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Despite the prevalence and costs of allergic diseases caused by pollen, we know little about the distributions of allergenic and non-allergenic pollen inside and outside homes at the continental scale. To better understand patterns in potential pollen diversity across the United States, we used DNA sequencing of a chloroplast marker gene to identify the plant DNA found in settled dust collected on indoor and outdoor surfaces across 459 homes. House location was the best predictor of the relative abundance of plant taxa found in outdoor dust samples. Urban, southern houses in hotter climates that were further from the coast were more likely to have more DNA from grass and moss species, while rural houses in northern, cooler climates closer to the coast were more likely to have higher relative abundances of DNA from Pinus and Cedrus species. In general, those plant taxa that were more abundant outdoors were also more abundant indoors, but indoor dust had uniquely high abundances of DNA from food plants and plants associated with lawns. Approximately 14 % of the plant DNA sequences found outside were from plant taxa that are known to have allergenic pollen compared to just 8 % inside. There was little geographic pattern in the total relative abundance of these allergens highlighting the difficulties associated with trying to predict allergen exposures based on geographic location alone. Together, this work demonstrates the utility of using environmental DNA sequencing to reconstruct the distributions of plant DNA inside and outside buildings, an approach that could prove useful for better understanding and predicting plant allergen exposures.

Editorial

It has been known for centuries that microorganisms are ubiquitous in the atmosphere, where they are capable of long-distance dispersal. Likewise, it is well-established that these airborne bacteria and fungi can have myriad effects on human health, as well as the health of plants and livestock. However, we have a limited understanding of how these airborne communities vary across different geographic regions or the factors that structure the geographic patterns of near-surface microbes across large spatial scales. We collected dust samples from the external surfaces of ∼1,200 households located across the United States to understand the continental-scale distributions of bacteria and fungi in the near-surface atmosphere. The microbial communities were highly variable in composition across the United States, but the geographic patterns could be explained by climatic and soil variables, with coastal regions of the United States sharing similar airborne microbial communities. Although people living in more urbanized areas were not found to be exposed to distinct outdoor air microbial communities compared with those living in more rural areas, our results do suggest that urbanization leads to homogenization of the airborne microbiota, with more urban communities exhibiting less continental-scale geographic variability than more rural areas. These results provide our first insight into the continental-scale distributions of airborne microbes, which is information that could be used to identify likely associations between microbial exposures in outdoor air and incidences of disease in crops, livestock, and humans.

Geographic range size can span orders of magnitude for plant and animal species, with the study of why range sizes vary having preoccupied biogeographers for decades. In contrast, there have been few comparable studies of how range size varies across microbial taxa and what traits may be associated with this variation. We determined the range sizes of 74,134 bacterial and archaeal taxa found in settled dust collected from 1,065 locations across the United States. We found that most microorganisms have small ranges and few have large ranges, a pattern similar to the range size distributions commonly observed for macrobes. However, contrary to expectations, those microbial taxa that were locally abundant did not necessarily have larger range sizes. The observed differences in microbial range sizes were generally predictable from taxonomic identity, phenotypic traits, genomic attributes, and habitat preferences, findings that provide insight into the factors shaping patterns of microbial biogeography.

We spend most of our lives inside homes, surrounded by arthropods that impact our property as pests and our health as disease vectors and producers of sensitizing allergens. Despite their relevance to human health and well-being, we know relatively little about the arthropods that exist in our homes and the factors structuring their diversity. As previous work has been limited in scale by the costs and time associated with collecting arthropods and the subsequent morphological identification, we used a DNA-based method for investigating the arthropod diversity in homes via high-throughput marker gene sequencing of home dust. Settled dust samples were collected by citizen scientists from both inside and outside more than 700 homes across the United States, yielding the first continental-scale estimates of arthropod diversity associated with our residences. We were able to document food webs and previously unknown geographic distributions of diverse arthropods - from allergen producers to invasive species and nuisance pests. Home characteristics, including the presence of basements, home occupants and surrounding land use, were more useful than climate parameters in predicting arthropod diversity in homes. These noninvasive, scalable tools and resultant findings not only provide the first continental-scale maps of household arthropod diversity, but our analyses also provide valuable baseline information on arthropod allergen exposures and the distributions of invasive pests inside homes.

Environmental and ecological research has long been characterized as operating along a continuum, with "basic" - representing "investigator-initiated" research - at one end and "applied" - representing "mission-ini- tiated" research - at the other. While federal agency science programs ideally occupy points along this contin- uum, the resulting science has not always been relevant to solving environmental problems. Here, we suggest that environmental problem-solving by federal agencies has been less effective than it might have been, because of a need for more effective, long-term strategic planning, cooperation across agencies, and incentives for scientists to participate in policy development and implementation. We make suggestions about what fed- eral agencies can do to improve the integration of science, policy, and natural resource management. First, we refer to agency examples, using regulatory (acid deposition) and land management (national forest) issues to illustrate how environmental research intersects with policy development and its implementation. Second, we discuss the barriers that inhibit the application of scientific knowledge in developing and implementing policy - from the perspective of a federal agency and of an individual scientist. Finally, we generate a series of specific recommendations, targeted at federal agencies, individual scientists, and decision makers.

Summary 1. Stream ecosystems are increasingly impacted by multiple stressors that lead to a loss of sensitive species and an overall reduction in diversity. A dominant paradigm in ecological restoration is that increasing habitat heterogeneity (HH) promotes restoration of biodiversity. This paradigm is reflected in stream restoration projects through the common practice of re-configuring channels to add meanders and adding physical structures such as boulders and artificial riffles to restore biodiversity by enhancing structural heterogeneity. 2. To evaluate the validity of this paradigm, we completed an extensive evaluation of published studies that have quantitatively examined the reach-scale response of invertebrate species richness to restoration actions that increased channel complexity/HH. We also evaluated studies that used manipulative or correlative approaches to test for a relationship between physical heterogeneity and invertebrate diversity in streams that were not in need of restoration. 3. We found habitat and macroinvertebrate data for 78 independent stream or river restoration projects described by 18 different author groups in which invertebrate taxa richness data in response to the restoration treatment were available. Most projects were successful in enhancing physical HH; however, only two showed statistically significant increases in biodiversity rendering them more similar to reference reaches or sites. 4. Studies manipulating structural complexity in otherwise healthy streams were generally small in scale and less than half showed a significant positive relationship with invertebrate diversity. Only one-third of the studies that attempted to correlate biodiversity to existing levels of in-stream heterogeneity found a positive relationship. 5. Across all the studies we evaluated, there is no evidence that HH was the primary factor controlling stream invertebrate diversity, particularly in a restoration context. The findings indicate that physical heterogeneity should not be the driving force in selecting restoration approaches for most degraded waterways. Evidence suggests that much more must be done to restore streams impacted by multiple stressors than simply re-configuring channels and enhancing structural complexity with meanders, boulders, wood, or other structures. 6. Thematic implications: as integrators of all activities on the land, streams are sensitive to a host of stressors including impacts from urbanisation, agriculture, deforestation, invasive species, flow regulation, water extractions and mining. The impacts of these individually or in combination typically lead to a decrease in biodiversity because of reduced water quality, biologically unsuitable flow regimes, dispersal barriers, altered inputs of organic matter or sunlight, degraded habitat, etc. Despite the complexity of these stressors, a large number of stream restoration projects focus primarily on physical channel characteristics. We show that this is not a wise investment if ecological recovery is the goal. Managers should critically diagnose the stressors impacting an impaired stream and invest resources first in repairing those problems most likely to limit restoration.

The emergence of 17-year periodical cicadas in Maryland, USA, in 2004 provided a unique opportunity to study the effect of a large, but temporally limited, resource pulse of arthropod detritus on stream ecosystem function. Cicada emergence was quantified in the forests adjacent to two small streams with different histories of riparian disturbance (Intact and Disturbed sites). We estimated the input of cicada detritus to the streams, described its retention and breakdown dynamics, and measured whole-stream respiration over the cicada flight season (May–July). Average emergence density was significantly greater at the Intact site, but average cicada detritus input rates were greater at the Disturbed site. Cicada detritus was locally retained within both streams and rapidly broke down. Daily whole-stream respiration (CR24) at both sites responded dramatically to the cicada pulse, with CR24 doubling pre-cicada measurements following the period of greatest cicada input (Intact: 12.82 → 23.78 g O2 m−2 d−1; Disturbed: 2.76 → 5.77 g O2 m−2 d−1). CR24 returned to baseline levels when cicada input decreased at the Intact site, but more than doubled again at the Disturbed site (13.14 g O2 m−2 d−1), despite a decline in cicada input rate. Differences in respiration response may be a function of differences in cicada input rates as well as differences in microbial community activity. The strong effects on stream ecosystem function exerted by a short but intense input of periodical cicada detritus may provide insights regarding the response of streams to other irregular resource pulses.

SUMMARY 1. The organic matter dynamics of streams dominated by herbs and grass on their banks are poorly understood, despite the fact that such streams are common worldwide. Further, herbs and grasses can provide large quantities of detritus to stream food webs, and particularly small streams can be heavily shaded by overhanging vegetation, perhaps limiting in-stream primary production. 2. We quantified the standing crop of edge vegetation and associated macroinvertebrate communities along three headwater streams with herbaceous and grass riparian vegetation on agricultural land in the Piedmont of Maryland, U.S.A., measured the decomposition of four common species of herbs and grasses using experimental leaf packs, and removed edge vegetation experimentally to determine the effect of shading on benthic algal production. 3. Large standing crops of plant material (average range: 68–276 g ash-free dry mass per m )2 ), composed largely of monocotyledons, were found at all three study streams. These values are similar to those for coarse particulate organic matter in deciduous forested streams in the eastern U.S.A. In addition, diverse assemblages of shredding macroinvertebrates were observed at all three study sites. 4. Decomposition of the herbs was faster than that of the grasses, and both decomposed faster than most deciduous tree leaf litter. The decomposition rates of the herbs and grasses were significantly related to leaf quality as measured by leaf nitrogen content. Macroinvertebrate shredders colonized all experimental leaf packs, and the colonization of the herbs was faster than that of the grasses. 5. The accrual of chlorophyll-a after the removal of shading vegetation was faster than that measured prior to removal as well as that in an unmanipulated control reach. 6. Given that the standing crop of organic matter in streams with herbs and grass along their banks was similar to that in forested streams, that the organic matter was rich in nitrogen and used by detritivores, and riparian shading limited algal growth, we suggest that herbaceous and grass plant material may be an important allochthonous food resource in such systems.

We spend the majority of our lives indoors; yet, we currently lack a comprehensive understanding of how the microbial communities found in homes vary across broad geographical regions and what factors are most important in shaping the types of microorganisms found inside homes. Here, we investigated the fungal and bacterial communities found in settled dust collected from inside and outside approximately 1200 homes located across the continental US, homes that represent a broad range of home designs and span many climatic zones. Indoor and outdoor dust samples harboured distinct microbial communities, but these differences were larger for bacteria than for fungi with most indoor fungi originating outside the home. Indoor fungal communities and the distribution of potential allergens varied predictably across climate and geographical regions; where you live determines what fungi live with you inside your home. By contrast, bacterial communities in indoor dust were more strongly influenced by the number and types of occupants living in the homes. In particular, the female : male ratio and whether a house had pets had a significant influence on the types of bacteria found inside our homes highlighting that who you live with determines what bacteria are found inside your home.

There is a long history of archaeologists and forensic scientists using pollen found in a dust sample to identify its geographic origin or history. Such palynological approaches have important limitations as they require time-consuming identification of pollen grains, a priori knowledge of plant species distributions, and a sufficient diversity of pollen types to permit spatial or temporal identification. We demonstrate an alternative approach based on DNA sequencing analyses of the fungal diversity found in dust samples. Using nearly 1,000 dust samples collected from across the continental U.S., our analyses identify up to 40,000 fungal taxa from these samples, many of which exhibit a high degree of geographic endemism. We develop a statistical learning algorithm via discriminant analysis that exploits this geographic endemicity in the fungal diversity to correctly identify samples to within a few hundred kilometers of their geographic origin with high probability. In addition, our statistical approach provides a measure of certainty for each prediction, in contrast with current palynology methods that are almost always based on expert opinion and devoid of statistical inference. Fungal taxa found in dust samples can therefore be used to identify the origin of that dust and, more importantly, we can quantify our degree of certainty that a sample originated in a particular place. This work opens up a new approach to forensic biology that could be used by scientists to identify the origin of dust or soil samples found on objects, clothing, or archaeological artifacts.

Although inland waters make up only about 1% of the earth’s surface, these fresh waters contain about 10% of all animal species, the majority of which are invertebrates. Inhabiting ground, surface, and running waters, diverse assemblages of freshwater invertebrates play key roles in ecological processes that ensure that our water is clean and that organic matter in a lake, stream, or wetland is not lost or accumulated in excess. Unfortunately, freshwater invertebrates and the ecosystems they live in are under severe threat from habitat degradation and loss, pollution and reduced water quality, altered hydrologic regimes, and invasion by exotic species.

Most of our time is spent indoors where we are exposed to a wide array of different microorganisms living on surfaces and in the air of our homes. Despite their ubiquity and abundance, we have a limited understanding of the microbial diversity found within homes and how the composition and diversity of microbial communities change across different locations within the home. Here we examined the diversity of bacterial communities found in nine distinct locations within each of forty homes in the Raleigh-Durham area of North Carolina, USA, using high-throughput sequencing of the bacterial 16S rRNA gene. We found that each of the sampled locations harbored bacterial communities that were distinct from one another with surfaces that are regularly cleaned typically harboring lower levels of diversity than surfaces that are cleaned infrequently. These location-specific differences in bacterial communities could be directly related to usage patterns and differences in the likely sources of bacteria dispersed onto these locations. Finally, we examined whether the variability across homes in bacterial diversity could be attributed to outdoor environmental factors, indoor habitat structure, or the occupants of the home. We found that the presence of dogs had a significant effect on bacterial community composition in multiple locations within homes as the homes occupied by dogs harbored more diverse communities and higher relative abundances of dog-associated bacterial taxa. Furthermore, we found a significant correlation between the types of bacteria deposited on surfaces outside the home and those found inside the home, highlighting that microbes from outside the home can have a direct effect on the microbial communities living on surfaces within our homes. Together this work provides the first comprehensive analysis of the microbial communities found in the home and the factors that shape the structure of these communities both within and between homes.

An ever expanding body of research investigates the human microbiome in general and the skin microbiome in particular. Microbiomes vary greatly from individual to individual. Understanding the factors that account for this variation, however, has proven challenging, with many studies able to account statistically for just a small proportion of the inter-individual variation in the abundance, species richness or composition of bacteria. The human armpit has long been noted to host a high biomass bacterial community, and recent studies have highlighted substantial inter-individual variation in armpit bacteria, even relative to variation among individuals for other body habitats. One obvious potential explanation for this variation has to do with the use of personal hygiene products, particularly deodorants and antiperspirants. Here we experimentally manipulate product use to examine the abundance, species richness, and composition of bacterial communities that recolonize the armpits of people with different product use habits. In doing so, we find that when deodorant and antiperspirant use were stopped, culturable bacterial density increased and approached that found on individuals who regularly do not use any product. In addition, when antiperspirants were subsequently applied, bacterial density dramatically declined. These culture-based results are in line with sequence-based comparisons of the effects of long-term product use on bacterial species richness and composition. Sequence-based analyses suggested that individuals who habitually use antiperspirant tended to have a greater richness of bacterial OTUs in their armpits than those who use deodorant. In addition, individuals who used antiperspirants or deodorants long-term, but who stopped using product for two or more days as part of this study, had armpit communities dominated by Staphylococcaceae, whereas those of individuals in our study who habitually used no products were dominated byCorynebacterium. Collectively these results suggest a strong effect of product use on the bacterial composition of armpits. Although stopping the use of deodorant and antiperspirant similarly favors presence of Staphylococcaceae overCorynebacterium, their differential modes of action exert strikingly different effects on the richness of other bacteria living in armpit communities.

Despite the rapid expansion of the built environment, we know little about the biology of species living in human-constructed habitats. Camel crickets (Rhaphidophoridae) are commonly observed in North American houses and include a range of native taxa as well as the Asian Diestrammena asynamora (Adelung), a species occasionally reported from houses though considered to be established only in greenhouses. We launched a continental-scale citizen science campaign to better understand the relative distributions and frequency of native and nonnative camel crickets in human homes across North America. Participants contributed survey data about the presence or absence of camel crickets in homes, as well as photographs and specimens of camel crickets allowing us to identify the major genera and/or species in and around houses. Together, these data offer insight into the geographical distribution of camel crickets as a presence in homes, as well as the relative frequency and distribution of native and nonnative camel crickets encountered in houses. In so doing, we show that the exotic Diestrammena asynamora not only has become a common presence in eastern houses, but is found in these environments far more frequently than native camel crickets. Supplemental pitfall trapping along transects in 10 urban yards in Raleigh, NC revealed that D. asynamora can be extremely abundant locally around some homes, with as many as 52 individuals collected from pitfalls in a single yard over two days of sampling. The number of D. asynamora individuals present in a trap was negatively correlated with the trap’s distance from a house, suggesting that these insects may be preferentially associated with houses but also are present outside. In addition, we report the establishment in the northeastern United States of a second exotic species, putatively Diestrammena japanica Blatchley, which was previously undocumented in the literature. Our results offer new insight into the relative frequency and distribution of camel crickets living in human homes, and emphasize the importance of the built environment as habitat for two little-known invading species of Orthoptera.