Seston dynamics and tripton sedimentation in the pelagic zone of a shallow eutrophic lake

The transport of organic matter from the water column to the sediment and the relationship between the dynamics of the settleable fraction and that of the total suspended particulate matter were studied in shallow eutrophic Lake Wingra, Wisconsin. Tripton sedimentation was closely related to the dynamics of seston with a lag of 2 to 4 weeks. Sedimentation rate of tripton ranged from 0 to 8 g m^–2 day^–1 (in May and August respectively). Relative t0 the standing crop 0f seston the maximum sedimentation rate was 8% seston per day (in September). The annual tripton sedimentation was estimated at 632 g dry weight or 215 g C per m² which was equivalent t0 55% of the annual phytoplankton production and 42% of the phytoplankton and macrophytes annual production. It was estimated that 70% of the settling organic matter is decomposed annually, consequently only a small fraction 0f tripton is involved in the long term accumulation of bottom deposits. Factors influencing tripton sedimentation are discussed.Research supported by the Eastern Deciduous Forest Biome US-IBP, funded by the National Science Foundation under Interagency Agreement AG-199 BMS69-01147 A09 with the Energy Research and Development Administration-Oak Ridge National Laboratory. Contribution N0. 233 from the Eastern Deciduous Forest Biome US-IBP.Research supported by the Eastern Deciduous Forest Biome US-IBP, funded by the National Science Foundation under Interagency Agreement AG-199 BMS69-01147 A09 with the Energy Research and Development Administration-Oak Ridge National Laboratory. Contribution N0. 233 from the Eastern Deciduous Forest Biome US-IBP.     

Analysis of an east tennessee oak hickory forest by canonical correlation of species and environmental parameters

Summary A new multivariate analytical technique, canonical group correlation (CGC) is developed to correlate abiotic and biotic characterization of communities. This technique is applied to the plant communities of a 97.5 ha oak-hickory watershed. This analysis has validated inferences drawn in earlier studies which used only species data. We have concluded that the dominant factors discriminating the four distinct types of vegetation which exist in the region being studied are age and slope position. Slope position is inferred to be correlated with a moisture gradient. This information is depicted by the location of the four community types in two canonical spaces. One space is determined by vegetational parameters (species composition), the other by environmental parameters. A linear transformation between the two spaces is derived. This transformation can be used to predict successional development.Research supported by the Eastern Deciduous Forest Biome, US-IBP, funded by the National Sciences Foundation under Interagency Agreement AG-199, 40-193-69 with the Atomic Energy Commission, Oak Ridge National Laboratory. This is Contribution No. 291 from the Eastern Deciduous Forest Biome, US-IBP, and Publication No. 1054, Environmental Sciences Division, Oak Ridge National Laboratory.Nomenclature follows Little (1953).     

Comparison of species ordinations resulting from alternative indices of interspecific association and different numbers of included species

Summary Several measures of interspecific association are compared. Dispersion and covariance are limited in value because they respond to the commonness of the species compared. Correlation is not so limited but it responds to discrepancies in commonness among the species. The practical result of these relationships between commonness and association is that only the most common species can occupy periferal positions in a species ordination. Rare species are relegated to positions near the center not on the basis of their phytosociological pattern but simply because of their rarity. Both Cole's index of association and the tetrachoric correlation overcome the problem imposed by the relationship between ordination position and species commonness and they both produce very similar results. The effect of differing numbers of species on the ordination configuration is examined using both Pearson's correlation and Cole's index. The basic pattern of the ordination is set with the first few species when Cole's index is used, however, since rare species are given more weight in the analysis with this index, the addition of several very rare species can change the configuration of the ordination.Nomenclature of species is given in Table 1.Research supported by the Eastern Deciduous Forest Biome Project, US-IBP, funded by the National Science Foundation under Interagency Agreement AG-199, BMS69-01147 A09 with the Energy Research and Development Administration — Oak Ridge National Laboratory. Research also supported by the U.S. Energy Research and Development Administration under contract with the Union Carbide Corporation. Contribution No. 240 from the EDFB, US-IBP. Publication No. 790. Environmental Sciences Division, ORNL.     

Phytoplankton community response to reservoir aging, 1968–92

The effects of reservoir aging on the phytoplankton community of amidwestern U.S. reservoir constructed in 1965 (Pawnee Reservoir) werestudied by comparing algal biovolume and species composition from April 1992through November 1992 to surveys conducted in 1968–73 and 1990. Meansummer total phosphorus, nitrate-nitrogen, Secchi disk depth, totalsuspended solids, chlorophyll a, and phytoplankton species composition datacharacterized Pawnee Reservoir during 1968–69 as a high nutrient,relatively clear water environment. Phytoplankton biomass was relativelylow, consisting mainly of cyanophytes and non-flagellated chlorophytes.During 1970–73, water clarity was poor, total suspended solids werehigh, and total phosphorus was lower, but was still greater than 100 µgl^–1. The 1970–73 phytoplankton biomass was high and wasdominated by cyanophytes. Mean summer total phosphorus remained >100µg l^–1, water clarity remained poor, but phytoplanktonbiomass decreased significantly during 1990–92. The dramatic drop inchlorophyll a and low mean volatile suspended solids indicated thatinorganic suspended sediments, rather than phytoplankton, accounted for themajority of the turbidity in 1990-92. In addition to lower phytoplanktonbiomass, community composition shifted away from buoyancy-regulatingcyanophytes toward flagellated chlorophytes. These data suggest that asreservoirs located in agricultural watersheds age, (1) inorganic suspendedsediments have a significant effect on the light environment as well asphytoplankton biomass and species composition, (2) the control ofphytoplankton biomass and species composition shifts away from nutrients tolight and suspended sediments, and (3) there is a 1–2 year lag in theresponse of phytoplankton biomass to maximum nutrient loading during thetrophic upsurge period. Thus, sedimentation has been shown to be a primarydeterminant of plankton and benthic macroinvertebrate community compositionas Pawnee Reservoir aged.     

Nitrogen and phosphorus recycling in Lake Sammamish,a temperate mesotrophic lake

This paper presents nitrogen and phosphorus budgets for spring and summer for the trophogenic (0–9 m) and tropholytic (9–27 m) zones of Lake Sammamish. The objective of constructing the budgets is to evaluate the efficiency of nutrient recycling and increase knowledge of the overall nutrient dynamics.The budgets reveal that uptake and solubilization are the dominant fluxes and that nutrient recycling is generally efficient, with the possible exception of early spring during the diatom bloom. This leads to greater reductions in the dissolved N and P pools in spring than summer. Sedimentation is greater in spring because of a pulse immediately following the diatom bloom.Solubilization of particulates is much less in the tropholytic zone than the trophogenic zone. This is due to slower decomposition rates there and to the efficiency of solubilization in the overlying trophogenic zone which results in a relatively small particulate influx. Turnover times for the N and P pools are therefore much faster in the trophogenic zone than in the tropholytic zone. In the trophogenic zone, however, the dissolved N pool turns over much more slowly than the dissolved P pool because of its larger size relative to algal growth requirements.Overall there is a net loss of N and P from the water column in spring primarily due to sedimentation and denitrification whilst in summer there is a small net gain because of sediment release and a slight excess of inflow over outflow.The work was supported by National Science Foundation grants DEB 74-20744, BMS 74-20744 and GB 36810F to the International Biological Program, Western Coniferous Biome (US/IBP) and grant R 008512 from the US Environmental Protection Agency. Contribution no. 373 by the Western Coniferous Biome.The work was supported by National Science Foundation grants DEB 74-20744, BMS 74-20744 and GB 36810F to the International Biological Program, Western Coniferous Biome (US/IBP) and grant R 008512 from the US Environmental Protection Agency. Contribution no. 373 by the Western Coniferous Biome.     

Disparities and Trends in Indoor Exposure to Secondhand Smoke among U.S. Adolescents: 2000-2009

Introduction

Secondhand smoke (SHS) exposure causes disease and death among nonsmokers. With a plethora of smoke-free legislation implemented and a steady decrease in cigarette consumption noted over the past decade in the U.S., this study assessed trends in indoor SHS exposure among U.S. adolescents in grades 6–12 during 2000–2009.

Methods

Data were obtained from the 2000–2009 National Youth Tobacco Survey – a national survey of U.S. middle and high school students. SHS exposure within an indoor area within the past seven days was self-reported. Trends in indoor SHS exposure during 2000–2009 were assessed overall and by socio-demographic characteristics, using the Wald''s test in a binary logistic regression. Within-group comparisons were performed using chi-squared statistics (p<0.05).

Results

The proportion of U.S. middle and high school students who were exposed to indoor SHS declined from 65.5% in 2000 to 40.5% in 2009 (p<0.05 for linear trend). Significant declines were also observed across all population subgroups. Between 2000 and 2009, prevalence of indoor SHS exposure declined significantly among both middle (58.5% to 34.3%) and high school (71.5% to 45.4%) students. Prevalence of indoor SHS exposure was significantly higher among girls (44.0% in 2009) compared to boys (37.2% in 2009) during each survey year. Similarly, prevalence of indoor SHS exposure during 2000–2009 was highest among non-Hispanic whites (44.2% in 2009) and lowest among non-Hispanic Asians (30.2% in 2009). During each survey year, prevalence was highest among the oldest age group (≥18 years) and lowest among the youngest (9–11 years). Also, prevalence was significantly higher among current cigarette smokers (83.8% in 2009) compared to nonsmokers (34.0% in 2009).

Conclusion

Significant declines in indoor SHS exposure among U.S. middle and high school students occurred during 2000–2009. While the results are encouraging, additional efforts are needed to further reduce youth indoor SHS exposure.     

A probability-based indicator of ecological condition

We introduce a new method for quantifying the ecological condition (C) of sites based on documented species’ responses to environmental stress. Preliminary research is needed to establish species-specific logistic functions, representing probabilities of finding individual species across an explicit reference gradient, ranging from maximally stressed (C = 0) to minimally stressed (C = 10) localities. Each function takes into account the species’ tolerance to stress, the species’ overall ubiquity, and the probability of detecting the species when it is present. Given a set of standardized species-specific functions, the ecological condition of any site can be derived by iteration, converging on the value of C that best “predicts” the species that are actually present. Species from multiple taxonomic groups can be included in the calculations, and results are not directly affected by species richness or sampling area. We demonstrate a successful application of this method for bird species assemblages in the U.S. portion of the Great Lakes coastal zone. Approximately, 28% of the bird species observed in the Eastern Deciduous Forest Ecological Province and 35% of the species in the Laurentian Mixed Forest Ecological Province showed strong relationships with a reference gradient of land cover variables. Functional stress–response relationships of these species can be used effectively to estimate ecological condition at new sites. The estimated condition based on bird species generally mirrors the reference condition, but deviations from the expected 1:1 relationship provide meaningful insights about ecological condition of the target areas. Sensitivity analysis using different numbers of species shows that our method is robust and can be applied consistently with 25–30 species exhibiting strong stress–response functions.     

Phytoplankton and bacterial assemblages in ballast water of U.S. military ships as a function of port of origin, voyage time, and ocean exchange practices

We characterized the physical/chemical conditions and the algal and bacterial assemblages in ballast water from 62 ballast tanks aboard 28 ships operated by the U.S. Military Sealift Command and the Maritime Administration, sampled at 9 ports on the U.S. West Coast and 4 ports on the U.S. East Coast. The ballast tank waters had been held for 2–176 days, and 90% of the tanks had undergone ballast exchange with open ocean waters. Phytoplankton abundance was highly variable (grand mean for all tanks, 3.21 × 10⁴ viable cells m⁻³; median, 7.9 × 10³ cells m⁻³) and was unrelated to physical/chemical parameters, except for a positive relationship between centric diatom abundance and nitrate concentration. A total of 100 phytoplankton species were identified from the ballast tanks, including 23 potentially harmful taxa (e.g. Chaetoceros concavicornis, Dinophysis acuminata, Gambierdiscus toxicus, Heterosigma akashiwo, Karlodinium veneficum, Prorocentrum minimum, Pseudo-nitzschia multiseries). Assemblages were dominated by chain-forming diatoms and dinoflagellates, and viable organisms comprised about half of the total cells. Species richness was higher in ballast tanks with coastal water, and in tanks containing Atlantic or Pacific Ocean source waters rather than Indian Ocean water. Total and viable phytoplankton numbers decreased with age of water in the tanks. Diversity also generally decreased with water age, and tanks with ballast water age >33 days did not produce culturable phytoplankton. Abundance was significantly higher in tanks with recently added coastal water than in tanks without coastal sources, but highly variable in waters held less than 30 days. Bacterial abundance was significantly lower in ballast tanks with Atlantic than Pacific Ocean source water, but otherwise was surprisingly consistent among ballast tanks (overall mean across all tanks, 3.13 ± 1.27 × 10¹¹ cells m⁻³; median, 2.79 × 10¹¹ cells m⁻³) and was unrelated to vessel type, exchange status, age of water, environmental conditions measured, or phytoplankton abundance. At least one of four pathogenic eubacteria (Listeria monocytogenes, Escherichia coli, Mycobacterium spp., Pseudomonas aeruginosa) was detected in 48% of the ballast tanks, but toxigenic strains of Vibrio cholerae were not detected. For ships with tanks of similar ballasting history, the largest source of variation in phytoplankton and bacteria abundance was among ships; for ships with tanks of differing ballasting histories, and for all ships/tanks considered collectively, the largest source of variation was within ships. Significant differences in phytoplankton abundance, but not bacterial abundance, sometimes occurred between paired tanks with similar ballasting history; hence, for regulatory purposes phytoplankton abundance cannot be estimated from single tanks only. Most tanks (94%) had adequate records to determine the source locations and age of the ballast water and, as mentioned, 90% had had ballast exchange with open-ocean waters. Although additional data are needed from sediments that can accumulate at the bottom of ballast tanks, the data from this water-column study indicate that in general, U.S. Department of Defense (DoD) ships are well managed to minimize the risk for introduction of harmful microbiota. Nevertheless, abundances of viable phytoplankton with maximum dimension >50 μm exceeded proposed International Maritime Organization standards in 47% of the ballast tanks sampled. The data suggest that further treatment technologies and/or alternative management strategies will be necessary to enable DoD vessels to comply with proposed standards.     

Immunochemical cross-reactivity between intact purified myelin basic protein (MBP) and the synthetic encephalitogenic peptide S49

Three antisera to myelin basic protein—a rabbit antiserum pool against rat myelin, a rabbit antiserum pool against rat myelin basic protein (MBP), and a monkey antiserum against bovine MBP—were found to contain detectable levels of antibodies that would bind radiolabeled S49 (GSLPQKAQRPQDENG). Strongly encephalitogenic in Lewis rat, S49 is a synthetic peptide representing residues 69–84 of bovine MBP with a deletion of glycine-76 and histidine-77 to make it analogous to rat and guinea pig MBPs. The rabbit antimyelin antiserum and the monkey anti-MBP antiserum contained antibodies directed against a non-sequential determinant that required asparagine 84, the glycine-histidine deletion, and residues 69–71 for maximal activity. S49-reactive antibodies from the rabbit anti-MBP antiserum were directed solely against a sequential determinant comprising residues 69–71. S49-reactive antibodies from all three antisera reacted in liquid phase with purified intact rat, guinea pig, and bovine MBP showing that the determinant is exposed for B cell recognition even in bovine MBP and can serve both as immunogen and reactant.This work supported at Duke University Medical Center by Research Grant NS-10237 from the National Institutes of Health of the U.S. Public Health Service and the Medical Scientist Training Program Grant #5-T32-OMO-7171-08; at St. Luke's Hospital Center by NS-15322 from the National Institutes of Health of the U.S. Public Health Service; and at Northwestern University by Research Grant NS-06262 from the National Institutes of Health of the U.S. Public Health Service.     

Tuberculosis Infection in the United States: Prevalence Estimates from the National Health and Nutrition Examination Survey, 2011-2012

Background

Reexamining the prevalence of persons infected with tuberculosis (TB) is important to determine trends over time. In 2011–2012 a TB component was included in the National Health and Nutrition Examination Survey (NHANES) to estimate the reservoir of persons infected with TB.

Methods

Civilian, noninstitutionalized U.S. population survey participants aged 6 years and older were interviewed regarding their TB history and eligibility for the tuberculin skin test (TST) and interferon gamma release assay (IGRA) blood test. Once eligibility was confirmed, both tests were conducted. Prevalence and numbers of TST positive (10 mm or greater), IGRA positive, and both TST and IGRA positive were calculated by adjusting for the complex survey design after applying corrections for item nonresponse and digit preference in TST induration measurements. To examine TST positivity over time, data from NHANES 1999–2000 were reanalyzed using the same statistical methods. The TST was performed using Tubersol, a commercially available purified protein derivative (PPD), rather than PPD-S, which was the antigen used in NHANES 1999–2000. Prior patient history of TB vaccination was not collected in this study nor were patients examined for the presence of a Bacillus of Calmette and Guerin (BCG) vaccine scar.

Results

For NHANES 2011–2012, TST and IGRA results were available for 6,128 (78.4%) and 7,107 (90.9%) eligible participants, respectively. There was no significant difference between the percentage of the U.S. population that was TST positive in 2011–2012 (4.7% [95% CI 3.4–6.3]; 13,276,000 persons) compared with 1999–2000 (4.3%; 3.5–5.3). In 2011–2012 the percentage that was IGRA positive was 5.0% (4.2–5.8) and double TST and IGRA positivity was 2.1% (1.5–2.8). The point estimate of IGRA positivity prevalence in foreign-born persons (15.9%; 13.5–18.7) was lower than for TST (20.5%; 16.1–25.8) in 2011–2012. The point estimate of IGRA positivity prevalence in U.S.-born persons (2.8%; 2.0–3.8) was higher than for TST (1.5%; 0.9–2.6).

Conclusions

No statistically significant decline in the overall estimated prevalence of TST positivity was detected from 1999–2000 to 2011–2012. The prevalence of TB infection, whether measured by TST or IGRA, remains lower among persons born in the United States compared with foreign-born persons.     

Phytoplankton Growth and Microzooplankton Grazing in the Subtropical Northeast Atlantic

Dilution experiments were performed to estimate phytoplankton growth and microzooplankton grazing rates during two Lagrangian surveys in inner and eastern locations of the Eastern North Atlantic Subtropical Gyre province (NAST-E). Our design included two phytoplankton size fractions (0.2–5 µm and >5 µm) and five depths, allowing us to characterize differences in growth and grazing rates between size fractions and depths, as well as to estimate vertically integrated measurements. Phytoplankton growth rates were high (0.11–1.60 d⁻¹), especially in the case of the large fraction. Grazing rates were also high (0.15–1.29 d⁻¹), suggesting high turnover rates within the phytoplankton community. The integrated balances between phytoplankton growth and grazing losses were close to zero, although deviations were detected at several depths. Also, O₂ supersaturation was observed up to 110 m depth during both Lagrangian surveys. These results add up to increased evidence indicating an autotrophic metabolic balance in oceanic subtropical gyres.     

Predicting U.S. Tuberculosis Case Counts through 2020

In 2010, foreign-born persons accounted for 60% of all tuberculosis (TB) cases in the United States. Understanding which national groups make up the highest proportion of TB cases will assist TB control programs in concentrating limited resources where they can provide the greatest impact on preventing transmission of TB disease. The objective of our study was to predict through 2020 the numbers of U.S. TB cases among U.S.-born, foreign-born and foreign-born persons from selected countries of birth. TB case counts reported through the National Tuberculosis Surveillance System from 2000–2010 were log-transformed, and linear regression was performed to calculate predicted annual case counts and 95% prediction intervals for 2011–2020. Data were analyzed in 2011 before 2011 case counts were known. Decreases were predicted between 2010 observed and 2020 predicted counts for total TB cases (11,182 to 8,117 [95% prediction interval 7,262–9,073]) as well as TB cases among foreign-born persons from Mexico (1,541 to 1,420 [1,066–1,892]), the Philippines (740 to 724 [569–922]), India (578 to 553 [455–672]), Vietnam (532 to 429 [367–502]) and China (364 to 328 [249–433]). TB cases among persons who are U.S.-born and foreign-born were predicted to decline 47% (4,393 to 2,338 [2,113–2,586]) and 6% (6,720 to 6,343 [5,382–7,476]), respectively. Assuming rates of declines observed from 2000–2010 continue until 2020, a widening gap between the numbers of U.S.-born and foreign-born TB cases was predicted. TB case count predictions will help TB control programs identify needs for cultural competency, such as languages and interpreters needed for translating materials or engaging in appropriate community outreach.     

Georgian Bay phytoplankton: Ecology and response to contaminants

The phytoplankton productivity of Georgian Bay was studied during 1974. Lakewide samples were collected at 16 stations during monthly cruises from April to December and identification and enumeration was carried out by the Utermohl technique. Contaminant bioassays with metals added singly and as a mixture were performed in 1980 and 1981. Based on an overall average, Diatomeae (36–73%) was the most prevalent component of phytoplankton biomass followed by Chrysophyceae (5–38%), and Cyanophyta (3–27%). Biomass means of all stations by cruise indicated a range of 0.35 to 0.61 g·m^–3 with a bimodal seasonal pattern. Although ultraplankton made the highest mean percent contribution to the biomass (37%), the other size assemblages such as < 5 µm (26%) and netplankton (29%) were not unimportant.Size fractionation of primary productivity during 1974 revealed that a major portion of photosynthesis (39–70%) was in the <20 µm size fraction. Algal Fractionation Bioassays conducted during 1980 and 1981 indicated a significant inhibition of ultraplankton productivity. Additional bioassays with single metals and in combination showed differential toxicity to various phytoplankton size assemblages.The phytoplankton biomass and floristic composition indicate the Georgian Bay ecosystem to be oligotrophic. This ecosystem appears to be controlled by the physical dynamics of thermal and flow regimes. Compared with other Great Lakes, the low P/B quotients recorded in oligotrophic Georgian Bay is enigmatic and may be attributable to the observed sensitivity of phytoplankton to contaminants originating from anthropogenic and natural sources.     

Life Years Lost Associated with Obesity-Related Diseases for U.S. Non-Smoking Adults

The objectives of this paper are to predict life years lost associated with obesity-related diseases (ORDs) for U.S. non-smoking adults, and to examine the relationship between those ORDs and mortality. Data from the National Health Interview Survey, 1997–2000, were used. We employed mixed proportional hazard models to estimate the association between those ORDs and mortality and used simulations to project life years lost associated with the ORDs. We found that obesity-attributable comorbidities are associated with large decreases in life years and increases in mortality rates. The life years lost associated with ORDs is more marked for younger adults than older adults, for blacks than whites, for males than females, and for the more obese than the less obese. Using U.S. non-smoking adults aged 40 to 49 years as an example to illustrate percentage of the life years lost associated with ORDs, we found that the mean life years lost associated with ORDs for U.S. non-smoking black males aged 40 to 49 years with a body mass index above 40 kg/m² was 5.43 years, which translates to a 7.5% reduction in total life years. White males of the same age range and same degree of obesity lost 5.23 life years on average – a 6.8% reduction in total life years, followed by black females (5.04 years, a 6.5% reduction in life years), and white females (4.7 years, a 5.8% reduction in life years). Overall, ORDs increased chances of dying and lessened life years by 0.2 to 11.7 years depending on gender, race, BMI classification, and age.     

From Models to Measurements: Comparing Downed Dead Wood Carbon Stock Estimates in the U.S. Forest Inventory

The inventory and monitoring of coarse woody debris (CWD) carbon (C) stocks is an essential component of any comprehensive National Greenhouse Gas Inventory (NGHGI). Due to the expense and difficulty associated with conducting field inventories of CWD pools, CWD C stocks are often modeled as a function of more commonly measured stand attributes such as live tree C density. In order to assess potential benefits of adopting a field-based inventory of CWD C stocks in lieu of the current model-based approach, a national inventory of downed dead wood C across the U.S. was compared to estimates calculated from models associated with the U.S.’s NGHGI and used in the USDA Forest Service, Forest Inventory and Analysis program. The model-based population estimate of C stocks for CWD (i.e., pieces and slash piles) in the conterminous U.S. was 9 percent (145.1 Tg) greater than the field-based estimate. The relatively small absolute difference was driven by contrasting results for each CWD component. The model-based population estimate of C stocks from CWD pieces was 17 percent (230.3 Tg) greater than the field-based estimate, while the model-based estimate of C stocks from CWD slash piles was 27 percent (85.2 Tg) smaller than the field-based estimate. In general, models overestimated the C density per-unit-area from slash piles early in stand development and underestimated the C density from CWD pieces in young stands. This resulted in significant differences in CWD C stocks by region and ownership. The disparity in estimates across spatial scales illustrates the complexity in estimating CWD C in a NGHGI. Based on the results of this study, it is suggested that the U.S. adopt field-based estimates of CWD C stocks as a component of its NGHGI to both reduce the uncertainty within the inventory and improve the sensitivity to potential management and climate change events.     

Admixture in Africanized honey bees (Apis mellifera) from Panamá to San Diego,California (U.S.A.)

The Africanized honey bee (AHB) is a New World amalgamation of several subspecies of the western honey bee (Apis mellifera), a diverse taxon historically grouped into four major biogeographic lineages: A (African), M (Western European), C (Eastern European), and O (Middle Eastern). In 1956, accidental release of experimentally bred “Africanized” hybrids from a research apiary in Sao Paulo, Brazil initiated a hybrid species expansion that now extends from northern Argentina to northern California (U.S.A.). Here, we assess nuclear admixture and mitochondrial ancestry in 60 bees from four countries (Panamá; Costa Rica, Mexico; U.S.A) across this expansive range to assess ancestry of AHB several decades following initial introduction and test the prediction that African ancestry decreases with increasing latitude. We find that AHB nuclear genomes from Central America and Mexico have predominately African genomes (76%–89%) with smaller contributions from Western and Eastern European lineages. Similarly, nearly all honey bees from Central America and Mexico possess mitochondrial ancestry from the African lineage with few individuals having European mitochondria. In contrast, AHB from San Diego (CA) shows markedly lower African ancestry (38%) with substantial genomic contributions from all four major honey bee lineages and mitochondrial ancestry from all four clades as well. Genetic diversity measures from all New World populations equal or exceed those of ancestral populations. Interestingly, the feral honey bee population of San Diego emerges as a reservoir of diverse admixture and high genetic diversity, making it a potentially rich source of genetic material for honey bee breeding.     

Indian Signatures in the Westernmost Edge of the European Romani Diaspora: New Insight from Mitogenomes

In agreement with historical documentation, several genetic studies have revealed ancestral links between the European Romani and India. The entire mitochondrial DNA (mtDNA) of 27 Spanish Romani was sequenced in order to shed further light on the origins of this population. The data were analyzed together with a large published dataset (mainly hypervariable region I [HVS-I] haplotypes) of Romani (N = 1,353) and non-Romani worldwide populations (N>150,000). Analysis of mitogenomes allowed the characterization of various Romani-specific clades. M5a1b1a1 is the most distinctive European Romani haplogroup; it is present in all Romani groups at variable frequencies (with only sporadic findings in non-Romani) and represents 18% of their mtDNA pool. Its phylogeographic features indicate that M5a1b1a1 originated 1.5 thousand years ago (kya; 95% CI: 1.3–1.8) in a proto-Romani population living in Northwest India. U3 represents the most characteristic Romani haplogroup of European/Near Eastern origin (12.4%); it appears at dissimilar frequencies across the continent (Iberia: ∼31%; Eastern/Central Europe: ∼13%). All U3 mitogenomes of our Iberian Romani sample fall within a new sub-clade, U3b1c, which can be dated to 0.5 kya (95% CI: 0.3–0.7); therefore, signaling a lower bound for the founder event that followed admixture in Europe/Near East. Other minor European/Near Eastern haplogroups (e.g. H24, H88a) were also assimilated into the Romani by introgression with neighboring populations during their diaspora into Europe; yet some show a differentiation from the phylogenetically closest non-Romani counterpart. The phylogeny of Romani mitogenomes shows clear signatures of low effective population sizes and founder effects. Overall, these results are in good agreement with historical documentation, suggesting that cultural identity and relative isolation have allowed the Romani to preserve a distinctive mtDNA heritage, with some features linking them unequivocally to their ancestral Indian homeland.     

Association between Mycobacterium tuberculosis Complex Phylogenetic Lineage and Acquired Drug Resistance

Background

Development of resistance to antituberculosis drugs during treatment (i.e., acquired resistance) can lead to emergence of resistant strains and consequent poor clinical outcomes. However, it is unknown whether Mycobacterium tuberculosis complex species and lineage affects the likelihood of acquired resistance.

Methods

We analyzed data from the U.S. National Tuberculosis Surveillance System and National Tuberculosis Genotyping Service for tuberculosis cases during 2004–2011 with assigned species and lineage and both initial and final drug susceptibility test results. We determined univariate associations between species and lineage of Mycobacterium tuberculosis complex bacteria and acquired resistance to isoniazid, rifamycins, fluoroquinolones, and second-line injectables. We used Poisson regression with backward elimination to generate multivariable models for acquired resistance to isoniazid and rifamycins.

Results

M. bovis was independently associated with acquired resistance to isoniazid (adjusted prevalence ratio = 8.46, 95% CI 2.96–24.14) adjusting for HIV status, and with acquired resistance to rifamycins (adjusted prevalence ratio = 4.53, 95% CI 1.29–15.90) adjusting for homelessness, HIV status, initial resistance to isoniazid, site of disease, and administration of therapy. East Asian lineage was associated with acquired resistance to fluoroquinolones (prevalence ratio = 6.10, 95% CI 1.56–23.83).

Conclusions

We found an association between mycobacterial species and lineage and acquired drug resistance using U.S. surveillance data. Prospective clinical studies are needed to determine the clinical significance of these findings, including whether rapid genotyping of isolates at the outset of treatment may benefit patient management.     

Thymidine Incorporation by Free-Living and Particle-Bound Bacteria in a Eutrophic Dimictic Lake

The percentage of [methyl-³H]thymidine incorporated into samples from a dimictic eutrophic lake and retained on polycarbonate membranes of 3.0-, 1.0-, and 0.2-μm pore size was studied in a lake with filamentous cyanobacteria as the dominant phytoplankton type throughout the period of thermal stratification. Water samples were also examined by epifluorescence microscopy for evidence of algal senescence and bacterial colonization of intact and damaged cyanobacterial filaments. A small percentage (2 to 20%) of bacterial activity was retained by filters with pore sizes ≥ 1 μm in epilimnetic samples. Epilimnetic samples also had a small percentage of cyanobacterial filaments, either intact or damaged, which were visibly colonized by bacteria in summer and fall samples. A significant proportion (20 to 35%) of bacterial activity was retained by filters with pore sizes ≥ 1 μm in samples collected from the metalimnion and hypolimnion during late summer and fall. The proportion of damaged cyanobacterial filaments was higher in these samples than in those from the epilimnion or from those obtained early in the summer. Furthermore, the filaments in these samples were more heavily colonized by bacteria. Overall, particle-bound production accounted for only 2 to 19% of total bacterial production from April to August in all water layers. It appears that the supply of colonizable particles (damaged cyanobacterial filaments) is an important factor affecting the level of particle-bound bacterial activity in this lake.