Michael S. Owens

Metatranscriptomic analyses of plankton communities inhabiting surface and subpycnocline waters of the Chesapeake Bay during oxic-anoxic-oxic transitions.

ABSTRACT We used metatranscriptomics to study the gene transcription patterns of microbial plankton (0.2 to 64 μm) at a mesohaline station in the Chesapeake Bay under transitions from oxic to anoxic waters in spring and from anoxic to oxic waters in autumn. Samples were collected from surface (i.e., above pycnocline) waters (3 m) and from waters beneath the pycnocline (16 to 22 m) in both 2010 and 2011. Metatranscriptome profiles based on function and potential phylogeny were different between 2010 and 2011 and strongly variable in 2011. This difference in variability corresponded with a highly variable ratio of eukaryotic to bacterial sequences (0.3 to 5.5), reflecting transient algal blooms in 2011 that were absent in 2010. The similarity between metatranscriptomes changed at a lower rate during the transition from oxic to anoxic waters than after the return to oxic conditions. Transcripts related to photosynthesis and low-affinity cytochrome oxidases were significantly higher in shallow than in deep waters, while in deep water genes involved in anaerobic metabolism, particularly sulfate reduction, succinyl coenzyme A (succinyl-CoA)-to-propionyl-CoA conversion, and menaquinone synthesis, were enriched relative to in shallow waters. Expected transitions in metabolism between oxic and anoxic deep waters were reflected in elevated levels of anaerobic respiratory reductases and utilization of propenediol and acetoin. The percentage of archaeal transcripts increased in both years in late summer (from 0.1 to 4.4% of all transcripts in 2010 and from 0.1 to 6.2% in 2011). Denitrification-related genes were expressed in a predicted pattern during the oxic-anoxic transition. Overall, our data suggest that Chesapeake Bay microbial assemblages express gene suites differently in shallow and deep waters and that differences in deep waters reflect variable redox states.

Effect of Sediment Manipulation on the Biogeochemistry of Experimental Sediment Systems

Abstract Before biological or biogeochemical experimentation, sediments are often manipulated and defaunated with the use of many different approaches and only modest consideration of treatment effects on sediment biogeochemistry and fluxes. Mesocosm experiments require large quantities of sediment and no standard protocol to defaunate and equilibrate muddy sediments before initiation of experiments has been determined. Using fine-grained sediments, we examined a number of treatments: (1) intact with macroinfauna; (2) intact, macroinfauna individually removed; (3) homogenized surface sediment with macrofauna; (4) homogenized deep sediment without macroinfauna; and (5) intact deep sediment without macroinfauna. In weekly batch core flux incubations, we measured dissolved oxygen, dinitrogen gas, ammonium (NH4+), nitrate plus nitrite (NO3− + NO2−), silicate (Si), and soluble reactive phosphorus (SRP) fluxes over a 5-week period. In addition, we determined porewater ammonium concentrations over time. Different sediment preparation techniques, with the same muddy sediment, significantly affected nutrient and gas fluxes, and the amount of nutrient and gas fluxes differed between sediment preparation techniques. Severely manipulated sediments, such as homogenized treatments, had high initial effluxes but eventually equilibrated to lower and more constant nutrient and gas fluxes. Moreover, biogeochemical flux changes for all treatments became similar after about 2 to 3 weeks. Sieved sediments exhibited low fluxes over the entire 5-week period, and flux rates did not change over time. A feasible method for sediment preparation for mesocosm studies is to use homogenized deep sediment equilibrated over an almost 2-week period. Overall, sediment preparation and the time after sediment manipulation affect sediment biogeochemical processes and must be considered before initiating experiments.

Key respiratory genes elucidate bacterial community respiration in a seasonally anoxic estuary

Intense annual spring phytoplankton blooms and thermohaline stratification lead to anoxia in Chesapeake Bay bottom waters. Once oxygen becomes depleted in the system, microbial communities use energetically favourable alternative electron acceptors for respiration. The extent to which changes in respiration are reflected in community gene expression have only recently been investigated. Metatranscriptomes prepared from near-bottom water plankton over a 4-month time series in central Chesapeake Bay demonstrated changes consistent with terminal electron acceptor availability. The frequency of respiration-related genes in metatranscriptomes was examined by BLASTx against curated databases of genes intimately and exclusively involved in specific electron acceptor utilization pathways. The relative expression of genes involved in denitrification and dissimilatory nitrate reduction to ammonium were coincident with changes in nitrate, nitrite and ammonium concentrations. Dissimilatory iron and manganese reduction transcript ratios increase during anoxic conditions and corresponded with the highest soluble reactive phosphate and manganese concentrations. The sulfide concentration peaked in late July and early August and also matched dissimilatory sulfate reduction transcript ratios. We show that rather than abrupt transitions between terminal electron acceptors, there is substantial overlap in time and space of these various anaerobic respiratory processes in Chesapeake Bay.

Sediment-Water Nitrogen Exchange along the Potomac River Estuarine Salinity Gradient

ABSTRACT Cornwell, J.C.; Owens, M.S.; Boynton, W.R., and Harris, L.A., 2016. Sediment-water nitrogen exchange along the Potomac River estuarine salinity gradient. Observations of N2 efflux in estuarine sediments across the salinity gradient of the tidal Potomac River, a eutrophic subestuary of the Chesapeake Bay, were used to evaluate environmental controls of microbial denitrification. Rates of denitrification were measured using N2:Ar ratios in core incubations and were similar to other nitrogen-enriched estuaries, with summer and spring N2-N efflux rates averaging 54 ± 47 and 153 ± 97 μmol m−2 h−1, respectively. The paradigm of higher denitrification rates at lower salinities was not supported by observations during summer and spring conditions along this estuarine salinity gradient. Low bottom water oxygen concentrations in the lower, more saline part of the estuary resulted in low rates of coupled nitrification/denitrification. The most favorable region for denitrification in the tidal Potomac River occurred where changes in salinity were most rapid and oxygen concentrations were not depleted, with high rates observed within the estuarine turbidity maximum (ETM) zone. Overall, the key role of salinity in the tidal Potomac River in controlling denitrification appears to be in the focusing of materials into ETM and providing stratification in the lower estuary that restricts the vertical exchange of oxygen necessary for coupled nitrification/denitrification.

The Benthic Exchange of O2, N2 and Dissolved Nutrients Using Small Core Incubations.

The measurement of sediment-water exchange of gases and solutes in aquatic sediments provides data valuable for understanding the role of sediments in nutrient and gas cycles. After cores with intact sediment-water interfaces are collected, they are submerged in incubation tanks and kept under aerobic conditions at in situ temperatures. To initiate a time course of overlying water chemistry, cores are sealed without bubbles using a top cap with a suspended stirrer. Time courses of 4-7 sample points are used to determine the rate of sediment water exchange. Artificial illumination simulates day-time conditions for shallow photosynthetic sediments, and in conjunction with dark incubations can provide net exchanges on a daily basis. The net measurement of N2 is made possible by sampling a time course of dissolved gas concentrations, with high precision mass spectrometric analysis of N2:Ar ratios providing a means to measure N2 concentrations. We have successfully applied this approach to lakes, reservoirs, estuaries, wetlands and storm water ponds, and with care, this approach provides valuable information on biogeochemical balances in aquatic ecosystems.