Early Inoculation of Microbial Suspension in Suckling Piglets Affects the Transmission of Maternal Microbiota and the Associated Antibiotic Resistance Genes

Antibiotic resistance of microbes thriving in the animal gut is a growing concern for public health as it may serve as a hidden reservoir for antibiotic resistance genes (ARGs). We compared 16 control piglets to 24 piglets fed for 3 weeks with S1 or S2 fecal suspensions from two sows that were not exposed to antibiotics for at least 6 months: the first suspension decreased the erythromycin resistance gene ermB and the aminoglycoside phosphotransferase gene conferring resistance to kanamycine (aphA3), while the second decreased the tetracycline resistance gene tetL, with an unexpected increase in ARGs. Using 16S RNA sequencing, we identified microbial species that are likely to carry ARGs, such as the lincosamide nucleotidyltransferase lnuB, the cephalosporinase cepA, and the tetracycline resistance genes tetG and tetM, as well as microbes that never co-exist with the tetracycline resistance gene tetQ, the erythromycin resistance gene ermG and aphA3. Since 73% of the microbes detected in the sows were not detected in the piglets at weaning, a neutral model was applied to estimate whether a microbial species is more important than chance would predict. This model confirmed that force-feeding modifies the dynamics of gut colonization. In conclusion, early inoculation of gut microbes is an interesting possibility to stimulate gut microbiota towards a desirable state in pig production, but more work is needed to be able to predict which communities should be used.

Probiotics in poultry feed: A comprehensive review

The use of antibiotics to maintain animal well-being, promote growth and improve efficiency has been practised for more than 50 years. However, as early as the 1950s, researchers identified concern on the development of resistant bacteria for the antibiotics streptomycin and tetracycline used in turkeys and broilers respectively. These findings laid the groundwork for agricultural officials to impose stricter regulatory parameters on the use of antibiotics in poultry feeds. Probiotics are live micro-organisms included in the diet of animals as feed additives or supplements. Commonly known as a direct-fed microbial, probiotics provide beneficial properties to the host, primarily through action in the gastrointestinal tract (GIT) of the animal. Supplementation of probiotics in the diet can improve animal health and performance, through contributions to gut health and nutrient use. For instance, supplementation of probiotics has been demonstrated to benefit farm animals in immune modulation, structural modulation and increased cytokine production, which positively affect the intestinal mucosal lining against pathogens. Bacillus subtilis has been a popular bacterium used within the industry and was shown to improve intestinal villus height. Increasing the villus height and structure of the crypts in the GIT allows for the improvement of nutrient digestion and absorption. Tight junctions maintain important defences against pathogenic bacteria and cellular homeostasis. Heat stress can be a major environmental challenge in the poultry industry. Heat stress causes the bird to fluctuate its internal core temperature beyond their comfort zone. To overcome such challenges, poultry will attempt to balance its heat production and dissipation through behavioural and physiological adaptation mechanisms.

Janzen-Connell Effects Are a Weak Impediment to Competitive Exclusion

AbstractA goal of ecology is to identify the stabilizing mechanisms that maintain species diversity in the face of competitive exclusion and drift. For tropical forest tree communities, it has been hypothesized that high diversity is maintained via Janzen-Connell effects, whereby host-specific natural enemies prevent any one species from becoming too abundant. Here we explore the plausibility of this hypothesis with theoretical models. We confirm a previous result that when added to a model with drift but no competitive exclusion-that is, a neutral model where intrinsic fitnesses are perfectly equalized across species-Janzen-Connell effects maintain very high species richness that scales strongly with community size. However, when competitive exclusion is introduced-that is, when intrinsic fitnesses vary across species-the number of species maintained by Janzen-Connell effects is substantially reduced and scales much less strongly with community size. Because fitness variation is pervasive in nature, we conclude that the potential of Janzen-Connell effects to maintain diversity is probably weak and that the mechanism does not yet provide a sufficient explanation for the observed high diversity of tropical forest tree communities. We also show that, surprisingly, dispersal limitation can further reduce the ability of Janzen-Connell effects to maintain diversity.

Experimental assessment of biotic and abiotic filters driving community composition

Species occurrence in a site can be limited by both the abiotic environment and biotic interactions. These two factors operate in concert, but their relative importance is often unclear. By experimentally introducing seeds or plants into competition-free gaps or into the intact vegetation, we can disentangle the biotic and abiotic effects on plant establishment. We established a seed-sowing/transplant experiment in three different meadows. Species were introduced, as seeds and pregrown transplants, into competition-free gaps and the intact vegetation. They included 12 resident plants from the locality and 18 species typical for different habitats. Last two years, gaps were overgrown with vegetation from surrounding plants and we observed the competitive exclusion of our focal plants. We compared plant survival with the expected occurrence in target locality (Beals index). Many of the species with habitat preferences different from our localities were able to successfully establish from seeds and grow in the focal habitat if competition was removed. They included species typical for much drier conditions. These species were thus not limited by the abiotic conditions, but by competition. Pregrown transplants were less sensitive to competition, when compared to seedlings germinated from seeds. Beals index significantly predicted both species success in gaps and the ability to withstand competition. Survival in a community is dependent on the adaptation to both the abiotic environment and biotic interactions. Statistically significant correlation coefficients of the ratio of seedling survival in vegetation and gaps with Beals index suggest the importance of biotic interactions as a determinant of plant community composition. To disentangle the importance of abiotic and biotic effect on plant establishment, it is important to distinguish between species pool as a set of species typically found in given community type (determined by Beals index) and a set of species for which the abiotic conditions are suitable.

Linking patterns and processes of tree community assembly across spatial scales in tropical montane forests

Many studies have tried to assess the role of both deterministic and stochastic processes in community assembly, yet a lack of consensus exists on which processes are more prevalent and at which spatial scales they operate. To shed light on this issue, we tested two nonmutually exclusive, scale-dependent hypotheses: (1) that competitive exclusion dominates at small spatial scales; and (2) that environmental filtering does so at larger ones. To accomplish this, we studied the functional patterns of tropical montane forest communities along two altitudinal gradients, in Ecuador and Peru, using floristic and functional data from 60 plots of 0.1 ha. We found no evidence of either functional overdispersion or clustering at small spatial scales, but we did find functional clustering at larger ones. The observed pattern of clustering, consistent with an environmental filtering process, was more evident when maximizing the environmental differences among any pair of plots. To strengthen the link between the observed community functional pattern and the underlying process of environmental filtering, we explored differences in the climatic preferences of the most abundant species found at lower and higher elevations and examined whether their abundances shifted along the elevation gradient. We found (1) that greater community functional differences (observed between lower and upper tropical montane forest assemblies) were mostly the result of strong climatic preferences, maintained across the Neotropics; and (2) that the abundances of such species shifted along the elevational gradient. Our findings support the conclusion that, at large spatial scales, environmental filtering is the overriding mechanism for community assembly, because the pattern of functional clustering was linked to species' similarities in their climatic preferences, which ultimately resulted in shifts in species abundances along the gradient. However, there was no evidence of competitive exclusion at more homogeneous, smaller spatial scales, where plant species effectively compete for resources.

Early life supply of competitive exclusion products reduces colonization of extended spectrum beta-lactamase-producing Escherichia coli in broilers

Broilers are an important reservoir of extended spectrum beta-lactamase and AmpC beta-lactamase (ESBL/pAmpC)-producing bacteria. In previous studies, a single supply of a competitive exclusion (CE) product before challenge with a high dose of ESBL/pAmpC-producing Escherichia coli led to reduced colonization, excretion, and transmission, but could not prevent colonization. The hypothesized mechanism is competition; therefore, in this study the effect of a prolonged supply of CE products on colonization, excretion, and transmission of ESBL-producing E. coli after challenge with a low dose at day 0 or day 5 was investigated. Day-old broilers (Ross 308) (n = 220) were housed in isolators. Two CE products, containing unselected fermented intestinal bacteria (CEP) or a selection of pre- and probiotics (SYN), were supplied in drinking water from day 0 to 14. At day 0 or 5, broilers were challenged with 0.5 mL with 10¹ or 10² cfu/mL E. coli encoding the beta-lactamase gene bla_CTX-M-1 on an IncI plasmid (CTX-M-1-E. coli). Presence and concentration of CTX-M-1-E. coli were determined using cloacal swabs (days 0–14, 16, 19, and 21) and cecal content (day 21). Cox proportional hazard model and a mixed linear regression model were used to determine the effect of the intervention on colonization and excretion (log₁₀ cfu/g). When challenged on the day of hatch, no effect of CEP was observed. When challenged at day 5, both CEP and SYN led to a prevention of colonization with CTX-M-1-E. coli in some isolators. In the remaining isolators, we observed reduced time until colonization (hazard ratio between 3.71 × 10⁻³ and 3.11), excretion (up to −1.60 log₁₀ cfu/g), and cecal content (up to −2.80 log₁₀ cfu/g), and a 1.5 to 3-fold reduction in transmission rate. Colonization after a low-dose challenge with ESBL-producing E. coli can be prevented by CE products. However, if at least 1 bird is colonized it spreads through the whole flock. Prolonged supply of CE products, provided shortly after hatch, may be applicable as an intervention to reduce the prevalence of ESBL/pAmpC-producing bacteria in the broiler production chain.

Reproductive Traits of an Invasive Alien Population of Grey Squirrel (Sciurus carolinensis) in Central Italy

The reproductive cycle of an invasive alien Italian grey squirrel population was studied to understand its adaptation and limit its spread, in order to conserve the autochthonous red squirrel. Female and male genital traits were evaluated throughout the reproductive cycle, including the ovary, uterus, testicle, epididymis, seminiferous tubule morphometry, and germinative epithelium histology. Moreover, individual female fecundity was determined by counting uterine scars. Ovary width and uterus weight, length, and width reached their highest values in the luteal and pregnancy phases. On conducting a histological evaluation of the testicular germinal epithelium, four morphotypes related to the different reproductive phases of the male squirrels were identified: immature, pubertal, spermatogenesis, and regressive. Testicle and epididymis weights and seminiferous tubule diameters reached their largest values during spermatogenesis. Uterine scar analysis showed that 69% of the females had given birth to one or two litters, while 31% had no uterine scars. Litters were larger in the first breeding period than in the second; annual fecundity was 4.52 ± 1.88 uterine scars/female. Umbrian grey squirrels have adapted to their non-native range, showing two annual mating periods at times similar to those in their native range, and high reproductive success.

Predator coexistence through emergent fitness equalization

The competitive exclusion principle is one of the oldest ideas in ecology and states that without additional self-limitation two predators cannot coexist on a single prey. The search for mechanisms allowing coexistence despite this has identified niche differentiation between predators as crucial: without this, coexistence requires the predators to have exactly the same R* values, which is considered impossible. However, this reasoning misses a critical point: predators' R* values are not static properties, but affected by defensive traits of their prey, which in turn can adapt in response to changes in predator densities. Here I show that this feedback between defense and predator dynamics enables stable predator coexistence without ecological niche differentiation. Instead, the mechanism driving coexistence is that prey adaptation causes defense to converge to the value where both predators have equal R* values ("fitness equalization"). This result is highly general, independent of specific model details, and applies to both rapid defense evolution and inducible defenses. It demonstrates the importance of considering long-standing ecological questions from an eco-evolutionary viewpoint, and showcases how the effects of adaptation can cascade through communities, driving diversity on higher trophic levels. These insights offer an important new perspective on coexistence theory.

Virus population dynamics examined with experimental model systems

Experimental evolution permits exploring the effect of controlled environmental variables in virus evolution. Several designs in cell culture and in vivo have established basic concepts that can assist in the interpretation of evolutionary events in the field. Important information has come from cytolytic and persistent infections in cell culture that have unveiled the power of virus-cell coevolution in virus and cell diversification. Equally informative are comparisons of the response of viral populations when subjected to different passage régimens. In particular, plaque-to-plaque transfers in cell culture have revealed unusual genotypes and phenotypes that populate minority layers of viral quasispecies. Some of these viruses display properties that contradict features established in virology textbooks. Several hypotheses and principles of population genetics have found experimental confirmation in experimental designs with viruses. The possibilities of using experimental evolution to understand virus behavior are still largely unexploited.

Role of Sortase A in Lactobacillus gasseri Kx110A1 Adhesion to Gastric Epithelial Cells and Competitive Exclusion of Helicobacter pylori

We have previously shown that Lactobacillus gasseri Kx110A1, a human stomach isolate, can colonize mouse stomach and reduce the initial colonization of Helicobacter pylori. Here, we investigated the role of sortase-dependent proteins (SDPs) involved in these functions by the construction of a mutant for srtA, the gene encoding the housekeeping sortase that covalently anchors SDPs to the cell surface. The srtA mutant showed a decrease in hydrophobicity and autoaggregation under acidic conditions, indicating the effect of SDPs on cell surface properties. Correspondingly, the srtA mutant lost the capacity to adhere to gastric epithelial cells, thus resulting in an inability to provide a physical barrier to prevent H. pylori adherence. These results indicate that sortase A is a key determinant of the cell surface properties of L. gasseri Kx110A1 and contributes to Lactobacillus-mediated exclusion of H. pylori. Understanding the molecular mechanisms by which lactobacilli antagonize H. pylori might contribute to the development of novel therapeutic strategies that take advantage of health-promoting bacteria and reduce the burden of antibiotic resistance.

Identifying models of trait-mediated community assembly using random forests and approximate Bayesian computation

Ecologists often use dispersion metrics and statistical hypothesis testing to infer processes of community formation such as environmental filtering, competitive exclusion, and neutral species assembly. These metrics have limited power in inferring assembly models because they rely on often-violated assumptions. Here, we adapt a model of phenotypic similarity and repulsion to simulate the process of community assembly via environmental filtering and competitive exclusion, all while parameterizing the strength of the respective ecological processes. We then use random forests and approximate Bayesian computation to distinguish between these models given the simulated data. We find that our approach is more accurate than using dispersion metrics and accounts for uncertainty in model selection. We also demonstrate that the parameter determining the strength of the assembly processes can be accurately estimated. This approach is available in the R package CAMI; Community Assembly Model Inference. We demonstrate the effectiveness of CAMI using an example of plant communities living on lava flow islands.

Multistability and regime shifts in microbial communities explained by competition for essential nutrients

Microbial communities routinely have several possible species compositions or community states observed for the same environmental parameters. Changes in these parameters can trigger abrupt and persistent transitions (regime shifts) between such community states. Yet little is known about the main determinants and mechanisms of multistability in microbial communities. Here, we introduce and study a consumer-resource model in which microbes compete for two types of essential nutrients each represented by multiple different metabolites. We adapt game-theoretical methods of the stable matching problem to identify all possible species compositions of such microbial communities. We then classify them by their resilience against three types of perturbations: fluctuations in nutrient supply, invasions by new species, and small changes of abundances of existing ones. We observe multistability and explore an intricate network of regime shifts between stable states in our model. Our results suggest that multistability requires microbial species to have different stoichiometries of essential nutrients. We also find that a balanced nutrient supply promotes multistability and species diversity, yet make individual community states less stable.

Variability of the Ability of Complex Microbial Communities to Exclude Microbes Carrying Antibiotic Resistance Genes in Rabbits

Reducing antibiotic use is a necessary step toward less antibiotic resistance in livestock, but many antibiotic resistance genes can persist for years, even in an antibiotic-free environment. In this study, we investigated the potential of three fecal complex microbial communities from antibiotic-naive does to drive the microbiota of kits from antibiotic-exposed dams and outcompete bacteria-carrying antibiotic-resistant genes. The fecal complex microbial communities were either orally delivered or simply added as fresh fecal pellets in four to five nests that were kept clean from maternal feces. Additionally, four nests were cleaned for the maternal feces and five nests were handled according to the common farm practice (i.e., cleaning once a week) as controls. At weaning, we measured the relative abundance of 26 antibiotic resistance genes, the proportion of Enterobacteriaceae resistant to tetracycline and sulfonamide antibiotics, and the taxonomic composition of the microbiota by sequencing the 16S rRNA genes of one kit per nest. Changing the surrounding microbes of the kits can hinder the transmission of antibiotic resistance genes from one generation to the next, but the three communities widely differed in their ability to orient gut microbes and in their impact on antibiotic resistance genes. The most efficient delivery of the microbial community reduced the proportion of resistant Enterobacteria from 93 to 9%, decreased the relative abundance of eight antibiotic resistance genes, and changed the gut microbes of the kits at weaning. The least efficient did not reduce any ARG or modify the bacterial community. In addition, adding fecal pellets was more efficient than the oral inoculation of the anaerobic suspension derived from these fecal pellets. However, we were unable to predict the outcome of the exclusion from the data of the donor does (species composition and abundance of antibiotic resistance genes). In conclusion, we revealed major differences between microbial communities regarding their ability to exclude antibiotic resistance genes, but more work is needed to understand the components leading to the successful exclusion of antibiotic resistance genes from the gut. As a consequence, studies about the impact of competitive exclusion should use several microbial communities in order to draw general conclusions.

Abiotic conditions mediate intraguild interactions between mammalian carnivores

Intraguild (IG) interactions are common among mammalian carnivores, can include intraguild predation (IGP) and interspecific killing (IK), and are often asymmetrical, where a larger more dominant species (IG_predator ) kills a smaller one (IG_prey ). According to ecological theory, the potential for an IG_predator and IG_prey to coexist depends on whether the direct consumptive benefits for the IG_predator are substantial (IGP) or insignificant (IK), the extent to which the IG_prey is the superior exploitative competitor on shared prey resources, and overall ecosystem productivity. We used resource selection models and spatially explicit age and harvest data for two closely related mesopredators that engage in IG interactions, American martens (Martes americana; IG_prey ) and fishers (Pekania pennanti; IG_predator ), to identify drivers of distributions, delineate areas of sympatry and allopatry, and explore the role of an apex predator (coyote; Canis latrans) on these interactions. Model selection revealed that fisher use of this landscape was strongly influenced by late winter abiotic conditions, but other bottom-up (forest composition) and top-down (coyote abundance) factors also influenced their distribution. Overall, fisher probability of use was higher where late winter temperatures were warmer, snowpack was deeper, and measures of productivity were greater. Martens were constrained to areas of the landscape where the probability of fisher use, coyote abundance, and productivity were low and selected for forest conditions that presumably maximized prey availability. Marten age data indicated an increased proportion of juveniles outside of the predicted area of sympatry, suggesting that few animals survived >1.5 years in this area that supported higher densities of fishers and coyotes. Consistent with asymmetrical IG interaction theory, the IG_predator (fishers and, to a lesser degree, coyotes) competitively excluded the IG_prey (martens) from more productive, milder temperature habitats, whereas IG_predators and IG_prey coexisted in low productivity environments, where a combination of abiotic and biotic conditions enabled the IG_prey to be the superior exploitative competitor.

The past and future roles of competition and habitat in the range-wide occupancy dynamics of Northern Spotted Owls

Slow ecological processes challenge conservation. Short-term variability can obscure the importance of slower processes that may ultimately determine the state of a system. Furthermore, management actions with slow responses can be hard to justify. One response to slow processes is to explicitly concentrate analysis on state dynamics. Here, we focus on identifying drivers of Northern Spotted Owl (Strix occidentalis caurina) territorial occupancy dynamics across 11 study areas spanning their geographic range and forecasting response to potential management actions. Competition with Barred Owls (Strix varia) has increased Spotted Owl territory extinction probabilities across all study areas and driven recent declines in Spotted Owl populations. Without management intervention, the Northern Spotted Owl subspecies will be extirpated from parts of its current range within decades. In the short term, Barred Owl removal can be effective. Over longer time spans, however, maintaining or improving habitat conditions can help promote the persistence of northern spotted owl populations. In most study areas, habitat effects on expected Northern Spotted Owl territorial occupancy are actually greater than the effects of competition from Barred Owls. This study suggests how intensive management actions (removal of a competitor) with rapid results can complement a slower management action (i.e., promoting forest succession).

Bacteriocin production and adhesion properties as mechanisms for the anti-listerial activity of Lactobacillus plantarum 423 and Enterococcus mundtii ST4SA

Probiotics play an important role in maintaining a healthy and stable intestinal microbiota, primarily by preventing infection. Probiotic lactic acid bacteria (LAB) are known to be inhibitory to many bacterial enteric pathogens, including antibiotic-resistant strains. Whilst the positive role that probiotics have on human physiology, specifically in the treatment or prevention of specific infectious diseases of the gastro-intestinal tract (GIT) is known, the precise mechanistic basis of these effects remains a major research goal. In this study, molecular evidence to underpin the protective and anti-listerial effect of Lactobacillus plantarum 423 and Enterococcus mundtii ST4SA against orally administered Listeria monocytogenes EGDe in the GIT of mice is provided. Bacteriocins plantaricin 423 and mundticin ST4SA, produced by L. plantarum 423 and E. mundtii ST4SA, respectively, inhibited the growth of L. monocytogenes in vitro and in vivo. Bacteriocin-negative mutants of L. plantarum 423 and E. mundtii ST4SA failed to exclude L. monocytogenes EGDe from the gastrointestinal tract (GIT) of mice. Furthermore, L. plantarum 423 and E. mundtii ST4SA failed to inhibit recombinant strains of L. monocytogenes EGDe in vivo that expressed the immunity proteins of the two bacteriocins. These results confirmed that bacteriocins plantaricin 423 and mundticin ST4SA acted as anti-infective mediators in vivo. Compared to wild type strains, mutants of L. plantarum 423 and E. mundtii ST4SA, in which the adhesion genes were knocked out, were less effective in the exclusion of L. monocytogenes EGDe from the GIT of mice. This work demonstrates the importance of bacteriocin and adhesion genes as probiotic anti-infective mechanisms.

Ecological Drivers of Species Distributions and Niche Overlap for Three Subterranean Termite Species in the Southern Appalachian Mountains, USA

In both managed and unmanaged forests, termites are functionally important members of the dead-wood-associated (saproxylic) insect community. However, little is known about regional-scale environmental drivers of geographic distributions of termite species, and how these environmental factors impact co-occurrence among congeneric species. Here we focus on the southern Appalachian Mountains-a well-known center of endemism for forest biota-and use Ecological Niche Modeling (ENM) to examine the distributions of three species of Reticulitermes termites (i.e., R. flavipes, R. virginicus, and R. malletei). To overcome deficiencies in public databases, ENMs were underpinned by field-collected high-resolution occurrence records coupled with molecular taxonomic species identification. Spatial overlap among areas of predicted occurrence of each species was mapped, and aspects of niche similarity were quantified. We also identified environmental factors that most strongly contribute to among-species differences in occupancy. Overall, we found that R. flavipes and R. virginicus showed significant niche divergence, which was primarily driven by dry-season precipitation. Also, all three species were most likely to co-occur in the mid-latitudes of the study area (i.e., northern Alabama and Georgia, eastern Tennessee and western North Carolina), which is an area of considerable topographic complexity. This work provides important baseline information for follow-up studies of local-scale drivers of these species' distributions. It also identifies specific geographic areas where future assessments of the frequency of true syntopy vs. micro-allopatry, and associated interspecific competitive interactions, should be focused.

Macroscale analysis of mistletoe host ranges in the Andean-Patagonian forest

The number of host species infected by a mistletoe (host range) is critical in that it influences prevalence, virulence and overall distribution of the parasite; however, macroecological analyses of this life history feature are lacking for many regions. The Andean-Patagonian forest, found along the southern Andes from 35 °S to Tierra del Fuego at 55 °S, contains 12 mistletoe species in three families (Loranthaceae, Misodendraceae and Santalaceae). By tabulating herbarium records, the host ranges and geographical distributions of these mistletoes were explored. Our results show that these parasites occur on 43 plant species in 24 families but with varying degrees of specificity. All Misodendrum species and Desmaria mutabilis (Loranthaceae) are specialists that use Nothofagus as their primary hosts. Tristerix and Notanthera (Loranthaceae) and Antidaphne and Lepidoceras (Santalaceae) are generalists parasitizing more than six host species from several genera and families. Although many of the mistletoe species are sympatric, there is low overlap in host use. Our data show that in the southern South American bioregion, generalist mistletoes have smaller geographic ranges than specialists. This contrast with a previous hypothesis that predicted mistletoes with large geographic ranges would also have large host ranges, and conversely, less diverse regions would have more specialised mistletoes.

Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter

Chickens are a key food source for humans yet their microbiome contains bacteria that can be pathogenic to humans, and indeed potentially to chickens themselves. Campylobacter is present within the chicken gut and is the leading cause of bacterial foodborne gastroenteritis within humans worldwide. Infection can lead to secondary sequelae such as Guillain-Barré syndrome and stunted growth in children from low-resource areas. Despite the global health impact and economic burden of Campylobacter, how and when Campylobacter appears within chickens remains unclear. The lack of day to day microbiome data with replicates, relevant metadata, and a lack of natural infection studies have delayed our understanding of the chicken gut microbiome and Campylobacter. Here, we performed a comprehensive day to day microbiome analysis of the chicken cecum from day 3 to 35 (12 replicates each day; final n = 379). We combined metadata such as chicken weight and feed conversion rates to investigate what the driving forces are for the microbial changes within the chicken gut over time, and how this relates to Campylobacter appearance within a natural habitat setting. We found a rapidly increasing microbial diversity up to day 12 with variation observed both in terms of genera and abundance, before a stabilization of the microbial diversity after day 20. In particular, we identified a shift from competitive to environmental drivers of microbial community from days 12 to 20 creating a window of opportunity whereby Campylobacter can appear. Campylobacter was identified at day 16 which was 1 day after the most substantial changes in metabolic profiles observed. In addition, microbial variation over time is most likely influenced by the diet of the chickens whereby significant shifts in OTU abundances and beta dispersion of samples often corresponded with changes in feed. This study is unique in comparison to the most recent studies as neither sampling was sporadic nor Campylobacter was artificially introduced, thus the experiments were performed in a natural setting. We believe that our findings can be useful for future intervention strategies and help reduce the burden of Campylobacter within the food chain.

Co-occurrence of related asexual, but not sexual, lineages suggests that reproductive interference limits coexistence

We used randomizations to analyse patterns of co-occurrence of sexual and apomictic (asexual) members of the North American Crepis agamic complex (Asteraceae). We expect strong asymmetry in reproductive interactions in Crepis: apomicts produce clonal seeds with no need for pollination and are not subject to reproductive interference from co-occurring relatives. However, because they still produce some viable pollen, apomicts can reduce reproductive success of nearby sexual relatives, potentially leading to eventual local exclusion of sexuals. Consistent with this, randomizations reveal that sexuals are over-represented in isolated sites, while apomicts freely co-occur. Incorporation of taxonomic and phylogenetic evidence indicates that this pattern is not driven by local origins of asexuals. Our evidence that patterns of local co-occurrence are structured by reproductive interference suggests an underappreciated role for these interactions in community assembly, and highlights the need for explicit tests of the relative contributions of ecological and reproductive interactions in generating patterns of limiting similarity.

Divergent Secondary Metabolites and Habitat Filtering Both Contribute to Tree Species Coexistence in the Peruvian Amazon

Little is known about the mechanisms promoting or limiting the coexistence of functionally divergent species in hyperdiverse tropical tree genera. Density-dependent enemy attacks have been proposed to be a major driver for the local coexistence of chemically divergent congeneric species. At the same time, we expect local soil conditions to favor the coexistence of species sharing similar functional traits related to resource use strategies, while environmental heterogeneity would promote the diversity of these traits at both local and large spatial scales. To test how these traits mediate species coexistence, we used functional trait data for 29 species from the tree genus Protium (Burseraceae), collected in 19 plots (2 ha each) in the Peruvian Amazon. We characterized the presence-absence of 189 plant secondary metabolites (SM) for 27 of these species, and 14 functional traits associated with resource use strategies (RUT) for 16 species. Based on these data, we found that SM were significantly more dissimilar than null expectations for species co-occurring within plots, whereas RUT were significantly more similar. These results were consistent with the hypothesis that density-dependent enemy attacks contribute to the local coexistence of congeneric species displaying divergent chemical defenses, whereas local habitat conditions filter species with similar RUT. Using measurements of nine soil properties in each plot, we also found a significant turnover of RUT traits with increasing dissimilarity of soil texture and nutrient availabilities, providing support for the hypothesis that soil heterogeneity maintains functional diversity at larger spatial scales (from 500 m up to ca. 200 km) in Protium communities. Our study provides new evidence suggesting that density-dependent enemy attacks and soil heterogeneity both contribute to maintaining high species richness in diverse tropical forests.

Range-constrained co-occurrence simulation reveals little niche partitioning among rock-dwelling Montenegrina land snails (Gastropoda: Clausiliidae)

AIM

Taxon co-occurrence analysis is commonly used in ecology, but it has not been applied to range-wide distribution data of partly allopatric taxa because existing methods cannot differentiate between distribution-related effects and taxon interactions. Our first aim was to develop a taxon co-occurrence analysis method that is also capable of taking into account the effect of species ranges and can handle faunistic records from museum databases or biodiversity inventories. Our second aim was to test the independence of taxon co-occurrences of rock-dwelling gastropods at different taxonomic levels, with a special focus on the Clausiliidae subfamily Alopiinae, and in particular the genus Montenegrina.

LOCATION

Balkan Peninsula in south-eastern Europe (46N-36N, 13.5E-28E).

METHODS

We introduced a taxon-specific metric that characterizes the occurrence probability at a given location. This probability was calculated as a distance-weighted mean of the taxon's presence and absence records at all sites. We applied corrections to account for the biases introduced by varying sampling intensity in our dataset. Then we used probabilistic null-models to simulate taxon distributions under the null hypothesis of no taxon interactions and calculated pairwise and cumulated co-occurrences. Independence of taxon occurrences was tested by comparing observed co-occurrences to simulated values.

RESULTS

We observed significantly fewer co-occurrences among species and intra-generic lineages of Montenegrina than expected under the assumption of no taxon interaction.

MAIN CONCLUSIONS

Fewer than expected co-occurrences among species and intrageneric clades indicate that species divergence preceded niche partitioning. This suggests a primary role of non-adaptive processes in the speciation of rock-dwelling gastropods. The method can account for the effects of distributional constraints in range-wide datasets, making it suitable for testing ecological, biogeographical, or evolutionary hypotheses where interactions of partly allopatric taxa are in question.

Avi-Lution® supplemented at 1.0 or 2.0 g/kg in feed improves the growth performance of broiler chickens during challenge with bacitracin-resistant Clostridium perfringens

Avi-Lution® is a defined, patented, synbiotic product containing Saccharomyces cerevisiae, Enterococcus faecium, and Bacillus spp. Broiler chickens (n = 1,250) were experimentally treated as uninoculated controls (uCon), inoculated controls (iCon) with Clostridium perfringens, or inoculated and treated with bacitracin methylene disalicylate (BMD) at 55 mg/kg as an infected/treated control or Avi-Lution® at 1.0 (AvL1) or 2.0 (AvL2) g/kg in feed for 42 d. Each treatment was applied to 10 replicate pens of 25 straight-run, newly hatched chicks. Pens treated with AvL1, AvL2, or BMD showed improved growth, feed efficiency, or mortality from necrotic enteritis compared with iCon pens at d 14, 28, and 42. No differences in these measurements, however, were observed between pens treated with AvL1 and AvL2, which suggests that Avi-Lution® was effective at 1.0 g/kg in feed. Despite improved performance, BMD, AvL1, and AvL2 treatments did not decrease the severity of intestinal lesion scores through 42 d of age compared with the infected control. These results demonstrate that Avi-Lution® improved growth performance and feed conversion rates in broilers challenged with Clostridium perfringens despite no difference in severity of intestinal lesion scores.

Salmonella Excludes Salmonella in Poultry: Confirming an Old Paradigm Using Conventional and Barcode-Tagging Approaches

Salmonella is one of the major foodborne bacterial pathogens, and the consumption of contaminated chicken meats isa primary route of Salmonella transmission into human food chains. However, the mechanism of Salmonella transmission within the chicken flock is not fully understood, including competition among Salmonella strains during chicken infection. The purpose of the present study was to evaluate the competitive exclusion (CE) between different or same Salmonella species consecutively challenged through the oral route. Two different approaches were used to evaluate the CE effect, including tracking Salmonella colonization by wild-type strains with difference in natural antibiotic resistance or DNA barcode-tagged isogenic strains. When day-of-hatch chicks were administered by wild-type S. Typhimurium (ST) on day 1, followed by infection on day 2 by S. Enteritidis (SE) or vice versa, most of the birds were colonized only by the first strains administered (82% by ST or 83% by SE). When similar experiments were performed using two different isogenic barcode-tagged SE strains, Illumina sequencing analysis of the barcode region showed that the first barcode-tagged strains administered were dominant strains, ranging from 92 to 99% of the Salmonella recovered from ceca. These results provide quantitative evidence supporting the CE theory that oral administration of Salmonella will produce predominant inhibition over the subsequent colonization of ceca by the following administration one day later by different or same Salmonella species. We also showed that the use of barcode-tagged isogenic strains in combination with deep profiling of barcodes by Illumina sequencing can serve as a quantitative method for studying complex dynamics of Salmonella infection, transmission and colonization in poultry.

Conductive Particles Enable Syntrophic Acetate Oxidation between Geobacter and Methanosarcina from Coastal Sediments

Coastal sediments are rich in conductive particles, possibly affecting microbial processes for which acetate is a central intermediate. In the methanogenic zone, acetate is consumed by methanogens and/or syntrophic acetate-oxidizing (SAO) consortia. SAO consortia live under extreme thermodynamic pressure, and their survival depends on successful partnership. Here, we demonstrate that conductive particles enable the partnership between SAO bacteria (i.e., Geobacter spp.) and methanogens (Methanosarcina spp.) from the coastal sediments of the Bothnian Bay of the Baltic Sea. Baltic methanogenic sediments were rich in conductive minerals, had an apparent isotopic fractionation characteristic of CO₂-reductive methanogenesis, and were inhabited by Geobacter and Methanosarcina. As long as conductive particles were delivered, Geobacter and Methanosarcina persisted, whereas exclusion of conductive particles led to the extinction of Geobacter. Baltic Geobacter did not establish a direct electric contact with Methanosarcina, necessitating conductive particles as electrical conduits. Within SAO consortia, Geobacter was an efficient [¹³C]acetate utilizer, accounting for 82% of the assimilation and 27% of the breakdown of acetate. Geobacter benefits from the association with the methanogen, because in the absence of an electron acceptor it can use Methanosarcina as a terminal electron sink. Consequently, inhibition of methanogenesis constrained the SAO activity of Geobacter as well. A potential benefit for Methanosarcina partnering with Geobacter is that together they competitively exclude acetoclastic methanogens like Methanothrix from an environment rich in conductive particles. Conductive particle-mediated SAO could explain the abundance of acetate oxidizers like Geobacter in the methanogenic zone of sediments where no electron acceptors other than CO₂ are available.

Acetate-oxidizing bacteria are known to thrive in mutualistic consortia in which H₂ or formate is shuttled to a methane-producing Archaea partner. Here, we discovered that such bacteria could instead transfer electrons via conductive minerals. Mineral SAO (syntrophic acetate oxidation) could be a vital pathway for CO₂-reductive methanogenesis in the environment, especially in sediments rich in conductive minerals. Mineral-facilitated SAO is therefore of potential importance for both iron and methane cycles in sediments and soils. Additionally, our observations imply that agricultural runoff or amendments with conductive chars could trigger a significant increase in methane emissions.