Utilizing pyrosequencing and quantitative PCR to characterize fungal populations among house dust samples

Molecular techniques are an alternative to culturing and counting methods in quantifying indoor fungal contamination. Pyrosequencing offers the possibility of identifying unexpected indoor fungi. In this study, 50 house dust samples were collected from homes in the Yakima Valley, WA. Each sample was analyzed by quantitative PCR (QPCR) for 36 common fungi and by fungal tag-encoded flexible (FLX) amplicon pyrosequencing (fTEFAP) for these and additional fungi. Only 24 of the samples yielded amplified results using fTEFAP but QPCR successfully amplified all 50 samples. Over 450 fungal species were detected by fTEFAP but most were rare. Twenty-two fungi were found by fTEFAP to occur with at least an average of ≥0.5% relative occurrence. Many of these fungi seem to be associated with plants, soil or human skin. Combining fTEFAP and QPCR can enhance studies of fungal contamination in homes.     

Using variance components to estimate power in a hierarchically nested sampling design

We used variance components to assess allocation of sampling effort in a hierarchically nested sampling design for ongoing monitoring of early life history stages of the federally endangered Devils Hole pupfish (DHP) (Cyprinodon diabolis). Sampling design for larval DHP included surveys (5 days each spring 2007–2009), events, and plots. Each survey was comprised of three counting events, where DHP larvae on nine plots were counted plot by plot. Statistical analysis of larval abundance included three components: (1) evaluation of power from various sample size combinations, (2) comparison of power in fixed and random plot designs, and (3) assessment of yearly differences in the power of the survey. Results indicated that increasing the sample size at the lowest level of sampling represented the most realistic option to increase the survey’s power, fixed plot designs had greater power than random plot designs, and the power of the larval survey varied by year. This study provides an example of how monitoring efforts may benefit from coupling variance components estimation with power analysis to assess sampling design.     

Responses of Physical, Chemical, and Biological Indicators of Water Quality to a Gradient of Agricultural Land Use in the Yakima River Basin, Washington

The condition of 25 stream sites in the Yakima River Basin, Washington, were assessed by the U.S. Geological Survey's National Water-Quality Assessment Program. Multimetric condition indices were developed and used to rank sites on the basis of physical, chemical, and biological characteristics. These indices showed that sites in the Cascades and Eastern Cascades ecoregions were largely unimpaired. In contrast, all but two sites in the Columbia Basin ecoregion were impaired, some severely. Agriculture (nutrients and pesticides) was the primary factor associated with impairment and all impaired sites were characterized by multiple indicators of impairment. All indices of biological condition (fish, invertebrates, and algae) declined as agricultural intensity increased. The response exhibited by invertebrates and algae suggested a threshold response with conditions declining precipitously at relatively low levels of agricultural intensity and little response at moderate to high levels of agricultural intensity. This pattern of response suggests that the success of mitigation will vary depending upon where on the response curve the mitigation is undertaken. Because the form of the community condition response is critical to effective water-quality management, the National Water-Quality Assessment Program is conducting studies to examine the response of biota to gradients of land-use intensity and the relevance of these responses to water-quality management. These land-use gradient pilot studies will be conducted in several urban areas starting in 1999.     

Vegetation response to hydrologic and geomorphic factors in an arid region of the Baja California Peninsula

Remotely sensed imageries were used to analyze the response of desert vegetation to physiographic factors and accumulated precipitation in drier and wetter years within a region of >16,500 km² sampled with 5,000 random pixels of 30 m. Vegetation development was indexed by the annual maximum values for greenness (SAVI) and canopy water content (NDII). Precipitation was interpolated from the 0.25° grid of the Tropical Rainfall Measurement Mission satellite-based estimates, showing a regional average of ～55 mm in the wetter year. The vegetation indices were only weakly related to total precipitation, often in a negative sense. Terrain factors that most often affected the vegetation indices, in multiple regression models, were Topographic Wetness Index, elevation, and slope gradient; these often had different signs for SAVI and for NDII. Models for NDII on intrusive igneous rocks gave better results than on extrusive igneous rocks. The strongest patterns in vegetation development were the contrast among Pacific coast, Cordillera, and Gulf coast subregions and the generally stronger results for NDII than SAVI.     

Predictive model for chloroform during disinfection of water for consumption,city of Montevideo

The objective of this study was to predict chloroform formation resulting from the process of disinfecting water, particularly trihalomethane which is most frequently produced. A statistical model was used which included repeated measurements of water parameters used for monitoring water quality at 51 sites covering the municipal water system of Montevideo. Samples were taken considering different seasons from June 2009 to July 2011 in Montevideo. Total samples (n?=?330) were analytically studied using the headspace-gas chromatography method coupled with mass spectrometry. Chloroform was the dependent variable and the covariables were pH, temperature, free chlorine, and total chlorine. A Tobit analysis with an unstructured correlation matrix was performed, and a significant interaction was found between pH and free chlorine for the prediction of chloroform formation. We concluded that parameters for the continuous control of water quality for consumption can be used to predict the levels of chloroform that may be present. Given the large measurement to variability found in the repeated measurements, the use of averages that include more than one season is not recommended to determine the degree of compliance with acceptable levels established by norms.     

The problem of estimating recent genetic connectivity in a changing world

Accurate understanding of population connectivity is important to conservation because dispersal can play an important role in population dynamics, microevolution, and assessments of extirpation risk and population rescue. Genetic methods are increasingly used to infer population connectivity because advances in technology have made them more advantageous (e.g., cost effective) relative to ecological methods. Given the reductions in wildlife population connectivity since the Industrial Revolution and more recent drastic reductions from habitat loss, it is important to know the accuracy of and biases in genetic connectivity estimators when connectivity has declined recently. Using simulated data, we investigated the accuracy and bias of 2 common estimators of migration (movement of individuals among populations) rate. We focused on the timing of the connectivity change and the magnitude of that change on the estimates of migration by using a coalescent‐based method (Migrate‐n) and a disequilibrium‐based method (BayesAss). Contrary to expectations, when historically high connectivity had declined recently: (i) both methods over‐estimated recent migration rates; (ii) the coalescent‐based method (Migrate‐n) provided better estimates of recent migration rate than the disequilibrium‐based method (BayesAss); (iii) the coalescent‐based method did not accurately reflect long‐term genetic connectivity. Overall, our results highlight the problems with comparing coalescent and disequilibrium estimates to make inferences about the effects of recent landscape change on genetic connectivity among populations. We found that contrasting these 2 estimates to make inferences about genetic‐connectivity changes over time could lead to inaccurate conclusions.     

Bacterial source tracking guides management of boat head waste in a coastal resort area

Fecal contamination of water bodies causes a public health problem and economic loss. To control such contamination management actions need to be guided by sound science. From 2007–2009 a study was undertaken to determine the sources of fecal bacteria contamination to the marine waters adjoining the Town of Wrightsville Beach, North Carolina, USA. The research effort included sampling for fecal coliform and Enterococcus bacteria, sampling for optical brighteners, dye studies, and use of molecular bacterial source tracking techniques including polymerase chain reaction (PCR) and terminal restriction fragment polymorphism (T-RFLP) fingerprinting of the Bacteroides–Prevotella group. Of the 96 samples collected from nine locations during the study, the water contact standard for Enterococcus was exceeded on 13 occasions. The T-RFLP fingerprint analyses demonstrated that the most widespread source of fecal contamination was human, occurring in 38% of the samples, with secondary ruminant and avian sources also detected. Optical brightener concentrations were low, reflecting a lack of sewage line leakage or spills. A lack of sewer leaks and lack of septic systems in the town pointed toward discharge from boat heads into the marine waters as the major cause of fecal contamination; this was supported by dye studies. Based on these data, the Town initiated action to have the U.S. Environmental Protection Agency declare the coastal waters (out to 3 nautical miles), the nearby Atlantic Intracoastal Waterway and its tributaries a no-discharge zone (NDZ) to alleviate the human fecal pollution. The Town garnered supporting resolutions from other local communities who jointly petitioned the North Carolina Department of Environmental and Natural Resources. This State regulatory agency supported the local government resolutions and sent an application for an NDZ to the EPA in April 2009. The EPA concurred, and in February 2010 the coastal waters of New Hanover County, NC, became the first marine area on the U.S. eastern seaboard between Delaware and the Florida Keys to be declared a no-discharge zone.     

Millennial‐Length Records of Streamflow From Three Major Upper Colorado River Tributaries1

Gray, Stephen T., Jeffrey J. Lukas, and Connie A. Woodhouse, 2011. Millennial‐Length Records of Streamflow From Three Major Upper Colorado River Tributaries. Journal of the American Water Resources Association (JAWRA) 47(4):702‐712. DOI: 10.1111/j.1752‐1688.2011.00535.x Abstract: Drought, climate change, and shifting consumptive use are prompting a widespread reassessment of water availability in the Upper Colorado River basin. Here, we present millennial‐length records of water year (October‐September) streamflow for key Upper Colorado tributaries: the White, Yampa, and Little Snake Rivers. Based on tree rings, these records represent the first paleohydrological reconstructions from these subbasins to overlap with a series of Medieval droughts (∼ad 800 to 1300). The reconstructions show marked interannual variability imbedded in nonstationary behavior over decadal to multidecadal time scales. These reconstructions suggest that, even in a millennial context, gaged flows from a handful of years (e.g., 1977 and 2002) were extremely dry. However, droughts of much greater duration and magnitude than any in the instrumental record were regular features prior to 1900. Likewise these reconstructions point to the unusual wetness of the gage period, and the potential for recent observations to paint an overly optimistic picture of regional water supplies. The future of the Upper Colorado River will be determined by a combination of inherent hydroclimatic variability and a broad range of human‐induced changes. It is then essential that regional water managers, water users, and policy makers alike consider a broader range of hydroclimatic scenarios than is offered by the gage record alone.     

Suppressed recovery of plant community composition and biodiversity on dredged fill of a hurricane-induced inlet through a barrier island

In September 2003, Hurricane Isabel created an inlet over 500 m wide and 10 m deep that connected the Atlantic Ocean and Pamlico Sound. This breach was subsequently filled with sediments dredged from the adjacent sound. The purpose of this study was to determine if the barrier island terrestrial plant communities were naturally re-establishing through primary succession. In 2006–2008, we compared plant communities, soil carbon and nitrogen, and Aeolian transport of sediments in undisturbed back-dunes, undisturbed shrub thickets, putative back-dunes, and putative shrub thickets. We found that species richness and evenness were low on the filled area relative to adjacent plant communities that had persisted through the storm. Plants on the filled area were almost entirely limited to a band of primarily Spartina patens found at the margin of the sound and there were no signs of establishing the typical zonation of back dune grasses, shrubs, and salt marsh. Evaluation of soil quality suggests that nutrients and organic material are not limiting recovery. Aeolian transport, however, was demonstrably higher across the filled area, where no dense stands of taller plants buffered the airflow. Plant re-establishment is suppressed by wind erosion inhibiting deposition of seeds. Recovery of the site will likely depend on the rhizomatous spread of S. patens from the sound shore. S. patens can then potentially facilitate the colonization of other species by buffering the wind and trapping seeds of other plants. Ironically, this slow recovery may benefit federally threatened bird species that require sparse vegetation for nesting success.     

Adoption and cuckoldry lead to alloparental care in the tessellated darter (Etheostoma olmstedi), a non-group-living species with no evidence of nest site limitation

While extensive empirical and theoretical work has focused on the evolution of costly cooperation (particularly in group-living species), less attention has been paid to more low-risk or immediately beneficial forms of cooperation. In some non-group-living darters, alloparental care (or allocare) by subordinates has been noted to result from by-product benefits as small territorial (subordinate) males adopt and provide care to the abandoned eggs of large territorial (dominant) males. In the tessellated darter (Etheostoma olmstedi), allocare also results from sneak fertilization. However, information on the rate of allocare by tessellated darters is contradictory: prior behavioral work suggested that it is very common, while a genetic examination showed males to primarily care for their own young. We found behavioral and genetic evidence of very high levels of allocare at our study location. The relative size of the assigned fathers of young to the alloparental male is consistent with the idea that initial allocare primarily results from sneak fertilization (“cuckoldry-based allocare”), but later allocare results from subordinate males caring at previously abandoned nests (“adoption-based allocare”). Larger males appeared to breed more frequently at different nests, but did not father more individual offspring than smaller males. Finally, low relatedness between abandoning and alloparenting males suggests that kin selection does not contribute to alloparental care. We discuss how variation in nest availability may explain the inconsistent findings of the rate of alloparental care in the tessellated darter, and how increased research in this and similar systems can expand our understanding of the evolution of cooperation.