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. 2020 Oct 30;8(11):1699.
doi: 10.3390/microorganisms8111699.

The Diversity, Composition, and Putative Functions of Gill-Associated Bacteria of Bathymodiolin Mussel and Vesicomyid Clam from Haima Cold Seep, South China Sea

Juan Ling  1   2 , Hongxiang Guan  3 , Lihua Liu  3 , Jun Tao  4 , Jie Li  1   2 , Junde Dong  1   2 , Si Zhang  1   2
Affiliations

The Diversity, Composition, and Putative Functions of Gill-Associated Bacteria of Bathymodiolin Mussel and Vesicomyid Clam from Haima Cold Seep, South China Sea

Juan Ling et al. Microorganisms. .

Abstract

The Haima cold seep, which is one of the two active cold seeps in the South China Sea, is known for its great ecological importance. The seep bivalves are assumed to depend mainly on their bacterial symbiosis for survival and growth. However, information on the bacterial diversity, composition, and putative function of gill-associated of dominant dwelling animals in Haima cold seep remain elusive. Herein, we adopted a high-throughput sequencing of 16S rRNA gene amplicons, and function prediction methods (Functional Annotation of Prokaryotic Taxa (FAPROTAX) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICURUSTs)) to purposely illustrate the taxonomic and phylogenetic diversity, composition, and putative functions of the symbionts in bathymodiolin mussel Gigantidas haimaensis (Bivalvia: Mytilidae: Gigantidas) and vesicomyid clam Archivesica marissinica (Bivalvia: Glossoidea: Vesicomyidae). The predominant microbes of both species were Proteobacteria and Gammaproteobacteria on the phylum and class level, respectively. The taxonomic and phylogenetic diversity of gill microbial communities in G. haimaensis were significantly different from those in A. marissinica (p < 0.05). Nine functional groups, including seven carbon-related biogeochemical groups, were identified through the FAPROTAX analysis. However, the most dominant groups for G. haimaensis and A. marissinica were both chemoheterotrophic. G. haimaensis and A. marissinica shared many pathways, however, 16 obtained Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups (42.11%) significantly differed between the two species (p < 0.05). These findings would provide insight into the functions of microbes in the element cycling and energy flow as well as the host-symbiont relationship of bivalves in the Haima cold seep environment.

Keywords: Haima cold seep; gill-associated microbial community; mussel and clam; potential function.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; the collection, analyses, or interpretation of data; the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Photograph of the two species of bivalves Gigantidas haimaensis and Archivesica marissinica from Haima cold seep. The in situ photo showing the population of G. haimaensis (A) and A. marissinica (B). The photo of single G. haimaensis (C) and A. marissinica (D).
Figure 2
Figure 2
The taxonomic composition of bathymodiolin mussel G. haimaensis (Group A) and vesicomyid clam A. marissinica (Group B) at the phylum level (A) and the genus level (B), respectively.
Figure 3
Figure 3
Phylogenetic relationship and annotation of ZOTUs (zero-radius operational taxonomic units) obtained in the gill of bathymodiolin mussel G. haimaensis and vesicomyid clam A. marissinica. From inner to outer: ring 1 represents all the ZOTUs detected this study; rings 2 and 3 indicate the phylogenetic classification of ZOTUss at the phylum and class level, respectively, and their legends were in the left part; rings 4 and 5 with heatmaps show the relative abundance of ZOTUs in abundance in each group. The legends were in the left part with G. haimaensis (Group A) and A. marissinica (Group B). The outer rings 6 and 7 with histograms demonstrated a relative abundance of ZOTUs in G. haimaensis (blue) and A. marissinica (in red).
Figure 4
Figure 4
The alpha diversity indices including (A) ZOTUs (zero-radius operational taxonomic units) richness, (B) Simpson, (C) Shannon diversity index, and (D) Faith’s phylogenetic diversity index for obtained gill-associated microbial communities of G. haimaensis (Group A) and A. marissinica (Group B).
Figure 5
Figure 5
Phylogenic tree of the gill-associated microbes in G. haimaensis (A) and A. marissinica (B) for their top 10 high abundance ZOTUs (zero-radius operational taxonomic units) and their reference sequences, respectively, inferred from the Neighbor-Joining (NJ) analysis. The ZOTUs in (A) indicated the top 10 ZOTUs in G. haimaensis, and the ZOTUs in (B) indicated the top 10 ZOTUs in A. marissinica. The bootstrap values (> 50%) of relevant nodes are shown based on 1000 replicates. Sequences from this study are shown in bold. Scale bars: 2% of the estimated sequence divergence.
Figure 5
Figure 5
Phylogenic tree of the gill-associated microbes in G. haimaensis (A) and A. marissinica (B) for their top 10 high abundance ZOTUs (zero-radius operational taxonomic units) and their reference sequences, respectively, inferred from the Neighbor-Joining (NJ) analysis. The ZOTUs in (A) indicated the top 10 ZOTUs in G. haimaensis, and the ZOTUs in (B) indicated the top 10 ZOTUs in A. marissinica. The bootstrap values (> 50%) of relevant nodes are shown based on 1000 replicates. Sequences from this study are shown in bold. Scale bars: 2% of the estimated sequence divergence.
Figure 6
Figure 6
Variation analysis of gill-associated microbial community between G. haimaensis (Group A) and A. marissinica (Group B) at the ZOTUs (zero-radius operational taxonomic units) level. Red bars and dots stand for G. haimaensis, and blue bars and dots stand for A. marissinica.
Figure 7
Figure 7
The bubble plot of the function groups predicted against the FAPROTAX database for G. haimaensis (Group A) and A. marissinica (Group B).
Figure 8
Figure 8
The heatmap of KO groups predicted by PICRUSt analysis in G. haimaensis (Group A) and A. marissinica (Group B) at KEGG level 2.
Figure 9
Figure 9
Variation analysis of gill-associated microbial community between G. haimaensis (Group A) and A. marissinica (Group B) at KEGG level 2. Red bars and dots stand for G. haimaensis, and blue bars and dots stand for A. marissinica.
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