Transcriptomic responses of sponge holobionts to in situ, seasonal anoxia and hypoxia

Climate change is expanding marine oxygen-minimum zones (deep areas with little to no dissolved oxygen), and enhanced nutrient runoff is causing coastal eutrophication and subsequent deoxygenation. Deoxygenation can be fatal for many marine animals; however, some sponge species (phylum: porifera) are tolerant of hypoxia and anoxia. Indeed, two sponge species, Eurypon sp. 2 and Hymeraphia stellifera, survive anoxia for months at a time. To understand their tolerance mechanisms, we sequenced the metagenomes and transcriptomes of these sponges and performed differential gene expression analyses on the sponges, their mitochondria and their microbial symbionts under in situ conditions of normoxia, hypoxia and anoxia. Each species possessed a unique microbiome, but the microbiome of each species was dominated by a species-specific Thaumarchaeon and a Gammaproteobacterium. Sponges and their microbial symbionts contain significant and underrepresented marine genetic resources. This sequencing effort yielded two novel, reference transcriptomes for the poriferan species (increasing the number of publicly available poriferan transcriptomes by approximately 15%), and four novel metagenome-assembled genomes for their microbial symbionts. Gene expression for the sponge hosts and their symbionts was species-and oxygen-level dependent, though there were some shared interspecific responses to deoxygenation. In general, few changes occurred in the expression of sponge metabolic genes as a function of oxygenation level, indicating that they may remain metabolically active under anoxia. However, ATP synthesis genes were significantly upregulated under hypoxia when compared to normoxia, and genes for DNA replication were downregulated. Mitochondrial gene expression was effectively unchanged under both hypoxia and anoxia. Nevertheless, both anoxia and hypoxia caused upregulation of heat shock proteins (HSPs), indicating cellular level adaptations to deoxygenation stress. Thaumarchaeota symbionts also upregulated stress response genes in hypoxia, while maintaining expression of oxygen-dependent metabolic pathways under hypoxia and anoxia. Gammaproteobacteria symbionts showed relatively few noteworthy changes in gene expression in response to anoxia but decreased metabolic gene expression in hypoxia. There was no clear evidence of upregulated anaerobic respiration in the transcriptomes of the sponge holobionts under anoxia or hypoxia. Moreover, the Thaumarchaeota were identified as ammonia-oxidizing archaea that were closely related to a free-living species capable of oxygen production. If the symbionts can produce oxygen for their hosts, this could underline their deoxygenation tolerance and explain the lack of anaerobic respiration noted under anoxia. The marine genetic resources sequenced in this project aide our understanding of deoxygenation tolerance and could provide a blueprint for limiting the risks to marine animals in future oceans facing localized and global deoxygenation.