Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem

Abstract

The Columbia River (CR) is a powerful economic and environmental driver in the US Pacific Northwest. Microbial communities in the water column were analyzed from four diverse habitats: (1) an estuarine turbidity maximum (ETM), (2) a chlorophyll maximum of the river plume, (3) an upwelling-associated hypoxic zone, and (4) the deep ocean bottom. Three size fractions, 0.1–0.8, 0.8–3, and 3–200 μm were collected for each habitat in August 2007, and used for DNA isolation and 454 sequencing, resulting in 12 metagenomes of >5 million reads (>1.6 Gbp). To characterize the dominant microorganisms and metabolisms contributing to coastal biogeochemistry, we used predicted peptide and rRNA data. The 3- and 0.8-μm metagenomes, representing particulate fractions, were taxonomically diverse across habitats. The 3-μm size fractions contained a high abundance of eukaryota with diatoms dominating the hypoxic water and plume, while cryptophytes were more abundant in the ETM. The 0.1-μm metagenomes represented mainly free-living bacteria and archaea. The most abundant archaeal hits were observed in the deep ocean and hypoxic water (19% of prokaryotic peptides in the 0.1-μm metagenomes), and were homologous to Nitrosopumilus maritimus (ammonia-oxidizing Thaumarchaeota). Bacteria dominated metagenomes of all samples. In the euphotic zone (estuary, plume and hypoxic ocean), the most abundant bacterial taxa (≥40% of prokaryotic peptides) represented aerobic photoheterotrophs. In contrast, the low-oxygen, deep water metagenome was enriched with sequences for strict and facultative anaerobes. Interestingly, many of the same anaerobic bacterial families were enriched in the 3-μm size fraction of the ETM (2–10X more abundant relative to the 0.1-μm metagenome), indicating possible formation of anoxic microniches within particles. Results from this study provide a metagenome perspective on ecosystem-scale metabolism in an upwelling-influenced river-dominated coastal margin.

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

“…In contrast, nosZ and norB transcripts were enriched up to 28-fold in PA fractions, particularly at upper OMZ depths (Figure 5b), and affiliated with a community taxonomically distinct from that catalyzing upstream steps of denitrification (Figure 5d), as also reported in Dalsgaard et al (2014). These results support metagenome data from the Chilean OMZ (Ganesh et al, 2014) and from an estuarine site (Smith et al, 2013) showing nor/nos enrichment in PA fractions, suggesting a conserved PA niche. After scaling based on 16S gene counts (a proxy for cell counts), absolute counts of nosZ and Figure 1f and the FL/PA ratio (for FL counts only), with the values then divided by 1 000 000 for presentation.…”

Microbial Surface Colonization and Biofilm Development in Marine Environments

“…In non-and less-eutrophic marine environments such as pristine estuaries and offshore waters, where the majority of the particles are biogenic and thus organically enriched (123), significantly different community structures of particle-associated and free-living microorganisms are commonly found (108,114,(127)(128)(129). Particle-associated bacterial communities are frequently enriched in the marine Roseobacter clade (MRC) bacteria of the Alphaproteobacteria; the Alteromonadaceae and Vibrionaceae groups of the Gammaproteobacteria; as well as the Deltaproteobacteria, Bacteroidetes, and Planctomycetes (108,127,(130)(131)(132)(133)(134)(135)(136)(137). Many of these bacteria produce extracellular enzymes for biopolymer degradation, and some require suboxic or anoxic microniches within particles to support microaerophilic or anaerobic metabolism.…”

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

“…However, for the sample from the Sargasso Sea GS001, most of the homologous sequences to Thalassoarchaea where found in the 3-to 0.8-mm filter (GS001b) instead of the smaller fraction (inset in Figure 6). Recently, some data sets have been published that come from river estuaries or plumes (similar to the environment from which MG2-GG3 metagenome was obtained) (Smith et al, 2013;Satinsky et al, 2014). These metagenomes have large numbers of reads homologous to both MG2-GG3 and Thalassoarchaea.…”