, symbiotic adhesion and stability, host–microbe interaction and protein transportation. The genes involved in defense mechanisms, such as the restriction-modification system, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, and toxin-antitoxin system were commonly enriched in both shallow and deep sponge-associated Thaumarchaeota. Our study demonstrates the significant effects of both depth and symbiosis on forming genomic characteristics of Thaumarchaeota, and provides novel insights into their niche adaptation in deep-sea sponges.

Lineage-specific energy and carbon metabolism of sponge symbionts and contributions to the host carbon pool

Marine sponges host a wide diversity of microorganisms, which have versatile modes of carbon and energy metabolism. In this study we describe the major lithoheterotrophic and autotrophic processes in 21 microbial sponge-associated phyla using novel and existing genomic and transcriptomic datasets. We show that the main microbial carbon fixation pathways in sponges are the Calvin–Benson–Bassham cycle (energized by light in Cyanobacteria, by sulfur compounds in two orders of Gammaproteobacteria, and by a wide range of compounds in filamentous Tectomicrobia), the reductive tricarboxylic acid cycle (used by Nitrospirota), and the 3-hydroxypropionate/4-hydroxybutyrate cycle (active in Thaumarchaeota). Further, we observed that some sponge symbionts, in particular Acidobacteria, are capable of assimilating carbon through anaplerotic processes. The lithoheterotrophic lifestyle was widespread and CO oxidation is the main energy source for sponge lithoheterotrophs. We also suggest that the molybdenum-binding subunit of dehydrogenase (encoded by coxL) likely evolved to benefit also organoheterotrophs that utilize various organic substrates. Genomic potential does not necessarily inform on actual contribution of autotrophs to light and dark carbon budgets. Radioisotope assays highlight variability in the relative contributions of photo- and chemoautotrophs to the total carbon pool across different sponge species, emphasizing the importance of validating genomic potential with physiology experimentation.