Changes in community structures and functions of the gut microbiomes of deep-sea cold seep mussels during in situ transplantation experiment

(2023) 5:17 Xiao et al. Animal Microbiome https://doi.org/10.1186/s42523-023-00238-8 Animal Microbiome Open Access RESEARCH Changes in community structures and functions of the gut microbiomes of deep‑sea cold seep mussels during in situ transplantation experiment Yao Xiao1,2, Hao Wang3, Yi Lan1,2, Cheng Zhong1,2, Guoyong Yan1,2, Zhimeng Xu1,2, Guangyuan Lu1,4, Jiawei Chen1,2, Tong Wei1,2, Wai Chuen Wong1,2, Yick Hang Kwan5 and Pei‑Yuan Qian1,2* Abstract Background Many deep-sea invertebrates largely depend on chemoautotrophic symbionts for energy and nutrition, and some of them have reduced functional digestive tracts. By contrast, deep-sea mussels have a complete digestive system although symbionts in their gills play vital roles in nutrient supply. This digestive system remains functional and can utilise available resources, but the roles and associations among gut microbiomes in these mussels remain unknown. Specifically, how the gut microbiome reacts to environmental change is unclear. Results The meta-pathway analysis showed the nutritional and metabolic roles of the deep-sea mussel gut microbi‑ ome. Comparative analyses of the gut microbiomes of original and transplanted mussels subjected to environmental change revealed shifts in bacterial communities. Gammaproteobacteria were enriched, whereas Bacteroidetes were slightly depleted. The functional response for the shifted communities was attributed to the acquisition of carbon sources and adjusting the utilisation of ammonia and sulphide. Self-protection was observed after transplantation. Conclusion This study provides the first metagenomic insights into the community structure and function of the gut microbiome in deep-sea chemosymbiotic mussels and their critical mechanisms for adapting to changing environ‑ ments and meeting of essential nutrient demand. Keywords Gigantidas mussel, Metagenome, Nutritional role, Haima seep, In situ experiment *Correspondence: Pei‑Yuan Qian 1 Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, People’s Republic of China 2 Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People’s Republic of China 3 Center of Deep‑Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, People’s Republic of China 4 Research Center for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 51807, People’s Republic of China 5 Department of Biology, HADAL and Nordcee, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark Background The gut microbiome plays an essential role in nutrient assimilation, converting photosynthesis-derived food components into absorbable metabolites in most animals [1, 2]. Apart from photosynthesis, chemosynthesis is a crucial process that enables animals to gain nutrition in deep-sea cold seep and hydrothermal vent ecosystems [3]. These extreme habitats are characterised by darkness, high hydrostatic pressure, and lack of photosynthesisderived nutrients [4]. Invertebrates, such as bathymodioline mussels and siboglinid tubeworms, have successfully colonised these hostile ecosystems and often formed © The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Xiao et al. Animal Microbiome (2023) 5:17 dense communities. The ecological success of deep-sea mussels and tubeworms relies on chemosynthetic symbionts fuelled by the simple reduction of molecules, such as methane and hydrogen sulphide, into organic compounds that are passed from symbionts to the host. Compared with tubeworms, which have a degenerated digestive system, mussels have a fully developed digestive system consisting of a mouth, a stomach, two digestive glands, an intestine, and other organs, although the gut is reduced in size [5]. The transmission electron microscope (TEM) image of a mussel stomach showed filled nutritional particles, and a stable isotope experiment detected a low δ13C value in the gut [6, 7]. Bathymodiolus thermophilus can ingest and assimilate free-living bacteria through filter-feeding in a highly pressurised flow-through acrylic aquarium [8]. These observations clearly indicate that the digestive systems of deep-sea mussels have nutritional and physiological functions. Deep-sea mussels have a mixotrophic diet that includes heterotrophic and autotrophic nutritional processes, and the retained ability of filter-feeding affords them flexibility in using carbon sources and obtaining ecological benefits. However, most previous studies on deep-sea mussels focused on the prominent trophic role of chemosynthetic endosymbiotic bacteria and did not consider the function of the gut microbiome. The nutritional role of heterotrophy is poorly understood, and the adaptation of the gut microbiome associated with the nutritional cycling in deep-sea mussels at genomic level has not been explored. Gigantidas haimaensis is a newly described species of the deep-sea bathymodioline mussel from the Haima cold seep in the South China Sea and houses methaneoxidising bacteria (MOB) inside their gill epithelial cells [9]. Symbiotic bacteria can capture bubble-forming gaseous methane advected to near-surface sediments in the cold seep area for microbial oxidation. Depending on upflow rates, disturbance frequencies and other physical factors, the total methane emission varies in active seep areas [10], and these variations result in different methane concentrations around cold seep mussels. Cold seep mussels were previously believed to use methane as the sole carbon and energy source, and they can adapt to a wide range of methane concentrations (0.7–33.7 µM) to survive in extreme environments [11, 12]. The growth and physiological conditions of cold seep mussels are shaped by methane concentration [13]. Notably, observations from the gill indices and fluorescence in situ hybridisation showed that Bathymodiolus azoricus exhibits a marked decrease in dry weight and total symbiont abundance in the absence of methane [14]. In this study, we found that the gut microbiome can assimilate nutrients from the genomic view and Page 2 of 13 hypothesised that t (...truncated)