Search

The microbial fermentation behind sourdough bread is among our oldest technologies, yet there are many opportunities for sourdough science to learn from traditional bakers. We analyzed 16S rRNA sequences in R to assess the bacterial community structure and performance of 40 starters grown from 10 types of flour over 14 days, and identified six distinct stages of succession. At each stage, bacterial taxa correlate with determinants of bread quality including pH, rise, and aromatic profile. Day 1 starter cultures were dominated by microorganisms commonly associated with plants and flour, and by aromas similar to toasted grain/cereal. Bacterial diversity peaked from days 2–6 as taxa shifted from opportunistic/generalist bacteria associated with flour inputs, toward specialized climax bacterial communities (days 10–14) characterized by acid-tolerant taxa and fruity (p < 3.03e−03), sour (p < 1.60e−01), and fermented (p < 1.47e−05) aromas. This collection of traits changes predictably through time, regardless of flour type, highlighting patterns of bacterial constraints and dynamics that are conserved across systems and scales. Yet, while sourdough climax communities exhibit similar markers of maturity (i.e., pH ≤ 4 and enriched in Lactobacillus (mean abundance 48.1%), Pediococcus (mean abundance 22.7%), and/or Gluconobacter (mean abundance 19.1%)), we also detected specific taxa and aromas associated with each type of flour. Our results address important ecological questions about the relationship between community structure and starter performance, and may enable bakers to deliberately select for specific sourdough starter and bread characteristics.

Gastrointestinal (GI) morphology plays an important role in nutrition, health, and epidemiology; yet limited data on GI variation have been collected since 1885. Here we demonstrate that students can collect reliable data sets on gut morphology; when they do, they reveal greater morphological variation for some structures in the GI tract than has been documented in the published literature. We discuss trait variability both within and among species, and the implications of that variability for evolution and epidemiology. Our results show that morphological variation in the GI tract is associated with each organ’s role in food processing. For example, the length of many structures was found to vary significantly with feeding strategy. Within species, the variability illustrated by the coefficients of variation suggests that selective constraints may vary with function. Within humans, we detected significant Pearson correlations between the volume of the liver and the length of the appendix (t-value = 2.5278, df = 28, p = 0.0174, corr = 0.4311) and colon (t-value = 2.0991, df = 19, p = 0.0494, corr = 0.4339), as well as between the lengths of the small intestine and colon (t-value = 2.1699, df = 17, p = 0.0445, corr = 0.4657), which are arguably the most vital organs in the gut for nutrient absorption. Notably, intraspecific variation in the small intestine can be associated with life history traits. In humans, females demonstrated consistently and significantly longer small intestines than males (t-value15 = 2.245, p = 0.0403). This finding supports the female canalization hypothesis, specifically, increased female investment in the digestion and absorption of lipids.

The practice of sourdough bread-making is an ancient science that involves the development, maintenance, and use of a diverse and complex starter culture. The sourdough starter culture comes in many different forms and is used in bread-making at both artisanal and commercial scales, in countries all over the world. While there is ample scientific research related to sourdough, there is no standardized approach to using sourdough starters in science or the bread industry; and there are few recommendations on future directions for sourdough research. Our review highlights what is currently known about the microbial ecosystem of sourdough (including microbial succession within the starter culture), methods of maintaining sourdough (analogous to land management) on the path to bread production, and factors that influence the sensory qualities of the final baked product. We present new hypotheses for the successful management of sourdough starters and propose future directions for sourdough research and application to better support and engage the sourdough baking community.

Salmonella enterica serovar Javiana is the fourth most reported serovar of laboratory-confirmed human Salmonella infections in the U.S. and in Tennessee (TN). Although Salmonella ser. Javiana is a common cause of human infection, the majority of cases are sporadic in nature rather than outbreak-associated. To better understand Salmonella ser. Javiana microbial population structure in TN, we completed a phylogenetic analysis of 111 Salmonella ser. Javiana clinical isolates from TN collected from Jan. 2017 to Oct. 2018. We identified mobile genetic elements and genes known to confer antibiotic resistance present in the isolates, and performed a pan-genome-wide association study (pan-GWAS) to compare gene content between clades identified in this study. The population structure of TN Salmonella ser. Javiana clinical isolates consisted of three genetic clades: TN clade I (n = 54), TN clade II (n = 4), and TN clade III (n = 48). Using a 5, 10, and 25 hqSNP distance threshold for cluster identification, nine, 12, and 10 potential epidemiologically-relevant clusters were identified, respectively. The majority of genes that were found to be over-represented in specific clades were located in mobile genetic element (MGE) regions, including genes encoding integrases and phage structures (91.5%). Additionally, a large portion of the over-represented genes from TN clade II (44.9%) were located on an 87.5 kb plasmid containing genes encoding a toxin/antitoxin system (ccdAB). Additionally, we completed phylogenetic analyses of global Salmonella ser. Javiana datasets to gain a broader insight into the population structure of this serovar. We found that the global phylogeny consisted of three major clades (one of which all of the TN isolates belonged to) and two cgMLST eBurstGroups (ceBGs) and that the branch length between the two Salmonella ser. Javiana ceBGs (1,423 allelic differences) was comparable to those from other serovars that have been reported as polyphyletic (929–2,850 allelic differences). This study demonstrates the population structure of TN and global Salmonella ser. Javiana isolates, a clinically important Salmonella serovar and can provide guidance for phylogenetic cluster analyses for public health surveillance and response.

Ecosystem models require the specification of initial conditions, and these initial conditions have some level of uncertainty. It is important to allow for uncertainty when presenting model results, because it reduces the risk of errant or non-representative results. It is crucial that model results are presented as an envelope of what is likely, rather than presenting only one instance. We perturbed the initial conditions of the Chatham Rise Atlantis model and analysed the effect of this uncertainty on the model’s dynamics by comparing the model outputs resulting from many initial condition perturbations. At the species group level, we found some species groups were more sensitive than others, with lower trophic level species groups generally more sensitive to perturbations of the initial conditions. We recommend testing for robust system dynamics by assessing the consistency of ecosystem indicators in response to fishing pressure under perturbed initial conditions. In any set of scenarios explored using complex end-to-end ecosystem models, we recommend that associated uncertainty analysis be included with perturbations of the initial conditions.

Intriguing and potentially commercially useful microorganisms are found in our surroundings and new tools allow us to learn about their genetic potential and evolutionary history. Engaging students from different disciplines and courses in the search for microbes requires an exciting project with innovative but straightforward procedures and goals. Here we describe an interdisciplinary program to engage students from different courses in the sampling, identification and analysis of the DNA sequences of a unique yet common microbe, Delftia spp. A campus-wide challenge was created to identify the prevalence of this genus, able to precipitate gold, involving introductory level environmental and life science courses, upper-level advanced laboratory modules taken by undergraduate students (juniors and seniors), graduate students and staff from the campus. The number of participants involved allowed for extensive sampling while undergraduate researchers and students in lab-based courses participated in the sample processing and analyses, helping contextualize and solidify their learning of the molecular biology techniques. The results were shared at each step through publicly accessible websites and workshops. This model allows for the rapid discovery of Delftia presence and prevalence and is adaptable to different campuses and experimental questions.

Domestic cats preying on wildlife is a frequent conservation concern but typical approaches for assessing impacts rely on owner reports of prey returned home, which can be biased by inaccurate reporting or by cats consuming prey instead of bringing it home. Isotopes offer an alternative way to quantify broad differences in animal diets. By obtaining samples of pet food from cat owners we predicted that we would have high power to identify cats feeding on wild birds or mammals, given that pet food is thought to have higher C isotope values, due to the pervasive use of corn and/or corn by-products as food ingredients, than native prey. We worked with citizen scientists to quantify the isotopes of 202 cat hair samples and 239 pet food samples from the US and UK. We also characterized the isotopes of 11 likely native prey species from the southeastern US and used mixing models to assess the diet of 47 cats from the same region. Variation in C and N isotope values for cat food was very high, even within the same brand/flavor, suggesting that pet food manufacturers use a wide range of ingredients, and that these may change over time. Cat food and cat hair from the UK had lower C values than the US, presumably reflecting differences in the amount of corn used in the food chains of the two countries. This high variation in pet food reduced our ability to classify cats as hunters of native prey, such that only 43% of the animals could be confidently assigned. If feral or free ranging cats were considered, this uncertainty would be even higher as pet food types would be unknown. Our results question the general assumption that anthropogenic foods always have high C isotope values, because of the high variability we documented within one product type (cat food) and between countries (US vs. UK), and emphasize the need to test a variety of standards before making conclusions from isotope ecology studies.

The decline in the number of hours Americans spend outdoors, exacerbated by urbanization, has affected people’s familiarity with local wildlife. This is concerning to conservationists, as people tend to care about and invest in what they know. Children represent the future supporters of conservation, such that their knowledge about and feelings toward wildlife have the potential to influence conservation for many years to come. Yet, little research has been conducted on children’s attitudes toward wildlife, particularly across zones of urbanization. We surveyed 2,759 4–8th grade children across 22 suburban, exurban, and rural schools in North Carolina to determine their attitudes toward local, domestic, and exotic animals. We predicted that children who live in rural or exurban areas, where they may have more direct access to more wildlife species, would list more local animals as “liked” and fewer as “scary” compared to children in suburban areas. However, children, regardless of where they lived, provided mostly non-native mammals for open-ended responses, and were more likely to list local animals as scary than as liked. We found urbanization to have little effect on the number of local animals children listed, and the rankings of “liked” animals were correlated across zones of urbanization. Promising for conservation was that half of the top “liked” animals included species or taxonomic groups containing threatened or endangered species. Despite different levels of urbanization, children had either an unfamiliarity with and/or low preference for local animals, suggesting that a disconnect between children and local biodiversity is already well-established, even in more rural areas where many wildlife species can be found.

Ecosystem and multi-species models are used to understand ecosystem-wide effects of fishing, such as population expansion due to predation release, and further cascading effects. Many are based on fisheries models that focus on a single, depleted population, and may not always behave as expected in a multi-species context. The spawning stock recruitment (SSR) relationship, a curve linking the number of juvenile fish to the existing adult biomass, can produce dynamics that are counter-intuitive and change scenario outcomes. We analysed the Beverton–Holt SSR curve and found a population with low resilience when depleted becomes very productive under persistent predation release. To avoid implausible increases in biomass, we propose limiting recruitment to its unfished level. This allows for specification of resilience when a population is depleted, without sudden and excessive increase when the population expands. We demonstrate this dynamic and solution within an end-to-end ecosystem model, focusing on myctophids under fishing-induced predation release. We present one possible solution, but the specification of stock-recruitment models should continue to be a topic of discussion amongst multi-species and ecosystem modellers and empiricists going forward.

Urban trees serve a critical conservation function by supporting arthropod and vertebrate communities but are often subject to arthropod pest infestations. Native trees are thought to support richer arthropod communities than exotic trees but may also be more susceptible to herbivorous pests. Exotic trees may be less susceptible to herbivores but provide less conservation value as a consequence. We tested the hypotheses that native species in Acer and Quercus would have more herbivorous pests than exotic congeners and different communities of arthropod natural enemies. The density of scale insects, common urban tree pests, was greatest on a native Acer and a native Quercus than exotic congeners in both years of our research (2012 and 2016) and sometimes reached damaging levels. However, differences in predator and parasitoid abundance, diversity, and communities were not consistent between native and exotic species in either genus and were generally similar. For example, in 2012 neither predator nor parasitoid abundance differed among native and exotic Acer congeners but in 2016 a native species, A. saccharum, had the least of both groups. A native, Q. phellos, had significantly more predators and parasitoids in 2012 than its native and exotic congeners but no differences in 2016. Parasitoid communities were significantly different among Acer species and Quercus species due in each case to greater abundance of a single family on one native tree species. These native and exotic tree species could help conserve arthropod natural enemies and achieve pest management goals.

Given the abundance, broad distribution, and diversity of roles that ants play in many ecosystems, they are an ideal group to serve as ecosystem indicators of climatic change. At present, only a few whole-genome sequences of ants are available (19 of >16,000 species), mostly from tropical and sub-tropical species. To address this limited sampling, we sequenced genomes of temperate-latitude species from the genus Aphaenogaster, a genus with important seed dispersers. In total, we sampled seven colonies of six species: Aphaenogaster ashmeadi, Aphaenogaster floridana, Aphaenogaster fulva, Aphaenogaster miamiana, Aphaenogaster picea, and Aphaenogaster rudis. The geographic ranges of these species collectively span eastern North America from southern Florida to southern Canada, which encompasses a latitudinal gradient in which many climatic variables are changing rapidly. For the six genomes, we assembled an average of 271,039 contigs into 47,337 scaffolds. The Aphaenogaster genomes displayed high levels of completeness with 96.1% to 97.6% of Hymenoptera BUSCOs completely represented, relative to currently sequenced ant genomes which ranged from 88.2% to 98.5%. Additionally, the mean genome size was 370.5 Mb, ranging from 310.3 to 429.7, which is comparable to that of other sequenced ant genomes (212.8–396.0 Mb) and flow cytometry estimates (210.7–690.4 Mb). In an analysis of currently sequenced ant genomes and the new Aphaenogaster sequences, we found that after controlling for both spatial autocorrelation and phylogenetics ant genome size was marginally correlated with sample site climate similarity. Of all examined climate variables, minimum temperature, and annual precipitation had the strongest correlations with genome size, with ants from locations with colder minimum temperatures and higher levels of precipitation having larger genomes. These results suggest that climate extremes could be a selective force acting on ant genomes and point to the need for more extensive sequencing of ant genomes.

The Chatham Rise is a highly productive deep-sea ecosystem that supports numerous substantial commercial fisheries, and is a likely candidate for an ecosystem based approach to fisheries management in New Zealand. We present the first end-to-end ecosystem model of the Chatham Rise, which is also to the best of our knowledge, the first end-to-end ecosystem model of any deep-sea ecosystem. We describe the process of data compilation through to model validation and analyse the importance of knowledge gaps with respect to model dynamics and results. The model produces very similar results to fisheries stock assessment models for key fisheries species, and the population dynamics and system interactions are realistic. Confidence intervals based on bootstrapping oceanographic variables are produced. The model components that have knowledge gaps and are most likely to influence model results were oceanographic variables, and the aggregate species groups ‘seabird’ and ‘cetacean other’. We recommend applications of the model, such as forecasting biomasses under various fishing regimes, include alternatives that vary these components.

Background Functional groups serve two important functions in ecology: they allow for simplification of ecosystem models and can aid in understanding diversity. Despite their important applications, there has not been a universally accepted method of how to define them. A common approach is to cluster species on a set of traits, validated through visual confirmation of resulting groups based primarily on expert opinion. The goal of this research is to determine a suitable procedure for creating and evaluating functional groups that arise from clustering nominal traits. Methods To do so, we produced a species by trait matrix of 22 traits from 116 fish species from Tasman Bay and Golden Bay, New Zealand. Data collected from photographs and published literature were predominantly nominal, and a small number of continuous traits were discretized. Some data were missing, so the benefit of imputing data was assessed using four approaches on data with known missing values. Hierarchical clustering is utilised to search for underlying data structure in the data that may represent functional groups. Within this clustering paradigm there are a number of distance matrices and linkage methods available, several combinations of which we test. The resulting clusters are evaluated using internal metrics developed specifically for nominal clustering. This revealed the choice of number of clusters, distance matrix and linkage method greatly affected the overall within- and between- cluster variability. We visualise the clustering in two dimensions and the stability of clusters is assessed through bootstrapping. Results Missing data imputation showed up to 90% accuracy using polytomous imputation, so was used to impute the real missing data. A division of the species information into three functional groups was the most separated, compact and stable result. Increasing the number of clusters increased the inconsistency of group membership, and selection of the appropriate distance matrix and linkage method improved the fit. Discussion We show that the commonly used methodologies used for the creation of functional groups are fraught with subjectivity, ultimately causing significant variation in the composition of resulting groups. Depending on the research goal dictates the appropriate strategy for selecting number of groups, distance matrix and clustering algorithm combination.

High-throughput sequencing techniques have opened up the world of microbial diversity to scientists, and a flurry of studies in the most remote and extreme habitats on earth have begun to elucidate the key roles of microbes in ecosystems with extreme conditions. These same environmental extremes can also be found closer to humans, even in our homes. Here, we used high-throughput sequencing techniques to assess bacterial and archaeal diversity in the extreme environments inside human homes (e.g., dishwashers, hot water heaters, washing machine bleach reservoirs, etc.). We focused on habitats in the home with extreme temperature, pH, and chemical environmental conditions. We found a lower diversity of microbes in these extreme home environments compared to less extreme habitats in the home. However, we were nonetheless able to detect sequences from a relatively diverse array of bacteria and archaea. Habitats with extreme temperatures alone appeared to be able to support a greater diversity of microbes than habitats with extreme pH or extreme chemical environments alone. Microbial diversity was lowest when habitats had both extreme temperature and one of these other extremes. In habitats with both extreme temperatures and extreme pH, taxa with known associations with extreme conditions dominated. Our findings highlight the importance of examining interactive effects of multiple environmental extremes on microbial communities. Inasmuch as taxa from extreme environments can be both beneficial and harmful to humans, our findings also suggest future work to understand both the threats and opportunities posed by the life in these habitats.

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 by Corynebacterium. 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 over Corynebacterium, their differential modes of action exert strikingly different effects on the richness of other bacteria living in armpit communities.

Although humans and arthropods have been living and evolving together for all of our history, we know very little about the arthropods we share our homes with apart from major pest groups. Here we surveyed, for the first time, the complete arthropod fauna of the indoor biome in 50 houses (located in and around Raleigh, North Carolina, USA). We discovered high diversity, with a conservative estimate range of 32–211 morphospecies, and 24–128 distinct arthropod families per house. The majority of this indoor diversity (73%) was made up of true flies (Diptera), spiders (Araneae), beetles (Coleoptera), and wasps and kin (Hymenoptera, especially ants: Formicidae). Much of the arthropod diversity within houses did not consist of synanthropic species, but instead included arthropods that were filtered from the surrounding landscape. As such, common pest species were found less frequently than benign species. Some of the most frequently found arthropods in houses, such as gall midges (Cecidomyiidae) and book lice (Liposcelididae), are unfamiliar to the general public despite their ubiquity. These findings present a new understanding of the diversity, prevalence, and distribution of the arthropods in our daily lives. Considering their impact as household pests, disease vectors, generators of allergens, and facilitators of the indoor microbiome, advancing our knowledge of the ecology and evolution of arthropods in homes has major economic and human health implications.

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.

Because microorganisms are sensitive to temperature, ongoing global warming is predicted to influence microbial community structure and function. We used large-scale warming experiments established at two sites near the northern and southern boundaries of US eastern deciduous forests to explore how microbial communities and their function respond to warming at sites with differing climatic regimes. Soil microbial community structure and function responded to warming at the southern but not the northern site. However, changes in microbial community structure and function at the southern site did not result in changes in cellulose decomposition rates. While most global change models rest on the assumption that taxa will respond similarly to warming across sites and their ranges, these results suggest that the responses of microorganisms to warming may be mediated by differences across the geographic boundaries of ecosystems.

Climate change affects communities both directly and indirectly via changes in interspecific interactions. One such interaction that may be altered under climate change is the ant-plant seed dispersal mutualism common in deciduous forests of eastern North America. As climatic warming alters the abundance and activity levels of ants, the potential exists for shifts in rates of ant-mediated seed dispersal. We used an experimental temperature manipulation at two sites in the eastern US (Harvard Forest in Massachusetts and Duke Forest in North Carolina) to examine the potential impacts of climatic warming on overall rates of seed dispersal (using Asarum canadense seeds) as well as species-specific rates of seed dispersal at the Duke Forest site. We also examined the relationship between ant critical thermal maxima (CTmax) and the mean seed removal temperature for each ant species. We found that seed removal rates did not change as a result of experimental warming at either study site, nor were there any changes in species-specific rates of seed dispersal. There was, however, a positive relationship between CTmax and mean seed removal temperature, whereby species with higher CTmax removed more seeds at hotter temperatures. The temperature at which seeds were removed was influenced by experimental warming as well as diurnal and day-to-day fluctuations in temperature. Taken together, our results suggest that while temperature may play a role in regulating seed removal by ants, ant plant seed-dispersal mutualisms may be more robust to climate change than currently assumed.