Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp.

Abstract

Sponges are widely distributed in the global ocean and harbor diverse symbiotic microbes with mutualistic relationships. However, sponge symbionts in the deep sea remain poorly studied at the genome level. Here, we report a new glass sponge species of the genus Bathydorus and provide a genome-centric view of its microbiome. We obtained 14 high-quality prokaryotic metagenome-assembled genomes (MAGs) affiliated with the phyla Nitrososphaerota, Pseudomonadota, Nitrospirota, Bdellovibrionota, SAR324, Bacteroidota, and Patescibacteria. In total, 13 of these MAGs probably represent new species, suggesting the high novelty of the deep-sea glass sponge microbiome. An ammonia-oxidizing Nitrososphaerota MAG B01, which accounted for up to 70% of the metagenome reads, dominated the sponge microbiomes. The B01 genome had a highly complex CRISPR array, which likely represents an advantageous evolution toward a symbiotic lifestyle and forceful ability to defend against phages. A sulfur-oxidizing Gammaproteobacteria species was the second most dominant symbiont, and a nitrite-oxidizing Nitrospirota species could also be detected, but with lower relative abundance. Bdellovibrio species represented by two MAGs, B11 and B12, were first reported as potential predatory symbionts in deep-sea glass sponges and have undergone dramatic genome reduction. Comprehensive functional analysis indicated that most of the sponge symbionts encoded CRISPR–Cas systems and eukaryotic-like proteins for symbiotic interactions with the host. Metabolic reconstruction further illustrated their essential roles in carbon, nitrogen, and sulfur cycles. In addition, diverse putative phages were identified from the sponge metagenomes. Our study expands the knowledge of microbial diversity, evolutionary adaption, and metabolic complementarity in deep-sea glass sponges.

The addition of discrimination inhibitors stimulations discrimination potential and N2O emissions were linked to predation among microorganisms in long term nitrogen application and straw returning systems

“…Since the key taxa of AOA was not identified, the relevant functions were analyzed by NCBI similar sequence alignment ( Supplementary Table 3 ). By comparison, the key AOA species may be Nitrososphaerota archaeon, which can obtain energy during ammonia oxidation and utilize carbon dioxide as a chemoautotrophic carbon source ( Wei et al, 2023 ). The interactions between protists and AOA or AOB may provide substrates and motivation for the soil nitrification process and stimulate nitrogen transformation.…”

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects

“…Notably, almost all the symbiotic MAGs in the sponge Bathydorus sp. SQW35 have genes encoding Cas proteins and an ammonia-oxidizing Nitrososphaerota MAG B01, dominating the internal sponge environment, exhibits a highly complex CRISPR array [ 109 ]. This complex array signifies a favorable evolutionary adaptation to a symbiotic lifestyle and reflects a potent ability to resist phage attacks within the sponge’s ecosystem.…”

“…(3) Use of CRISPR as a marker to track microbe-virus interactions in the ocean. Strikingly, comparative analysis of CRISPR sequences in prokaryotic genomes and viral genomes enables the identification of host–virus pairs, uncovering new infection relationships, and analyzing virus–host interactions [ 59 , 90 , 104 , 109 , 139 , 140 , 141 , 142 , 143 ]. For instance, thy A gene, a fragment of the cold-active Colwelliaphage 9A, was discovered in the CRISPR sequences of Syntrophus aciditrophicus , suggesting a history of viral infection in the organism [ 113 ].…”