Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities

Functional gene arrays (FGAs) are a special type of microarrays containing probes for key genes involved in microbial functional processes, such as biogeochemical cycling of carbon, nitrogen, sulfur, phosphorus, and metals, biodegradation of environmental contaminants, energy processing, and stress responses. GeoChips are considered as the most comprehensive FGAs. Experimentally established probe design criteria and a computational pipeline integrating sequence retrieval, probe design and verification, array construction, data analysis, and automatic update are used to develop the GeoChip technology. GeoChip has been systematically evaluated and demonstrated to be a powerful tool for rapid, specific, sensitive, and quantitative analysis of microbial communities in a high-throughput manner. Several generations of GeoChip have been developed and applied to investigate the functional diversity, composition, structure, function, and dynamics of a variety of microbial communities from different habitats, such as water, soil, marine, bioreactor, human microbiome, and extreme ecosystems. GeoChip is able to address fundamental questions related to global change, bioenergy, bioremediation, agricultural operation, land use, human health, environmental restoration, and ecological theories and to link the microbial community structure to environmental factors and ecosystem functioning.     

Assessing the carbon balance of circumpolar Arctic tundra using remote sensing and process modeling.

This paper reviews the current status of using remote sensing and process-based modeling approaches to assess the contemporary and future circumpolar carbon balance of Arctic tundra, including the exchange of both carbon dioxide and methane with the atmosphere. Analyses based on remote sensing approaches that use a 20-year data record of satellite data indicate that tundra is greening in the Arctic, suggesting an increase in photosynthetic activity and net primary production. Modeling studies generally simulate a small net carbon sink for the distribution of Arctic tundra, a result that is within the uncertainty range of field-based estimates of net carbon exchange. Applications of process-based approaches for scenarios of future climate change generally indicate net carbon sequestration in Arctic tundra as enhanced vegetation production exceeds simulated increases in decomposition. However, methane emissions are likely to increase dramatically, in response to rising soil temperatures, over the next century. Key uncertainties in the response of Arctic ecosystems to climate change include uncertainties in future fire regimes and uncertainties relating to changes in the soil environment. These include the response of soil decomposition and respiration to warming and deepening of the soil active layer, uncertainties in precipitation and potential soil drying, and distribution of wetlands. While there are numerous uncertainties in the projections of process-based models, they generally indicate that Arctic tundra will be a small sink for carbon over the next century and that methane emissions will increase considerably, which implies that exchange of greenhouse gases between the atmosphere and Arctic tundra ecosystems is likely to contribute to climate warming.     

The transformative power of commoning and alternative food networks

ABSTRACT

A commoning framework offers a critical lens to fully appreciate the scope and impact of alternative food networks (AFNs). Fieldwork from an AFN in southern China is drawn upon to show how commoning enacts changes in how members contextualise and anchor their social relations to one another with regards to sourcing food as a commons. A commoning framework gives a fuller picture of how the constitutive effects of AFNs reside not in their introduction of a new uniformity but in their navigation of the multiplicity of the social through its proposition and co-construction of a new ‘cognitive praxis’.     

Chromium in intertidal sediments of the Clyde,UK: potential for remobilisation and bioaccumulation

Detailed surveys of intertidal sediments have been performed along the north and south shores of the Inner Clyde estuary, UK. Surface sediment data reveal significant spatial variation in Cr content and an association with major sediment characteristics and location within the estuary. Depth variation for Cr and other heavy metals cannot be explained by variation in major geochemical controls such as grain size and organic matter and highlights the impact of historical contamination on sediment quality. These elevated levels at depth may still have environmental impact through redox-reactivity, in association with iron and manganese. Sequential extraction of sediments and pore water analysis of Cr(VI) and Cr(III) provide detailed information on release potential from the sediments. The implication of Cr mobility for biota in the estuary has been assessed by the analysis of a common marine bivalve, Mytilus edulis (Blue Mussel) and a burrowing polychaete, Nereis diversicolor (rag worm) from a number of survey sites. Bioconcentration factors for Mytilus indicate that the weakly held portion of sediment Cr is available for uptake and in the case of Nereis, bioaccumulation appears to be inhibited by sediment organic matter.     

A gateway to nature: Teenagers' narratives on smoking marijuana outdoors

Increasingly, many youth are disconnected from the natural world; rather, they inhabit a technological world. Although experiences in nature have long been a source of fascination, little is known about how youth independently access and make sense of nature. We focus on the experiences of youth who chose to use marijuana in nature. A substance such as marijuana is often viewed as a “gateway” leading to “harder” drug use; rarely do we consider how marijuana might be a gateway to positive experiences. Narrative analysis was used to explore how young people, aged 14–18, describe their marijuana use in nature, an important aspect of the culture and context of marijuana use. Youth's constructions of nature are revealed in four narratives in which they situate themselves: freedom in nature, the pleasure of leisure, in awe of the natural world and making meaning of the world. One subnarrative, flowing through space, was also uncovered. The findings point to the importance of these nature experiences for youth who expressed how they were able to be in nature in new ways. Participants articulated their yearning for and ability to establish a connection within their natural world.     

Urban–rural differences in atmospheric mercury speciation

Measurements of gaseous elemental mercury (GEM), particulate mercury (Hg_p), and reactive gaseous mercury (RGM) were concurrently recorded at an urban site in Detroit and a rural site in Dexter, both in Michigan for the calendar year 2004. Their average concentrations (±standard deviation) for the urban area were 2.5 ± 1.4 ng m^?3, 18.1 ± 61.0 pg m^?3, and 15.5 ± 54.9 pg m^?3, respectively, while their rural counterparts were 1.6 ± 0.6 ng m^?3, 6.1 ± 5.5 pg m^?3, and 3.8 ± 6.6 pg m^?3, respectively. The medians of urban-to-rural ratios of Hg concentrations indicate approximately 1-fold, 2-fold, and 3-fold gradients between Detroit and Dexter for GEM, Hg_p, and RGM, respectively. The urban–rural differences in Hg also varied considerably on different temporal scales and with wind flow patterns, which was most evident in RGM. Our results show that while Hg at both sites was impacted by regional sources, meteorological conditions, and photochemical transformations, the extent of variations in the observed urban-to-rural gradients, particularly in RGM, cannot be fully accounted for by these processes. Both analyses of the annual data and case studies indicate that the more variable and episodic nature of Hg, particularly RGM, seen in Detroit compared with Dexter, was the result of direct impact from local anthropogenic sources.     

Measurement of particle concentrations in a dental office

Particles in a dental office can be generated by a number of instruments, such as air-turbine handpieces, low-speed handpieces, ultrasonic scalers, bicarbonate polishers, polishing cups, as well as drilling and air sprays inside the oral cavity. This study examined the generation of particles during dental drilling and measured particle size, mass, and trace elements. The air sampling techniques included both continuous and integrated methods. The following particle continuous measurements were taken every minute: (1) size-selective particle number concentration (Climet); (2) total particle number concentration (PTRAK), and; (3) particle mass concentration (DustTrak). Integrated particle samples were collected for about 5 h on each of five sampling days, using a PM_2.5 sampler (ChemComb) for elemental/organic carbon analysis, and a PM₁₀ sampler (Harvard Impactor) for mass and elemental analyses. There was strong evidence that these procedures result in particle concentrations above background. The dental procedures produced number concentrations of relatively small particles (<0.5 μm) that were much higher than concentrations produced for the relatively larger particles (>0.5 μm). Also, these dental procedures caused significant elevation above background of certain trace elements (measured by X-ray fluorescence) but did not cause any elevation of elemental carbon (measured by thermal optical reflectance). Dental drilling procedures aerosolize saliva and products of drilling, producing particles small enough to penetrate deep into the lungs. The potential health impacts of the exposure of dental personnel to such particles need to be evaluated. Increased ventilation and personal breathing protection could be used to minimize harmful effects.     

Elemental composition of Malawian rice

Widespread potential dietary deficiencies of calcium (Ca), iron (Fe), iodine (I), selenium (Se) and zinc (Zn) have been identified in Malawi. Several deficiencies are likely to be compounded by high phytic acid (PA) consumption. Rice (Oryza sativa) is commonly consumed in some Malawian populations, and its mineral micronutrient content is important for food security. The considerable irrigation requirements and flooded conditions of paddy soils can also introduce or mobilise potentially toxic elements including arsenic (As), cadmium (Cd) and lead (Pb). The aim of this study was to determine the mineral composition of rice sampled from farmers’ fields and markets in Malawi. Rice was sampled from 18 extension planning areas across Malawi with 21 white (i.e. polished) and 33 brown samples collected. Elemental composition was determined by inductively coupled plasma-mass spectrometry (ICP-MS). Arsenic speciation was performed using high-performance liquid chromatography (HPLC)-ICP-MS. Concentration of PA was determined using a PA-total phosphorus assay. Median total concentrations (mg kg^?1, dry weight) of elements important for human nutrition in brown and white rice, respectively, were: Ca = 66.5 and 37.8; Cu = 3.65 and 2.49; Fe = 22.1 and 7.2; I = 0.006 and <0.005; Mg = 1130 and 265; Mn = 18.2 and 9.6; Se = 0.025 and 0.028; and Zn = 17.0 and 14.4. In brown and white rice samples, respectively, median PA concentrations were 5438 and 1906 mg kg^?1, and median PA:Zn molar ratios were 29 and 13. Concentrations of potentially toxic elements (mg kg^?1, dry weight) in brown and white rice samples, respectively, were: As = 0.030 and 0.006; Cd  ≤ 0.002 and 0.006; Pb = 0.008 and 0.008. Approximately 95 % of As was found to be inorganic As, where this could be quantified. Malawian rice, like the more widely consumed staple grain maize, contains inadequate Ca, I, Se or Zn to meet dietary requirements. Biofortification strategies could significantly increase Se and Zn concentrations and require further investigation. Concentrations of Fe in rice grain varied greatly, and this was likely due to contamination of rice samples with soil. Risk of As, Cd or Pb toxicity due to rice consumption in Malawi appears to be minimal.