Constrained Correspondence Analysis Research Articles

Large-scale seabird community structure along oceanographic gradients in the Scotia Sea and northern Antarctic Peninsula

IntroductionThe Scotia Sea and Antarctic Peninsula are warming rapidly and changes in species distribution are expected. In predicting habitat shifts and considering appropriate management strategies for marine predators, a community-level understanding of how these predators are distributed is desirable. Acquiring such data, particularly in remote areas, is often problematic given the cost associated with the operation of research vessels. Here we use cruise vessels as sampling platforms to explore seabird distribution relative to habitat characteristics.MethodsData on seabird at-sea distribution were collected using strip-transect counts throughout the Antarctic Peninsula and Scotia Sea in the austral summer of 2019-2020. Constrained correspondence analysis (CCA) and generalized additive models (GAM) were used to relate seabird community composition, density, and species richness to environmental covariates.ResultsSpecies assemblages differed between oceanographic areas, with sea surface temperature and distance to coast being the most important predictors of seabird distribution. Our results further revealed a geographic separation of distinct communities rather than hotspot regions in the study area in summer.DiscussionThese findings highlight the importance of large-scale environmental characteristics in shaping seabird community structure, presumably through underlying prey distribution and interspecific interactions. The present study contributes to the knowledge of seabird distribution and habitat use as well as the baseline for assessing the response of Antarctic seabird communities to climate warming. We argue that cruise vessels, when combined with structured research surveys, can provide a cost-effective additional tool for the monitoring of community and ecosystem level changes.

Ecological and structural differentiation of the Sudanian woodlands in the Biosphere Reserve of Pendjari, Benin

Aims: This study aims to: i) differentiate the plant associations in the Biosphere Reserve of Pendjari (BRP), ii) determine the ecological characteristics of their habitats and iii) present distribution maps on different soil types. Study area: The BRP, located in the Sudanian Zone of Benin. Methods: 202 phytosociological relevés were sampled according to the Braun-Blanquet method within the BRP. Ordination was performed using Detrended Correspondence Analysis to evaluate vegetation patterns. Soil parameters were used to characterize the vegetation types. Results: The numerical analysis of 202 plots and 249 plant species showed two major floristic groups that correlated with a moisture gradient: drylands versus wetlands. The dryland group was a mixture of woodland and shrub savanna, the dominant ecosystems of the study area. The wetland group encompassed species primarily from riparian forest, tree savanna and grass savanna on floodplains. Syntaxonomical analysis of the dryland group showed rocky and gravelly soil associations (Burkeo africanae-Detarietum microcarpi) and soils associated with or without fine gravels (Andropogono gayani-Terminalietum avicennioidis, Andropogono gayani-Senegalietum dudgeonii and Terminalietum leiocarpae). Syntaxonomical analysis of the wetland group showed riparian forest associations on sandy-clay soil (Coletum laurifoliae, Borassetum aethiopi and Hyparrhenio glabriusculae-Mitragynetum inermis) and floodplain associations on silt-clay soil (Terminalio macropterae-Mitragynetum inermis, Brachiario jubatae-Terminalietum macropterae, Sorghastro bipennati-Vachellietum hockii). Conclusions: Eleven new associations were identified in this study. If the distribution of plant associations was determined by different soil properties, the soil humidity would be one of the main ecological factors determining the establishment of plant species and thus plant association development. Taxonomic reference: Akoègninou et al. (2006), Angiosperm Phylogeny Group classification for the orders and families of flowering plants (APG IV, 2016). Abbreviations: BRP = Biosphere Reserve of Pendjari; CBD = Convention on Biological Diversity; CCA = Constrained Correspondence Analysis; DCA = Detrended Correspondence Analysis; GPS UTM = Global Positioning System Universal Transverse Mercator.

DOP66 Ileal resections from fibrotic-CD patients present microbiota dysbiosis, altered metabolomic profiles and metabolite-sensing GPCRs expression

Abstract Background Crohn’s Disease (CD) is a subtype of IBD characterized by a chronic transmural inflammation of the gastrointestinal tract associated with several complications being intestinal fibrosis the most frequent. CD patients present microbiota dysbiosis and altered metabolomic profiles. GPCRs constitute a family of receptors which could be involved in inflammatory and fibrotic processes associated to CD. We aim to characterize microbiota composition, tissue metabolomic profile and metabolite-sensing GPCRs expression in ileal resections from fibrotic CD patients. Methods Ileal resections from B2-CD (n=21) and non-IBD (n=13) patients were obtained. Microbiota characterization was performed by 16S rRNA gene Illumina Miseq sequencing. Bioinformatic analysis of sequencing data was performed using constrained correspondence analysis and non-parametric Wilcoxon test to compare species proportions. Bacterial load was estimated by qPCR. Metabolomic analysis was performed by NMR. Results are expressed as μg metabolite/g tissue. Murine intestinal fibrosis was induced in C67BL/6 mice by: a) the heterotopic intestinal transplant model and b) chronic administration of 4 cycles of increasing DSS percentages. Gene expression of GPCRs was analyzed by qPCR. Data were expressed as fold induction vs control (mean±SEM) and compared by a t-test. Correlations were analyzed with the Spearman coefficient. Results First, microbiota analysis revealed a reduction in bacterial diversity and load in fibrotic CD patients. Then, in B2-CD samples we found at genus level Enterococcus genera significantly decreased and at species level Ruminococcus bromii and Faecalibacterium prausnitzii also reduced compared to controls. From the metabolomic analysis, altered levels of metabolites were found in ileal resections from fibrotic CD patients as summarized in Table 1. Next, B2-CD patients exhibited differential expression of metabolite-sensing GPCRs vs non-IBD as shown in Table 2. Moreover, gene expression of fibrotic markers was analyzed in B2-CD patients and significantly increased levels of COL1A1 (13.22±4.38), COL3A1 (1.84±0.52), and COL4A1(7.75±2.19), were found vs controls. Of interest, GPR81, GPR84, GPR4 and GPR68 positively correlated with profibrotic markers, specifically with COL1A1 and COL4A1. Finally, in line with human results, we also analyzed the expression of metabolite-sensing GPCRs in two different murine colitis models and results obtained are represented in Table 3. Conclusion Fibrotic CD patients exhibit microbial dysbiosis, joined with altered levels of metabolites and gene expression of metabolite-sensing GPCRs, which are also affected in murine colitis models. Their correlation with profibrotic markers points them as protagonists of intestinal fibrosis.

Testing environmental effects on taxonomic composition with canonical correspondence analysis: alternative permutation tests are not equal

After applying canonical correspondence analysis to metagenomics data with hugely different library sizes (site totals) it became evident that Canoco and the R-packages ade4 and vegan can yield (at least up to 2022) very different P-values in statistical tests of the relationship between taxonomic composition (species composition) and predictors (environmental variables and/or treatments). The reason is that vegan and Canoco up to version 5.12 apply residualized response permutation (but ignore the model intercept), whereas ade4 applies predictor permutation. Predictor permutation, when extended to residualized predictor permutation, is applicable in partial constrained ordination. This paper shows by simulation that residualized response permutation can yield a very inflated Type I error rate, if the abundance data are both overdispersed and highly variable in site total. In contrast, residualized predictor permutation controlled the type I error rate and had good power, also when the predictors were skewed or binary. After square-root or log transformation of the abundance data, the differences between the permutation methods became small. Residualized predictor permutation is recommended, particularly in testing trait–environment relationships using double constrained correspondence analysis, because this method also critically depends on the species totals, which are generally highly variable. It is implemented in Canoco 5.15 and the R-code of this paper.

Hay meadows' overriding effect shapes ground beetle functional diversity in mountainous landscapes

AbstractMountain regions are hotspots of biodiversity, and are particularly sensitive to human activities and global changes. Characterizing biodiversity using trait‐based approaches may improve the understanding of the evolutionary and mechanistic basis of ecological patterns in species distribution. The investigation of trait–environment relationships, however, is challenging, especially when a hierarchical sampling design is used, as this may lead to misidentification of associations. Here, we investigate how functional traits in ground beetles (Coleoptera: Carabidae), a taxon often used as a bioindicator of climate and environmental changes, vary with environmental features in a mountainous landscape. The study was conducted in the Stelvio National Park (Central Italian Alps), collecting individuals with pitfall traps deployed within plots (small spatial scale), located along altitudinal transects (large spatial scale). To investigate the trait–environment association, we used double constrained correspondence analysis, which permits the selection of important traits and environmental variables while accounting for the hierarchical structure of the sampling design. The trait–environment association was largely one‐dimensional, with hay meadow acting as main environmental driver, negatively related to brachypterous wing‐form (indicator of poor dispersal ability) and, to a lesser extent, to specialized diet and (only for the large scale) body length. Secondarily, these traits were related negatively to soil pH and, for the larger spatial scale, positively to canopy cover and elevation. Double constrained correspondence analysis with specialized permutation schemes for statistical testing was effective and robust to analyze the data of the hierarchical sampling.

Plural valuation in space: mapping values of grasslands and their ecosystem services

ABSTRACT The agricultural management of grasslands not only is strongly linked to fodder production but also provides other valuable ecosystem services such as carbon sequestration, nutrient regulation, and recreation. Capturing the values that society places on such ecosystem services is a step to provide management recommendations. To elicit the societal value of grasslands and their ecosystem services, it is important to consider multiple dimensions, namely, instrumental, intrinsic, and relational values. We conducted surveys with citizens in 2018 and 2020 in two study areas in Bavaria, Germany: one grassland-dominated and one with mixed agricultural land use. In the surveys, the respondents were invited to map up to seven points in their respective regions where they perceived grasslands to be ‘especially valuable’. Also, the respondents could provide reasons for this selection. These verbatims were classified into instrumental, intrinsic, and several sub-types of relational values using Qualitative Content Analysis. Next, we conducted a hotspot analysis that revealed spatial hotspots and coldspots for each value type . Besides some overlaps, we found that hotspots of instrumental, intrinsic, and relational values varied in space. A Constrained Correspondence Analysis underlined the trade-offs between instrumentally valued grasslands that are perceived as suitable to supply provisioning services and intrinsically valued grasslands that are closely related to relational values such as care. The results show that grasslands and their ecosystem services are valued for a variety of reasons on different locations, and point out the need for further investigations of the spatial distribution of values associated with ecosystem services.

Emission Rates of Species-Specific Volatiles Vary across Communities of Clarkia Species: Evidence for Multimodal Character Displacement.

AbstractA current frontier of character displacement research is to determine whether displacement occurs via multiple phenotypic pathways and varies across communities with different species compositions. Here, we conducted the first test for context-dependent character displacement in multimodal floral signals by analyzing variation in floral scent in a system that exhibits character displacement in flower size and that has multiple types of sympatric communities. In a greenhouse common garden experiment, we measured quantitative variation in volatile emission rates of the progeny of two species of Clarkia from replicated parental communities that contain one, two, or four Clarkia species. The first two axes of a constrained correspondence analysis, which explained 24% of the total variation in floral scent, separated the species and community types. Of the 23 compounds that were significantly correlated with these axes, nine showed patterns consistent with character displacement. Two compounds produced primarily by C. unguiculata and two compounds produced primarily by C. cylindrica were emitted in higher amounts in sympatry. Character displacement in some volatiles varied across sympatric parental communities and occurred in parallel with displacement in flower size, demonstrating that this evolutionary process can be context dependent and may occur through multiple pathways.

P718 Characterization of microbiota and metabolomic profile in human colonic surgical resections of UC patients

Abstract Background Ulcerative colitis (UC) is characterized by a diffuse, continuous, and chronic inflammation of mucosa and submucosa layers in the colon whose etiology is still unknown. Intestinal microbiota dysbiosis and alterations in the metabolomic profile have been reported in mucosal biopsies from Inflammatory Bowel Disease (IBD) patients. We aim to characterize the microbiota composition and metabolomic profile in colonic resections of UC patients. Methods Colonic resections from UC (n=18) and non-IBD (n=20) patients were obtained. Microbiota identification, composition and classification was performed by 16S rRNA gene Illumina Miseq sequencing. The bioinformatic analysis of sequencing data was performed using constrained correspondence analysis (CCA) and non-parametric Wilcoxon test to compare species and genera proportions. Bacterial load was estimated by qPCR. Metabolomic analysis was performed using Nuclear Magnetic Resonance (NMR) to study polar metabolites and Gas-Chromatography or Liquid-Chromatography Mass-Spectrometry to study non-polar metabolites. Results Microbiota analysis revealed differences at genus and species level between UC and non-IBD patients. Cellulosimicrobium was found at 10-fold higher levels in UC samples while Escherichia genus was 3.88 times more abundant in controls. A reduction in bacterial load was seen in UC samples. Levels of short-chain fatty acids (FA), medium-chain FA, long-chain FA, carboxylic acids and amino acids were obtained from the metabolomics analysis and a positive correlation between propionic, aspartic and hydroxybutyric acids and Cellulosimicrobium and Pseudomonas was found (Fig1B). Gut commensals such as unclassified Agathobacter, Blautia faecis, Oscillospiraceae or Faecalibacterium prausnitzii positively correlated with the abundance of butyric acid, acetic acid and succinic acid; meanwhile Subdoligranulum, Lachnospireace or unclassified Blautia negatively correlated with some medium or long chain fatty acids (Fig1B). Fig1. Correlations between bacterial species and metabolites in (A) controls and (B) UC patients. Performed with mixOmics library in R. Conclusion Significant differences in microbiota composition and abundance are found in UC patients, which undergo a clear gut dysbiosis in colonic tissue. Correlation analysis suggests Cellulosimicrobium and Pseudomonas as sources of propionic, aspartic and hydroxybutyric acid. These results point at Cellulosimicrobium as a potential candidate in UC pathology.

Temporal Aspect of the Terrestrial Invertebrate Response to Moisture Dynamic in Technosols formed after Reclamation at a Post-Mining Site in Ukrainian Steppe Drylands

Abstract Different approaches were applied to assess soil moisture optima and tolerance of the ecological niche temporal projection of terrestrial invertebrates within an experimental polygon created to investigate the reclamation processes after deep underground hard-rock mining in the Ukrainian steppe drylands. Sampling was carried out in 2013–2015 on a variant of artificial soil (technosols). To investigate the spatiotemporal variation in the abundance, species richness and species composition of invertebrate assemblages the animals were sampled using pitfall traps. The readily available water for plants, precipitation, wind speed, atmospheric temperature, atmospheric humidity, and atmospheric pressure were used as environmental predictors. The two-dimension geographic coordinates of the sampling locations were used to generate a set of orthogonal eigenvector-based spatial variables. Time series of sampling dates were used to generate a set of orthogonal eigenvector-based temporal variables. Weighted averaging, generalized linear mixed models, Huisman-Olff-Fresco models expanded by Jansen-Oksanen, correspondence analysis, and constrained correspondence analysis were used to estimate soil moisture species optima and tolerance. The moisture content in the technosols was revealed to be the most important factor determining the temporal dynamics of terrestrial invertebrate community in conditions of semi-arid climate and the ecosystem which formed as a result of the reclamation process. The species response to the soil water content is affected not only by the soil water content but also by the complex of the other environmental, temporal, and spatial factors. The effect of other factors on the species response must be extracted previously to find real estimations of the species optima and tolerance.

Holobiont effect accounts for more methane emission variance than the additive and microbiome effects on dairy cattle

Rumen microbiota has been previously related to phenotypic complex traits of relevance in dairy cattle. The joint analysis of the host's genetic background and its microbiota can be statistically modelled using similarity matrices between microorganism communities in the different hosts. Microbiota relationship matrices (K) enable considering the whole microbiota and the cumbersome interrelations between taxa, rather than analyzing single taxa one at the time. Several methods have been proposed to ordinate these matrices. The aim of this study was to compare the performance of twelve K built from different microbiome distance metrics, within a variance component estimation framework for methane concentration in dairy cattle. Phenotypic, genomic and rumen microbiome information from simulations (n = 1000) and real data (cows = 437) were analyzed. Four models were considered: an additive genomic model (GBLUP), a microbiome model (MBLUP), a genetic and microbiome effects model (HBLUP) and a genetic, microbiome and genetic × microbiome interaction effects model (HiBLUP). Results from simulation were obtained from 25 replicates. Results from simulated data suggested that Ks with flattened off-diagonal elements were more accurate in variance components estimation for all compared models that included Ks information (MBLUP, HBLUP and HiBLUP). Multidimensional scaling (MDS), redundancy analysis (RDA) and constrained correspondence analysis (CCA) performed better in simulation to estimate heritability and microbiability. The models including Ks from the MDS, RDA and CCA methods were also between the most plausible models in the real data set, according to the deviance information criteria (DIC). Real data was analyzed under the same framework as in the simulation. The most plausible model in real data was HiBLUP. Estimates variated depending on K; methane heritability (0.15–0.17) and microbiability (0.15–0.21) were lower than the proportion of the phenotypic variance attributable to the host-microbiome holobiont effect (0.42–0.59), which we have defined here as “holobiability”. The holobiability including the genomic × microbiome interaction from the HiBLUP was between 0.01 and 0.15 larger than the holobiability explained from the sum of the genetic and microbiome effects without interaction between them, from the HBLUP, depending on K. The findings in this study support the potential of the joint analysis of genomic and microbiome information. Accounting for the hologenome effect (genomic and microbiome) could improve the accuracy in variance component estimation of complex traits relevant in livestock science.

The Small-Scale Variation of Herb-Layer Community Structure in a Riparian Mixed Forest

The role of spatial variables, soil properties and overstorey structure in spatial variation of the herb-layer community in a riparian mixed forest was shown. The research were conducted in the "Dnipro-Orils’kiy" Nature Reserve (Ukraine). The research polygon was laid in a forest in the floodplain of the River Protich, which is a left inflow of the River Dnipro. Plant abundance was quantified by measuring cover within experimental polygon. The experimental polygon consisted of 7 transects and each transect was made up of 15 test points. The distance between rows in the site was 3 m. At the site we established a plot of 45×21 m, with 105 subplots of 3×3 m organized in a regular grid. Vascular plant species lists were recorded for each 3×3 m subplot along with visual estimates of species cover projection. The plant community was represented by 43 species, of which 18.6% were phanerophytes, 39.5% were hemikriptophytes, 9.3% were therophytes, 7.0% were geophytes. An overall test of random labelling revealed the total nonrandom distribution of the tree stems within the site. Constrained correspondence analysis (CCA) was applied as ordination approach. The forward selection procedure allowed us to select 6 soil variables, which explain 28.3% of the herb-layer community variability. The list of the important soil variables includes soil mechanical impedance (at the depth 0–5, 30–35, 75–80, and 95–10 cm), soil moisture, and soil bulk density. The variation explained by pure spatial variables is equal to 11.0 %. The majority of the tree-distance structured variation in plant community composition was broad-scaled. The significant relationship was found between the pure spatial component of the community variation and a lot of phytoindicator estimations of which the variability of damping and humidity were of the greatest importance. Trees stand was demonstrated to be a considerable factor structuring both the herb-layer community and spatial variation of the physical properties of soil.

Diversity and composition of moss guilds on uprooted trees in Central European mountain forests: effects of uprooting components and environmental variables

Key messageThe size of the structural components of the root–pit–mound complex was crucial for high moss species richness. Root plates, pits, and mounds were similar in terms of moss species composition, which was mostly determined by forest type.ContextUprooted trees may be colonized by different terricolous mosses including common species and specialists.AimsThe main aim of the present study was to analyze the relative effects of tree uprooting on mosses.MethodsWe used the parametric ZIGLMM and GLMM models to explain the richness and abundance of the moss species and double constrained correspondence analysis (dc-CA) to analyze species composition.ResultsThe size of components of RPM complexes had a positive effect on moss species richness. The species cover of mosses was positively correlated with elevation. Species richness was partly dependent on forest type and species cover on component type and age of the RPM complex. The most important factor diversifying species composition was the type of forest. Species traits were also related to forest communities.ConclusionUprooted trees are worth keeping in forest community, especially large ones. Moreover, the conservation value of uprooted trees in woodlands is higher if they are dispersed in different forest types.

The Small-Scale Variation of Herb-Layer Community Structure in a Riparian Mixed Forest

The role of spatial variables, soil properties and overstorey structure in spatial variation of the herb-layer community in a riparian mixed forest was shown. The research were conducted in the "Dnipro-Orils’kiy" Nature Reserve (Ukraine). The research polygon was laid in a forest in the floodplain of the River Protich, which is a left inflow of the River Dnipro. Plant abundance was quantified by measuring cover within experimental polygon. The experimental polygon consisted of 7 transects and each transect was made up of 15 test points. The distance between rows in the site was 3 m. At the site we established a plot of 45×21 m, with 105 subplots of 3×3 m organized in a regular grid. Vascular plant species lists were recorded for each 3×3 m subplot along with visual estimates of species cover projection. The plant community was represented by 43 species, of which 18.6% were phanerophytes, 39.5% were hemikriptophytes, 9.3% were therophytes, 7.0% were geophytes. An overall test of random labelling revealed the total nonrandom distribution of the tree stems within the site. Constrained correspondence analysis (CCA) was applied as ordination approach. The forward selection procedure allowed us to select 6 soil variables, which explain 28.3% of the herb-layer community variability. The list of the important soil variables includes soil mechanical impedance (at the depth 0–5, 30–35, 75–80, and 95–10 cm), soil moisture, and soil bulk density. The variation explained by pure spatial variables is equal to 11.0 %. The majority of the tree-distance structured variation in plant community composition was broad-scaled. The significant relationship was found between the pure spatial component of the community variation and a lot of phytoindicator estimations of which the variability of damping and humidity were of the greatest importance. Trees stand was demonstrated to be a considerable factor structuring both the herb-layer community and spatial variation of the physical properties of soil.

Microbial community compositions and sulfate-reducing bacterial profiles in malodorous urban canal sediments.

Anthropogenically impacted urban canals represent distinct freshwater ecosystems that could shape microbial communities in underlying sediments; however, knowledge of the relationships between environmental factors and microbial community compositions and their functions in such an environment is limited. This study characterized the microbial community compositions of malodorous canal sediments at six locations along the Saen Saep Canal in Thailand. 16S rRNA gene amplicon sequencing (MiSeq, Illumina) revealed dominant genera classified as fermentative bacteria, methanogens, and sulfate-reducing bacteria (SRB), all of which emphasized anaerobic environments. SRB, as the primary producers of malodorous hydrogen sulfide, accounted for 8.2-30.4% of the total sequences. dsrB gene clone libraries further identified the SRB species. A constrained correspondence analysis demonstrated a spatial pattern of SRB that correlated with physicochemical parameters in which nitrate and sulfate in sediments were the most influencing factors. Overall, a better understanding of the SRB and other related microorganisms in canal sediments can assist in the future implementation of appropriate olfactory abatement and management methodologies in urban canals.

The response of invertebrate communities to a moisture gradient in artificial soils of Ukrainian steppe arid zone

Animals were sampled within the experimental area using traps to investigate the spatial and temporal variation in abundance, species richness, and species composition of invertebrate communities. A total of 60 traps were operated simultaneously during each sampling period. Traps were emptied 26 times every 7-9 days each year. Plant water availability, precipitation, wind speed, air temperature (minimum, maximum, daily mean), air humidity, and atmospheric pressure were used as ecological predictors of invertebrate community status and structure. Two-dimensional geographic coordinates of sampling locations were used to create a set of orthogonal spatial variables based on eigenvectors. We used time series of sampling dates to produce a set of orthogonal eigenvector time variables. The moisture content in technosols was the most important factor determining the terrestrial invertebrate community's temporal dynamics under semi-arid climate and reclaimed ecosystem conditions. Each ecological group of terrestrial invertebrates is homogeneous in terms of moisture gradient (xerophilic, xerozoophilic, mesophilic) and has a specific set of patterns best explain the species response to water content in technosols. However, one should consider the fact that the species response to soil water content is influenced not only by soil water content but also by a complex of other environmental, temporal and spatial factors. That is why the effect of other factors on the species response must be extracted previously to find real estimations of the species optima and tolerance. This task can be solved using the constrained correspondence analysis (CCA) or constrained redundancy analysis (RDA) depending on the type of response to ecological factors prevailing in the community – monotone or unimodal. We found that in more dry conditions, the prevalent species responses are unimodal asymmetric, in moister – bimodal, and in moderate conditions, the distributions are symmetric unimodal. The asymmetric species response to soil moisture in different parts of the soil humidity range may be assumed as predominantly due to the abiotic factors in the gradient's aridest margin and due predominantly to the biotic factors in the most humid margin of the gradient.

Functional Changes of the Community of Microbes With Ni-Dependent Enzyme Genes Accompany Adaptation of the Ruminal Microbiome to Urea-Supplemented Diets.

Urea is an inexpensive non-protein nitrogen source commonly supplemented to the diets of ruminants. It is cleaved to ammonia by bacterial ureases, which require Ni as a catalyst for ureolysis. The key event in the changes of the ruminal microbiome after urea supplementation remains unknown. We have therefore investigated changes in the ruminal microbiome and its community with Ni-dependent enzyme genes following urea supplementation and analyzed the associations of rumen environmental factors, including fermentation variables and Ni concentrations, with the compositional and functional changes of these communities. We found that urea supplementation increased urease activity and the concentrations of ammonia and Ni, and tended to increase concentrations of short chain fatty acids and acetate, whereas it decreased rumen pH and the L-/D-lactate ratio. With standards for genome completeness >60% and strain heterogeneity <10%, 20 bacterial species containing five Ni-dependent enzyme genes were detected in the metagenome sequences. For the five Ni-dependent enzyme genes, urea supplementation increased the relative abundances of genes of urease and acetyl-CoA synthase, whereas it decreased the relative abundances of genes of glyoxalase I, [NiFe]-hydrogenase, and lactate racemase. For the 20 microbes with Ni-dependent enzyme genes, urea supplementation increased the relative abundances of five bacteria exhibiting high capacities for the utilization of hemicellulose and pectin for butyrate and fatty acid biosynthesis. For the ruminal microbiome, urea supplementation increased the metagenomic capacities for hemicellulose and pectin degradation, butyrate generation, fatty acid biosynthesis, and carbon fixation, whereas it decreased the metagenomic capacities for starch degradation, propionate generation, and sulfur and nitrogen metabolism. Constrained correspondence analysis identified rumen ammonia and Ni concentrations as likely driving factors in the reshaping of the ruminal microbiome and, together with pH, of the community of microbes with Ni-dependent enzyme genes. Thus, the functional change of the latter community is probably an important event in the adaptation of the ruminal microbiome to urea-supplemented diets. This result provides a new perspective for the understanding of the effects of urea supplementation on rumen fermentation.

The small-scale variation of herb-layer community structure in a riparian mixed forest

The ground vegetation layer is the most diverse plant community in forest ecosystems. We have shown the role of spatial variables, soil properties and overstorey structure in spatial variation of the herb-layer community in a riparian mixed forest . The research was conducted in the "Dnipro-Orils’kiy" Nature Reserve (Ukraine). The research polygon was located in the forest in the floodplain of the River Protich, which is a left tributary of the River Dnipro. Plant abundance was quantified by measuring cover within an experimental polygon. The experimental polygon consisted of 7 transects, each comprising 15 test points. The distance between the rows in the site was 3 m. At the site we established a plot of 45 × 21 m, with 105 subplots of 3 × 3 m organized in a regular grid. A list of vascular plant species was composed for each 3 × 3 m subplot along with visual estimates of species cover projection. The plant community was represented by 43 species, of which 18.6% were phanerophytes, 39.5% were hemicryptophytes, 9.3% were therophytes, 7.0% were geophytes. An overall test of random labelling revealed the total nonrandom distribution of the tree stems within the site. The species-specific test of random labelling showed the nonrandom segregated distribution of Acer tataricum, Pyrus communis, Quercus robur, and Ulmus laevis. Crataegus monogyna and Euonymus europaeus were distributed randomly. The nearest neighbour of Acer tataricum was less likely to be Ulmus laevis. There was no direct spatial connection between Acer tataricum and other trees. Crataegus monogyna, Pyrus communis, Quercus robur and Euonymus europaeus were not segregated from all other species. The nearest neighbour of Ulmus laevis was less likely to be Acer tataricum. Constrained correspondence analysis (CCA) was applied as ordination approach. The forward selection procedure allowed us to select 6 soil variables which explain 28.3% of the herb-layer community variability. The list of the important soil variables includes soil mechanical impedance (at the depth 0–5, 30–35, 75–80, and 95–10 cm), soil moisture, and soil bulk density. The variation explained by pure spatial variables accounted for 11.0 %. The majority of the tree-distance structured variation in plant community composition was broad-scaled. The spatial scalograms were left-skewed asymmetric. Significant relationship was found between the pure spatial component of the community variation and a number of phytoindicator estimations, most important of which were the variability of damping and humidity. Tree stand was obseerved to be a considerable factor structuring both the herb-layer community and spatial variation of the physical properties of soil.

Double constrained ordination for assessing biological trait responses to multiple stressors: A case study with benthic macroinvertebrate communities

Benthic macroinvertebrate communities are used as indicators for anthropogenic stress in freshwater ecosystems. To better understand the relationship between anthropogenic stress and changes in macroinvertebrate community composition, it is important to understand how different stressors and species traits are associated, and how these associations influence variation in species occurrence and abundances. Here, we show the capacity of the multivariate technique of double constrained correspondence analysis (dc-CA) to analyse trait-environment relationships, and we compare it with the redundancy analysis method on community weighted mean values of traits (CWM-RDA), which is frequently used for this type of analysis. The analyses were based on available biomonitoring data for macroinvertebrate communities from the Danube River. Results from forward selection of traits and environmental variables using dc-CA analyses showed that aquatic stages, reproduction techniques, dispersal tactics, locomotion and substrate relations, altitude, longitudinal and transversal distribution, and substrate preferendum were significantly related to habitat characteristics, hydromorphological alterations and water quality measurements such as physico-chemical parameters, heavy metals, pesticides and pharmaceuticals. Environmental variables significantly associated with traits using the CWM-RDA method were generally consistent with those found in dc-CA analysis. However, the CWM-RDA does neither test nor explicitly select traits, while dc-CA tests and selects both traits and environmental variables. Moreover, the dc-CA analysis revealed that the set of environmental variables was much better in explaining the community data than the available trait set, a kind of information that can neither be obtained from CWM-RDA nor from RLQ (Environment, Link and Trait data), which is a close cousin of dc-CA but not regression-based. Our results suggest that trait-based analysis based on dc-CA may be useful to assess mechanistic links between multiple anthropogenic stressors and ecosystem health, but more data sets should be analysed in the same manner.

Livestock browsing affects the species composition and structure of cloud forest in the Dhofar Mountains of Oman

AbstractQuestionsIt is frequently reported that overstocking of camels, cattle and goats is degrading the Anogeissus cloud forest, which is endemic to a 200‐km stretch of coastal mountains in southern Arabia. However, livestock impacts on the vegetation have not been assessed. Furthermore, we have a limited understanding of the impacts of large‐bodied browsing livestock, such as camels, in woodland and forest rangelands. Therefore, in this study, we examine the effects of livestock browsing on the species composition, density, and phytomorphology of woody vegetation in the Anogeissus cloud forests in the Dhofar Mountains of Oman.LocationData were collected at 30 sites in the Jabal Qamar mountain range in western Dhofar, Oman.MethodsThe point‐centred quarter method was used to sample the composition, density and structure of woody vegetation. Constrained correspondence analysis was used to quantify the effects of livestock browsing on woody plant species composition, whilst effects on plant density were analysed using mixed‐effects models. Standardised major axis regression was used to examine differences in height–diameter allometry (stunting) under different stocking rates.ResultsFog density, topographic position and long‐term stocking rates were found to be important factors affecting woody species composition. We found lower species diversity and plant density, and higher frequencies of unpalatable species, under higher stocking rates. Juveniles showed a stronger response to stocking rates than adults, and several common species exhibited stunted morphology under high stocking rates.ConclusionsBrowsing by large‐bodied livestock, such as camels and cattle, can substantially alter the species composition, structure, and phytomorphology of woody vegetation in semi‐arid woodlands and forests. Juveniles are particularly susceptible to browsing which alters woody vegetation demography and inhibits regeneration potential. Our results support previous suggestions of overstocking in Dhofar and highlight the importance of swift measures to reduce livestock browsing pressure in the Anogeissus cloud forests.

Comparison of BG-Lure and BG-Sweetscents attractants for field sampling of phlebotomine sand flies

Phlebotomines are important vectors of bacteria, viruses and protozoan parasites. Protozoans of the genus Leishmania which cause visceral and cutaneous leishmaniases, are among the most important etiologic agents transmitted by sand flies. Different blends of human and animal volatiles have been evaluated for use in surveillance and/or control of hematophagous insects. With regard to phlebotomine sand flies there are few records of attraction under laboratory and field conditions. This study was carried out at two collecting sites located in a Brazilian town with a high prevalence of cutaneous leishmaniasis. The aim of the present study was to evaluate the effect of adding two kinds of commercial bait which mimic human odors to light traps to attract sand flies and compare the results with those of light traps without any additional bait. The commercial baits, BG-Lure® and BG-Sweetscent®, were developed to catch anthropophilic mosquitoes. Three treatments were evaluated: 1 - HP light trap with BG-Lure® added; 2 - HP light trap with BG-Sweetscent® added and 3- HP light trap without any attractant. A total of 3,682 sand flies were collected during the study. Constrained correspondence analysis was applied to perform ordination of the captured community of sand fly species that could be explained by attractant, sampling site and sex. The most abundant species: Pintomyia nevesi, Nyssomyia whitmani and Nyssomyia antunesi were further investigated by fitting generalized linear mixed models. Only Ny. whitmani showed a slight indication of an increase in catches with BG-Lure®.