Multi-species Model Research Articles

The effect of synbiotic-fluoride therapy on multi-species biofilm

ObjectivesThe study objective was to examine the effect of synbiotic-fluoride (SF) therapy within a multi-species cariogenic biofilm model system comprising of S. mutans, S. sanguinis, and S. gordonii. MethodsThe SF therapy was prepared using 2% L-arginine (Arg), 0.2% NaF and probiotic L. rhamnosus GG (LRG). The 8 treatment groups were: Group 1: No treatment, Group 2: 2% Arg, Group 3: 0.2% NaF, Group 4: LRG, Group 5: 2% Arg+0.2% NaF, Group 6: 2% Arg+LRG, Group 7: 0.2% NaF+LRG, and Group 8: SF therapy (2% Arg+0.2% NaF +LRG). Multi-species biofilm model over 96 h comprising Streptococcus mutans, Streptococcus sanguinis, and Streptococcus gordonii was utilized. The biofilms received cariogenic challenge and SF therapy 2 × /day. The extracellular matrix components were analyzed for carbohydrates, proteins, and extra-cellular DNA (eDNA). The live/dead cells were imaged and quantified using confocal microscopy. The viable/dead bacterial concentrations were estimated using propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR). The gene expressions for gtfB, sagP, arcA, argG, and argH were measured using real-time reverse transcriptase qPCR. ResultsCarbohydrates and protein content with SF therapy were higher than non-LRG containing groups, while eDNA content was lower than other groups (p<0.05). Live bacterial proportions determined using confocal imaging with SF therapy were the lowest (p<0.05). The 2% Arg+LRG and SF therapy showed higher viable L. rhamnosus GG than 0.2% NaF+LRG (p<0.05). The dead S. mutans with SF therapy were higher than the other groups (p<0.05) with no difference from 2% Arg+0.2% NaF and 2% Arg+LRG (p>0.05). The SF therapy significantly downregulates gtfB and upregulates sagP, arcA, argG, argH gene expression (p<0.05). ConclusionSynbiotic-fluoride therapy effectuates multi-fold changes in the multi-species biofilm matrix and cellular components leading to superior ecological homeostasis than its individual contents, prebiotics (arginine), probiotic (L. rhamnosus GG), and fluorides (NaF). Clinical significanceThe ecological-based synbiotic-fluoride caries-preventive therapy aids in maintaining biofilm homeostasis to preempt/restore dysbiosis thereby sustaining dynamic-diverse health-associated microbial stability significant as a preventive regimen for high caries-risk patients.

Phylogenomic evolutionary insights in the fern family Gleicheniaceae

The pantropical fern family Gleicheniaceae comprises approximately 157 species. Seven genera are currently recognized in the family, although their monophyly is still uncertain due to low sampling in phylogenetic studies. We examined the monophyly of the genera through extended sampling, using the first phylogenomic inference of the family including data from both nuclear and plastid genomes. Seventy-six samples were sequenced (70 Gleicheniaceae species and six outgroups) using high throughput sequencing, including all seven currently recognized genera. Plastid and nuclear data were recovered and assembled; the nuclear data was phased to reduce paralogy as well as hybrid noise in the final recovered topology. Maximum likelihood trees were built for each locus, and a concatenated dataset was built for both datasets. A species tree based on a multispecies coalescent model was generated, and divergence time analyses performed. We here present the first genomic phylogenetic inferences concerning Gleicheniaceae, confirming the monophyly of most genera except Sticherus, which we recovered as paraphyletic. Although most of the extant genera of Gleicheniaceae originated during the Mesozoic, several genera show Neogene and even Quaternary diversifications, and our results suggest that reticulation and polyploidy may have played significant roles during this diversification. However, some genera, such as Rouxopteris and Stromatopteris, appear to represent evolutionary relicts.

Abstract 5713: Assessing the real-world utility of cell-free microbial DNA in diagnosing early-stage lung cancer

Abstract Introduction: Links between cancer and microbes date back four millennia (Sepich-Poore et al. 2021. Science). Recently, we found that microbial DNA is detectable in tumor tissues and patient blood from many human cancer types (Poore et al. 2020. Nature). These intratumoral and bloodborne microbiomes were distinct between cancer types, between normal and malignant tissues, and present in cell-free plasma samples. However, the practical utility of cell-free microbial DNA (cf-mbDNA) as a bona fide liquid biopsy diagnostic, including its applicability in early-stage disease in treatment-naïve individuals, distinguishing histological subtypes, and discriminating against non-cancer-but-diseased patients remains unknown. Thus, we constructed an age and sex-matched cohort of &amp;gt;1000 individuals with lung cancer, lung disease, and no disease (healthy) to evaluate the utility of a cf-mbDNA-driven liquid biopsy diagnostic. Methods: Shallow shotgun metagenomic sequencing with gold-standard positive and negative controls was performed using 400 µL of patient plasma. Direct genome alignments separated human and microbial reads, and generated genome-wide binned and species-level abundances, respectively. Novel taxonomic diversity was captured by additionally performing de novo co-assemblies in tandem with tumor and blood samples from The Cancer Genome Atlas (TCGA). Multi-modal, stacked machine learning classifiers then evaluated the diagnostic performance of microbial-only and multi-species (microbial + human) information. Results: Cf-mbDNA provides strong diagnostic performance in treatment-naïve, cancer-bearing individuals versus age and sex-matched healthy controls, as early as stage I disease (AUROCs≥0.90). Furthermore, cf-mbDNA outperforms histological classification compared to human genomic information. Multi-species models paired with routinely-available clinicodemographic information provided robust discrimination of lung cancer versus lung diseases (AUROC≥0.80). Importantly, the addition of cell-free microbial information produced an integrated model surpassing the diagnostic performance of PET-CT and clinical risk models for lung nodule malignancy determination in a blinded validation cohort of Stage I lung cancer and non-cancer lung disease samples. Conclusion: Cf-mbDNA features comprise a novel class of biomarkers that are combinable with host analytes, and show promise for real-world, early-stage, lung cancer diagnosis. Citation Format: Serena Fraraccio, Stephen Wandro, Akanksha Singh-Taylor, Sandrine Miller-Montgomery, Eddie Adams, Rob Knight, Leopoldo N. Segal, Harvey I. Pass, Gregory D. Sepich-Poore. Assessing the real-world utility of cell-free microbial DNA in diagnosing early-stage lung cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5713.

Numerical Research on Migration Law of Typical Chlorinated Organic Matter in Shallow Groundwater of Yangtze Delta Region

With the reform of China’s urbanization increasing in popularity, the security issues posed by urban groundwater, especially groundwater in industrial areas, have attracted scholars’ attention. This research aimed to predict and quantify the migration process of contaminants in a microconfined aquifer by conducting a groundwater contamination investigation in an abandoned chemical plant in the Jiangsu Province of China. First, data such as regional hydrogeological parameters and types of contaminants were obtained via hydrogeological drilling, groundwater well monitoring, pumping tests, and laboratory permeability tests, which helped identify the most serious pollution factor: chloroform. Then, a groundwater flow model was built using the Groundwater Modeling System (GMS) and verified using the general-purpose parameter estimation (PEST) package. In addition, based on the three-dimensional multi-species model for transport (MT3DMS) in GMS, a transport model was established. The results illustrate that the plume range of chloroform diffuses with water flow, but, because of its slow diffusion rate and inability to degrade naturally, the concentration of the contaminant has remained several times higher than the safety standard for a long time. The contaminant spread vertically to the soil layer above the microconfined aquifer under pressure, resulting in direct pollution. In addition, the contaminant in the microconfined aquifer is anticipated to migrate down to the clay layer and become enriched. However, the first confined aquifer has not been seriously polluted in the past 20 years. Finally, a sensitivity analysis of the parameters shows that groundwater contamination in the Yangtze delta region is greatly affected by precipitation recharge and hydraulic conductivity.

Becoming-monster: Ecoaesthetics and feminist criticism of Chinese animation White Snake (2019)1

This article examines Chinese animation Baishe: Yuanqi (White Snake) () and discusses how ecoaesthetics are intertwined with questions of gender representations. Ecoaesthetics are broadly defined to consider the relationship between the human and natural world via de-anthropocentrism – which is the criticism of a human-centred view of the world that surrounds us. The film White Snake focuses on a man who becomes a monster to be with the creature he loves. This article argues that White Snake provides a multi-species model for ecocriticism. On the one hand, the film presents ecological thoughts that showcases a contradictory but symbiotic relationship between human and non-humans; on the other hand, the film neglects the connection between ecoaesthetics and feminist criticism so that it ends up portraying an ecological system that is under the inveterate patriarchal reign and therefore violates ideas around equality in ecoaesthetics. I propose a notion becoming-monster to decipher this ambivalent ecoaesthetic representation. The representation of becoming-monster showcases the harmony that can potentially exist between the human and the non-human appealing de-anthropocentric actions while the ideal image of the equality between human and non-human others is in fact under the male gaze.

Computationally efficient high-fidelity plasma simulations by coupling multi-species kinetic and multi-fluid models on decomposed domains

A numerical method is developed for coupling a multi-species kinetic plasma model with a 5N-moment multi-fluid plasma model. The simulation domain is decomposed such that the local conditions satisfy the corresponding plasma model's region of validity. The method allows for hybrid simulations by formulating each model as a set of conservation laws and using a continuum numerical method to solve each model's governing equations in the subdomains of the decomposed domain. The models are coupled through fluxes across subdomain interfaces. Two methods are explored for the formulation of the fluxes that can be self-consistently represented by both plasma models. One method allows for flux calculations consistent with the 5N-moment multi-fluid plasma model and assumes thermodynamic equilibrium within each species of the kinetic plasma model. The second method ensures conservation of the distribution function as well as mass, momentum, and energy by formulating the fluxes using a composite underlying distribution function at the subdomain interfaces. The methods are compared in 1D1V simulations of a double rarefaction wave and a plasma sheath using the WARPXM framework, which solves each model using the discontinuous Galerkin finite element method. Both methods for formulating the fluxes perform well as the subdomain interface distribution function approaches a Maxwellian, with the consistent method being more robust to larger deviations. A simulation of the magnetized Kelvin-Helmholtz instability in 2D2V is also performed using the consistent method, which demonstrates the potential of the domain-decomposed hybrid method in facilitating speedup and reduction in required computational resources for high-fidelity plasma simulations, allowing for the investigation of problems that are beyond current capabilities.

Tropical agricultural wooded land uses support high site use of forest birds

Agricultural expansion has been responsible for the large-scale modification of forest ecosystems globally. In many regions, this has resulted in the creation of heterogenous landscapes comprised of cleared agricultural lands, and semi-natural and natural wooded land uses such as agroforests and secondary forests. These wooded land uses can play an important role in supporting forest biodiversity. In a tropical agricultural landscape of Northeast India, we investigate how wooded land uses affect site use by forest specialist, forest generalist and open-country bird species, in comparison to a protected area. We also investigate the effects of site vegetation characteristics, surrounding forest cover and distance to the protected area. Using multi-species occupancy models, we found that wooded land uses support high site use of the three forest specialization groups. We attribute the high site use of forest species in wooded land uses to the similarity in site vegetation characteristics between these land uses and the protected area. In addition, high forest cover at, and neighbouring, our sampling sites, and habitat connectivity also contributed towards supporting high site use of forest species. However, for some species across the three groups, a few site vegetation characteristics and surrounding forest cover had a subtle influence. Our study showcases the supplementary role of low-intensity agricultural landscapes as habitat for forest birds, provided that wooded land uses outside protected areas are well maintained. In so doing, it contributes valuable insights into land management practices that support biodiversity in heterogeneous agricultural landscapes.

Individual Tree-Crown Detection and Species Identification in Heterogeneous Forests Using Aerial RGB Imagery and Deep Learning

Automatic identification and mapping of tree species is an essential task in forestry and conservation. However, applications that can geolocate individual trees and identify their species in heterogeneous forests on a large scale are lacking. Here, we assessed the potential of the Convolutional Neural Network algorithm, Faster R-CNN, which is an efficient end-to-end object detection approach, combined with open-source aerial RGB imagery for the identification and geolocation of tree species in the upper canopy layer of heterogeneous temperate forests. We studied four tree species, i.e., Norway spruce (Picea abies (L.) H. Karst.), silver fir (Abies alba Mill.), Scots pine (Pinus sylvestris L.), and European beech (Fagus sylvatica L.), growing in heterogeneous temperate forests. To fully explore the potential of the approach for tree species identification, we trained single-species and multi-species models. For the single-species models, the average detection accuracy (F1 score) was 0.76. Picea abies was detected with the highest accuracy, with an average F1 of 0.86, followed by A. alba (F1 = 0.84), F. sylvatica (F1 = 0.75), and Pinus sylvestris (F1 = 0.59). Detection accuracy increased in multi-species models for Pinus sylvestris (F1 = 0.92), while it remained the same or decreased slightly for the other species. Model performance was more influenced by site conditions, such as forest stand structure, and less by illumination. Moreover, the misidentification of tree species decreased as the number of species included in the models increased. In conclusion, the presented method can accurately map the location of four individual tree species in heterogeneous forests and may serve as a basis for future inventories and targeted management actions to support more resilient forests.

Larval Dispersal Modeling Reveals Low Connectivity among National Marine Protected Areas in the Yellow and East China Seas.

Marine protected areas (MPAs) are vital for protecting biodiversity, maintaining ecosystem integrity, and tackling future climate change. The effectiveness of MPA networks relies on connectivity, yet connectivity assessments are often skipped in the planning process. Here we employed a multi-species biophysical model to examine the connectivity patterns formed among the 21 national MPAs in the Yellow and East China Seas. We simulated the potential larval dispersal of 14 oviparous species of five classes. Larvae of non-migratory species with pelagic larval duration (PLD) were assumed to be passive floating particles with no explicit vertical migration. A total of 217,000 particles were released according to spawning period, living depth, and species distribution, and they were assumed to move with currents during the PLD. Most larvae were dispersed around the MPAs (0-60 m isobaths) and consistent with the currents. Larval export increased with PLD and current velocity, but if PLD was too long, few larvae survived due to high daily mortality during pelagic dispersal. The overall connectivity pattern exhibited a north-to-south dispersal trend corresponding to coastal currents. Our results indicated that the national MPAs in the Yellow and East China Seas did not form a well-connected network and nearly 30% of them were isolated. These MPAs formed three distinct groups, one in the Yellow Sea ecoregion and two in the East China Sea ecoregion. Four MPAs (all in coastal Zhejiang) emerged as key nodes for ensuring multi-generational connectivity. Under the pressure of future climate change, high self-recruitment and low connectivity present significant challenges for building well-connected MPA networks. We suggest adding new protected areas as stepping stones for bioecological corridors. Focused protection of the Yellow Sea ecoregion could have a good effect on the southern part of the population recruitment downstream. Conservation management should be adjusted according to the life cycles and distributions of vulnerable species, as well as seasonal changes in coastal currents. This study provides a scientific basis for improving ecological connectivity and conservation effectiveness of MPAs in the Yellow and East China Seas.

Multi-decadal distribution changes of commercially important demersal species in the central-western Sea of Japan based on a multi-species spatiotemporal model

Understanding long-term changes in the distribution of commercially important species is a key first step for developing appropriate management plans. We estimated multi-decadal changes in the distributions of seven demersal fish species in the central-western Sea of Japan by fitting a multi-species spatiotemporal model to catch and effort data from a Japanese offshore trawl fishery from 1982 to 2020. We then identified any spatiotemporal patterns and discussed their relationship to oceanographic factors. Large distribution expansions were detected for Pacific cod (Gadus macrocephalus) and blackthroat seaperch (Doederleinia berycoides) in the southwestern region of the study area in the 2000s and 2010s. Combined with previous findings and an interannual trend of water temperature, it is thought that these changes could have been caused by expansions in the distribution of optimal thermal condition for stock-recruitment relationships. Species that did not experience large changes in distribution, such as cold-water flounders [the flathead flounder (Hippoglossoides dubius) and Korean flounder (Glyptocephalus stelleri)], mainly inhabit deep waters that are thought to be dominated by a colder and homogeneous water mass, meaning that their habitats were more likely to remain stable over time. Our results will contribute to improvement of adaptive stock managements for commercially important demersal species.

Beaver activity and red squirrel presence predict bird assemblages in boreal Canada

AbstractWetlands and predation in boreal ecosystems play essential roles throughout the breeding season for bird assemblages. We found a positive association of beaver activity and a negative influence of American red squirrels (Tamiasciurus hudsonicus) on bird assemblages. We used a multispecies hierarchical model to investigate whether bird communities differ between two major wetland habitats in boreal Canada: beaver ponds and peatland ponds. In addition to including variables such as forest cover and latitude, we adopted a structural equation model approach to estimate the occupancy of American red squirrels and its potential influence on bird communities. Using automated recording stations deployed at 50 ponds, we detected 96 bird species in 2018 and 2019. Bird species were grouped into four taxonomic guilds according to their habitat successional requirements: early successional species, late successional species, generalists, and wetland species. Beaver ponds harbored higher species richness, a pattern driven primarily by early successional species. The occupancy of almost a quarter of the species was lower in the presence of red squirrels. Late successional species responded positively to the cover of forest surrounding the pond. Our results highlight the value of considering acoustic data of red squirrels to quantify habitat quality in boreal forests. We conclude that beaver activity shapes bird assemblages through modification of their habitat, and that some bird guilds are associated negatively with the presence of American red squirrels.

Evaluation of the impact of formaldehyde fumigation during the hatching phase on contamination in the hatch cabinet and early performance in broiler chickens

Commercial hatch cabinet environments promote replication of microorganisms. These pathogenic or apathogenic microorganisms may serve as pioneer colonizers of the gastrointestinal tract (GIT) of poultry. Some of these pioneer colonizers, such as Escherichia coli and Enterococcus spp., are opportunistic pathogens that lead to reduced performance in commercial poultry. Effective hatchery sanitation is imperative to limit contamination of naïve neonatal chicks and poults. Formaldehyde fumigation has been traditionally used to reduce the pathogen load in commercial hatch cabinets. To investigate potential alternatives to formaldehyde fumigation, models to mimic the microbial bloom in a laboratory setting must be utilized. The purpose of the present study was to evaluate the impact of a multispecies environmental challenge model (PM challenge) with and without formaldehyde fumigation during the hatching phase on early performance in broiler chicks. Three experiments were conducted to evaluate microbial contamination in the hatch cabinet environment (air samples, fluff samples), enteric colonization at day-of-hatch (DOH), and 7-day performance. In all experiments, significantly (P < 0.05) more gram-negative bacteria were recovered from the GIT at DOH in the PM challenge control group as compared to the nonchallenged control (NC) group and the formaldehyde-treated group (PM+F). There were no statistical differences in 7-day body weight gain or feed conversion ratio between the PM challenge control group, the NC group or the PM+F group. These data suggest this model could be utilized to evaluate alternatives to formaldehyde fumigation for controlling the microbial load during the hatching phase in a laboratory setting.

Enhanced reductive degradation of chloramphenicol by sulfidated microscale zero-valent iron: Sulfur-induced mechanism, competitive kinetics, and new transformation pathway

Crystalline iron sulfide (FeSx, i.e., FeS or FeS2) minerals as sulfur sources were used to prepare the mechanochemically sulfidated microscale zero-valent iron ((FeSx+ZVI)bm). Metastable FeS and FeS2 precursors were generated via aqueous coprecipitation and applied to fabricate FeSx@ZVI samples. (FeSx+ZVI)bm and FeSx@ZVI exhibited better chloramphenicol (CAP) degradation than ZVI due to the increase in specific surface areas, the decrease of electrochemical impedance, the formation of galvanic cells, and sulfur-induced pitting and local acidity. (FeSx+ZVI)bm had better CAP removal capacity than FeSx@ZVI under different S/Fe molar ratios, initial pH, and oxygen conditions. At the same time, FeSx@ZVI showed better electron utilization under oxic conditions, related to their Fe0 and sulfur spatial distribution. Nitro reduction and dechlorination of CAP by (FeSx+ZVI)bm produced nitroso, azoxy, amine, and monodechlorination products, while dechlorination was not involved in the degradation process of CAP by FeSx@ZVI. A new transformation pathway of nitroso-CAP to amine-CAP mediated by azoxy products is proposed via coupling a chain decay multispecies model and DFT calculations. The larger competitive reaction rates among O2, CAP, and its degradation products was determined by their lower LUMO energy. The contribution of direct electron transfer to nitro reduction was greater than that of atomic hydrogen, but the opposite was true for dechlorination. FeSx@ZVI had a larger DET contribution than (FeSx+ZVI)bm, and FeS2 promoted the DET contribution better than FeS. Toxicity assessment indicated that the rapid transformation of nitroso and azoxy products was crucial for eliminating the biotoxicity of CAP.

Estimating population dynamics trajectories of raptors from a multi-species hierarchical distance sampling model

Community dynamics are essential for ecosystems as they support the functioning of food webs and maintain biodiversity. However, the fluctuations of species abundances are rarely analyzed simultaneously despite their interconnectedness across space and time. We developed a Bayesian multi-species model that estimates community- and taxon-level parameters related to dynamics, abundance, detection probability, and environmental stochasticity. From this model, we analyze the variability of populations of a community of raptors composed of accipiters (sharp-shinned hawk [Accipiter striatus], and Cooper's hawk [A. cooperii]), buteos (red-tailed hawk [Buteo jamaicensis], and red-shouldered hawk [B. lineatus]) and owls (great horned owl [Bubo virginianus], and barred owl [Strix varia]). We show that migration pulses of accipiters, buteos, and dispersal of fledging owls drive variation in raptor abundances, indicating a defined production and dispersal period. Also, large-scale climatic processes such as the North Atlantic Oscillation (NAO) influenced the variation in abundances of raptors. When the NAO was in a positive phase, the abundance of raptors decreased, and inversely. Local weather did not affect raptor population abundances. Our approach facilitated the modelling of species-specific effects of environmental variation and guild-level dynamics that could be used for ecosystem-based conservation measures.

Effect of Probiotic Lactobacillus plantarum on Streptococcus mutans and Candida albicans Clinical Isolates from Children with Early Childhood Caries.

Probiotics interfere with pathogenic microorganisms or reinstate the natural microbiome. Streptococcus mutans and Candida albicans are well-known emerging pathogenic bacteria/fungi for dental caries. In this study, three probiotic Lactobacilli strains (Lactobacillus plantarum 8014, L. plantarum 14917, and Lactobacillus salivarius 11741) were tested on S. mutans and C. albicans clinical isolates using a multispecies biofilm model simulating clinical cariogenic conditions. The ten pairs of clinical isolates of S. mutans and C. albicans were obtained from children with severe early childhood caries. Our study findings show a remarkable inhibitory effect of L. plantarum 14917 on S. mutans and C. albicans clinical isolates, resulting in significantly reduced growth of S. mutans and C. albicans, a compromised biofilm structure with a significantly smaller microbial and extracellular matrix and a less virulent microcolony structure. FurTre, plantaricin, an antimicrobial peptide produced by L. plantarum, inhibited the growth of S. mutans and C. albicans. The mechanistic assessment indicated that L. plantarum 14917 had a positive inhibitory impact on the expression of S. mutans and C. albicans virulence genes and virulent structure, such as C. albicans hypha formation. Future utilization of L. plantarum 14917 and/or its antimicrobial peptide plantaricin could lead to a new paradigm shift in dental caries prevention.

Novel Source–Sink Model for Space Environment Evolution with Orbit Capacity Assessment

The increasing number of anthropogenic space objects (ASOs) in low Earth orbit (LEO) poses a threat to the safety and sustainability of the space environment. Multiple companies are planning to launch large constellations of hundreds to thousands of satellites in the near future, increasing the probability of collisions and debris generation. This paper analyzes the long-term evolution of the LEO ASO population with the goal of estimating LEO orbital capacity. This is carried out by introducing a new probabilistic source–sink model. The developed source–sink model is a multishell multispecies model, which includes different object species, such as active and derelict satellites, and debris. Furthermore, debris are divided into the following two subgroups: trackable and nontrackable debris, the last ones representing a significant hazard for active satellites. In addition, the proposed model accounts for collision events and atmospheric drag effects, which include the influence of solar activity. Indeed, the Jacchia–Bowman 2008 thermospheric density model is exploited. The results prove that considering untracked debris within the model produces more collisions, and therefore a smaller population of active satellites affecting the safety of LEO and its orbital capacity.

The Antimicrobial Activity of Curcumin and Xanthohumol on Bacterial Biofilms Developed over Dental Implant Surfaces.

In search for natural products with antimicrobial properties for use in the prevention and treatment of peri-implantitis, the purpose of this investigation was to evaluate the antimicrobial activity of curcumin and xanthohumol, using an in vitro multi-species dynamic biofilm model including Streptococcus oralis, Actinomyces naeslundii, Veillonella parvula, Fusobacterium nucleatum, Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans. The antimicrobial activities of curcumin (5 mM) and xanthohumol (100 μM) extracts, and the respective controls, were evaluated with 72-h biofilms formed over dental implants by their submersion for 60 seconds. The evaluation was assessed by quantitative polymerase chain reaction (qPCR), confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). For the data analysis, comparisons were tested applying ANOVA tests with post-hoc Bonferroni corrections to evaluate the antimicrobial activity of both extracts. With qPCR, statistically significant reductions in bacterial counts were observed for curcumin and xanthohumol, when compared to the negative control. The results with CLSM and SEM were consistent with those reported with qPCR. It was concluded that both curcumin and xanthohumol have demonstrated antimicrobial activity against the six bacterial species included in the dynamic in vitro biofilm model used.

Increasing the uptake of multispecies models in fisheries management

AbstractMultispecies models have existed in a fisheries context since at least the 1970s, but despite much exploration, advancement, and consideration of multispecies models, there remain limited examples of their operational use in fishery management. Given that species and fleet interactions are inherently multispecies problems and the push towards ecosystem-based fisheries management, the lack of more regular operational use is both surprising and compelling. We identify impediments hampering the regular operational use of multispecies models and provide recommendations to address those impediments. These recommendations are: (1) engage stakeholders and managers early and often; (2) improve messaging and communication about the various uses of multispecies models; (3) move forward with multispecies management under current authorities while exploring more inclusive governance structures and flexible decision-making frameworks for handling tradeoffs; (4) evaluate when a multispecies modelling approach may be more appropriate; (5) tailor the multispecies model to a clearly defined purpose; (6) develop interdisciplinary solutions to promoting multispecies model applications; (7) make guidelines available for multispecies model review and application; and (8) ensure code and models are well documented and reproducible. These recommendations draw from a global assemblage of subject matter experts who participated in a workshop entitled “Multispecies Modeling Applications in Fisheries Management”.

Semi-natural habitats on organic strawberry farms and in surrounding landscapes promote bird biodiversity and pest control potential

Agricultural intensification and expansion have degraded biodiversity in agroecosystems, jeopardizing the ecosystem services provided by wildlife. Birds can act as particularly important purveyors of ecosystem services to farmers by consuming arthropod pests. Some bird species, however, may sometimes act as pests themselves by consuming crops. Further, on-farm management practices (e.g., crop diversity, vegetative structure) and the complexity of the surrounding landscape can shift the balance of bird-mediated ecosystem services and disservices through changes in bird community composition. Here, we explored how organic strawberry farms in California could be managed to bolster bird biodiversity and shift community composition from strawberry-consuming to pest-eating species. Using multi-species N-mixture models we found that semi-natural habitat at the landscape (1000 m) and farm (50 m) scales were positively associated with mean abundance of all birds, with varying effects on different species. In particular, we found that the mean local abundance of species that consume Lygus spp. (a major pest), but not strawberry-consuming species, increased with semi-natural habitat at the farm scale. Nest density in developed areas within farms also increased with greater semi-natural habitat in the landscape, while nest density in semi-natural habitat within farms decreased with increasing semi-natural habitat in the landscape. Further, nest density of Lygus spp. eating birds increased with increasing local semi-natural habitat. These results suggest that increasing semi-natural habitat at the landscape and local scales can bolster bird abundance across farms, while pest control can be promoted locally by conserving or restoring semi-natural vegetation at the farm scale.

Rapid, recurring, structured survey versus bioblitz for generating biodiversity data and analysis with a multispecies abundance model.

A bioblitz inexpensively and quickly generates biodiversity data, but bioblitzes are often conducted with haphazard, unreplicated sampling. Results tend to be taxonomically, geographically, or temporally biased, lack metadata, and consist of lists of observed taxa that do not enable further analyses or correction for imperfect detection. A rapid, recurring, structured survey (RRSS) uses a structured sampling design and temporal and spatial replication to survey randomly selected sites on a conservation property. We participated in a loosely structured bioblitz and a subsequent RRSS at Big Canoe Creek Nature Preserve in Springville (St. Clair County), Alabama (USA) to compare observed richness derived from the 2 survey approaches. The RRSS data structure enabled us to fit models that accounted for imperfect detection to estimate abundances, occupancy probabilities, and habitat associations. The loosely structured bioblitz data could not be used in such models. We present a new integrated multispecies abundance model that we applied to avian RRSS data. Our model extension enables estimation for the community, employs data augmentation to estimate the number of undetected species, and incorporates covariates. The RRSS generated a more comprehensive and less biased list of observed taxonomic richness than the loosely structured bioblitz (e.g., 73 vs. 45 bird species and 104 vs. 63 insect families from the RRSS vs. loosely structured bioblitz, respectively). Models fit to the RRSS data identified seasonal patterns in avian community composition and allowed for estimation of habitat-occupancy relationships for insect taxa. The RRSS protocol has potential for broad transferability as a standardized, quick, and inexpensive way to inventory biodiversity and estimate ecological parameters while providing an outreach opportunity.