Ecological complex networks representing predator-prey interactions are crucial for analyzing the structure, function, and dynamics of ecosystems. However, gathering data on what species eat is challenging and resource intensive, and the difficulty of capturing the interactions across diverse taxa and broad spatio-temporal scales has confined existing networks taxonomically or geographically. To address these challenges, we explored an analytical approach to a predator-prey network constructed using crowd-sourced observations encompassing thousands of interactions and taxonomic groups across multiple spatio-temporal dimensions, which we present here. Our work is among the first to model a large-scale global foodweb from crowdsourced data and underscores the potential of such networks to uncover structurally important species across food chains, trophic levels and motifs, despite the extensive gaps in data collection. This work demonstrates the opportunities and challenges of combining citizen science with ecological network analysis while candidly assessing limitations of using crowdsourced data for holistic ecosystem research.

ABSTRACT While the domestication of plants and animals is widely recognized for its role in the rise of human civilization, humans have also cultivated microbes over millennia to produce food and beverages. One microbe in particular, Saccharomyces cerevisiae , is associated with a wide variety of human-fermentation environments, including wine, beer, and notably bread, such that it is often referred to as “baker’s yeast.” To better illuminate the domestication history of baking associated yeast, we isolated 38 Saccharomyces cerevisiae strains from sourdough starters donated by bakers throughout North America and compared them to thousands of S. cerevisiae isolates from a variety of wild and human-fermentation environments. We identified 6 major clades with two primary domestication hubs, Mediterranean liquid-state fermentation and Asian solid-state fermentation, diverging across Eurasia that gave rise to human-associated lineages. Population genomic analyses demonstrate that S. cerevisiae strains found in sourdough starters are genetically distinct from commercial baking strains and do not come from the surrounding wild environment. Our results show that sourdough yeast strains are closely related to each other and have shared ancestry with strains isolated from various Asian solid state grain fermentations such Japanese sake, Asian rice wines, Chinese distilled spirits (baijiu), and Chinese steamed bread (mantou). We found evidence of significant admixture throughout S. cerevisiae populations, including baking-associated lineages, likely facilitated by human activity. Pangenome gene content largely captures S. cerevisiae traditional genomic sequence-based population structure and reflects human cultural practices, with differences in gene content and copy number between baking associated strains and other groups. Overall, we show that many generalized hallmarks of domestication, such as genome contraction, loss of genetic diversity, and lack of niche expansion, are not universal features of S. cerevisiae domestication, and that baking-associated yeasts have a complex evolutionary history heavily shaped by human culture.

Nectar yeasts are a highly specialized group of fungi that may play key roles in pollination ecology. Nectar yeasts lack an independent dispersal mechanism to access new habitats with fresh resources. Yeasts, bumble bee pollinators and flowering plants likely take part in a series of diffuse mutualisms, wherein yeast attract bees that provide phoretic travel between flowers. This interaction is thought to provide bees with improved foraging efficiency and plants with increased pollinator visitation and associated pollination services. However, the underlying mechanisms driving bee pollinator preferences for nectar with yeast and differences among yeast species in eliciting pollinator behavior are relatively unexplored. We used an integrative approach to elucidate the underpinnings of bee pollinator preference for nectars that contain yeasts. We conducted a survey of local flower nectar for presence and species diversity of yeast. Using two prominent, local nectar yeast species (Metschnikowia reukaufii and Metschnikowia koreensis), we conducted observational field trials to ascertain the effects of the presence and identity of nectar yeast on bee visitation rates. We also analyzed the volatile profiles of both yeast species to explore if olfactory cues were associated with differential foraging behavior. We found that M. reukaufii was the most common nectar yeast in our study area in the southeastern United States, as did previously published global surveys. Intriguingly, we found co-occurrence of multiple yeast species in 22% of nectar samples, all of which contained M. reukaufii and another yeast typically from the Metschnikowia genus, such as M. koreensis. In a field trial, we found that bee pollinators had higher visitation to flowers supplemented with M. koreensis over sterile flowers, while no difference in bee foraging behaviour was evident in response to M. reukaufii. Despite this behavioural difference, the volatile profiles of both yeast species were not significantly different from one another. The ecology and species interactions of wild yeasts are poorly understood, yet may play vital roles in many ecosystems. Our research highlights the importance of studying facultative mutualisms and the necessity of testing their underlying assumptions. Elucidating the mechanisms behind insect-microbe symbioses will open new horizons in pollination ecology and conservation.

Shotgun metagenomics holds great potential for identifying parasite DNA in biological samples, but its effectiveness is limited by widespread contamination in publicly available reference genomes, which hinders accurate detection. In this study, we systematically quantify and remove contamination from 831 published endoparasite genomes to create ParaRef, a curated reference database for species-level parasite detection. We show that decontamination significantly reduces false detection rates and improves overall detection accuracy. Our study highlights the pervasive issue of contamination in public databases and offers a resource that will enhance the reliability of parasite detection using metagenomics.

The world's governments have agreed on actions to address the challenge of antibiotic resistance. This raises the question of what level of national action is associated with improved outcomes, including both slower growth and lower levels of antibiotic resistance. Answering this question is challenged by variation in data availability and quality as well as disruptive events such as the COVID-19 pandemic. We investigate the association between level of national action and temporal trends in multiple indicators related to health system capacity, antibiotic use (ABU), absolute rates of resistance (ABR) and a Drug Resistance Index (DRI). Using the Global Database for Tracking Antimicrobial Resistance (TrACSS) to construct an index of national action, we apply cross-sectional regression across 73 countries to estimate the association between the level of action in 2016 and trends in national indicators (2000-2016). We find that national action is consistently associated with improved linear or categorical trends in all groups of indicators. Reductions are associated with a relatively high action index (range 0-4) for ABU (median 2.8, 25-75% quartile 2.6-3.3), ABR (3.0, 2.4-3.4), and DRI (3.5, 3.1-3.6). These associations are robust to the inclusion of other contextual factors related to socio-economic conditions, human population density, animal production and climate. Since 2016, a majority of both Low- and Middle-Income Countries (LMICs) and High-Income Countries (HICs) report increased action on repeated questions, while one third of countries report reduced action. The main limitations in interpretation are heterogeneity in data availability and in when actions have been implemented. Our findings highlight the importance of national action to address the domestic situation related to antibiotic resistance and indicate the value of both incremental changes in reducing adversity of outcomes and the need for high levels of action in delivering reduced levels of resistance.

The saola is one of the most elusive large mammals, standing at the brink of extinction. We constructed a reference genome and resequenced 26 saola individuals, confirming the saola as a basal member of the Bovini. Despite its small geographic range, we found that the saola is partitioned into two populations with high genetic differentiation (FST = 0.49). We estimate that these populations diverged and started declining 5,000-20,000 years ago, possibly due to climate changes and exacerbated by increasing human activities. The saola has long tracts without genomic diversity; however, most of these tracts are not shared by the two populations. Saolas carry a high genetic load, yet their gradual decline resulted in the purging of the most deleterious genetic variation. Finally, we find that combining the two populations, e.g., in an eventual captive breeding program, would mitigate the genetic load and increase the odds of species survival.

Studying the ecology of ancient organisms requires a tremendous amount of data, as in the case of prehistoric sharks where our knowledge is based mostly on teeth. Shark Tooth Forensics is a participatory science project tackling the problem of deciphering the ecology of ancient sharks with assistance from public school students. Traditionally, paleontological data collection protocols use research staff or a cadre of trained volunteers to collect paleontological data, whereas participatory science provides a means to increase the number of people involved in paleontological research. Students contributing to our project search for fossil shark teeth in sediments from various geologic time periods, and measure and record the teeth they discover for accessioning in natural history museums. Statistical analyses reveal that middle school students provide measurements of shark teeth that are indistinguishable from those same measurements taken by research staff. However, it is necessary to collect data from large student populations, ~10–30 students, before obtaining a statistically reliable sample. In addition, we find students are able to recognize shark teeth from a variety of species, not just stereotypical triangular teeth of species like the Great White ( Carcharodon carcharias ). Teachers can utilize Shark Tooth Forensics curricular activities that use student data in curriculum as a way to gain more personal investment. We estimate over 2,000 students have already participated, and with the potential for this project to last for decades, many thousands more will have the opportunity to discover fossil sharks and reconstruct the lives of these ancient fish.

Ants originated over 150 million years ago through an irreversible transition to superorganismal colony life. Comparative analyses of 163 ant genomes, including newly generated whole-genome sequences of 145 ant species, reveal extensive genome rearrangements correlated with speciation rates. Meanwhile, conserved syntenic blocks are enriched with co-expressed genes involved in basal metabolism and caste differentiation. Gene families related to digestion, endocrine signaling, cuticular hydrocarbon synthesis, and chemoreception expanded in the ant ancestor, while many caste-associated genes underwent positive selection in the formicoid ancestor. Elaborations and reductions of queen-worker dimorphism and other social traits left convergent signatures of intensified or relaxed selection in conserved signaling and metabolic pathways, suggesting that a core gene set was used to diversify organizational complexity. Previously uncharacterized genetic regulators of caste development were confirmed by functional experiments. This study reconstructs the genetic underpinning of social traits and their integration within gene-regulatory networks shaping caste phenotypes.

Fermented foods have been consumed for thousands of years and have been used as a model system to study community succession and other ecological questions. Additionally, cooking classes offer opportunities to learn about food preparation and history. In the present study, scientists and chefs delivered cooking-class style workshops in which participants learned the recipes of one of three fermented foods and the microbial ecology within these foods. Participants prepared jars of chow chow, kimchi, or kombucha to set up experiments to study microbial community succession and pH changes. The fermented foods were also used to test the following hypotheses: that increasing the number of substrates results in increased alpha diversity, and that phylogenetically diverse substrates will lead to greater beta diversity among microbial communities. Microbial communities contained lactic and acetic acid bacteria described previously in fermented foods, and indicator species were identified for cabbage and radish substrates in kimchi. Finally, we qualitatively comment on the experience of developing workshops with chefs and the use of participatory science in these experiments.IMPORTANCEThe present study demonstrates the utility of using fermented foods as an inexpensive and effective tool to investigate ecological phenomena and engage the public in microbiology and ecology through cooking-class style workshops. We also model a creative, interdisciplinary collaboration between scientists and chefs.

Humans have historically relied on acetic acid bacteria (AAB) for food fermentation, yet their origins must trace back to free-living species outside of human environments. In nature, plants, fruit flies, and social insects host AAB. However, the evolutionary transitions of AAB from symbiotic hosts to fermented foods remain ambiguous. Here, we conduct a comprehensive phylogenomic analysis of 570 publicly available AAB genomes. We find that the ∼170My evolutionary history of this group is concordant with the rise of angiosperms, corbiculate bees, and the consequential accelerated availability of environmental carbohydrates. Unlike other ferment-associated microbes, ferment-associated AAB have exclusively evolved from clades inhabiting flowers and fruits, but not insect hosts. Genomic features are similar in plant- and ferment-associated AAB, yet markers of early adaptation to ferments are also present. Conversely, social insect-associated AAB have reduced genome sizes, which may have limited their functional capability to disperse into ferments. Plant- and ferment-associated AAB coincide in the ability to metabolise diverse plant carbohydrates, though both have adapted to produce habitat-specific carbohydrate-active enzymes. In contrast, metabolic capacity is reduced in social insect-associated AAB. By tracing the phylogenomics of this clade, we understand how evolution forged AAB capable of performing metabolic work for humans, shaping the history and potential futures of fermentation. ### Competing Interest Statement The authors have declared no competing interest.

Does fermentation enhance the safety of beverages? This study investigates kombucha's resilience to microbial invasion from human hands. Kombucha, an ancient fermented tea, relies on a biofilm known as a symbiotic community of bacteria and yeast (SCOBY) and a starter culture to ferment sweet tea, producing various metabolites including gluconic acid, acetic acid, ethanol, and carbon dioxide. While fermented foods have been historically associated with potential health benefits, direct evidence comparing the prevalence of human pathogens in fermented versus non-fermented beverages has been lacking. To address this, we conducted a citizen science experiment at Arizona State University, introducing swabs from people's palms into both kombucha and a sweet tea control. Over 30 days, we monitored the bacterial and fungal composition using 16S and ITS rRNA sequencing. Our findings reveal that kombucha maintained a relatively stable microbial profile and physical appearance, with a typical SCOBY biofilm developing. In stark contrast, the sweet tea experienced a dramatic change in microbial composition and was visibly compromised by rapidly growing microorganisms. Importantly, this suggests that the complex microbial ecosystem of kombucha can limit the growth of foreign microbes introduced from human hands. Given that human pathogens were absent from the kombucha while present in the tea samples, our results indicate that the antimicrobial properties of fermentation byproducts and the physical barrier of the SCOBY may contribute to this resilience. Further research is warranted to fully elucidate the mechanisms underlying kombucha's resistance to microbial invasion.

Milk fermentation has a rich history in which food culture, the environment, and microbes intersect. However, traditional practices and their associated microbes have largely been replaced by industrial processes. We investigate a historical fermentation originating from Turkey and Bulgaria - ant yogurt. By examining the traditional practice, gastronomic applications, and experimentally derived yogurts, we uncover that the red wood ant holobiont facilitates fermentation. Bacteria hosted by the ants can proliferate in the milk. Specifically, live ants contribute lactic and acetic acid bacteria, including Frutilactobacillus sanfranciscensis, normally related to sourdough. Consequently, the bacterial community introduces lactic and acetic acid, while the ants provide formic acid, collectively advantageous for yogurt acidification and coagulation. Last, the ants and bacteria produce potential casein-active proteases that may further alter the yogurt texture. Our findings highlight the value of integrating traditional and biological frameworks to uncover the origins and applications of fermented food microbes.

Increasing urban temperatures due to the urban heat island effect are associated with widespread biodiversity declines. Because cities are distributed across diverse climatic zones, the effects of urban heat on biodiversity may vary geographically. Here, we examined how urban warming influences ant communities across four U.S. cities that span 6.6° of latitude and differ by 4.1 °C in average summer temperature. We sampled urban ants using baits placed at the base of a single common tree species along an urban temperature gradient within each city. When pooling results across all cities, ant species richness increased towards the equator, consistent with broader macroecological trends. Within cities, however, ant richness consistently declined with increasing urban temperatures, regardless of latitude. In addition to temperature, we observed that ant richness was positively correlated with humidity and negatively correlated with impervious surface cover. Our findings contrast with studies of other urban arthropods, where responses to urban heat vary by latitude. The consistent negative effect of urban warming on ant diversity suggests that urban heat stress may be a conserved factor affecting biodiversity across temperate latitudes, particularly within eastern North America. While we did not detect an increasing sensitivity to urban warming at lower latitudes, the greater overall biodiversity in low-latitude cities implies that urbanization could pose a significant threat to these species-rich communities. Given the rapid expansion of urban areas, especially in warm regions, understanding the combined impacts of urbanization and climate change on biodiversity remains critical for conservation efforts.

A new ant species was discovered in the heart of New York City in 2011, which garnered national headlines and created the memorable nickname “ManhattAnt.” New York City is one of the oldest and largest cities in North America and has been the site of introduction for some of North America’s most damaging invasive pests. Nevertheless, there has been little follow up research on the ManhattAnt since its discovery, and it has yet to be formally identified. Here we use genetic and morphological approaches to confirm the identity of the ManhattAnt and characterize its introduced range and colony structure. Results from genetic analyses placed the ManhattAnt within the Lasius emarginatus species complex, and morphological comparisons ruled out closely related species to identify the ManhattAnt as the European ant L. emarginatus with 93–99% certainty depending on the nest sample. Since its initial discovery, the ManhattAnt has become one of the most common ants in New York City and has spread at a rate of 2km/yr into New Jersey and onto Long Island. Based on the climate it inhabits within its native range, L. emarginatus could expand to cover much of the eastern United states from Massachusetts to Georgia. Although many successful invasive ants display supercoloniality with little aggression between neighboring nests, we found no evidence that L. emarginatus colonies in New York City are supercolonial. Continued monitoring of L. emarginatus is warranted, as it has been increasingly reported as an indoor pest and is known to form mutualisms with honeydew producing pests of street trees.

Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.

Anthropogenic land cover change is a major driver of biodiversity loss, with urbanisation and farmland practices responsible for some of the most drastic modifications of natural habitats. The relative importance of different land covers for shaping insect communities, however, is unclear. This study examines the effect of urban and farmland covers, along with land cover heterogeneity, at a landscape scale on species richness, evenness and biomass of flying insects using citizen science carnet sampling across Denmark. Increasing urban cover had a negative effect on insect richness but an even stronger negative effect on biomass. Increased land cover heterogeneity did not mitigate the negative effect of urban cover. Insect assemblages also became more even with increased urban cover. Farmland cover had no significant effect on insect richness, evenness or biomass. Based on our findings, the urban cover has a strong negative impact on insect communities, indicating that urbanisation could contribute to insect declines. Moreover, our findings indicate that insect loss occurs more through loss of biomass than loss of species, which may affect the ecosystem‐level consequences of urbanisation.

Objectives Campylobacter spp. are one of the leading foodborne pathogens in the world, and chickens are a known reservoir. This is significant considering broiler chicken is the top consumed meat worldwide. In the USA, backyard poultry production is increasing, but little research has been done to investigate prevalence and antimicrobial resistance associated with Campylobacter in these environments.Methods Our study encompasses a farm-to-genome approach to identify Campylobacter and investigate its antimicrobial resistance phenotypically and genotypically. We travelled to 10 backyard and 10 integrated commercial broiler farms to follow a flock throughout production. We sampled at days 10, 31 and 52 for backyard and 10, 24 and 38 for commercial farms. Bird faecal (n = 10) and various environmental samples (soil n = 5, litter/compost n = 5, and feeder and waterer swabs n = 6) were collected at each visit and processed for Campylobacter.Results Our results show a higher prevalence of Campylobacter in samples from backyard farms (21.9%) compared to commercial (12.2%). Most of our isolates were identified as C. jejuni (70.8%) and the remainder as C. coli (29.2%). Antimicrobial susceptibility testing reveals phenotypic resistance to ciprofloxacin (40.2%), an important treatment drug for Campylobacter infection, and tetracycline (46.6%). A higher proportion of resistance was found in C. jejuni isolates and commercial farms. Whole-genome sequencing revealed resistance genes, such as tet(O) and gyrA_T86I point mutation, that may confer resistance.Conclusion Overall, our research emphasizes the need for interventions to curb prevalence of resistant Campylobacter spp. on broiler production systems.

Climate warming disproportionately impacts countries in the Global South by increasing extreme heat exposure. However, geographic disparities in adaptation capacity are unclear. Here, we assess global inequality in green spaces, which urban residents critically rely on to mitigate outdoor heat stress. We use remote sensing data to quantify daytime cooling by urban greenery in the warm seasons across the ~500 largest cities globally. We show a striking contrast, with Global South cities having ~70% of the cooling capacity of cities in the Global North (2.5 ± 1.0 °C vs. 3.6 ± 1.7 °C). A similar gap occurs for the cooling adaptation benefits received by an average resident in these cities (2.2 ± 0.9 °C vs. 3.4 ± 1.7 °C). This cooling adaptation inequality is due to discrepancies in green space quantity and quality between cities in the Global North and South, shaped by socioeconomic and natural factors. Our analyses further suggest a vast potential for enhancing cooling adaptation while reducing global inequality.

Extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) is an emerging pathogen of high concern given its resistance to extended-spectrum cephalosporins. Broiler chicken, which is the number one consumed meat in the United States and worldwide, can be a reservoir of ESBL E. coli. Backyard poultry ownership is on the rise in the United States, yet there is little research investigating prevalence of ESBL E. coli in this setting. This study aims to identify the prevalence and antimicrobial resistance profiles (phenotypically and genotypically) of ESBL E. coli in some backyard and commercial broiler farms in the U.S. For this study ten backyard and ten commercial farms were visited at three time-points across flock production. Fecal (n = 10), litter/compost (n = 5), soil (n = 5), and swabs of feeders and waterers (n = 6) were collected at each visit and processed for E. coli. Assessment of ESBL phenotype was determined through using disk diffusion with 3rd generation cephalosporins, cefotaxime and ceftazidime, and that with clavulanic acid. Broth microdilution and whole genome sequencing were used to investigate both phenotypic and genotypic resistance profiles, respectively. ESBL E. coli was more prevalent in backyard farms with 12.95% of samples testing positive whereas 0.77% of commercial farm samples were positive. All isolates contained a blaCTX-M gene, the dominant variant being blaCTX-M-1, and its presence was entirely due to plasmids. Our study confirms concerns of growing resistance to fourth generation cephalosporin, cefepime, as roughly half (51.4%) of all isolates were found to be susceptible dose-dependent and few were resistant. Resistance to non-beta lactams, gentamicin and ciprofloxacin, was also detected in our samples. Our study identifies prevalence of blaCTX-M type ESBL E. coli in U.S. backyard broiler farms, emphasizing the need for interventions for food and production safety.

Globally, human house types are diverse, varying in shape, size, roof type, building materials, arrangement, decoration and many other features. Here we offer the first rigorous, global evaluation of the factors that influence the construction of traditional (vernacular) houses. We apply macroecological approaches to analyse data describing house features from 1900 to 1950 across 1000 societies. Geographic, social and linguistic descriptors for each society were used to test the extent to which key architectural features may be explained by the biophysical environment, social traits, house features of neighbouring societies or cultural history. We find strong evidence that some aspects of the climate shape house architecture, including floor height, wall material and roof shape. Other features, particularly ground plan, appear to also be influenced by social attributes of societies, such as whether a society is nomadic, polygynous or politically complex. Additional variation in all house features was predicted both by the practices of neighouring societies and by a society's language family. Collectively, the findings from our analyses suggest those conditions under which traditional houses offer solutions to architects seeking to reimagine houses in light of warmer, wetter or more variable climates.