Metaproteomics of aquatic microbial communities in a deep and stratified estuary

Abstract

Here we harnessed the power of metaproteomics to assess the metabolic diversity and function of stratified aquatic microbial communities in the deep and expansive Lower St. Lawrence Estuary, located in eastern Canada. Vertical profiling of the microbial communities through the stratified water column revealed differences in metabolic lifestyles and in carbon and nitrogen processing pathways. In productive surface waters, we identified heterotrophic populations involved in the processing of high and low molecular weight organic matter from both terrestrial (e.g. cellulose and xylose) and marine (e.g. organic compatible osmolytes) sources. In the less productive deep waters, chemosynthetic production coupled to nitrification by MG-I Thaumarchaeota and Nitrospina appeared to be a dominant metabolic strategy. Similar to other studies of the coastal ocean, we identified methanol oxidation proteins originating from the common OM43 marine clade. However, we also identified a novel lineage of methanol-oxidizers specifically in the particle-rich bottom (i.e. nepheloid) layer. Membrane transport proteins assigned to the uncultivated MG-II Euryarchaeota were also specifically detected in the nepheloid layer. In total, these results revealed strong vertical structure of microbial taxa and metabolic activities, as well as the presence of specific "nepheloid" taxa that may contribute significantly to coastal ocean nutrient cycling.

Environmental Microbial Community Proteomics: Status, Challenges and Perspectives

“…Moreover, hexulose-6-phosphate synthase, the key enzyme of the RuMP pathway of OM43, is also detected in all Atlantic Ocean samples. In addition, methanol oxidation proteins originating from the common OM43 marine clade are also identified in a deep and stratified estuary [50]. These results support the in situ activities of the OM43 clade using one-carbon compounds for energy production.…”

Production and persistence of bacterial and labile organic matter at the hypoxic water–sediment interface of the St. Lawrence Estuary

“…These trends are in agreement with transmissivity values measured in situ, with values below 94% found in the surface waters of S18 and S22 or near the bottom of the LSLE stations (S20.5 and S22; Table ). The increase in turbidity near the bottom of the LSLE stations (S20.5 and S22) can be associated with the presence of a nepheloid layer (Colatriano et al ). This nepheloid layer might be absent or thinner (i.e., below the deepest sampling depth) at S18 in the GSL.…”

“…Although the presence of microbial OM near the water–sediment interface of the LSLE is clear, the strong increase in THAA concentrations and yields in this zone is probably not caused by a particularly intense bacterial production. A recent study of aquatic microbial communities in the LSLE (at a station between S20.5 and S22) revealed that the nepheloid layer is characterized by lower bacterial abundance and bacterial productivity compared to surface waters (2 and 39 times lower, respectively; Colatriano et al ). The accumulation of AA and bacterial molecules in the nepheloid layer of the LSLE is thus likely caused by another factor.…”

“…A metaproteomic study by Colatriano et al () in the LSLE revealed the presence of microbial taxa that are specialized for the nepheloid layer. This is supported here by a different relative composition of the d ‐AA bacterial biomarkers in this zone.…”

Nitrospina bacteria in a rocky intertidal habitat (Quintay Bay, central Chile)

“…Members of this phylum have been detected in the field and are basically related to marine chemolithotrophic nitrification (Pachiadaki et al., ). Nitrospina ‐like bacteria have been detected from the surface down to the deep ocean (DeLong et al., ; Nunoura et al., ; Santoro, Casciotti, & Francis, ; Watson & Waterbury, ) including in oxygen minimum zones (OMZs) (Beman, Shih, & Popp, ; Fuchsman, Kirkpatrick, Brazelton, Murray, & Staley, ; Labrenz, Jost, & Jurgens, ; Zaikova et al., ), oxic/anoxic sediments (Davis, Stakes, Wheat, & Moyer, ; Jorgensen et al., ; Rani, Koh, Rhee, Fujitani, & Park, ), and deep estuarine environments (Colatriano et al., ). These bacteria reach abundances as high as 9.25% of total 16S‐rRNA gene sequences recovered in bacterial sequence libraries obtained from the eastern tropical North Pacific (Beman et al., ), and up to one‐third of the bacterial 16S‐rRNA gene sequences in deep hypersaline ponds in the Red Sea (Ngugi, Blom, Stepanauskas, & Stingl, ).…”