Julia A. Maresca

Nutrient release and ammonium sorption by poultry litter and wood biochars in stormwater treatment.

The feasibility of using biochar as a filter medium in stormwater treatment facilities was evaluated with a focus on ammonium retention. Successive batch extractions and batch ammonium sorption experiments were conducted in both deionized (DI) water and artificial stormwater using poultry litter (PL) and hardwood (HW) biochars pyrolyzed at 400°C and 500°C. No measureable nitrogen leached from HW biochars except 0.07 μmol/g of org-N from 400°C HW biochar. PL biochar pyrolyzed at 400°C leached 120-127 μmol/g of nitrogen but only 7.1-8.6 μmol/g of nitrogen when pyrolyzed at 500°C. Ammonium sorption was significant for all biochars. At a typical ammonium concentration of 2mg/L in stormwater, the maximum sorption was 150 mg/kg for PL biochar pryolyzed at 400°C. In stormwater, ion competition (e.g. Ca(2+)) suppressed ammonium sorption compared to DI water. Surprisingly, ammonium sorption was negatively correlated to the BET surface area of the tested biochars, but increased linearly with cation exchange capacity. Cation exchange capacity was the primary mechanism controlling ammonium sorption and was enhanced by pyrolysis at 400°C, while BET surface area was enhanced by pyrolysis at 500°C. The optimal properties (BET surface area, CEC, etc.) of biochar as a sorbent are not fixed but depend on the target pollutant. Stormwater infiltration column experiments in sand with 10% biochar removed over 90% of ammonium with influent ammonium concentration of 2mg/L, compared to only 1.7% removal in a sand-only column, indicating that kinetic limitations on sorption were minor for the storm conditions studied. Hardwood and poultry litter biochar pyrolyzed at 500°C and presumably higher temperature may be viable filter media for stormwater treatment facilities, as they showed limited release of organic and inorganic nutrients and acceptable ammonium sorption.

Heterotrophic bacteria from an extremely phosphate‐poor lake have conditionally reduced phosphorus demand and utilize diverse sources of phosphorus

Heterotrophic Proteobacteria and Actinobacteria were isolated from Lake Matano, Indonesia, a stratified, ferruginous (iron-rich), ultra-oligotrophic lake with phosphate concentrations below 50 nM. Here, we describe the growth of eight strains of heterotrophic bacteria on a variety of soluble and insoluble sources of phosphorus. When transferred to medium without added phosphorus (P), the isolates grow slowly, their RNA content falls to as low as 1% of cellular dry weight, and 86-100% of the membrane lipids are replaced with amino- or glycolipids. Similar changes in lipid composition have been observed in marine photoautotrophs and soil heterotrophs, and similar flexibility in phosphorus sources has been demonstrated in marine and soil-dwelling heterotrophs. Our results demonstrate that heterotrophs isolated from this unusual environment alter their macromolecular composition, which allows the organisms to grow efficiently even in their extremely phosphorus-limited environment.

Freshwater Bacteria Release Methane as a By-Product of Phosphorus Acquisition

ABSTRACT Freshwater lakes emit large amounts of methane, some of which is produced in oxic surface waters. Two potential pathways for aerobic methane production exist: methanogenesis in oxygenated water, which has been observed in some lakes, and demethylation of small organic molecules. Although methane is produced via demethylation in oxic marine environments, this mechanism of methane release has not yet been demonstrated in freshwater systems. Genes related to the C-P lyase pathway, which cleaves C-P bonds in phosphonate compounds, were found in a metagenomic survey of the surface water of Lake Matano, which is chronically P starved and methane rich. We demonstrate that four bacterial isolates from Lake Matano obtain P from methylphosphonate and release methane and that this activity is repressed by phosphate. We further demonstrate that expression of phnJ, which encodes the enzyme that releases methane, is higher in the presence of methylphosphonate and lower when both methylphosphonate and phosphate are added. This gene is also found in most of the metagenomic data sets from freshwater environments. These experiments link methylphosphonate degradation and methane production with gene expression and phosphate availability in freshwater organisms and suggest that some of the excess methane in the Lake Matano surface water, and in other methane-rich lakes, may be produced by P-starved bacteria. IMPORTANCE Methane is an important greenhouse gas and contributes substantially to global warming. Although freshwater environments are known to release methane into the atmosphere, estimates of the amount of methane emitted by freshwater lakes vary from 8 to 73 Tg per year. Methane emissions are difficult to predict in part because the source of the methane can vary: it is the end product of the energy-conserving pathway in methanogenic archaea, which live predominantly in anoxic sediments or waters but have also been identified in some oxic freshwater environments. More recently, methane release from small organic molecules has been observed in oxic marine environments. Here we show that demethylation of methylphosphonate may also contribute to methane release from lakes and that phosphate can repress this activity. Since lakes are typically phosphorus limited, some methane release in these environments may be a by-product of phosphorus metabolism rather than carbon or energy metabolism. Methane emissions from lakes are currently predicted using primary production, eutrophication status, extent of anoxia, and the shape and size of the lake; to improve prediction of methane emissions, phosphorus availability and sources may also need to be included in these models.

Characterization of an unconventional rhodopsin from the freshwater Actinobacterium Rhodoluna lacicola

UNLABELLED Rhodopsin-encoding microorganisms are common in many environments. However, knowing that rhodopsin genes are present provides little insight into how the host cells utilize light. The genome of the freshwater actinobacterium Rhodoluna lacicola encodes a rhodopsin of the uncharacterized actinorhodopsin family. We hypothesized that actinorhodopsin was a light-activated proton pump and confirmed this by heterologously expressing R. lacicola actinorhodopsin in retinal-producing Escherichia coli. However, cultures of R. lacicola did not pump protons, even though actinorhodopsin mRNA and protein were both detected. Proton pumping in R. lacicola was induced by providing exogenous retinal, suggesting that the cells lacked the retinal cofactor. We used high-performance liquid chromatography (HPLC) and oxidation of accessory pigments to confirm that R. lacicola does not synthesize retinal. These results suggest that in some organisms, the actinorhodopsin gene is constitutively expressed, but rhodopsin-based light capture may require cofactors obtained from the environment. IMPORTANCE Up to 70% of microbial genomes in some environments are predicted to encode rhodopsins. Because most microbial rhodopsins are light-activated proton pumps, the prevalence of this gene suggests that in some environments, most microorganisms respond to or utilize light energy. Actinorhodopsins were discovered in an analysis of freshwater metagenomic data and subsequently identified in freshwater actinobacterial cultures. We hypothesized that actinorhodopsin from the freshwater actinobacterium Rhodoluna lacicola was a light-activated proton pump and confirmed this by expressing actinorhodopsin in retinal-producing Escherichia coli. Proton pumping in R. lacicola was induced only after both light and retinal were provided, suggesting that the cells lacked the retinal cofactor. These results indicate that photoheterotrophy in this organism and others may require cofactors obtained from the environment.

Using total internal reflection fluorescence microscopy to visualize rhodopsin-containing cells.

ABSTRACT Sunlight is captured and converted to chemical energy in illuminated environments. Although (bacterio)chlorophyll-based photosystems have been characterized in detail, retinal-based photosystems, rhodopsins, have only recently been identified as important mediators of light energy capture and conversion. Recent estimates suggest that up to 70% of cells in some environments harbor rhodopsins. However, because rhodopsin autofluorescence is low—comparable to that of carotenoids and significantly less than that of (bacterio)chlorophylls—these estimates are based on metagenomic sequence data, not direct observation. We report here the use of ultrasensitive total internal reflection fluorescence (TIRF) microscopy to distinguish between unpigmented, carotenoid-producing, and rhodopsin-expressing bacteria. Escherichia coli cells were engineered to produce lycopene, β-carotene, or retinal. A gene encoding an uncharacterized rhodopsin, actinorhodopsin, was cloned into retinal-producing E. coli. The production of correctly folded and membrane-incorporated actinorhodopsin was confirmed via development of pink color in E. coli and SDS-PAGE. Cells expressing carotenoids or actinorhodopsin were imaged by TIRF microscopy. The 561-nm excitation laser specifically illuminated rhodopsin-containing cells, allowing them to be differentiated from unpigmented and carotenoid-containing cells. Furthermore, water samples collected from the Delaware River were shown by PCR to have rhodopsin-containing organisms and were examined by TIRF microscopy. Individual microorganisms that fluoresced under illumination from the 561-nm laser were identified. These results verify the sensitivity of the TIRF microscopy method for visualizing and distinguishing between different molecules with low autofluorescence, making it useful for analyzing natural samples.

Biochar-Amended Media for Enhanced Nutrient Removal in Stormwater Facilities

Nutrients from roadway stormwater runoff contribute to eutrophication of water bodies. Although bioretention facilities remove many stormwater pollutants by precipitation, filtration, sorption, microbial degradation and plant uptake, limited removal of nitrogen compounds is often reported. This project explores a new technology incorporating biochar into the upper unsaturated soil media of bioretention facilities to enhance removal of nitrogen compounds. Biochar is a thermal decomposition product from biomass heated at relatively low temperature (<700C) with limited oxygen. Several studies have examined biochar as a surface sorbent to remove contaminants in the environment, utilizing the high internal porosity and surface area of this carbonaceous material. In this work, we report on biochar’s ability to increase removal of nitrogen compounds in bioretention media in two ways: sorption of ammonium, and increasing water retention and thus retention time for nitrogen cycling. Laboratory experiments were conducted to evaluate the ability of two types of biochar Soil Reef (SR) biochar (a commercial wood biochar) and poultry litter (PL) biochar to remove ammonium-nitrogen (NH4 -N). Ammonium sorption batch experiments showed 74%, 43%, and 37% of the input NH4 + was adsorbed by 0.2 g of, respectively, PL400-L (400 C pre-leached with DI water), PL500-L, and SR-L biochar in 10 mL 0.5 mg/L NH4 + solution. Water retention measurements indicated the volumetric water content of a uniform sand amended with 7% SR-L or PL300-L biochar was 4.5 or 2.3 times higher than pure sand at matric potential of -37 cm H2O. In conjunction with these laboratory data, we propose a pilot-scale test facility for quantifying nitrogen compound removal with biochar-amended bioretention media. 197 World Environmental and Water Resources Congress 2014: Water without Borders

Distribution and diversity of rhodopsin-producing microbes in the Chesapeake Bay

ABSTRACT Although sunlight is an abundant source of energy in surface environments, less than 0.5% of the available photons are captured by (bacterio)chlorophyll-dependent photosynthesis in plants and bacteria. Metagenomic data indicate that 30 to 60% of the bacterial genomes in some environments encode rhodopsins, retinal-based photosystems found in heterotrophs, suggesting that sunlight may provide energy for more life than previously suspected. However, quantitative data on the number of cells that produce rhodopsins in environmental systems are limited. Here, we use total internal reflection fluorescence microscopy to show that the number of free-living microbes that produce rhodopsins increases along the salinity gradient in the Chesapeake Bay. We correlate this functional data with environmental data to show that rhodopsin abundance is positively correlated with salinity and with indicators of active heterotrophy during the day. Metagenomic and metatranscriptomic data suggest that the microbial rhodopsins in the low-salinity samples are primarily found in Actinobacteria and Bacteroidetes, while those in the high-salinity samples are associated with SAR-11 type Alphaproteobacteria. IMPORTANCE Microbial rhodopsins are common light-activated ion pumps in heterotrophs, and previous work has proposed that heterotrophic microbes use them to conserve energy when organic carbon is limiting. If this hypothesis is correct, rhodopsin-producing cells should be most abundant where nutrients are most limited. Our results indicate that in the Chesapeake Bay, rhodopsin gene abundance is correlated with salinity, and functional rhodopsin production is correlated with nitrate, bacterial production, and chlorophyll a. We propose that in this environment, where carbon and nitrogen are likely not limiting, heterotrophs do not need to use rhodopsins to supplement ATP synthesis. Rather, the light-generated proton motive force in nutrient-rich environments could be used to power energy-dependent membrane-associated processes, such as active transport of organic carbon and cofactors, enabling these organisms to more efficiently utilize exudates from primary producers.

Biochemical Analysis of Microbial Rhodopsins

Ion‐pumping rhodopsins transfer ions across the microbial cell membrane in a light‐dependent fashion. As the rate of biochemical characterization of microbial rhodopsins begins to catch up to the rate of microbial rhodopsin identification in environmental and genomic sequence data sets, in vitro analysis of their light‐absorbing properties and in vivo analysis of ion pumping will remain critical to characterizing these proteins. As we learn more about the variety of physiological roles performed by microbial rhodopsins in different cell types and environments, observing the localization patterns of the rhodopsins and/or quantifying the number of rhodopsin‐bearing cells in natural environments will become more important. Here, we provide protocols for purification of rhodopsin‐containing membranes, detection of ion pumping, and observation of functional rhodopsins in laboratory and environmental samples using total internal reflection fluorescence microscopy.