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.

Keywords: CRISPR; ammonia-oxidizing archaea; phage; symbiont Bdellovibrio; the South China Sea.

Figure 1

New glass sponge from the South China Sea. (A) A photograph of the sponge Bathydorus sp. SQW35. The left scale bar unit is 10 mm, and the body length is about 350 mm. (B) The coxI-based maximum-likelihood phylogenetic tree was constructed using the “TIM2+F+I+G4” model. The scale bar represents 0.2 substitutions per nucleotide position.

Figure 2

Phylogenomic tree of sponge-associated MAGs and their relative abundance. (A) Phylogenomic maximum-likelihood tree of the 14 sponge-associated MAGs was constructed using the “LG+F+R7” model. Sponge-associated MAGs of Bathydorus sp. SQW35 are marked with red in the tree. All the reference genomes are listed in Supplementary Table 12. (B) Relative abundance of sponge-associated MAGs in the metagenomes of Bathydorus sp. SQW35. The relative abundance of MAGs was calculated with coverM v0.2.0 using metagenome reads after eliminating reads assigned to eukaryotic contigs.

Figure 3

Phylogenomic tree of the sponge-associated AOA MAGs. The phylogenomic maximum-likelihood tree of sponge-associated AOA MAGs was constructed using the “LG+F+R7” model. Bathydorus sp. SQW35 sponge-associated MAGs are marked with red. Sponge-associated reference MAGs from other environments are marked with blue. Methanosarcina barkeri and Methanosarcina mazei Go1 (p_Euryarchaeota) are used as outgroups. All the reference genomes are listed in Supplementary Table 12.

Figure 4

Global distribution of the sponge symbiont Nitrososphaerota B01. To investigate the distribution of B01 in sponges and surrounding environmental samples, its 16S rRNA gene sequence as a query was searched against the Sponge Microbiome Project (SMP) using BLASTN, and the target sequences with identity values of >96% were selected and assigned to Id100 (identity = 100%), Id99 (identity ≥ 99% but < 100%), Id98, Id97, and Id96 groups. The relative abundance of the B01 relatives in the SMP samples was calculated. Target sponge species and environmental samples were labeled on the world map.

Figure 5

Phylogenomic tree of the sponge-associated Bdellovibrionota MAGs. The maximum-likelihood tree was constructed using the “LG+F+R7” model. Escherichia coli DSM 30083, Escherichia coli 98NK2, and Escherichia coli ECA-727 were used as outgroups. Sponge-associated Bdellovibrionota MAGs B11 and B12 were colored in red. Free-living Bdellovibrionota MAGs with completeness > 90% were colored in blue.

Figure 6

Metabolic diagram of the symbiotic consortium in Bathydorus sp. SQW35. Solid lines refer to the metabolic pathways in which >50% of genes/enzymes were identified, and dash lines indicate missing key genes/enzymes. The pie chart shows the relative abundance of the main symbiotic MAGs in the sponge microbiome.