Contrasting bacterial and archaeal distributions reflecting different geochemical processes in a sediment core from the Pearl River Estuary

Abstract

Microbial community structure and metabolic activities have profound impacts on biogeochemical processes in marine sediments. Functional bacteria such as nitrate- and sulfate-reducing bacteria respond to redox gradients by coupling specific reactions amenable to relevant energy metabolisms. However, similar functional patterns have not been observed for sedimentary archaea (except for anaerobic methanotrophs and methanogens). We coupled taxonomic composition with comprehensive geochemical species to investigate the participation of distinct bacteria and archaea in sedimentary geochemical cycles in a sediment core (300 cm) from Pearl River Estuary (PRE). Geochemical properties (NO₃^-, dissolved Mn and Fe, SO₄²⁺, NH₄⁺; dissolved inorganic carbon (DIC), δ¹³C_DIC, dissolved organic carbon (DOC), total organic carbon (TOC), δ¹³C_TOC, and fluorescent dissolved organic matter (FDOM)) exhibited strong depth variability of different trends. Bacterial 16S rRNA- and dsrB gene abundance decreased sharply with depth while archaeal and bathyarchaeotal 16S rRNA gene copies were relatively constant. This resulted in an increase in relative abundance of archaea from surface (11.6%) to bottom (42.8%). Network analysis showed that bacterial groups of Desulfobacterales, Syntrophobacterales and Gammaproteobacteria were significantly (P < 0.0001) associated with SO₄^2- and dissolved Mn while archaeal groups of Bathyarchaeota, Group C3 and Marine Benthic Group D (MBGD) showed close positive correlations (P < 0.0001) with NH₄⁺, δ¹³C_TOC values and humic-like FDOM. Our study suggested that these bacterial groups dominated in redox processes relevant to sulfate or metal oxides, while the archaeal groups are more like to degrade recalcitrant organic compounds in anaerobic sediments.

Keywords: Bacterial and archaeal communities; Depth variability; Geochemical cycles; Pearl River estuarine sediments.

Fig. 1

Characteristics of pore water chemistry (NO₃⁻, NH₄⁺, dissolved Mn, Fe, and SO₄²⁻, DIC, DOC, and fluorescent components) and sediment total organic carbon (TOC). Collection of pore water for geochemical analyses was conducted onboard the ship as quickly as possible using Rhizon samplers

Fig. 2

Depth-variations in microbial 16S rRNA- and dsrB gene copies based on qPCR. a Bacterial 16S rRNA- and dsrB genes; b archaeal 16S rRNA- and bathyarchaeotal 16S rRNA genes

Fig. 3

Depth distributions of relative abundances of bacteria (a) and archaea (b). Dark blue = bacterial groups, green = total archaea and dark red = different archaeal groups

Fig. 4

Principal coordinates analysis (PCoA) (a) and linear discriminant analysis (LDA) effect size (LEfSe) of microbial groups (b) with a LDA threshold of 3.5. In (b), dark red = archaeal groups and dark blue = bacterial groups

Fig. 5

Network interactions revealed relationships between microbial and geochemical factors with a threshold of 0.65 for spearman’s coefficient and 0.0001 for P-value. Purple lines indicated positive correlations with electron donors. Gray lines indicated positive correlations with electron acceptors. Circles: Archaeal OTUs; Diamonds: Bacterial OTUs; Triangles: Geochemical factors. The numbers representing generated OTU IDs were shown in Additional file 4: Table S3

Fig. 6

The maximum likelihood tree of 16S rRNA gene sequences showing the phylogenetic affiliations of the bacterial (a) and archaeal (b) OTUs significantly related to geochemical factors (Spearman, $\rho$ > 0.65, P < 0.0001). MHVG marine hydrothermal vent group. MBGD marine benthic group B

Fig. 6

The maximum likelihood tree of 16S rRNA gene sequences showing the phylogenetic affiliations of the bacterial (a) and archaeal (b) OTUs significantly related to geochemical factors (Spearman, $\rho$ > 0.65, P < 0.0001). MHVG marine hydrothermal vent group. MBGD marine benthic group B