Christof Meile

Ecological Genomics of Marine Roseobacters

ABSTRACT Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir-related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.

Genome characteristics of a generalist marine bacterial lineage

Members of the marine Roseobacter lineage have been characterized as ecological generalists, suggesting that there will be challenges in assigning well-delineated ecological roles and biogeochemical functions to the taxon. To address this issue, genome sequences of 32 Roseobacter isolates were analyzed for patterns in genome characteristics, gene inventory, and individual gene/pathway distribution using three predictive frameworks: phylogenetic relatedness, lifestyle strategy and environmental origin of the isolate. For the first framework, a phylogeny containing five deeply branching clades was obtained from a concatenation of 70 conserved single-copy genes. Somewhat surprisingly, phylogenetic tree topology was not the best model for organizing genome characteristics or distribution patterns of individual genes/pathways, although it provided some predictive power. The lifestyle framework, established by grouping isolates according to evidence for heterotrophy, photoheterotrophy or autotrophy, explained more of the gene repertoire in this lineage. The environment framework had a weak predictive power for the overall genome content of each strain, but explained the distribution of several individual genes/pathways, including those related to phosphorus acquisition, chemotaxis and aromatic compound degradation. Unassembled sequences in the Global Ocean Sampling metagenomic data independently verified this global-scale geographical signal in some Roseobacter genes. The primary findings emerging from this comparative genome analysis are that members of the lineage cannot be easily collapsed into just a few ecologically differentiated clusters (that is, there are almost as many clusters as isolates); the strongest framework for predicting genome content is trophic strategy, but no single framework gives robust predictions; and previously unknown homologs to genes for H2 oxidation, proteorhodopsin-based phototrophy, xanthorhodpsin-based phototrophy, and CO2 fixation by Form IC ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) expand the possible mechanisms for energy and carbon acquisition in this remarkably versatile bacterial lineage.

Seasonal oscillation of microbial iron and sulfate reduction in saltmarsh sediments (Sapelo Island, GA, USA)

Seasonal variations in anaerobic respiration pathways were investigated at three saltmarsh sites using chemical data, sulfate reduction rate measurements, enumerations of culturable populations of anaerobic iron-reducing bacteria (FeRB), and quantification of in situ 16S rRNA hybridization signals targeted for sulfate-reducing bacteria (SRB). Bacterial sulfate reduction in the sediments followed seasonal changes in temperature and primary production of the saltmarsh, with activity levels lowest in winter and highest in summer. In contrast, a dramatic decrease in the FeRB population size was observed during summer at all sites. The collapse of FeRB populations during summer was ascribed to high rates of sulfide production by SRB, resulting in abiotic reduction of bioavailable Fe(III) (hydr)oxides. To test this hypothesis, sediment slurry incubations at 10, 20 and 30 °C were carried out. Increases in temperature and labile organic carbon availability (acetate or lactate additions) increased rates of sulfate reduction while decreasing the abundance of culturable anaerobic FeRB. These trends were not reversed by the addition of amorphous Fe(III) (hydr)oxides to the slurries. However, when sulfate reduction was inhibited by molybdate, no decline in FeRB growth was observed with increasing temperature. Addition of dissolved sulfide adversely impacted propagation of FeRB whether molybdate was added or not. Both field and laboratory data therefore support a sulfide-mediated limitation of microbial iron respiration by SRB. When total sediment respiration rates reach their highest levels during summer, SRB force a decline in the FeRB populations. As sulfate reduction activity slows down after the summer, the FeRB are able to recover.

Carbon geochemistry of cold seeps: Methane fluxes and transformation in sediments from Kazan mud volcano, eastern Mediterranean Sea

Abstract Despite growing concerns about potential enhancement of global warming and slope failure by methane produced by gas hydrate dissociation, much uncertainty surrounds estimates of gas hydrate reservoir sizes, as well as methane fluxes and oxidation rates at the sea floor. For cold seep sediments of the eastern Mediterranean Sea, depth-dependent methane concentrations and rates of anaerobic oxidation of methane (AOM) are constrained by modeling the measured pore-water sulfate profile. The calculated dissolved methane distribution and flux are sensitive to the advective flow velocity, which is estimated from the depth distributions of conservative pore-water constituents (Na, B). Near-complete anaerobic oxidation of the upward methane flux of ∼6.0 mol m−2 yr−1 is supported by the depth distributions of indicative biomarkers, and the carbon isotopic compositions of organic matter and dissolved inorganic carbon. Pore-water and solid-phase data are consistent with a narrow depth interval of AOM, 14–18 cm below the sediment–water interface. Based on an isotopic mass balance, the biomass of the microbial population carrying out oxidation of methane coupled to sulfate reduction at the given methane flux represents ∼20% of the total organic carbon, which is a significant pool of in situ formed organic matter. Model results indicate that the asymptotic methane concentration is reached a few meters below the sediment surface. The predicted asymptotic concentration is close to the in situ saturation value with respect to gas hydrate, suggesting that the rate of shallow gas hydrate formation is controlled by the ascending methane flux. The proposed model approach can be used to predict the formation of gas hydrate, and to quantify methane fluxes plus transformation rates in surface sediments where fluid advection is an important transport mechanism.

Quantifying bioirrigation using ecological parameters: a stochastic approach

Irrigation by benthic macrofauna has a major influence on the biogeochemistry and microbial community structure of sediments. Existing quantitative models of bioirrigation rely primarily on chemical, rather than ecological, information and the depth-dependence of bioirrigation intensity is either imposed or constrained through a data fitting procedure. In this study, stochastic simulations of 3D burrow networks are used to calculate mean densities, volumes and wall surface areas of burrows, as well as their variabilities, as a function of sediment depth. Burrow networks of the following model organisms are considered: the polychaete worms Nereis diversicolor and Schizocardium sp., the shrimp Callianassa subterranea, the echiuran worm Maxmuelleria lankesteri, the fiddler crabs Uca minax, U. pugnax and U. pugilator, and the mud crabs Sesarma reticulatum and Eurytium limosum. Consortia of these model organisms are then used to predict burrow networks in a shallow water carbonate sediment at Dry Tortugas, FL, and in two intertidal saltmarsh sites at Sapelo Island, GA. Solute-specific nonlocal bioirrigation coefficients are calculated from the depth-dependent burrow surface areas and the radial diffusive length scale around the burrows. Bioirrigation coefficients for sulfate obtained from network simulations, with the diffusive length scales constrained by sulfate reduction rate profiles, agree with independent estimates of bioirrigation coefficients based on pore water chemistry. Bioirrigation coefficients for O2 derived from the stochastic model, with the diffusion length scales constrained by O2 microprofiles measured at the sediment/water interface, are larger than irrigation coefficients based on vertical pore water chemical profiles. This reflects, in part, the rapid attenuation with depth of the O2 concentration within the burrows, which reduces the driving force for chemical transfer across the burrow walls. Correction for the depletion of O2 in the burrows results in closer agreement between stochastically-derived and chemically-derived irrigation coefficient profiles.

Modeling biogeochemical processes in subterranean estuaries : Effect of flow dynamics and redox conditions on submarine groundwater discharge of nutrients

A two-dimensional density-dependent reactive transport model, which couples groundwater flow and biogeochemical reactions, is used to investigate the fate of nutrients (NO3 −, NH4 +, and PO4) in idealized subterranean estuaries representing four end-members of oxic/anoxic aquifer and seawater redox conditions. Results from the simplified model representations show that the prevalent flow characteristics and redox conditions in the freshwater-seawater mixing zone determine the extent of nutrient removal and the input of nitrogen and phosphorus to coastal waters. At low to moderate groundwater velocities, simultaneous nitrification and denitrification can lead to a reversal in the depth of freshwater NO3 − and NH4 +-PO4 plumes, compared to their original positions at the landward source. Model results suggest that autotrophic denitrification pathways with Fe2+ or FeS2 may provide an important, often overlooked link between nitrogen and phosphorus biogeochemistry through the precipitation of iron oxides and subsequent binding of phosphorus. Simulations also highlight that deviations of nutrient data from conservative mixing curves do not necessarily indicate nutrient removal.

Solute-specific pore water irrigation: Implications for chemical cycling in early diagenesis

In one-dimensional (1D) early diagenetic models, bioirrigation is typically represented by a nonlocal mass transfer or bioirrigation coefficient, . Usually, all pore water species are assigned the same . Here, we show that this assumption can lead to significant errors in estimates of bioirrigation intensities. Using a simplified early diagenetic reaction network, we compute the 3D concentration fields of major pore water species around a vertical burrow, as well as the solute fluxes across the burrow wall. From these results, corresponding 1D vertical profiles are derived. The profiles show pronounced differences from one solute to another. Dissolved O2 systematically exhibits the highest values, while fast oxygenation kinetics near the burrow wall result in near-zero values for aqueous Fe . For nitrate, use of a species-averaged profile may even lead to an erroneous prediction of the direction of the irrigation flux across the water-sediment interface. The large differences in profiles reflect the variable effects of biogeochemical processes on pore water concentration fields of reactive solutes near the burrow wall. Even for inert solutes, however, determination of can be ambiguous. Transient simulations mimicking the intrusion into the sediment of an inert tracer during an incubation experiment yield apparent mixing intensities that depend on the incubation time.

Tube‐dwelling invertebrates: tiny ecosystem engineers have large effects in lake ecosystems

There is ample evidence that tube-dwelling invertebrates such as chironomids significantly alter multiple important ecosystem functions, particularly in shallow lakes. Chironomids pump large water volumes, and associated suspended and dissolved substances, through the sediment and thereby compete with pelagic filter feeders for particulate organic matter. This can exert a high grazing pressure on phytoplankton, microorganisms, and perhaps small zooplankton and thus strengthen benthic-pelagic coupling. Furthermore, intermittent pumping by tube-dwelling invertebrates oxygenates sediments and creates a dynamic, three-dimensional mosaic of redox conditions. This shapes microbial community composition and spatial distribution, and alters microbe-mediated biogeochemical functions, which often depend on redox potential. As a result, extended hotspots of element cycling occur at the oxic-anoxic interfaces, controlling the fate of organic matter and nutrients as well as fluxes of nutrients between sediments and water. Surprisingly, the mechanisms and magnitude of interactions mediated by these organisms are still poorly understood. To provide a synthesis of the importance of tube-dwelling invertebrates, we review existing research and integrate previously disregarded functional traits into an ecosystem model. Based on existing research and our models, we conclude that tube-dwelling invertebrates play a central role in controlling water column nutrient pools, and hence water quality and trophic state. Furthermore, these tiny ecosystem engineers can influence the thresholds that determine shifts between alternate clear and turbid states of shallow lakes. The large effects stand in contrast to the conventional limnological paradigm emphasizing predominantly pelagic food webs. Given the vast number of shallow lakes worldwide, benthic invertebrates are likely to be relevant drivers of biogeochemical processes at regional and global scales, thereby mediating feedback mechanisms linked to climate change.

Quantification of Extracellular Carbonic Anhydrase Activity in Two Marine Diatoms and Investigation of Its Role

eCA enhances CO2 supply for photosynthesis in two marine diatoms. Many microalgae induce an extracellular carbonic anhydrase (eCA), associated with the cell surface, at low carbon dioxide (CO2) concentrations. This enzyme is thought to aid inorganic carbon uptake by generating CO2 at the cell surface, but alternative roles have been proposed. We developed a new approach to quantify eCA activity in which a reaction-diffusion model is fit to data on 18O removal from inorganic carbon. In contrast to previous methods, eCA activity is treated as a surface process, allowing the effects of eCA on cell boundary-layer chemistry to be assessed. Using this approach, we measured eCA activity in two marine diatoms (Thalassiosira pseudonana and Thalassiosira weissflogii), characterized the kinetics of this enzyme, and studied its regulation as a function of culture pH and CO2 concentration. In support of a role for eCA in CO2 supply, eCA activity specifically responded to low CO2 rather than to changes in pH or HCO3−, and the rates of eCA activity are nearly optimal for maintaining cell surface CO2 concentrations near those in the bulk solution. Although the CO2 gradients abolished by eCA are small (less than 0.5 μm concentration difference between bulk and cell surface), CO2 uptake in these diatoms is a passive process driven by small concentration gradients. Analysis of the effects of short-term and long-term eCA inhibition on photosynthesis and growth indicates that eCA provides a small energetic benefit by reducing the surface-to-bulk CO2 gradient. Alternative roles for eCA in CO2 recovery as HCO3− and surface pH regulation were investigated, but eCA was found to have minimal effects on these processes.

Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth’s marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal were examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species can cause the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), none of the potential intermediates considered here is able to support metabolic activity matching the measured rates. Correspondence to: C. Meile (cmeile@uga.edu)