Kai Ziervogel

Marine snow formation in the aftermath of the Deepwater Horizon oil spill in the Gulf of Mexico

The large marine snow formation event observed in oil-contaminated surface waters of the Gulf of Mexico (GoM) after the Deepwater Horizon accident possibly played a key role in the fate of the surface oil. We characterized the unusually large and mucus-rich marine snow that formed and conducted roller table experiments to investigate their formation mechanisms. Once marine snow lost its buoyancy, its sinking velocity, porosity and excess density were then similar to those of diatom or miscellaneous aggregates. The hydrated density of the component particles of the marine snow from the GoM was remarkably variable, suggesting a wide variety of component types. Our experiments suggest that the marine snow appearing at the surface after the oil spill was formed through the interaction of three mechanisms: (1) production of mucous webs through the activities of bacterial oil-degraders associated with the floating oil layer; (2) production of oily particulate matter through interactions of oil components with suspended matter and their coagulation; and (3) coagulation of phytoplankton with oil droplets incorporated into aggregates. Marine snow formed in some, but not all, experiments with water from the subsurface plume of dissolved hydrocarbons, emphasizing the complexity of the conditions leading to the formation of marine snow in oil-contaminated seawater at depth.

Chemical dispersants can suppress the activity of natural oil-degrading microorganisms

Significance Oil spills are a significant source of hydrocarbon inputs into the ocean. In response to oil spills, chemical dispersants are applied to the oil-contaminated seawater to disperse surface slicks into smaller droplets that are presumed to be more bioavailable to microorganisms. We provide evidence that chemical dispersants applied to either deep water or surface water from the Gulf of Mexico did not stimulate oil biodegradation. Direct measurement of alkane and aromatic hydrocarbon oxidation rates revealed either suppression or no stimulation of oil biodegradation in the presence of dispersants. However, dispersants affected microbial community composition and enriched bacterial populations with the ability to use dispersant-derived compounds as growth substrates, while oil-alone amendments enriched for natural hydrocarbon degraders. During the Deepwater Horizon oil well blowout in the Gulf of Mexico, the application of 7 million liters of chemical dispersants aimed to stimulate microbial crude oil degradation by increasing the bioavailability of oil compounds. However, the effects of dispersants on oil biodegradation rates are debated. In laboratory experiments, we simulated environmental conditions comparable to the hydrocarbon-rich, 1,100 m deep plume that formed during the Deepwater Horizon discharge. The presence of dispersant significantly altered the microbial community composition through selection for potential dispersant-degrading Colwellia, which also bloomed in situ in Gulf deep waters during the discharge. In contrast, oil addition to deepwater samples in the absence of dispersant stimulated growth of natural hydrocarbon-degrading Marinobacter. In these deepwater microcosm experiments, dispersants did not enhance heterotrophic microbial activity or hydrocarbon oxidation rates. An experiment with surface seawater from an anthropogenically derived oil slick corroborated the deepwater microcosm results as inhibition of hydrocarbon turnover was observed in the presence of dispersants, suggesting that the microcosm findings are broadly applicable across marine habitats. Extrapolating this comprehensive dataset to real world scenarios questions whether dispersants stimulate microbial oil degradation in deep ocean waters and instead highlights that dispersants can exert a negative effect on microbial hydrocarbon degradation rates.

Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia

Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel production and bioremediation. Here we demonstrate the use of a new, efficient approach to recover genomes of active polysaccharide degraders from natural, complex microbial assemblages, using a combination of fluorescently labeled substrates, fluorescence-activated cell sorting, and single cell genomics. We employed this approach to analyze freshwater and coastal bacterioplankton for degraders of laminarin and xylan, two of the most abundant storage and structural polysaccharides in nature. Our results suggest that a few phylotypes of Verrucomicrobia make a considerable contribution to polysaccharide degradation, although they constituted only a minor fraction of the total microbial community. Genomic sequencing of five cells, representing the most predominant, polysaccharide-active Verrucomicrobia phylotype, revealed significant enrichment in genes encoding a wide spectrum of glycoside hydrolases, sulfatases, peptidases, carbohydrate lyases and esterases, confirming that these organisms were well equipped for the hydrolysis of diverse polysaccharides. Remarkably, this enrichment was on average higher than in the sequenced representatives of Bacteroidetes, which are frequently regarded as highly efficient biopolymer degraders. These findings shed light on the ecological roles of uncultured Verrucomicrobia and suggest specific taxa as promising bioprospecting targets. The employed method offers a powerful tool to rapidly identify and recover discrete genomes of active players in polysaccharide degradation, without the need for cultivation.

Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the Deepwater Horizon oil spill site.

The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities.

Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard

ABSTRACT Heterotrophic microbial communities in seawater and sediments metabolize much of the organic carbon produced in the ocean. Although carbon cycling and preservation depend critically on the capabilities of these microbial communities, their compositions and capabilities have seldom been examined simultaneously at the same site. To compare the abilities of seawater and sedimentary microbial communities to initiate organic matter degradation, we measured the extracellular enzymatic hydrolysis rates of 10 substrates (polysaccharides and algal extracts) in surface seawater and bottom water as well as in surface and anoxic sediments of an Arctic fjord. Patterns of enzyme activities differed between seawater and sediments, not just quantitatively, in accordance with higher cell numbers in sediments, but also in their more diversified enzyme spectrum. Sedimentary microbial communities hydrolyzed all of the fluorescently labeled polysaccharide and algal extracts, in most cases at higher rates in subsurface than surface sediments. In seawater, in contrast, only 5 of the 7 polysaccharides and 2 of the 3 algal extracts were hydrolyzed, and hydrolysis rates in surface and deepwater were virtually identical. To compare bacterial communities, 16S rRNA gene clone libraries were constructed from the same seawater and sediment samples; they diverged strongly in composition. Thus, the broader enzymatic capabilities of the sedimentary microbial communities may result from the compositional differences between seawater and sedimentary microbial communities, rather than from gene expression differences among compositionally similar communities. The greater number of phylum- and subphylum-level lineages and operational taxonomic units in sediments than in seawater samples may reflect the necessity of a wider range of enzymatic capabilities and strategies to access organic matter that has already been degraded during passage through the water column. When transformations of marine organic matter are considered, differences in community composition and their different abilities to access organic matter should be taken into account.

Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison

We compared the function and composition of free-living and particle-associated microbial communities at an inshore site in coastal North Carolina and across a depth profile on the Blake Ridge (offshore). Hydrolysis rates of six different polysaccharide substrates were compared for particle-associated (>3 μm) and free-living (<3 to 0.2 μm) microbial communities. The 16S rRNA- and rDNA-based clone libraries were produced from the same filters used to measure hydrolysis rates. Particle-associated and free-living communities resembled one another; they also showed similar enzymatic hydrolysis rates and substrate preferences. All six polysaccharides were hydrolyzed inshore. Offshore, only a subset was hydrolyzed in surface water and at depths of 146 and 505 m; just three polysaccharides were hydrolyzed at 505 m. The spectrum of bacterial taxa changed more subtly between inshore and offshore surface waters, but changed greatly with depth offshore. None of the OTUs occurred at all sites: 27 out of the 28 major OTUs defined in this study were found either exclusively in a surface or in a mid-depth/bottom water sample. This distinction was evident with both 16S rRNA and rDNA analyses. At the offshore site, despite the low community overlap, bacterial communities maintained a degree of functional redundancy on the whole bacterial community level with respect to hydrolysis of high-molecular-weight substrates.

Verrucomicrobia Are Candidates for Polysaccharide-Degrading Bacterioplankton in an Arctic Fjord of Svalbard

ABSTRACT In Arctic marine bacterial communities, members of the phylum Verrucomicrobia are consistently detected, although not typically abundant, in 16S rRNA gene clone libraries and pyrotag surveys of the marine water column and in sediments. In an Arctic fjord (Smeerenburgfjord) of Svalbard, members of the Verrucomicrobia, together with Flavobacteria and smaller proportions of Alpha- and Gammaproteobacteria, constituted the most frequently detected bacterioplankton community members in 16S rRNA gene-based clone library analyses of the water column. Parallel measurements in the water column of the activities of six endo-acting polysaccharide hydrolases showed that chondroitin sulfate, laminarin, and xylan hydrolysis accounted for most of the activity. Several Verrucomicrobia water column phylotypes were affiliated with previously sequenced, glycoside hydrolase-rich genomes of individual Verrucomicrobia cells that bound fluorescently labeled laminarin and xylan and therefore constituted candidates for laminarin and xylan hydrolysis. In sediments, the bacterial community was dominated by different lineages of Verrucomicrobia, Bacteroidetes, and Proteobacteria but also included members of multiple phylum-level lineages not observed in the water column. This community hydrolyzed laminarin, xylan, chondroitin sulfate, and three additional polysaccharide substrates at high rates. Comparisons with data from the same fjord in the previous summer showed that the bacterial community in Smeerenburgfjord changed in composition, most conspicuously in the changing detection frequency of Verrucomicrobia in the water column. Nonetheless, in both years the community hydrolyzed the same polysaccharide substrates.

Latitudinal gradients in degradation of marine dissolved organic carbon.

Heterotrophic microbial communities cycle nearly half of net primary productivity in the ocean, and play a particularly important role in transformations of dissolved organic carbon (DOC). The specific means by which these communities mediate the transformations of organic carbon are largely unknown, since the vast majority of marine bacteria have not been isolated in culture, and most measurements of DOC degradation rates have focused on uptake and metabolism of either bulk DOC or of simple model compounds (e.g. specific amino acids or sugars). Genomic investigations provide information about the potential capabilities of organisms and communities but not the extent to which such potential is expressed. We tested directly the capabilities of heterotrophic microbial communities in surface ocean waters at 32 stations spanning latitudes from 76°S to 79°N to hydrolyze a range of high molecular weight organic substrates and thereby initiate organic matter degradation. These data demonstrate the existence of a latitudinal gradient in the range of complex substrates available to heterotrophic microbial communities, paralleling the global gradient in bacterial species richness. As changing climate increasingly affects the marine environment, changes in the spectrum of substrates accessible by microbial communities may lead to shifts in the location and rate at which marine DOC is respired. Since the inventory of DOC in the ocean is comparable in magnitude to the atmospheric CO2 reservoir, such a change could profoundly affect the global carbon cycle.

Natural oil slicks fuel surface water microbial activities in the northern Gulf of Mexico

We conducted a series of roller tank incubations with surface seawater from the Green Canyon oil reservoir, northern Gulf of Mexico, amended with either a natural oil slick (GCS-oil) or pristine oil. The goal was to test whether bacterial activities of natural surface water communities facilitate the formation of oil-rich marine snow (oil snow). Although oil snow did not form during any of our experiments, we found specific bacterial metabolic responses to the addition of GCS-oil that profoundly affected carbon cycling within our 4-days incubations. Peptidase and β-glucosidase activities indicative of bacterial enzymatic hydrolysis of peptides and carbohydrates, respectively, were suppressed upon the addition of GCS-oil relative to the non-oil treatment, suggesting that ascending oil and gas initially inhibits bacterial metabolism in surface water. Biodegradation of physically dispersed GCS-oil components, indicated by the degradation of lower molecular weight n-alkanes as well as the rapid transformation of particulate oil-carbon (C: N >40) into the DOC pool, led to the production of carbohydrate- and peptide-rich degradation byproducts and bacterial metabolites such as transparent exopolymer particles (TEP). TEP formation was highest at day 4 in the presence of GCS-oil; in contrast, TEP levels in the non-oil treatment already peaked at day 2. Cell-specific enzymatic activities closely followed TEP concentrations in the presence and absence of GCS-oil. These results demonstrate that the formation of oil slicks and activities of oil-degrading bacteria result in a temporal offset of microbial cycling of organic matter, affecting food web interactions and carbon cycling in surface waters over cold seeps.

Near-surface heating of young rift sediment causes mass production and discharge of reactive dissolved organic matter

Ocean margin sediments have been considered as important sources of dissolved organic carbon (DOC) to the deep ocean, yet the contribution from advective settings has just started to be acknowledged. Here we present evidence showing that near-surface heating of sediment in the Guaymas Basin, a young extensional depression, causes mass production and discharge of reactive dissolved organic matter (DOM). In the sediment heated up to ~100 °C, we found unexpectedly low DOC concentrations in the pore waters, reflecting the combined effect of thermal desorption and advective fluid flow. Heating experiments suggested DOC production to be a rapid, abiotic process with the DOC concentration increasing exponentially with temperature. The high proportions of total hydrolyzable amino acids and presence of chemical species affiliated with activated hydrocarbons, carbohydrates and peptides indicate high reactivity of the DOM. Model simulation suggests that at the local scale, near-surface heating of sediment creates short and massive DOC discharge events that elevate the bottom-water DOC concentration. Because of the heterogeneous distribution of high heat flow areas, the expulsion of reactive DOM is spotty at any given time. We conclude that hydrothermal heating of young rift sediments alter deep-ocean budgets of bioavailable DOM, creating organic-rich habitats for benthic life.