Core Microbiota Drive the Prevalence of Extracellular Antibiotic Resistome in the Water Compartments

Unlike intracellular chromosome, extracellular DNA (eDNA) may accelerate the spreading of antibiotic resistance genes (ARGs) through natural transformation, but one of the core issues regarding to the taxonomic characterization of eDNA in the complex water environments is largely unknown. Hence, Illumina Miseq sequencing was used to identify the genotype of eDNA from wastewater (WW), river water (RW) and stormwater (SW) runoff. High-throughput qPCR targeting 384 genes was implemented to detect extracellular ARGs (eARGs) and mobile genetic elements (eMGEs). We obtained 2,708,291 high quality sequences from 66 eDNA samples. The SW exhibited the significant higher Shannon Index. Subsequently, we identified 34 core bacteria sources of eDNA widely distributed in the three water compartments. Among which, Pseudomonas, Flavobacterium, Limnohabitans, Burkholderiaceae_unclassified, Methylotenera and Acinetobacter were the most prevalent. A total of 302 eARGs and eMGEs were detected, suggesting that eDNA is an important antibiotic resistance reservoir. Among the 127 shared genes of the three groups, 15 core resistance genes were filtered, including IS6100, sul1 NEW, intI1, ISPps1-pseud, aac3-Via, qacH_351 and ISSm2-Xanthob. The Procrustes analysis and Variance Partitioning Analysis (VPA) demonstrated that core bacteria and MGEs were significantly correlated with eARGs. These results suggested that the occurrence and changes of eARGs in the water compartments may be largely attributed to the core microbiota and eMGEs.

Quantifying soil, microbial, and plant community changes following wetland restoration on private land

<p>Extensive global and national wetland loss has reduced ecosystem services to people and undermines the sustainability of ecosystems. Restoration projects aim to regain the biophysical conditions of remnant wetlands that produce an abundance of ecosystem services. Ecological restoration practices manipulate community succession to enhance ecological functions, and these different successional stages may be reflected in the soil physio-chemical characteristics, plants, and soil microbes, which in turn produce a variety of ecosystem services. Considerable potential for wetland restoration on private property exists in New Zealand, but it remains unknown how successful restoration is when undertaken through a landholder’s own prerogative. Relative to restoration of public land, private restoration projects are often small scale, personally funded and preference driven. In this thesis, I quantify the outcomes of small-scale private wetland restoration projects by measuring changes in plant and soil microbial communities, and soil physiochemical characteristics. I explore the relationships among variation in plant, soil and microbial datasets and test for causes of this variation. Using a paired sampling design, I sampled 18 restored wetlands and 18 unrestored wetlands on private property in the Wairarapa region. I used a Whitaker plot design to sample wetland plant communities at multiple scales and took soil samples that I analysed for physio-chemical properties. Additionally, I quantified the biomass and community composition of the microbes in the soil samples using phospholipid fatty acid analysis. In my second chapter, I use linear mixed-effect models, principal components analysis, and non-metric multidimensional scaling to ask: How does wetland restoration alter the plant community, soil physio-chemical characteristics, and the soil microbial community? In my third chapter, I employ Procrustes analysis to look at the association of variation in plants, microbes, and soil characteristics to explore whether successional processes of these attributes are concurrent within wetlands. I then use hierarchical cluster analysis to determine which of the wetlands are at similar successional stages and identified site contexts and restoration treatments that were in common among similar wetlands. These analyses provide insight to the conditions that advance successional processes in restored wetlands. Specifically, I ask 1) How do plant, microbial, and soil characteristics co-vary during wetland restoration? 2) How do indicators of wetland succession respond to restoration? 3) Are different restoration practices and site contexts influencing wetland outcomes during restoration? Private wetland restoration enhanced succession in plant, soil, and microbial properties towards those more similar to undisturbed wetland conditions. Specifically, restoration added ~13 native plant species, increased totalfungal and arbuscular mycorrhizal biomass, and total microbial biomass by 25%. Restoration increased soil moisture by 93%, soil organic carbon by 20%, and saturated hydraulic conductivity by 27%. It also reduced bulk density by 0.19 g-1 cm3 and plant available phosphorus (Olsen P) by 23%. Procrustes analysis revealed a lack of congruence in the recovery of plant, microbial, and soil indicators of succession, signifying that the plant community succeeded faster than the microbial community and soil characteristics. Variation in soil and microbial properties separated restored wetlands into two groups of early and later succession wetlands, which was independent of the number of years since restoration began at the sites but corresponded to elements of wetland hydrology. Soil and microbial characteristics in hydrologically connected wetlands recovered more quickly following restoration than hydrologically isolated wetlands. Private restoration increased spatial heterogeneity of outcomes at the plot scale, which depended on site factors. My data suggests that private wetland restoration is effective in increasing plant, soil, and microbial characteristics that produce ecosystem services. Additionally, wetland restoration increased environmental heterogeneity and the capacity for ecosystem service delivery, which may contribute to increased resilience of the Wairarapa landscape.</p>

Quantifying soil, microbial, and plant community changes following wetland restoration on private land

<p>Extensive global and national wetland loss has reduced ecosystem services to people and undermines the sustainability of ecosystems. Restoration projects aim to regain the biophysical conditions of remnant wetlands that produce an abundance of ecosystem services. Ecological restoration practices manipulate community succession to enhance ecological functions, and these different successional stages may be reflected in the soil physio-chemical characteristics, plants, and soil microbes, which in turn produce a variety of ecosystem services. Considerable potential for wetland restoration on private property exists in New Zealand, but it remains unknown how successful restoration is when undertaken through a landholder’s own prerogative. Relative to restoration of public land, private restoration projects are often small scale, personally funded and preference driven. In this thesis, I quantify the outcomes of small-scale private wetland restoration projects by measuring changes in plant and soil microbial communities, and soil physiochemical characteristics. I explore the relationships among variation in plant, soil and microbial datasets and test for causes of this variation. Using a paired sampling design, I sampled 18 restored wetlands and 18 unrestored wetlands on private property in the Wairarapa region. I used a Whitaker plot design to sample wetland plant communities at multiple scales and took soil samples that I analysed for physio-chemical properties. Additionally, I quantified the biomass and community composition of the microbes in the soil samples using phospholipid fatty acid analysis. In my second chapter, I use linear mixed-effect models, principal components analysis, and non-metric multidimensional scaling to ask: How does wetland restoration alter the plant community, soil physio-chemical characteristics, and the soil microbial community? In my third chapter, I employ Procrustes analysis to look at the association of variation in plants, microbes, and soil characteristics to explore whether successional processes of these attributes are concurrent within wetlands. I then use hierarchical cluster analysis to determine which of the wetlands are at similar successional stages and identified site contexts and restoration treatments that were in common among similar wetlands. These analyses provide insight to the conditions that advance successional processes in restored wetlands. Specifically, I ask 1) How do plant, microbial, and soil characteristics co-vary during wetland restoration? 2) How do indicators of wetland succession respond to restoration? 3) Are different restoration practices and site contexts influencing wetland outcomes during restoration? Private wetland restoration enhanced succession in plant, soil, and microbial properties towards those more similar to undisturbed wetland conditions. Specifically, restoration added ~13 native plant species, increased totalfungal and arbuscular mycorrhizal biomass, and total microbial biomass by 25%. Restoration increased soil moisture by 93%, soil organic carbon by 20%, and saturated hydraulic conductivity by 27%. It also reduced bulk density by 0.19 g-1 cm3 and plant available phosphorus (Olsen P) by 23%. Procrustes analysis revealed a lack of congruence in the recovery of plant, microbial, and soil indicators of succession, signifying that the plant community succeeded faster than the microbial community and soil characteristics. Variation in soil and microbial properties separated restored wetlands into two groups of early and later succession wetlands, which was independent of the number of years since restoration began at the sites but corresponded to elements of wetland hydrology. Soil and microbial characteristics in hydrologically connected wetlands recovered more quickly following restoration than hydrologically isolated wetlands. Private restoration increased spatial heterogeneity of outcomes at the plot scale, which depended on site factors. My data suggests that private wetland restoration is effective in increasing plant, soil, and microbial characteristics that produce ecosystem services. Additionally, wetland restoration increased environmental heterogeneity and the capacity for ecosystem service delivery, which may contribute to increased resilience of the Wairarapa landscape.</p>

A Python toolbox for Automatic Face Alignment (AFA)

We describe AFA, an open-source Python package for automating the most common step in the preparation of facial stimuli for behavioral and neuro-imaging experiments – spatial alignment of faces (https://github.com/SourCherries/auto-face-align ). Face alignment is also important in the analysis of image statistics, and as a preprocessing step for machine learning. Automation of face alignment via AFA provides a reliable and efficient alternative to the very common practice of manual image-editing in graphics editors like Photoshop. As an open-source Python package, AFA encourages a clear and transparent specification of experimental method. AFA is based on facial landmark detection that is powered by the reliable and open-source DLIB library; and critical alignment code based on Generalized Procrustes Analysis (GPA) has been extensively unit-tested. AFA documentation and modularity provides opportunity for the modification and extensibility of AFA by the scientific community. As examples, we include functions for automatically generating image apertures that conceal areas outside the inner face; for image morphing between facial identities; and for shape-based averaging of facial identity. All of these are examples of stimulus preparation that have previously required manual landmark selection.

Match of the Bimaxillary Basal Bone Arches and Its Variations among Individuals

Introduction. This study is aimed at illustrating the bimaxillary basal bone contours, to clarify the match of the basal bone arches of the upper and lower, especially the posterior segments, including the second molar and retromolar region. Methods. Based on 100 cone-beam computed tomography (CBCT) images (50 males and 50 females), we obtained 100 pairs of basal bone arches, which were the horizontal inner cortex contours passing the furcation of the first molar paralleled to the lower occlusal plane. The Generalized Procrustes Analysis (GPA) was applied to depict average contours and calculate the ratio and difference width of both upper and lower dental arches in different positions. Variations of the basal bone morphology among individuals were revealed using Principal Component Analysis (PCA). Results. The width discrepancy occurred at 7-7 segment (male: upper 65.62 mm and lower 68.81 mm and female: upper 62.98 mm and lower 68.38 mm) and the retromolar region (male: upper 64.67 mm and lower 71.96 mm and female: upper 62.34 mm and lower 71.44 mm). The ratio ( p = 0.006 ) and difference value ( p = 0.009 ) of 7-7 segment and the ratio of retromolar region ( p = 0.044 ) differed in genders. Setting 2 mm overjet, the upper basal bone arch was wider than the lower by approximate 2 mm on both sides, except the second molar and retromolar region. According to PCA, the variation of basal bone arches appeared mainly at terminal segments. Conclusions. For both male and female, the bimaxillary basal bone matched except terminal segments. Mismatch of female bimaxillary posterior basal bone was more pronounced than male. The basal bone arches of male were wider and longer than that of female.

Metagenomic Assembly Reveals the Fate of the Core Antibiotic Resistome, its Hosts and Mobility in Animal Manure and After Compost

Background Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal husbandry threaten human health worldwide; however, the core resistome, mobility of ARGs, and the composition of ARG hosts in animal manure and the following composts remain unclear. In the present study, metagenomic assembly was used to comprehensively decipher the core resistome and its potential mobility and hosts in animal manure and compost. Results In total, 201 ARGs were shared among different animal (layer, broiler, swine, beef cow, and dairy cow) manures and accounted for 86–99% of total relative abundance of ARGs, which mainly comprised multidrug, macrolide-lincosamide-streptogramin (M-L-S), tetracycline, beta-lactam, aminoglycoside, and sulfonamide resistance genes. Moreover, efficient composting reduced the total relative abundance of ARGs in manure from 0.938 to 0.405 copies per 16S rRNA gene; however, it did not have any remarkable effect on the multidrug, sulfonamide, and trimethoprim resistance genes. Procrustes analysis indicated that composting can reduce antibiotic residues and decrease the correlation between antibiotics and resistance genes. Furthermore, the ARG hosts included Proteobacteria (50.08%), Firmicutes (37.77%), Bacteroidetes (6.49%), and Actinobacteria (5.24%). In manure, aminoglycoside resistance genes were majorly found in Enterococcus, Streptococcus, and Enterobacter; tetracycline resistance genes (TRGs) were found in Pseudomonas, Lactobacillus, and Streptococcus; and multidrug resistance genes were mainly found in Escherichia coli. In our samples, ARGs were more prevalent in plasmids than in chromosomes. The broad host range and diverse mobile genetic elements may be two key factors for ARGs, such as sul1 and aadA, which could survive during composting. The multidrug resistance genes represented the dominant ARGs in pathogenic antibiotic-resistant bacteria (PARB) in manure, and composting could effectively control PARB. Conclusions Our experiments revealed the core resistome in animal manure, classified and relative quantified the ARG hosts, and assessed the mobility of ARGs. Composting can mitigate ARGs in animal manure by altering the bacterial hosts; however, some ARGs can escape from the removal with the survivor heat-tolerant hosts or transfer to these hosts. These findings will help optimize composting strategies for the effective treatment of ARGs and their hosts in farms.

Foliar Fungal Endophytes in a Tree Diversity Experiment Are Driven by the Identity but Not the Diversity of Tree Species

Symbiotic foliar fungal endophytes can have beneficial effects on host trees and might alleviate climate-induced stressors. Whether and how the community of foliar endophytes is dependent on the tree neighborhood is still under debate with contradicting results from different tree diversity experiments. Here, we present our finding regarding the effect of the tree neighborhood from the temperate, densely planted and 12-years-old Kreinitz tree diversity experiment. We used linear models, redundancy analysis, Procrustes analysis and Holm-corrected multiple t-tests to quantify the effects of the plot-level tree neighborhood on the diversity and composition of foliar fungal endophytes in Fagus sylvatica, Quercus petraea and Picea abies. Against our expectations, we did not find an effect of tree diversity on endophyte diversity. Endophyte composition, however, was driven by the identity of the host species. Thirteen endophytes where overabundant in tree species mixtures, which might indicate frequent spillover or positive interactions between foliar endophytes. The independence of the diversity of endophytes from the diversity of tree species might be attributed to the small plot size and the high density of tree individuals. However, the mechanistic causes for these cryptic relationships still remain to be uncovered.

Palatal vault morphometric analysis of the effects of two early orthodontic treatments in anterior open bite growing subjects: a controlled clinical study

Background The purpose of this study was to evaluate the palatal morphological changes in Anterior Open Bite (AOB) pre-pubertal subjects treated with Rapid Maxillary Expansion and Bite-Block (RME/BB) or Quad Helix with crib (QH/C) when compared with a Control Group (CG) by using Geometric Morphometric Analysis (GMM). Methods AOB group (AOBG) included 30 subjects (20 females, 10 males, mean age 8.1 ± 0.8ys) with dentoskeletal AOB. AOBG was divided in two subgroups according to the treatment strategy: RME/BB group (RME/BBg) included 15 subjects (10 females, 5 males, QH/C group (QH/Cg) comprised 15 subjects (10 females, 5 males). The two subgroups were compared with a CG of 15 subjects (10 females, 5 males) matched for sex, age, vertical pattern, and observation period. Digital upper dental casts were collected before treatment (T1) and at the end of the active treatment (T2). Landmarks and semilandmarks were digitized on dental casts and GMM was applied. Procrustes analysis and principal component analysis (PCA) were performed. Results At T2, RME/BBg when compared with QH/Cg evidenced no statistically significant differences. Instead, RME/BBg showed an increased maxillary transverse dimension and a decreased palatal depth when compared with CG. The comparison QH/Cg vs. CG demonstrated a slight transversal maxillary expansion. Conclusions RME/BBg showed significant changes in the transversal and vertical dimensions with a clear maxillary expansion and a decrease of the palatal depth when compared with QH/Cg and CG. QH/Cg showed a significant slight maxillary expansion and no variation in vertical and sagittal planes when compared with CG.

Using trait data improves correlation between environment and community data only if abundances are considered

A straightforward way to explore variation between communities is to calculate dissimilarity indices and relate them with environmental and spatial variables. Communities are most often represented by the (relative) abundances of taxa they comprise; however, more recently, the distribution of traits of organisms included in the communities has been shown more strongly related to ecosystem properties. In this study, we test whether taxon- or trait-based dissimilarity is correlated more tightly with environmental difference and geographical distance and how the abundance scale influences this correlation. Our study system is grassland vegetation in Hungary, where we sampled vegetation plots spanning a long productivity gradient from open dry grasslands to marshes in three sites. We considered three traits for vascular plants: canopy height, specific leaf area and seed mass. We obtained field estimates of normalized vegetation difference index (NDVI) as proxy of productivity (water availability) for each plot. We calculated between-community dissimilarities using a taxon-based and a trait-based index, using raw and square-root transformed abundances and presence/absence data. We fitted distance-based redundancy analysis models with NDVI difference and geographical distance on the dissimilarity matrices and evaluated them using variance partitioning. Then, using the pooled data, we calculated non-metric multidimensional scaling ordinations (NMDS) from all types of dissimilarity matrices and made pairwise comparisons using Procrustes analysis. Data analysis was done separately for the three sites.We found that taxonomical dissimilarity matches environmental and spatial variables better when presence/absence data is used instead of abundance. This pattern was mainly determined by the increasing variation explained by space at the presence/absence scale. In contrast to this trend, with trait-based dissimilarity, accounting for abundance increased explained variation significantly due to the higher explanatory power of NDVI. With abundance data, considering traits improved environmental matching to a great extent in comparison with taxonomical information. However, with presence/absence data, traits brought no advantage over taxon-based dissimilarity in any respect. Changing the abundance scale caused larger difference between ordinations in the case of trait-based dissimilarity than with taxonomical dissimilarity.We conclude that considering relevant traits improves environmental matching only if abundances are also accounted for.Supporting informationAdditional graphs supporting the results are presented as appendix.Open researchData used in this research are publicly available from Dryad ###link to be supplied upon acceptance###