Phylogenetic diversity of NO reductases,new tools for nor monitoring,and insights into N2O production in natural and engineered environments

● 548 representative nor genes were collected to create complete phylogenetic trees. ● The distribution of nor and nod genes were detected in 18 different phyla. ● The most conserved amino acids in NOR were located adjacent to the active site. ● nor-universal and Clade-specific primers were designed, suggested, and tested. Nitric oxide reductases (NORs) have a central role in denitrification, detoxification of nitric oxide (NO) in host-pathogen interactions, and NO-mediated cell-cell signaling. In this study, we focus on the phylogeny and detection of qNOR and cNOR genes because of their nucleotide sequence similarity and evolutionary relatedness to cytochrome oxidases, their key role in denitrification, and their abundance in natural, agricultural, and wastewater ecosystems. We also include nitric oxide dismutase (NOD) due to its similarity to qNOR. Using 548 nor sequences from publicly accessible databases and sequenced isolates from N₂O-producing bioreactors, we constructed phylogenetic trees for 289 qnor/nod genes and 259 cnorB genes. These trees contain evidence of horizontal gene transfer and gene duplication, with 13.4% of the sequenced strains containing two or more nor genes. By aligning amino acid sequences for qnor + cnor, qnor, and cnor, we identified four highly conserved regions for NOR and NOD, including two highly conserved histidine residues at the active site for qNOR and cNOR. Extending this approach, we identified conserved sequences for: 1) all nor (nor-universal); 2) all qnor (qnor-universal) and all cnor (cnor-universal); 3) qnor of Comamonadaceae; 4) Clade-specific sequences; and 5) nod of Candidatus Methylomirabilis oxyfera. Examples of primer performance were confirmed experimentally.     

Evidence supporting the importance of terrestrial carbon in a large-river food web

Algal carbon has been increasingly recognized as the primary carbon source supporting large-river food webs; however, many of the studies that support this contention have focused on lotic main channels during low-flow periods. The flow variability and habitat-heterogeneity characteristic of these systems has the potential to significantly influence food web structure and must be integrated into models of large-river webs. We used stable-isotope analysis and IsoSource software to model terrestrial and algal sources of organic carbon supporting consumer taxa in the main channel and oxbow lakes of the Brazos River, Texas, USA, during a period of frequent hydrologic connectivity between these habitat types. Standardized sampling was conducted monthly to collect production sources and consumer species used in isotopic analysis. Predictability of hydrologic connections between habitat types was based on the previous 30 years of flow data. IsoSource mixing models identified terrestrial C3 macrophytes (riparian origin) as the primary carbon source supporting virtually all consumers in the main channel and most consumers in oxbow lakes. Small-bodied consumers (<100 mm) in oxbow lakes assimilated large fractions of algal carbon whereas this pattern was not apparent in the main channel. Estimates of detritivore trophic positions based on delta15N values indicated that terrestrial material was likely assimilated via invertebrates rather than directly from detritus. High flows in the river channel influenced algal standing stock, and differences in the importance of terrestrial and algal production sources among consumers in channel vs. oxbow habitats were associated with patterns of flooding. The importance of terrestrial material contradicts the findings of recent studies of large-river food webs that have emphasized the importance of algal carbon and indicates that there can be significant spatial, temporal, and taxonomic variation in carbon sources supporting consumers in large rivers.     

Cloning of urea transporters from the kidneys of two batoid elasmobranchs: evidence for a common elasmobranch urea transporter isoform

One of the two phloretin-sensitive, facilitated urea transporters identified from the kidneys of the myliobatiform, euryhaline elasmobranch, Dasyatis sabina, a 379 amino acid protein ([D. sabina]strUT-2), was very similar to the 380 amino acid isoform (shUT) present in the kidney of the squaliform, dogfish shark, Squalus acanthias (a species that can be considered marginally euryhaline since it utilizes upper estuarine, as well as ocean habitats). To test the proposal that this isoform is a conserved urea transporter (UT) expressed in the kidneys of diverse elasmobranchs, UTs were cloned from the kidneys of a rajiform elasmobranch, the stenohaline skate, Leucoraja ocellata and another dasyatid stingray, the marginally euryhaline, Dasyatis say. Utilizing 5′/3′ RACE, a 2,060 nt cDNA that encoded a phloretin-sensitive, 378 amino acid skate urea transporter ([L. ocellata]skUT-2) and a 1,683 nt cDNA that encoded a stingray 379 amino acid UT ([D. say]strUT-2) were obtained. These deduced UTs have a very high sequence identity with the known elasmobranch Uts. [L. ocellata]skUT-2 was 86% identical to [D. sabina]strUT-2 and 84% identical to [S. acanthias]shUT. [D. say]strUT-2 was 97% identical to the [D. sabina]strUT-2. These findings support the hypothesis that a conserved UT isoform is present in the kidneys of marine elasmobranchs, and is an important pathway for facilitated urea transport in the kidneys of marine elasmobranchs. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. H.A. Gefroh and E.E. Cwengros contributed equally to this study.     

USING CLIMATE FORECASTS FOR WATER MANAGEMENT: ARIZONA AND THE 1997–1998 EL NIÑO1

ABSTRACT: Unrelenting pressure on limited surface water supplies requires increasingly sophisticated water management approaches. Climate forecasts of seasonal precipitation and temperature are potentially useful, but the operational water management community currently underutilizes them. However, some agencies in Arizona took unprecedented advantage of forecasts for a potentially wet winter during the 1997–1998 El Niño event. This study investigates use of this information through a series of semi‐structured in‐depth interviews with key personnel from agencies responsible for emergency management and water supply; their jurisdictions ranged from urban to rural and local to regional. Interviews investigated information acquisition, interpretation, and incorporation into specific decisions and actions. While unprecedented actions were taken by some water management agencies and no agencies implemented inappropriate measures, some missed opportunities for more effective response, primarily through inaction. This study reveals a variety of technical factors and institutional characteristics affecting forecast use. Study findings emphasize the need for: (a) closer ongoing relationships between forecast producers and users, (b) increased institutional flexibility to exploit the increasing skill of seasonal climate forecasts, (c) demonstration projects of effective forecast use, and (d) a regional forum to facilitate information transfer between the hydro‐climatic research community and operational water managers.     

Do honey bees average directions in the waggle dance to determine a flight direction?

The waggle dance of the honey bee is a recruitment behavior used to communicate the location of a resource to a nest mate. There is, however, significant imprecision communicating the direction across waggle runs in a single dance. In this study, we ask whether honey bee recruits determine the direction of their flight based on an average of many waggle runs, or on a single waggle run. We show that the distribution of recruit flight directions is narrower than the distribution of directions indicated in the dance. We also show that there is a better fit between observed flight directions and the prediction of a multiple-waggle-run-averaging model than a last-waggle-run or other single-waggle-run models. These findings substantially weaken hypotheses about the adaptive nature of imprecision in honey bee recruitment.     

Toward Reversal of Eutrophic Conditions in a Subtropical Estuary: Water Quality and Seagrass Response to Nitrogen Loading Reductions in Tampa Bay, Florida, USA

Coastal waters have been significantly influenced by increased inputs of nutrients that have accompanied population growth in adjacent drainage basins. In Tampa Bay, Florida, USA, the population has quadrupled since 1950. By the late 1970s, eutrophic conditions including phytoplankton and macroalgal blooms and seagrass losses were evident. The focus of improving Tampa Bay is centered on obtaining sufficient water quality necessary for restoring seagrass habitat, estimated to have been 16,400 ha in 1950 but reduced to 8800 ha by 1982. To address these problems, targets for nutrient load reductions along with seagrass restoration goals were developed and actions were implemented to reach adopted targets. Empirical regression models were developed to determine relationships between chlorophyll a concentrations and light attenuation adequate for sustainable seagrass growth. Additional empirical relationships between nitrogen loading and chlorophyll a concentrations were developed to determine how Tampa Bay responds to changes in loads. Data show that when nitrogen load reduction and chlorophyll a targets are met, seagrass cover increases. After nitrogen load reductions and maintenance of chlorophyll a at target levels, seagrass acreage has increased 25% since 1982, although more than 5000 ha of seagrass still require recovery. The cooperation of scientists, managers, and decision makers participating in the Tampa Bay Estuary Program’s Nitrogen Management Strategy allows the Tampa Bay estuary to continue to show progress towards reversing many of the problems that once plagued its waters. These results also highlight the importance of a multi-entity watershed management process in maintaining progress towards science-based natural resource goals.     

Radium and radium-daughter nuclides in carbonates: a brief overview of strategies for determining chronologies

Radium isotopes have been used extensively to trace the movement of groundwater as well as oceanic water masses, but these radionuclides (and their daughters) are also useful chronometers for the determination of the time scales of other Earth and environmental processes. The purpose of this overview is to present the application of Ra and Ra daughters in the dating of carbonates. We show that the choice of dating method (decay of excess radionuclide or ingrowth of daughter) depends strongly on the parent/daughter activity ratios in the water in which the carbonate was precipitated. Thus freshly precipitated carbonates uniformly show excesses of ²²⁶Ra relative to its parent ²³⁰Th, and ²²⁶Ra decay can provide ages of carbonates over Holocene time scales. In contrast, carbonates are precipitated in waters of greatly varying ²¹⁰Pb/²²⁶Ra. Corals, deep-sea hydrothermal vent clams and the shelled cephalopod Nautilus live in waters with significant dissolved ²¹⁰Pb and all show excesses of ²¹⁰Pb in their carbonate. Bivalve molluscs from nearshore and coastal waters, and carbonates deposited from groundwater environments (e.g. travertines) in which ²¹⁰Pb is efficiently scavenged from solution, show deficiencies of ²¹⁰Pb relative to ²²⁶Ra. In contrast, fish otoliths strongly discriminate against ²¹⁰Pb regardless of the environment in which the fish lives. Deficiencies of ²²⁸Th relative to ²²⁸Ra are common in all carbonates. Useful time ranges for the ²¹⁰Pb/²²⁶Ra and ²²⁸Th/²²⁸Ra chronometers are ∼100 y and ∼10 y, respectively.     

Vitalizing effects of being outdoors and in nature

Five studies utilizing survey, experimental, and diary methods assessed the effects of being outdoors on subjective vitality. In Study 1, we used a vignette method to examine whether being outdoors was associated with vitality, above and beyond the influences of physical activity and social interactions. Study 2 explored the effects of being outdoors on vitality through an experimental design contrasting indoor and outdoor walks. In Study 3, participants were exposed to photographic scenes of either nature or buildings. Results showed that only the nature scenes enhanced subjective vitality. Studies 4 and 5 used a diary methodology to examine within-person variations in subjective energy as a function of being outdoors, again controlling for physical and social activity. Being outdoors was associated with greater vitality, a relation that was mediated by the presence of natural elements. Limitations of these studies are discussed, as well as their implications for research on energy and vitalization.     

Use of CALPUFF for exposure assessment in a near-field,complex terrain setting

CALPUFF is an atmospheric source-receptor model recommended by the U.S. Environmental Protection Agency for use on a case-by-case basis in complex terrain and wind conditions. The ability of the model to provide useful information for exposure assessments in areas with those topographical and meteorological conditions has received little attention. This is an important knowledge gap for use of CALPUFF outside of regulatory applications, such as exposure analyses conducted in support of risk assessments and health studies. We compared deposition of cadmium (Cd), lead (Pb), and zinc (Zn) calculated with CALPUFF as a result of emissions from a zinc smelter with corresponding concentrations of the metals measured in attic dust and soil samples obtained from the surrounding area. On a point-by-point analysis, predictions from CALPUFF explained 11% (lead) to 53% (zinc) of the variability in concentrations measured in attic dust. Levels of heavy metals in soil interpolated to 100 residential addresses from the distribution of concentrations measured in soil samples also agreed well with deposition predicted with CALPUFF: R² of 0.46, 0.76, and 079 for Pb, Cd, and Zn, respectively. Community-average concentrations of Cd, Pb, and Zn measured in soil were significantly (p < 0.0001) and strongly correlated (R² ranged from 0.77 to 0.98) with predicted deposition rates. These findings demonstrate that CALPUFF can provide reasonably accurate predictions of the patterns of long-term air pollutant deposition in the near-field associated with emissions from a discrete source in complex terrain. Because deposition estimates are calculated as a linear function of air concentrations, CALPUFF is expected to be reliable model for prediction of long-term average, near-field ambient air concentrations in complex terrain as well.     

Analytical Solutions to the Linearized Boussinesq Equation for Assessing the Effects of Recharge on Aquifer Discharge1

Boggs, Kevin G., Robert W. Van Kirk, Gary S. Johnson, Jerry P. Fairley, and P. Steve Porter, 2010. Analytical Solutions to the Linearized Boussinesq Equation for Assessing the Effects of Recharge on Aquifer Discharge. Journal of the American Water Resources Association (JAWRA) 46(6):1116–1132. DOI: 10.1111/j.1752-1688.2010.00479.x Abstract: There is a need to develop a general understanding of how variations in aquifer recharge are reflected in discharge. Analytical solutions to the linearized Boussinesq equation governing flow in an unconfined aquifer provide a unified mathematical framework to quantify relationships among lag time, attenuation and distance between aquifer recharge and discharge and the effect of an up-gradient no-flow boundary. We applied this framework to three types of recharge: (1) instantaneous, (2) periodic, and (3) constant rate for a finite duration. When the temporal scale of recharge exceeds the diffusive aquifer time scale, recharge will be reflected in discharge quickly and with little attenuation. When aquifer time scale is large, most recharge events are shorter in scale than that of the aquifer, resulting in large attenuation. Attenuation is more sensitive to boundary effects than lag time, and boundary effects increase as recharge time scale increases. Boundary effects can often be ignored when the recharge source is farther than 1/3 of the domain length away from the no-flow boundary. We illustrate analytical results with application to the economically critical Eastern Snake River Plain Aquifer in Idaho. In this aquifer, detectable annual and decadal cycles in discharge can result from recharge no farther than 20 and 60 km away from the discharge point, respectively. The effects of more distant, long-term recharge can be detected only after a time lag of several decades.