Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The ‘environmental packages’ apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

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Iron (Fe) and dissolved organic matter (DOM) cycling have been implicated in arsenic mobilization via microbially mediated Fe oxide reduction. To evaluate the sources and multiple roles of DOM in Bangladesh aquifers, we conducted spectroscopic analyses on various types of surface water and groundwater samples from a site representative of aquifer chemistry and hydrology. Surface water contained humic substances with oxidized quinone-like moieties and high concentrations of labile microbially derived DOM. In contrast, in shallow groundwater where dissolved iron and arsenic concentrations were high, the quinone-like moieties of humic substances were more reduced, with less abundant labile DOM than that of surface water. Instead, DOM at these depths was characterized by terrestrial (plant/soil) signatures. A sediment microcosm experiment demonstrated that Fe(II) and terrestrially derived DOM were released from sediment over time. The results provide new evidence to support a dual role of natural DOM in Bangladesh aquifers (1) as a labile substrate for Fe- and humic-reducing bacteria and (2) as an electron shuttle via humic substances to enhance microbial iron reduction. Fluorescence index, amino acid-like fluorescence, and redox index may serve as useful indicators of the type of DOM likely to be involved in Fe solubilization and potentially As mobilization reactions.

The human body is inhabited by billions of microbial cells and these microbial symbionts play critical roles in human health. Human-associated microbial communities are diverse, and the structure of these communities is variable across body habitats, through time, and between individuals. We can apply concepts developed by plant and animal ecologists to better understand and predict the spatial and temporal patterns in these communities. Due to methodological limitations and the largely unknown natural history of most microbial taxa, this integration of ecology into research on the human microbiome is still in its infancy. However, such integration will yield a deeper understanding of the role of the microbiome in human health and an improved ability to test ecological concepts that are more difficult to test in plant and animal systems. 137 Annu. Rev. Ecol. Evol. Syst. 2012.43:137-155. Downloaded from www.annualreviews.org by University of Colorado -Boulder on 11/30/12. For personal use only.

The ephemeral stream habitats of the McMurdo Dry Valleys of Antarctica support desiccation and freeze-tolerant microbial mats that are hot spots of primary productivity in an otherwise inhospitable environment. The ecological processes that structure bacterial communities in this harsh environment are not known; however, insights from diatom community ecology may prove to be informative. We examined the relationships between diatoms and bacteria at the community and taxon levels. The diversity and community structure of stream microbial mats were characterized using high-throughput pyrosequencing for bacteria and morphological identification for diatoms. We found significant relationships between diatom communities and the communities of cyanobacteria and heterotrophic bacteria, and co-occurrence analysis identified numerous correlations between the relative abundances of individual diatom and bacterial taxa, which may result from species interactions. Additionally, the strength of correlations between heterotrophic bacteria and diatoms varied along a hydrologic gradient, indicating that flow regime may influence the overall community structure. Phylogenetic consistency in the co-occurrence patterns suggests that the associations are ecologically relevant. Despite these community- and taxon-level relationships, diatom and bacterial alpha diversity were inversely correlated, which may highlight a fundamental difference between the processes that influence bacterial and diatom community assembly in these streams. Our results therefore demonstrate that the relationships between diatoms and bacteria are complex and may result from species interactions as well as niche-specific processes.

In this article, we describe a research approach to undertaking a small area census to identify informal economy activity, using a mixture of quantitative and qualitative tools. The method focuses on enterprise activity. The approach enables the researcher to record a broader spectrum of informal micro-enterprises through identifying businesses in situ within an area of sufficient scale to broadly reflect area-level market conditions and business dynamics. The approach comprises an enterprise census, a survey of all identified micro-enterprises in key sectors, indepth interviews, and participatory research techniques. The article reports on the application of this method in eight case sites, located in township settlements within five major cities in South Africa. The research identified 9,400 individual enterprises, entailing 10,220 primary and secondary activities, distributed within a population of 325,000 and comprising 97,000 households. The approach permits significant advances to our understanding of the spatial dynamics of the informal sector. The research data has enabled the researcher to make original contributions to understanding informal enterprise activities in grocery retailing, liquor trade, and traditional medicine sectors.

Bacterial communities can exert significant influence on the biogeochemical cycling of arsenic (As). This has globally important implications since As in drinking water affects the health of over 100 million people worldwide, including in the Ganges–Brahmaputra Delta region of Bangladesh where geogenic arsenic in groundwater can reach concentrations of more than 10 times the World Health Organization’s limit. Thus, the goal of this research was to investigate patterns in bacterial community composition across gradients in sediment texture and chemistry in an aquifer with elevated groundwater As concentrations in Araihazar, Bangladesh. We characterized the bacterial community by pyrosequencing 16S rRNA genes from aquifer sediment samples collected at three locations along a groundwater flow path at a range of depths between 1.5 and 15 m. We identified significant differences in bacterial community composition between locations in the aquifer. In addition, we found that bacterial community structure was significantly related to sediment grain size, and sediment carbon (C), manganese (Mn), and iron (Fe) concentrations. Deltaproteobacteria and Chloroflexi were found in higher proportions in silty sediments with higher concentrations of C, Fe, and Mn. By contrast, Alphaproteobacteria and Betaproteobacteria were in higher proportions in sandy sediments with lower concentrations of C and metals. Based on the phylogenetic affiliations of these taxa, these results may indicate a shift to more Fe-, Mn-, and humic substance-reducers in the high C and metal sediments. It is well-documented that C, Mn, and Fe may influence the mobility of groundwater arsenic, and it is intriguing that these constituents may also structure the bacterial community.

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