Heterotrophic extracellular enzymatic activities in the atlantic ocean follow patterns across spatial and depth regimes

Heterotrophic microbial communities use extracellular enzymes to initialize degradation of high molecular weight organic matter in the ocean. The potential of microbial communities to access organic matter, and the resultant rates of hydrolysis, affect the efficiency of the biological pump as well as the rate and location of organic carbon cycling in surface and deep waters. In order to investigate spatial- and depth-related patterns in microbial enzymatic capacities in the ocean, we measured hydrolysis rates of six high-molecular-weight polysaccharides and two low-molecular-weight substrate proxies at sites spanning 38°S to 10°N in the Atlantic Ocean, and at six depths ranging from surface to bottom water. In surface to upper mesopelagic waters, the spectrum of substrates hydrolyzed followed distinct patterns, with hydrolytic assemblages more similar vertically within a single station than at similar depths across multiple stations. Additionally, the proportion of total hydrolysis occurring above the pycnocline, and the spectrum of substrates hydrolyzed in mesopelagic and deep waters, was positively related to the strength of stratification at a site, while other physichochemical parameters were generally poor predictors of the measured hydrolysis rates. Spatial as well as depth-driven constraints on heterotrophic hydrolytic capacities result in broad variations in potential carbon-degrading activity in the ocean. The spectrum of enzymatic capabilities and rates of hydrolysis in the ocean, and the proportion of organic carbon hydrolyzed above the permanent thermocline, may influence the efficiency of the biological pump and net carbon export across distinct latitudinal and depth regions

Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia

Riverine bacterial communities play an essential role in the biogeochemical coupling of terrestrial and marine environments, transforming elements and organic matter in their journey from land to sea. However, precisely due to the fact that rivers receive significant terrestrial input, the distinction between resident freshwater taxa vs. land-derived microbes can often become ambiguous. Furthermore, ecosystem perturbations could introduce allochthonous microbial groups and reshape riverine bacterial communities. Using full- and partial-length 16S ribosomal RNA gene sequences, we analyzed the composition of bacterial communities in the Tar River of North Carolina from November 2010 to November 2011, during which a natural perturbation occurred: the inundation of the lower reaches of an otherwise drought-stricken river associated with Hurricane Irene, which passed over eastern North Carolina in late August 2011. This event provided the opportunity to examine the microbiological, hydrological, and geochemical impacts of a disturbance, defined here as the large freshwater influx into the Tar River, superimposed on seasonal changes or other ecosystem variability independent of the hurricane. Our findings demonstrate that downstream communities are more taxonomically diverse and temporally variable than their upstream counterparts. More importantly, pre- vs. post-disturbance taxonomic comparison of the freshwater-dominant Betaproteobacteria class and the phylum Verrucomicrobia reveal a disturbance signature of previously undetected taxa of diverse origins. We use known traits of closely-related taxa to interpret the ecological function of disturbance-associated bacteria, and hypothesize that carbon cycling was enhanced post-disturbance in the Tar River, likely due to the flux of organic carbon into the system associated with the large freshwater pulse. Our analyses demonstrate the importance of geochemical and hydrological alterations in structuring bacterial communities, and illustrate the response of temperate riverine bacteria on fine taxonomic scales to a disturbance

Nucleosome-mediated cooperativity between transcription factors

Cooperative binding of transcription factors (TFs) to cis-regulatory regions (CRRs) is essential for precision of gene expression in development and other processes. The classical model of cooperativity requires direct interactions between TFs, thus constraining the arrangement of TFs sites in a CRR. On the contrary, genomic and functional studies demonstrate a great deal of flexibility in such arrangements with variable distances, numbers of sites, and identities of the involved TFs. Such flexibility is inconsistent with the cooperativity by direct interactions between TFs. Here we demonstrate that strong cooperativity among non-interacting TFs can be achieved by their competition with nucleosomes. We find that the mechanism of nucleosome-mediated cooperativity is mathematically identical to the Monod-Wyman-Changeux (MWC) model of cooperativity in hemoglobin. This surprising parallel provides deep insights, with parallels between heterotropic regulation of hemoglobin (e.g. Bohr effect) and roles of nucleosome-positioning sequences and chromatin modifications in gene regulation. Characterized mechanism is consistent with numerous experimental results, allows substantial flexibility in and modularity of CRRs, and provides a rationale for a broad range of genomic and evolutionary observations. Striking parallels between cooperativity in hemoglobin and in transcription regulation point at a new design principle that may be used in range of biological systems

Structure and function of high Arctic pelagic, particle-associated and benthic bacterial communities

Arctic marine microbes are affected by environmental changes that may ultimately influence their functions in carbon cycling. Here, we investigated in concert the structure and enzymatic activities of pelagic, particle-associated and benthic bacterial communities in the central Arctic Ocean, and used these data to evaluate microbial structure–function relationships. Our findings showed influences of hydrographic conditions and particle association on community composition, and sharp pelagic-benthic contrasts. In addition to community compositional differences, regional and depth-related patterns in enzymatic activities were observed. Peptide hydrolysis rates were highest in surface waters, especially at ice-free and first year ice-covered regions, and decreased with depth. While the range of hydrolysed polysaccharides showed varying geographic patterns, particles often showed a wider spectrum of polysaccharide hydrolase activities. Summed benthic peptidase rates differed across stations but showed similar proportions of individual enzyme activities. Analysing for potential linkages between structure and function after subtracting the effect of environmental conditions revealed no direct link, indicating functional redundancy to carry out peptide hydrolysis among pelagic microbes. Thus, while community composition and activities are influenced by environmental conditions, bacterial functional redundancy suggests that compositional shifts – in response to the changing Arctic – may have complex and less predictable functional consequences than previously anticipated

Improved measurement of extracellular enzymatic activities in subsurface sediments using competitive desorption treatment

Extracellular enzymatic activities initiate microbially-driven heterotrophic carbon cycling in subsurface sediments. While measurement of hydrolytic activities in sediments is fundamental to our understanding of carbon cycling, these measurements are often technically difficult due to sorption of organic substrates to the sediment matrix. Most methods that measure hydrolysis of organic substrates in sediments rely on recovery of a fluorophore or fluorescently-labeled target substrate from a sediment incubation. The tendency for substrates to sorb to sediments results in lower recovery of an added substrate, and can result in data that are unusable or difficult to interpret. We developed a treatment using competitive desorption of a fluorescently-labeled, high molecular weight organic substrate that improves recovery of the labeled substrate from sediment subsamples. Competitive desorption treatment improved recovery of the fluorescent substrate by a median of 66%, expanded the range of sediments for which activity measurements could be made, and was effective in sediments from a broad range of geochemical contexts. More reliable measurements of hydrolytic activities in sediments will yield usable and more easily interpretable data from a wider range of sedimentary environments, enabling better understanding of microbially-catalyzed carbon cycling in subsurface environments

Improved measurement of extracellular enzymatic activities in subsurface sediments using competitive desorption treatment

Extracellular enzymatic activities initiate microbially-driven heterotrophic carbon cycling in subsurface sediments. While measurement of hydrolytic activities in sediments is fundamental to our understanding of carbon cycling, these measurements are often technically difficult due to sorption of organic substrates to the sediment matrix. Most methods that measure hydrolysis of organic substrates in sediments rely on recovery of a fluorophore or fluorescently-labeled target substrate from a sediment incubation. The tendency for substrates to sorb to sediments results in lower recovery of an added substrate, and can result in data that are unusable or difficult to interpret. We developed a treatment using competitive desorption of a fluorescently-labeled, high molecular weight organic substrate that improves recovery of the labeled substrate from sediment subsamples. Competitive desorption treatment improved recovery of the fluorescent substrate by a median of 66%, expanded the range of sediments for which activity measurements could be made, and was effective in sediments from a broad range of geochemical contexts. More reliable measurements of hydrolytic activities in sediments will yield usable and more easily interpretable data from a wider range of sedimentary environments, enabling better understanding of microbially-catalyzed carbon cycling in subsurface environments

A model of spatially restricted transcription in opposing gradients of activators and repressors

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102118/1/msb201248-sup-0001.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/102118/2/msb201248.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/102118/3/msb201248.reviewer_comments.pd

Comparison of multivariate microbial datasets with the Shannon index: An example using enzyme activity from diverse marine environments

a b s t r a c t Heterotrophic microbial communities contain substantial functional diversity, so studies of community function often generate multivariate data sets. Techniques for data reduction and analysis can help elucidate qualitative differences among sites from multivariate data sets that may be difficult to grasp intuitively from raw data. The Shannon index is one such technique, used commonly in ecological studies to quantify species evenness. Here, the Shannon index is used to compare quantitatively the extent to which complex microbial communities vary in their capability to access polysaccharides. It is maximized when hydrolysis rates for all polysaccharides are equal and minimized when the range among individual hydrolysis rates at a given site is large. Application of the technique to depth profiles of polysaccharide hydrolysis rates from four distinct pelagic marine environments indicates that, in three of four cases, surface water communities accessed substrates at a more even rate than in deeper waters. The technique could usefully be applied to other types of data obtained in studies of microbial activity and the geochemical effects

Changes in the spectrum and rates of extracellular enzyme activities in seawater following aggregate formation

Marine snow aggregates are heavily colonized by heterotrophic microorganisms that express high levels of hydrolytic activities, making aggregates hotspots for carbon remineralization in the ocean. To assess how aggregate formation influences the ability of seawater microbial communities to access organic carbon, we compared hydrolysis rates of six polysaccharides in coastal seawater after aggregates had been formed (via incubation on a roller table) with hydrolysis rates in seawater from the same site that had not incubated on a roller table (referred to as whole seawater). Hydrolysis rates in the aggregates themselves were up to three orders of magnitude higher on a volume basis than in whole seawater. The enhancement of enzyme activity in aggregates relative to whole seawater differed by substrate, suggesting that the enhancement was under cellular control, rather than due to factors such as lysis or grazing. A comparison of hydrolysis rates in whole seawater with those in aggregate-free seawater, i.e. the fraction of water from the roller bottles that did not contain aggregates, demonstrated a nuanced microbial response to aggregate formation. Activities of laminarinase and xylanase enzymes in aggregate-free seawater were higher than in whole seawater, while activities of chondroitin, fucoidan, and arabinogalactan hydrolyzing enzymes were lower than in whole seawater. These data suggest that aggregate formation enhanced production of laminarinase and xylanase enzymes, and the enhancement also affected the surrounding seawater. Decreased activities of chondroitin, fucoidan, and arabinoglactan-hydrolyzing enzymes in aggregate-free seawaters relative to whole seawater are likely due to shifts in enzyme production by the aggregate-associated community, coupled with the effects of enzyme degradation. Enhanced activities of laminarin- and xylan-hydrolyzing enzymes in aggregate-free seawater were due at least in part to cell-free enzymes. Measurements of enzyme lifetime using commercial enzymes suggest that hydrolytic cell-free enzymes may be active over timescales of days to weeks. Considering water residence times of up to 10 days in the investigation area (Apalachicola Bay), enzymes released from aggregates may be active over timescales long enough to affect carbon cycling in the Bay as well as in the adjacent Gulf of Mexico. Aggregate formation may thus be an important mechanism shaping the spectrum of enzymes active in the ocean, stimulating production of cell-free enzymes and leading to spatial and temporal decoupling of enzyme activity from the microorganisms that produced them

Oil-derived marine aggregates - hot spots of polysaccharide degradation by specialized bacterial communities

Aggregates generated in the laboratory from incubations of seawater and surface-water oil collected in the initial phase of the Deepwater Horizon oil spill resemble the oil-aggregates observed in situ. Here, we investigated the enzyme activities and microbial community composition of laboratory generated oil-aggregates, focusing on the abilities of these communities to degrade polysaccharides, which are major components of marine organic matter and are abundant constituents of exopolymeric substances (EPS) generated by oil-associated bacteria in response to the presence of oil. The patterns of polysaccharide-hydrolyzing enzyme activities in oil aggregates were very different from those in the water surrounding the aggregates after formation, and in the surface water that did not contain the oil. Specific oil aggregate-associated hydrolysis rates were also considerably higher than in the water surrounding the aggregates. The differences in initial hydrolysis profiles, and in evolution of these profiles with time, points to specialized metabolic abilities among the oil-aggregate communities compared to oil-water and ambient water communities. The composition of the oil-aggregate community indicates a multifunctional microbial assemblage containing primary oil-degrading and exopolysaccharide-producing members of the Gammaproteobacteria, and diverse members of the Alphaproteobacteria, Bacteroidetes and Planktomycetales that most likely participate in the breakdown of oil-derived bacterial biopolymers. Formation and aging of oil-aggregates encourages the growth and transformation of microbial communities that are specialized in degradation of petroleum, as well as their secondary degradation products