Distributions, abundances and activities of microbes associated with the nitrogen cycle in riparian and stream sediments of a river tributary.

River tributaries are ecologically important environments that function as sinks of inorganic nitrogen. To gain greater insight into the nitrogen cycle (N-cycle) in these environments, the distributions and activities of microbial populations involved in the N-cycle were studied in riparian and stream sediments of the Santa Fe River (SFR) tributaries located in northern Florida, USA. Riparian sediments were characterized by much higher organic matter content, and extracellular enzyme activities, including cellobiohydrolase, ß-d-glucosidase, and phenol oxidase than stream sediments. Compared with stream sediments, riparian sediments exhibited significantly higher activities of nitrification, denitrification, dissimilatory nitrate reduction to ammonia (DNRA) and anaerobic ammonia oxidation; correspondingly, with higher copies of amoA (a biomarker for enumerating nitrifiers), nirS and nirK (for denitrifiers), and nrfA (for DNRA bacteria). Among N-cycle processes, denitrification showed the highest activities and the highest concentrations of the corresponding gene (nirK and nirS) copy numbers. In riparian sediments, substantial nitrification activities (6.3 mg-N kg soil-1d-1 average) and numbers of amoA copies (7.3 × 107 copies g soil-1 average) were observed, and nitrification rates correlate with denitrification rates. The guild structures of denitrifiers and nitrifiers in riparian sediments differed significantly from those found in stream sediments, as revealed by analysis of nirS and archaeal amoA sequences. This study shows that riparian sediments serve as sinks for inorganic nitrogen loads from non-point sources of agricultural runoff, with nitrification and denitrification associated with elevated levels of carbon and nitrogen contents and extracellular enzyme activities.

Distribution, activities, and interactions of methanogens and sulfate-reducing prokaryotes in the Florida Everglades.

To gain insight into the mechanisms controlling methanogenic pathways in the Florida Everglades, the distribution and functional activities of methanogens and sulfate-reducing prokaryotes (SRPs) were investigated in soils (0 to 2 or 0 to 4 cm depth) across the well-documented nutrient gradient in the water conservation areas (WCAs) caused by runoff from the adjacent Everglades Agricultural Area. The methyl coenzyme M reductase gene (mcrA) sequences that were retrieved from WCA-2A, an area with relatively high concentrations of SO4 (2-) (≥39 µM), indicated that methanogens inhabiting this area were broadly distributed within the orders Methanomicrobiales, Methanosarcinales, Methanocellales, Methanobacteriales, and Methanomassiliicoccales. In more than 3 years of monitoring, quantitative PCR (qPCR) using newly designed group-specific primers revealed that the hydrogenotrophic Methanomicrobiales were more numerous than the Methanosaetaceae obligatory acetotrophs in SO4 (2-)-rich areas of WCA-2A, while the Methanosaetaceae were dominant over the Methanomicrobiales in WCA-3A (with relatively low SO4 (2-) concentrations; ≤4 µM). qPCR of dsrB sequences also indicated that SRPs are present at greater numbers than methanogens in the WCAs. In an incubation study with WCA-2A soils, addition of MoO4 (2-) (a specific inhibitor of SRP activity) resulted in increased methane production rates, lower apparent fractionation factors [αapp; defined as (amount of δ(13)CO2 + 1,000)/(amount of δ(13)CH4 + 1,000)], and higher Methanosaetaceae mcrA transcript levels compared to those for the controls without MoO4 (2-). These results indicate that SRPs play crucial roles in controlling methanogenic pathways and in shaping the structures of methanogen assemblages as a function of position along the nutrient gradient.

Projecting changes in Everglades soil biogeochemistry for carbon and other key elements, to possible 2060 climate and hydrologic scenarios.

Based on previously published studies of elemental cycling in Everglades soils, we projected how soil biogeochemistry, specifically carbon, nitrogen, phosphorus, sulfur, and mercury might respond to climate change scenarios projected for 2060 by the South Florida Water Management Model. Water budgets and stage hydrographs from this model with future scenarios of a 10% increased or decreased rainfall, a 1.5 °C rise in temperature and associated increase in evapotranspiration (ET) and a 0.5 m rise in sea level were used to predict resulting effects on soil biogeochemistry. Precipitation is a much stronger driver of soil biogeochemical processes than temperature, because of links among water cover, redox conditions, and organic carbon accumulation in soils. Under the 10% reduced rainfall scenario, large portions of the Everglades will experience dry down, organic soil oxidation, and shifts in soil redox that may dramatically alter biogeochemical processes. Lowering organic soil surface elevation may make portions of the Everglades more vulnerable to sea level rise. The 10% increased rainfall scenario, while potentially increasing phosphorus, sulfur, and mercury loading to the ecosystem, would maintain organic soil integrity and redox conditions conducive to normal wetland biogeochemical element cycling. Effects of increased ET will be similar to those of decreased precipitation. Temperature increases would have the effect of increasing microbial processes driving biogeochemical element cycling, but the effect would be much less than that of precipitation. The combined effects of decreased rainfall and increased ET suggest catastrophic losses in carbon- and organic-associated elements throughout the peat-based Everglades.

Seasonal dynamics of trace elements in tidal salt marsh soils as affected by the flow-sediment regulation regime.

Soil profiles were collected in three salt marshes with different plant species (i.e. Phragmites australis, Tamarix chinensis and Suaeda salsa) in the Yellow River Delta (YRD) of China during three seasons (summer and fall of 2007 and the following spring of 2008) after the flow-sediment regulation regime. Total elemental contents of As, Cd, Cu, Pb and Zn were determined using inductively coupled plasma atomic absorption spectrometry to investigate temporal variations in trace elements in soil profiles of the three salt marshes, assess the enrichment levels and ecological risks of these trace elements in three sampling seasons and identify their influencing factors. Trace elements did not change significantly along soil profiles at each site in each sampling season. The highest value for each sampling site was observed in summer and the lowest one in fall. Soils in both P. australis and S. salsa wetlands tended to have higher trace element levels than those in T. chinensis wetland. Compared to other elements, both Cd and As had higher enrichment factors exceeding moderate enrichment levels. However, the toxic unit (TU) values of these trace elements did not exceed probable effect levels. Correlation analysis showed that these trace elements were closely linked to soil properties such as moisture, sulfur, salinity, soil organic matter, soil texture and pH values. Principal component analysis showed that the sampling season affected by the flow-sediment regulation regime was the dominant factor influencing the distribution patterns of these trace elements in soils, and plant community type was another important factor. The findings of this study could contribute to wetland conservation and management in coastal regions affected by the hydrological engineering.

Efficacy of the seven feature, fifteen point histological scoring system and CD56 in interpretation of liver biopsies in persistent neonatal cholestasis: a five-year study.

CONTEXT: Neonatal cholestasis (NC) lasting more than 2 weeks affects one in 2500 live births. Extrahepatic biliary atresia (EHBA) and idiopathic neonatal hepatitis account for about 70% of all cases of NC. Differentiating these two conditions is important as patient management is very different for both the conditions. AIMS: To assess the usefulness of the seven-feature, 15-point histological scoring system in the interpretation of liver biopsy in NC and usefulness of immunostaining with CD56 (N-CAM) in EHBA. SETTINGS AND DESIGN: Retrospective study of 5 years' duration at a pediatric referral institute, where the case load of NC is high and definitive surgery for EHBA is undertaken after histological confirmation. MATERIALS AND METHODS: The study is of a 5-year duration conducted between June 2007 and May 2012. A total of 210 cases of NC were clinically diagnosed during this period. All the slides were reviewed with reference to a seven-feature, 15-point histological scoring system assessing its usefulness in the interpretation of liver biopsy in NC and utility of the immunohistochemical marker CD56 was also assessed as an aid in the characterization of bile ductular proliferation in EHBA. STATISTICAL ANALYSIS: Statistical analysis was performed and sensitivity and specificity of the histological scoring system for EHBA was analyzed. RESULTS: Of the 210 liver biopsies reviewed using the scoring system, 122 cases were diagnosed as EHBA and 88 cases were diagnosed as other causes of NC. The overall sensitivity of this scoring system was 95.5%, specificity was 93.1% and diagnostic accuracy was 94.6%. CONCLUSIONS: The seven-feature, 15-point histological scoring system has good diagnostic accuracy in the interpretation of liver histology in NC as advanced histopathological findings even at younger age require immediate surgery. CD-56 is a useful marker in the assessment of bile ductular proliferation in EHBA.

Calretinin immunohistochemistry: A new cost-effective and easy method for diagnosis of Hirschsprung's disease.

AIM: To evaluate the efficacy of calretinin immunostaining in diagnosing Hirschsprung's disease (HD). MATERIALS AND METHODS: Sixty cases were studied over a period of 1 year (July 2010-June 2011). There were 36 full-thickness biopsies and 24 resected specimens. Calretinin processing was done on the paraffin-embedded blocks after routine histopathological examination. RESULTS: Of the 36 biopsy specimens, in 19 cases HD was diagnosed by hematoxylin and eosin (H and E) staining earlier. In 2 patients, ganglion cells were seen and HD was ruled out. In 15 cases, there was a diagnostic dilemma and calretinin was used. Ganglion cells were found in 3 specimens and nerve fibers in 5. In all 24 resected specimens, calretinin correlated with the findings on H and E staining. CONCLUSIONS: Calretinin was extremely useful in solving the suspicious and indeterminate cases of HD. It can serve as a valuable cost-effective diagnostic aid in the centers where acetylcholinesterase enzyme histochemistry is not available.

Linking phosphorus sequestration to carbon humification in wetland soils by 31P and 13C NMR spectroscopy.

Phosphorus sequestration in wetland soils is a prerequisite for long-term maintenance of water quality in downstream aquatic systems, but can be compromised if phosphorus is released following changes in nutrient status or hydrological regimen. The association of phosphorus with relatively refractory natural organic matter (e.g., humic substances) might protect soil phosphorus from such changes. Here we used hydrofluoric acid (HF) pretreatment to remove phosphorus associated with metals or anionic sorption sites, allowing us to isolate a pool of phosphorus associated with the soil organic fraction. Solution (31)P and solid state (13)C NMR spectra for wetland soils were acquired before and after hydrofluoric acid pretreatment to assess quantitatively and qualitatively the changes in phosphorus and carbon functional groups. Organic phosphorus was largely unaffected by HF treatment in soils dominated by refractory alkyl and aromatic carbon groups, indicating association of organic phosphorus with stable, humified soil organic matter. Conversely, a considerable decrease in organic phosphorus following HF pretreatment was detected in soils where O-alkyl groups represented the major fraction of the soil carbon. These correlations suggest that HF treatment can be used as a method to distinguish phosphorus fractions that are bound to the inorganic soil components from those fractions that are stabilized by incorporation into soil organic matter.

Sirenomelia: a rare presentation.

We are presenting two cases of Sirenomelia (Mermaid Syndrome), which is an extreme example of the caudal regression syndrome. It invariably presents with lower limb fusion, sacral and pelvic bony anomalies, absent external genitalia, imperforate anus, and renal agenesis or dysgenesis. There are approximately 300 cases reported in the literature, 15% of which are associated with twinning, most often monozygotic. The syndrome of caudal regression is thought to be the result of injury to the caudal mesoderm early in gestation. One of our cases survived for 12 days after birth. This new born had an unusually high anorectal anomaly in which the colon was ending at the level of mid transverse colon, fused lower limbs and genital anomalies. Ultrasound of the abdomen revealed horseshoe kidney. Colostomy was performed on day 2 of life. The second case encountered was a stillborn baby on whom an autopsy was performed.

Spatial distributions and eco-partitioning of soil biogeochemical properties in the Everglades National Park.

Large-scale ecosystem restoration efforts, such as those in the Florida Everglades, can be long-term and resource intensive. To gauge success, restoration efforts must have a means to evaluate positive or negative results of instituted activities. Edaphic properties across the Everglades landscape have been determined to be a valuable metric for such evaluation, and as such, a baseline condition from which to make future comparisons and track ecosystem response is necessary. The objectives of this work were to document this baseline condition in the southern most hydrologic unit of the Everglades, Everglades National Park (ENP), and to determine if significant eco-partitioning of soil attributes exists that would suggest the need to focus monitoring efforts in particular eco-types within the ENP landscape. A total of 342 sites were sampled via soil coring and parameters such as total phosphorus (TP), total nitrogen (TN), total carbon (TC), total calcium, total magnesium, and bulk density were measured at three depth increments in the soil profile (floc, 0-10 cm, and 10-20 cm). Geostatistical analysis and GIS applications were employed to interpolate site-specific biogeochemical properties of soils across the entire extent of the ENP. Spatial patterns and eco-type comparisons suggest TC and TN to be highest in Shark River Slough (SRS) and the mangrove interface (MI), following trends of greatest organic soil accumulation. However, TP patterns suggest greatest storages in MI, SRS, and western marl and wet prairies. Eco-partitioning of soil constituents suggest local drivers of geology and hydrology are significant in determining potential areas to focus monitoring for future change detection.

Phosphorus transformations during decomposition of wetland macrophytes.

The microbially mediated transformation of detrital P entering wetlands has important implications for the cycling and long-term sequestration of P in wetland soils. We investigated changes in P forms in sawgrass (Cladium jamaicense Crantz) and cattail (Typha domingensis Pers.) leaf litter during 15 months of decomposition at two sites of markedly different nutrient status within a hard-water subtropical wetland (Water Conservation Area 2A, Florida). Leaf litter decomposition at the nutrient enriched site resulted in net sequestration of P from the environment in forms characteristic of microbial cells (i.e., phosphodiesters and pyrophosphate). In contrast, low P concentrations at the unenriched site resulted in little or no net sequestration of P, with changes in P forms limited to the loss of compounds present in the initial leaf litter. We conclude that under nutrient-rich conditions, P sequestration occurs through the accumulation of microbially derived compounds and the presumed concentration of endogenous macrophyte P. Under nutrient-poor conditions, standing P pools within wetland soils appear to be independent of the heterotrophic decomposition of macrophyte leaf litter. These conclusions have important implications for our ability to predict the nature, stability, and rates of P sequestration in wetlands in response to changes in nutrient loading.

Soil phosphorus forms in hydrologically isolated wetlands and surrounding pasture uplands.

Newly created and restored wetlands play an important role in sequestering excess nutrients at the landscape scale. In evaluating the long-term efficacy of nutrient management strategies to increase wetland capacity for sequestering P, information is needed on the forms of P found across the upland-wetland transition. To assess this, we studied soils (0-10 cm) from four wetlands within cow-calf pastures north of Lake Okeechobee, FL. Wetlands contained significantly (P < 0.05) greater concentrations of organic matter (219 g C kg(-1)), total P (371 mg P kg(-1)), and metals (Al, Fe) relative to surrounding pasture. When calculated on an aerial basis, wetland surface soils contained significantly greater amounts of total P (236 kg ha(-1)) compared with upland soils (114 kg ha(-1)), which was linked to the concomitant increase in organic matter with increasing hydroperiod. The concentration of P forms, determined by extraction with anion exchange membranes, 1 mol L(-1) HCl, and an alkaline extract (0.25 mol L(-1) NaOH and 50 mmol L(-1) ethylenediaminetetraacetic acid [EDTA]) showed significant differences between uplands and wetlands but did not alter as a proportion of total P. Speciation of NaOH-EDTA extracts by solution 31P nuclear magnetic resonance spectroscopy revealed that organic P was dominated by phosphomonoesters in both wetland and pasture soils but that myo-inositol hexakisphosphate was not detected in any sample. The tight coupling of total C and P in the sandy soils of the region suggests that the successful management of historically isolated wetlands for P sequestration depends on the long-term accumulation and stabilization of soil organic matter.

Phosphorus sorption and potential phosphorus storage in sediments of Lake Istokpoga and the upper chain of lakes, Florida, USA.

Phosphorus (P) can be an important nutrient in regulating primary productivity in lakes. The ability of lake sediments to retain P from external sources depends on the physiochemical characteristics of the sediment. To assess the P dynamics in Lake Istokpoga and the upper chain of lakes that drain into Lake Okeechobee, Florida, USA, sorption properties of batch sediment samples for Lakes Tohopekaliga, Cypress, Hatchineha, Kissimmee, and Istokpoga were characterized under aerobic and anaerobic conditions. Langmuir model parameters fit the experimental data well (in general, r(2) > 0.70). There were strong correlations between P sorption and total C, total P, Ca, Mg, Fe, and Al (r = 0.83-0.97). Equilibrium P concentration values ranged between 0.001 and 0.192 mg L(-1) for aerobic conditions. A single-point isotherm (initial concentration, 5 mg L(-1)) was found for a wide range of sediment types, which allows estimation of the maximum potential sorption (S(max)) as 1.7 times the sorption (S(max) = 1.7 S(5)). Results suggest that although these sediments have high P sorption capacities, the lake sediments may release P into the water column by desorption under aerobic conditions if water-column P concentrations are low enough (<0.036 mg L(-1) for Lake Tohopekaliga and <0.003-0.027 mg L(-1) for the other four lakes). Current watershed management strategies must balance efforts to reduce P inputs into the lakes from point and nonpoint sources against lowering the water-column P concentration to such a low level that the lake sediments become a source of P to downstream Lake Okeechobee.

Overestimation of organic phosphorus in wetland soils by alkaline extraction and molybdate colorimetry.

Accurate information on the chemical nature of soil phosphorus is essential for understanding its bioavailability and fate in wetland ecosystems. Solution phosphorus-31 nuclear magnetic resonance (31P NMR) spectroscopy was used to assess the conventional colorimetric procedure for phosphorus speciation in alkaline extracts of organic soils from the Florida Everglades. Molybdate colorimetry markedly overestimated organic phosphorus by between 30 and 54% compared to NMR spectroscopy. This was due in large part to the association of inorganic phosphate with organic matter, although the error was exacerbated in some samples by the presence of pyrophosphate, an inorganic polyphosphate that is not detected by colorimetry. The results have important implications for our understanding of phosphorus biogeochemistry in wetlands and suggest that alkaline extraction and solution 31p NMR spectroscopy is the only accurate method for quantifying organic phosphorus in wetland soils.

The reduction of internal phosphorus loading using alum in Spring Lake, Michigan.

The release of P from lake sediments, which occurs as a part of internal loading, may contribute a significant portion of the total P load to a lake. Phosphorus release rates from sediments in Spring Lake, Michigan, and the degree to which alum reduces P release from these sediments, were investigated during the summer of 2003. Triplicate sediment cores were sampled from four sites in the lake, and exposed to one of four treatments in the laboratory: (i) aerobic water column/alum, (ii) aerobic water column/no alum, (iii) anaerobic water column/alum, or (iv) anaerobic water column/no alum. Total P (TP) release rates were virtually undetectable in the alum treatments (both aerobic and anaerobic). Low, but detectable, release rates were measured in the aerobic/no alum treatment. The highest release rates were measured in the anaerobic/no alum treatments, and ranged from 1.6 to 29.5 mg P m(-2) d(-1) depending on how the calculations were derived. These fluxes translated to mean internal loads that ranged between 2.7 (low range) and 6.4 (high range) Mg yr(-1) when extrapolated to a whole-lake basis. Internal P loads accounted for between 55 and 65% of the total P load to Spring Lake. Although alum is a potentially effective means of reducing the sediment source of P, there is considerable uncertainty in how long an alum treatment would remain effective in this system given the current rates of external loading and the lack of information on wind-wave action and bioturbation in Spring Lake.