Despite increasing interest in the effects of triclosan and triclocarban on human biology, current knowledge is still limited on the impact of these additives to antimicrobial personal care products on the human microbiome. A carefully designed recent study published in mSphere by Poole and colleagues [A. C. Poole et al., mSphere 1(3):e00056-15, 2016, http://dx.doi.org/10.1128/mSphere.00056-15] highlights both the power of novel methodologies for microbiome elucidation and the longstanding challenge of employing small-cohort studies to inform risk assessment for chemicals of ubiquitous use in modern society.

Network reconstruction is a fundamental problem for understanding many complex systems with unknown interaction structures. In many complex systems, there are indirect interactions between two individuals without immediate connection but with common neighbors. Despite recent advances in network reconstruction, we continue to lack an approach for reconstructing complex networks with indirect interactions. Here we introduce a two-step strategy to resolve the reconstruction problem, where in the first step, we recover both direct and indirect interactions by employing the Lasso to solve a sparse signal reconstruction problem, and in the second step, we use matrix transformation and optimization to distinguish between direct and indirect interactions. The network structure corresponding to direct interactions can be fully uncovered. We exploit the public goods game occurring on complex networks as a paradigm for characterizing indirect interactions and test our reconstruction approach. We find that high reconstruction accuracy can be achieved for both homogeneous and heterogeneous networks, and a number of empirical networks in spite of insufficient data measurement contaminated by noise. Although a general framework for reconstructing complex networks with arbitrary types of indirect interactions is yet lacking, our approach opens new routes to separate direct and indirect interactions in a representative complex system.

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.

Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.

Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.

Traditionally, hazardous chemicals have been regulated in the U.S. on a one-by-one basis, an approach that is slow, expensive and can be inefficient, as illustrated by a decades-long succession of replacing one type of organohalogen flame retardants (OHFRs) with another one, without addressing the root cause of toxicity and associated public health threats posed. The present article expounds on the need for efficient monitoring strategies and pragmatic steps in reducing environmental pollution and adverse human health impacts. A promising approach is to combine specific bioassays with state-of-the-art chemical screening to identify chemicals and chemical mixtures sharing specific modes of action (MOAs) and pathways of toxicity (PoTs). This approach could be used to identify and regulate hazardous chemicals as classes or compound families, featuring similar biological end-points, such as endocrine disruption and mutagenicity. Opportunities and potential obstacles of implementing this approach are discussed.

Processed municipal sewage sludges (MSS) are an abundant, unwanted by-product of wastewater treatment, increasingly applied to agriculture and forestry for inexpensive disposal and soil conditioning. Due to their high organic carbon and lipid contents, MSS not only is rich in carbon and nutrients but also represents a “sink” for recalcitrant, hydrophobic, and potentially bioaccumulative compounds. Indeed, many organics sequestered and concentrated in MSS meet the US Environmental Protection Agency’s definition of being persistent, bioaccumulative, and toxic (PBT). In a strategic effort, our research team at the Biodesign Institute has created the National Sewage Sludge Repository (NSSR), a large repository of digested MSSs from 164 wastewater treatment plants from across the USA, as part of the Human Health Observatory (H2O) at Arizona State University (ASU). The NSSR likely represents the largest archive of digested MSS specimens in the USA. The present study summarizes key findings gleaned thus far from analysis of NSSR samples. For example, we evaluated the content of toxicants in MSS and computed estimates of nationwide inventories of mass produced chemicals that become sequestrated in sludge and later are released into the environment during sludge disposal on land. Ongoing efforts document co-occurrence of a variety of PBT compounds in both MSS and human samples, while also identifying a large number of potentially harmful MSS constituents for which human exposure data are still lacking. Finally, we summarize future opportunities and invite collaborative use of the NSSR by the research community. The H2O at ASU represents a new resource and research tool for environmental scientists and the larger research community. As illustrated in this work, this repository can serve to (i) identify and prioritize emerging contaminants, (ii) provide spatial and temporal trends of contaminants, (iii) inform and evaluate the effectiveness of environmental policy-making and regulations, and (iv) approximate, ongoing exposures and body burdens of mass-produced chemicals in human society.

In vitro rearing is an important and useful tool for honey bee (Apis mellifera L.) studies. However, it often results in intercastes between queens and workers, which are normally are not seen in hive-reared bees, except when larvae older than three days are grafted for queen rearing. Morphological classification (queen versus worker or intercastes) of bees produced by this method can be subjective and generally depends on size differences. Here, we propose an alternative method for caste classification of female honey bees reared in vitro, based on weight at emergence, ovariole number, spermatheca size and size and shape, and features of the head, mandible and basitarsus. Morphological measurements were made with both traditional morphometric and geometric morphometrics techniques. The classifications were performed by principal component analysis, using naturally developed queens and workers as controls. First, the analysis included all the characters. Subsequently, a new analysis was made without the information about ovariole number and spermatheca size. Geometric morphometrics was less dependent on ovariole number and spermatheca information for caste and intercaste identification. This is useful, since acquiring information concerning these reproductive structures requires time-consuming dissection and they are not accessible when abdomens have been removed for molecular assays or in dried specimens. Additionally, geometric morphometrics divided intercastes into more discrete phenotype subsets. We conclude that morphometric geometrics are superior to traditional morphometrics techniques for identification and classification of honey bee castes and intermediates.

The known occurrence of pharmaceuticals in the built and natural water environment, including in drinking water supplies, continues to raise concerns over inadvertent exposures and associated potential health risks in humans and aquatic organisms. At the same time, the number and concentrations of new and existing pharmaceuticals in the water environment are destined to increase further in the future as a result of increased consumption of pharmaceuticals by a growing and aging population and ongoing measures to decrease per-capita water consumption. This review examines the occurrence and movement of pharmaceuticals in the built and natural water environment, with special emphasis on contamination of the drinking water supply, and opportunities for sustainable pollution control. We surveyed peer-reviewed publications dealing with quantitative measurements of pharmaceuticals in U.S. drinking water, surface water, groundwater, raw and treated wastewater as well as municipal biosolids. Pharmaceuticals have been observed to reenter the built water environment contained in raw drinking water, and they remain detectable in finished drinking water at concentrations in the ng/L to μg/L range. The greatest promises for minimizing pharmaceutical contamination include source control (for example, inputs from intentional flushing of medications for safe disposal, and sewer overflows), and improving efficiency of treatment facilities.