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Front Microbiol
2017 Feb 02;8:715. doi: 10.3389/fmicb.2017.00715.
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Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic-Anoxic Interface of the Congo Deep-Sea Fan.
Bessette S
,
Moalic Y
,
Gautey S
,
Lesongeur F
,
Godfroy A
,
Toffin L
.
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Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3-5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic-anoxic interface of sedimentary habitats by using fluorescence in situ hybridization and comparative sequence analysis of particulate mono-oxygenase (pmoA) genes. Our findings revealed that sedimentary habitats of the recent lobe complex hosted type I and type II MOB cells and comparisons of pmoA community compositions showed variations among the different organic-rich habitats. Furthermore, the pmoA lineages were taxonomically more diverse compared to methane seep environments and were related to those found at cold seeps. Surprisingly, MOB phylogenetic lineages typical of terrestrial environments were observed at such water depth. In contrast, MOB cells or pmoA sequences were not detected at the previous lobe complex that is disconnected from the Congo River inputs.
FIGURE 1. Sampling sites and observed organic-rich habitats investigated in this study; adapted from (Rabouille et al., 2016). (A) Bathymetric map of the recent lobe complex of the Congo turbidite system with the location of the five sites studied during the Congolobe cruise. The recent lobe complex of the Congo deep sea fan covers an estimated area of 3,000 km2 and is composed of a series of lobes (labeled 1–5 from the oldest to the youngest) having a grape-like prograding downstream organization. (B–H) Sampling sites into chemosynthetic habitats observed using ROV Victor 6000 and core-tube sampler. Refer to Table 1 for label significance. (B) Reduced sediment at site A with vesicomyids clusters (Col_A_V). (C) Sparse vesicomyids at site B (Col_B_V). Ecosystems at site C : (D) Black patch of reduced sediment (Col_C_BP), (E) Microbial mat (Col_C_MM), (F) Vesicomyids clusters and adjacent brown sediment (Col_C_V). (G) Microbial mat at site F (Col_F_MM). (H) Brown sediment at site E (Col_E_BS).
FIGURE 2. Individual cells and cell aggregates of methane-oxidizing bacteria (MOB) at the oxic–anoxic interface of organic-rich sedimentary habitats at the recent lobe complex (site C) of the Congo deep-sea fan, visualized with specific fluorescent-labeled oligonucleotides probes. (A–C) Clusters of type I MOB detected with the specific Cy3-labeled probe Mγ84/705 in parallel with DAPI staining. (D–J) Shape, spatial organization, and size of Methylococcales (Cy3-labeled probe MTMC-701) in parallel with DAPI staining. (K,L) Type II MOB cells hybridized with Cy3-labeled probe Mα450 in parallel with DAPI staining. Image A was taken from a sample collected at microbial mat habitats (Col_C_MM); (B,C,D–L) from black patch habitat (Col_C_BP). The scale bar represents 2 μm length.
FIGURE 3. Phylogenetic affiliations and proportion of the pmoA amino acid sequences retrieved at surface organic-rich and seep sediments of habitats in the Congo lobe deep-sea fan (Col) and Haakon Mosby volcano (VKG) respectively based on neighbor-joining tree constructed using the ARB package and inferred with a PAM correction and 100 bootstrap replicates (158 curated amino acid positions).
FIGURE 4. Phylogenetic analysis of the inferred amino acid sequences encoded by the pmoA gene of type I methane-oxidizing bacteria. The neighbor-joining tree was constructed using the ARB package and inferred with a PAM correction and 100 bootstrap replicates (158 curated amino acid positions). Bootstrap values higher than 50% are indicated. Scale bar represents 10% estimated substitutions per amino acid position. Representative sequences for each OTUs from this study are depicted in black bold and the corresponding number of sequences in OTUs are indicated in brackets.
FIGURE 5. Phylogenetic analysis of the inferred amino acid sequences encoded by the pmoA gene of type II methane-oxidizing bacteria. The neighbor-joining tree was constructed using the ARB package and inferred with a PAM correction and 100 bootstrap replicates (158 curated amino acid positions). Bootstrap values higher than 50% are indicated. Scale bar represents 10% estimated substitutions per amino acid position. Representative sequences for each OTUs from this study are depicted in black bold and the corresponding number of sequences in OTUs are indicated in brackets.
FIGURE 6. Co-occurrence of pmoA OTUs between sites. Green squares represent sedimentary habitats and circles correspond to OTUs memberships detected within habitats, based on the Betweenness-Centrality property. Node sizes are proportional to the number of connections. Colors circles indicate OTUs methane-oxidizing bacteria types (type Ia red; type Ib yellow; type Id black; and type IIa blue). Numbers indicates OTU names. Congo lobe habitats are labeled as follow: Col_C_MM (C_MM); Col_C_BP (C_BP); Col_C_V_CT6 (C_V_CT6); Col_C_V_CT12 (C_V_CT12); Col_C_BS (C_BS); Col_F_MM (F_MM); Col_A_V (A_V); Col_B_V (B_V). Haakon Mosby mud volcano is represented by sample VKGMTB8.
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