Diversity and structure of bacterial and archaeal communities associated with the vulnerable sponge Halichondria cebimarensis

Sponges are essential components of the marine benthos and well known for their complex and abundant associated microbial communities. There are five endemic species of the genus Halichondria on the Brazilian coast and H. cebimarensis is one of the least studied. This sponge has a very limited geographic distribution and is classified as vulnerable. In order to understand the bacterial and archaeal communities associated with this sponge, samples of H. cebimarensis were collected from the southwestern Atlantic coast (Brazil, Sao Paulo state). Choanosome samples were separated and processed to be (i) inoculated in three different culture media; (ii) investigated by transmission electron microscopy; (iii) submitted to 16S rRNA metabarcoding. Forty isolates were obtained and 12 were identified as belonging to the Bacilli class. The culture-dependent approaches allowed us to access unique members of the microbial community. Our analyses revealed that this animal belongs to the Low Microbial Abundance group of sponges. Culture-independent approaches showed that the H. cebimarensis microbiome is dominated by the heterotrophic Gammaproteobacteria AqS2 (Ca. Amphirhobacter heronislandensis). This is the first study to reveal details of the microbiome of this vulnerable sponge and is an important step in understanding how this sponge functions, its biotechnological potential and a contribution to conservation efforts.

海绵是海洋底栖生物的核心组成部分，以其复杂多样的共生微生物群落而闻名。巴西沿岸分布有5种软海绵属（Halichondria）的特有物种，而H. cebimarensis是其中研究程度最低的物种之一。该海绵地理分布范围极为狭窄，被列为易危物种。为解析该海绵共生的细菌与古菌群落，研究人员于大西洋西南沿岸（巴西圣保罗州）采集了H. cebimarensis的样本。研究人员分离出海绵的髓质（choanosome）样本并开展三类处理：① 接种至三种不同的培养基中；② 通过透射电子显微镜进行观测；③ 进行16S rRNA元条形码测序分析。最终共获得40株分离菌株，其中12株经鉴定属于芽孢杆菌纲（Bacilli）。通过分离培养的研究策略，我们得以获取该微生物群落中的独特类群。分析结果显示，该海绵属于低微生物丰度海绵类群。非培养依赖的研究方法表明，H. cebimarensis的微生物组以异养γ-变形菌纲AqS2（Ca. Amphirhobacter heronislandensis）为优势类群。本研究首次揭示了这一易危海绵的微生物组细节，为解析该海绵的生态功能、挖掘其生物技术应用潜力以及推进海绵保护工作提供了重要支撑。