scholarly journals The Role of Edaphic and Vegetation Factors in Structuring Beta Diversity of the Soil Macrofauna Community of the Dnipro River Arena Terrace

2018 ◽  
Vol 37 (4) ◽  
pp. 301-327 ◽  
Author(s):  
Olexander Zhukov ◽  
Olga Kunah ◽  
Yulia Dubinina ◽  
Victoria Novikova
Keyword(s):  
Environmental Factors ◽  
Principal Components ◽  
Beta Diversity ◽  
Sequential Analysis ◽  
Permutation Test ◽  
Ecological Factors ◽  
Principal Component ◽  
Alpha Diversity ◽  
Soil Macrofauna

AbstractThe article presents the results of evaluation of the role of edaphic and vegetation factors on beta diversity of soil macrofauna by means of the MDM-approach. The multinomial diversity model (MDM) is a method for relating the Shannon diversity to ecological factors. The research was conducted in the ‘Dnipro-Orils’kiy’ Nature Reserve (Ukraine). The research polygon was laid in the forest within the Orlova ravine (48º31’13 “N, 34º48”15 “E). The study site comprises 1.0 ha of deciduous woodland bordered by an area of herbaceous cover within the ravine. In the soil of the studied polygon, 38 species of soil invertebrates were identified, which characterizes the gamma diversity. Alpha diversity, or the number of species on average at each sample point is 4.3. Beta diversity is 8.8. The principal component analysis of the edaphic parameters revealed four statistically significant principal components. For vegetation characteristics, six statistically significant principal components were identified. The sequential analysis of the effects shows that edaphic factors accounted for 20.9% (0.81 bit) of the available entropy (1.71–0.91). The largest decrease in the community entropy takes place under the action of the principal components 2 and 3 (0.06 bit and 0.05, respectively). A permutation test showed that these effects are statistically significant. In turn, 28.4% of the community β-diversity is attributable to vegetation factors. The greatest decrease in community entropy is related to the principal vegetation components 1, 3 and 4 (0.07, 0.05 and 0.04 bits, respectively). A permutation test indicated that this effect is statistically reliable. Geostatistical models substantially describe the varying effects on the beta-diversity of edaphic principal components 1 and 2, and the vegetation principal components 1 and 3. It was found that edaphic and plant factors play an important role in structuring the communities of soil macrofauna on the level of beta diversity. Community sensitivity to environmental factors varies in space and is spatially structured. For different environmental factors, specific spatial patterns of community sensitivity are allocated. Beta diversity may be due to the fact that the species of soil macrofauna communities also vary in the degree of sensitivity to various environmental factors. The species of soil microfauna are also divided according to their extent of sensitivity to different ecological factors.

Evaluation functions for integral mapping

2017 ◽  
Vol 921 (3) ◽  
pp. 24-29 ◽  
Author(s):  
S.I. Lesnykh ◽  
A.K. Cherkashin
Keyword(s):  
Principal Component Analysis ◽  
Environmental Factors ◽  
Principal Components ◽  
Principal Component ◽  
Evaluation Function ◽  
Final Value ◽  
Evaluation Functions ◽  
Geographical Environment ◽  
Environmental Background ◽  
Integral Mapping

The proposed procedure of integral mapping is based on calculation of evaluation functions on the integral indicators (II) taking into account the feature of the local geographical environment, when geosystems in the same states in the different environs have various estimates. Calculation of II is realized with application of a Principal Component Analysis for processing of the forest database, allowing to consider in II the weight of each indicator (attribute). The final value of II is equal to a difference of the first (condition of geosystem) and the second (condition of environmental background) principal components. The evaluation functions are calculated on this value for various problems of integral mapping. The environmental factors of variability is excluded from final value of II, therefore there is an opportunity to find the invariant evaluation function and to determine coefficients of this function. Concepts and functions of the theory of reliability for making the evaluation maps of the hazard of functioning and stability of geosystems are used.

scholarly journals The lung microbiota in Korean patients with non-tuberculous mycobacterial pulmonary disease

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Sung-Yoon Kang ◽  
Hyojung Kim ◽  
Sungwon Jung ◽  
Sang Min Lee ◽  
Sang Pyo Lee
Keyword(s):  
Principal Component Analysis ◽  
Respiratory Tract ◽  
Pulmonary Disease ◽  
Beta Diversity ◽  
Lower Respiratory Tract ◽  
Principal Component ◽  
Control Group ◽  
Flexible Bronchoscope ◽  
Bronchial Washing

Abstract Background The microbiota of the lower respiratory tract in patients with non-tuberculous mycobacterial pulmonary disease (NTM-PD) has not been fully evaluated. We explored the role of the lung microbiota in NTM-PD by analyzing protected specimen brushing (PSB) and bronchial washing samples from patients with NTM-PD obtained using a flexible bronchoscope. Results Bronchial washing and PSB samples from the NTM-PD group tended to have fewer OTUs and lower Chao1 richness values compared with those from the control group. In both bronchial washing and PSB samples, beta diversity was significantly lower in the NTM-PD group than in the control group (P = 2.25E-6 and P = 4.13E-4, respectively). Principal component analysis showed that the PSBs and bronchial washings exhibited similar patterns within each group but differed between the two groups. The volcano plots indicated differences in several phyla and genera between the two groups. Conclusions The lower respiratory tract of patients with NTM-PD has a unique microbiota distribution that is low in richness/diversity.

scholarly journals Sensitivity and resistance of communities: Evaluation on the example of the influence of edaphic, vegetation and spatial factors on soil macrofauna

2017 ◽  
Vol 25 (4) ◽  
Author(s):  
O. V. Zhukov ◽  
O. M. Kunah ◽  
Y. Y. Dubinina
Keyword(s):  
Environmental Factors ◽  
Species Interactions ◽  
Community Response ◽  
Ecological System ◽  
Environmental Stability ◽  
Relative Role ◽  
Soil Macrofauna ◽  
Floodplain Soil ◽  
Main Components

Environmental stability is a multifaceted concept and includes properties such as asymptotic stability, robustness, persistence, variability, elasticity and resistance. Resistance reflects the ability of a community or population to remain in a substantially unaltered state under external influence. The reverse of resistance is sensitivity. This article suggests a way to assess the sensitivity of animal communities to factors of various character and explain sensitivity and resistance of the macrofauna community near the floodplain of the river Dnieper within the "Dnipro-Orelsky" Nature Reserve to the effects of edaphic and plant factors, as well as spatial variables. It is shown that the regulatory impact of environmental factors is refracted through the properties of ecological systems themselves, namely resistance and sensitivity. If an ecological system does not react to changing environmental factors, such a system is indifferent with respect to these factors. In the case of regulatory influence of factors, there may be resistance, sensitivity and the proportionality of the response of the ecological system. The ratio of the specific role of a factor in the variability of a community to the contribution of the main components of the total variability of the attributive space makes it possible to assess the resistance, sensitivity and proportionality of response the ecological system to the action of that factor. If the ratio is >1, then this indicates sensitivity: level of variability of a community is higher than the relative role of environmental factors in the changing of the attributive space. If <1, this indicates resistance: the level of variability of a community is lower than the relative role of environmental factors in the changing of the attributive space. If the ratio =1 (≈1), changes in the community are proportional to the level of the main components of variation in comparison with other components. Ecological factors (both external environmental and internal due to species interactions and which have a neutral nature) cause different levels of community response to their impact. These differences refracted through different aspects of stability of a community can be described using the categories resistance, sensitivity and proportionality. The proposed procedure for quantification of specified properties of sustainability has established that the floodplain soil macrofauna is endowed with resistance to factors that prevail on the level of its variation. However, macrofauna is highly sensitive to minor factors. The community of the soil inhabitants is sensitive to fine-scale variations, which have a neutral nature.

scholarly journals Earthworms, ants and other arthropods as soil health indicators in traditional and no-fire agro-ecosystems from Eastern Brazilian Amazonia

2010 ◽  
Vol 26 (2) ◽  
Author(s):  
Guillaume Xavier Rousseau ◽  
Paulo Rogério Dos Santos Silva ◽  
Cláudio José Reis de Carvalho
Keyword(s):  
Land Use Changes ◽  
Soil Health ◽  
Cropping System ◽  
Principal Component ◽  
Health Indicators ◽  
Secondary Forests ◽  
Soil Macrofauna ◽  
Soil Biodiversity ◽  
Lack Of Information

Deforestation of the Amazonian rainforest and conversion to agriculture with the use of fire creates a mosaic of occupied lands and secondary forests. Considering the fundamental role of soil macrofauna and the lack of information about its resilience to deforestation, this study characterized the earthworms, ants and other soil arthropod communities in secondary forests of 40 and 20 years of age and in cropping system and pastures prepared with slash-and-burn or chop-and-mulch in the Brazilian Eastern Amazonia. Soil macrofauna was sampled according to the TSBF (Tropical Soil Biological and Fertility) methodology. Four sub-indices and one “macrofauna soil health index” were calculated using five principal component analyses. The macrofauna index identified better soil health in chop-andmulch crops, followed by the 40 yr-old forest and the chop-and-mulch pasture. These results confirmed the fundamental role of old secondary forests for soil biodiversity conservation and the potential of the chop-and-mulch technique to mitigate the effects of land use changes.

scholarly journals In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1936 ◽  
Author(s):  
Georg Steinert ◽  
Michael W. Taylor ◽  
Peter Deines ◽  
Rachel L. Simister ◽  
Nicole J. de Voogd ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Local Area ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Deep Reef ◽  
Host Identity ◽  
Tropical Reef ◽  
Seawater Samples

Sponges (phylum Porifera) are important members of almost all aquatic ecosystems, and are renowned for hosting often dense and diverse microbial communities. While the specificity of the sponge microbiota seems to be closely related to host phylogeny, the environmental factors that could shape differences within local sponge-specific communities remain less understood. On tropical coral reefs, sponge habitats can span from shallow areas to deeper, mesophotic sites. These habitats differ in terms of environmental factors such as light, temperature, and food availability, as well as anthropogenic impact. In order to study the host specificity and potential influence of varying habitats on the sponge microbiota within a local area, four tropical reef sponges,Rhabdastrella globostellata,Callyspongiasp.,Rhaphoxyasp., andAcanthella cavernosa, were collected from exposed shallow reef slopes and a deep reef drop-off. Based on 16S rRNA gene pyrosequencing profiles, beta diversity analyses revealed that each sponge species possessed a specific microbiota that was significantly different to those of the other species and exhibited attributes that are characteristic of high- and/or low-microbial-abundance sponges. These findings emphasize the influence of host identity on the associated microbiota. Dominant sponge- and seawater-associated bacterial phyla were Chloroflexi, Cyanobacteria, and Proteobacteria. Comparison of individual sponge taxa and seawater samples between shallow and deep reef sites revealed no significant variation in alpha diversity estimates, while differences in microbial beta diversity (variation in community composition) were significant forCallyspongiasp. sponges and seawater samples. Overall, the sponge-associated microbiota is significantly shaped by host identity across all samples, while the effect of habitat differentiation seems to be less predominant in tropical reef sponges.

Principals about principal components in statistical genetics

2018 ◽  
Vol 20 (6) ◽  
pp. 2200-2216 ◽  
Author(s):  
Fentaw Abegaz ◽  
Kridsadakorn Chaichoompu ◽  
Emmanuelle Génin ◽  
David W Fardo ◽  
Inke R König ◽  
...  
Keyword(s):  
Principal Components ◽  
Rare Variants ◽  
Association Studies ◽  
Meta Analysis ◽  
Principal Component ◽  
Statistical Genetics ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Study Results

Abstract Principal components (PCs) are widely used in statistics and refer to a relatively small number of uncorrelated variables derived from an initial pool of variables, while explaining as much of the total variance as possible. Also in statistical genetics, principal component analysis (PCA) is a popular technique. To achieve optimal results, a thorough understanding about the different implementations of PCA is required and their impact on study results, compared to alternative approaches. In this review, we focus on the possibilities, limitations and role of PCs in ancestry prediction, genome-wide association studies, rare variants analyses, imputation strategies, meta-analysis and epistasis detection. We also describe several variations of classic PCA that deserve increased attention in statistical genetics applications.

scholarly journals The role of edaphic, vegetational and spatial factors in structuring soil animal communities in a floodplain forest of the Dnipro river

2018 ◽  
Vol 45 (1) ◽  
pp. 8-23 ◽  
Author(s):  
Oleksandr V. Zhukov ◽  
Olga M. Kunah ◽  
Yuliya Y. Dubinina ◽  
Viktoriya O. Novikova
Keyword(s):  
Spatial Patterns ◽  
Principal Component ◽  
Fine Scale ◽  
Spatial Effects ◽  
Edaphic Factors ◽  
Soil Macrofauna ◽  
Medium Scale ◽  
Principal Coordinates ◽  
Broad Scale

Abstract This paper examines the role of ecological factors, derived from principal component analysis performed on edaphic and vegetational dataset as well as spatial variables, in structuring the soil macrofauna community of the Dnipro floodplain within the ‘Dnipro-Orilsky’ Nature Reserve (Ukraine). The soil macrofauna was defined as invertebrates visible to the naked eye (macroscopic organisms). The test points formed a regular grid with a mesh size of 3 m with 7 × 15 dimensions. Thus, the total test point number was 105. At each point, soil-zoological samples of 0.25 × 0.25 m were taken for quantifying the soil macrofauna. The spatial structure was modeled by a set of independent spatial patterns obtained by means of principal coordinates of neighbor matrices analysis (PCNM-variables). Spatial PCNM-variables explain significantly more variations of the community (19.9%) than edaphic factors (4.1%) and vegetation factors (3.2%). Spatial and combined environmental and spatial effects were divided into three components: broad-scale component was characterized by periodicity of spatial variation with a wavelength of 24.0–44.5 m, medium-scale – 11.1–20 m, fine-scale – 6.6–11.0 m. For a broad-scale component, environmental factors of a vegetational nature are more important, for medium-scale, edaphic factors are more important, for fine-scale, both vegetation and edaphic are important. For litter-dwelling animals, the most characteristic spatial patterns are on the broad and medium-scale levels. For endogeic and anecic animals, the most significant variability is on the fine-scale level.

scholarly journals Diversity of Ostrya carpinifolia Forests in Ravine Habitats of Serbia (S-E Europe)

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 59
Author(s):  
Dimitrije Sekulić ◽  
Branko Karadžić ◽  
Nevena Kuzmanović ◽  
Snežana Jarić ◽  
Miroslava Mitrović ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Endemic Species ◽  
Beta Diversity ◽  
Environmental Gradients ◽  
Species Turnover ◽  
Alpha Diversity ◽  
Moisture Gradient ◽  
Ostrya Carpinifolia ◽  
Quaternary Glaciations ◽  
High Diversity

We investigated vegetation in ravine habitats of Serbia, in order to classify hop hornbeam (Ostrya carpinifolia Scop.) forests in syntaxonomic terms, assess the effects of environmental factors on their floristic differentiation, and detect the biodiversity components of the analyzed communities. Both K-means clustering and Bayesian classification revealed five ecologically interpretable groups of forests that belong to the alliances Ostryo carpinifoliae-Fagion sylvaticae, Ostryo carpinifoliae-Tilion platyphylli, Fraxino orni-Ostryion carpinifoliae, Pseudofumario albae-Ostryion carpinifoliae, and Achilleo ageratifoliae-Ostryion carpinifoliae. Canonical correspondence analysis indicated that these alliances are clearly differentiated along a combined light–moisture gradient (from shade and mesic to sunny and xeric variants). The alpha diversity increases from xeric to mesic alliances. A lower alpha diversity in xeric forests may be explained by the stress conditions that prevent mesic species from colonizing the saxatile habitats. Extremely high—almost the greatest possible—values of both the species turnover and beta diversity were detected in all variants of the analyzed forests. Such high diversity may be the result of the strong environmental gradients in ravine habitats. The investigated forests represent an important pool of rare, paleo-endemic species that survived Quaternary glaciations in ravine refugia.

scholarly journals Gut microbiome transition across a lifestyle gradient in Himalaya

2018 ◽  
Author(s):  
Aashish R Jha ◽  
Emily R Davenport ◽  
Yoshina Gautam ◽  
Dinesh Bhandari ◽  
Sarmila Tandukar ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Water Source ◽  
Drinking Water Source ◽  
Human Gut ◽  
Bacterial Composition ◽  
Microbiome Composition ◽  
The World

The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles. However, it has been difficult to separate the contributions of human genetic and geographic factors from lifestyle/modernization. Here, we characterize the stool bacterial composition of four Himalayan populations to investigate how the gut community changes in response to shifts in human lifestyles. These groups led seminomadic hunting-gathering lifestyles until transitioning to varying dependence upon farming. The Tharu began farming 250-300 years ago, the Raute and Raji transitioned 30-40 years ago, and the Chepang retain many aspects of a foraging lifestyle. We assess the contributions of dietary and environmental factors on their gut microbiota and find that the gut microbiome composition is significantly associated with lifestyle. The Chepang foragers harbor elevated abundance of taxa associated with foragers around the world. Conversely, the gut microbiomes of populations that have transitioned to farming are more similar to those of Americans, with agricultural dependence and several associated lifestyle and environmental factors correlating with the extent of microbiome divergence from the foraging population. For example, our results show that drinking water source and solid cooking fuel are significantly associated with the gut microbiome. Despite the pronounced differences in gut bacterial composition across populations, we found little differences in alpha diversity across populations. These findings in genetically similar populations living in the same geographical region establish the key role of lifestyle in determining human gut microbiome composition and point to the next challenging steps of isolating dietary effects from other factors that change during modernization.

Urea uptake and urease activity in the Chesapeake Bay

2019 ◽  
Vol 77 (2) ◽  
pp. 139-168 ◽  
Author(s):  
Caroline M. Solomon
Keyword(s):  
Environmental Factors ◽  
Chesapeake Bay ◽  
Metabolic Pathways ◽  
Urease Activity ◽  
Principal Component ◽  
Culture Studies ◽  
Urea Uptake ◽  
The Relationship ◽  
Planktonic Communities

The importance of urea in supplying the nitrogen (N) required by planktonic communities has long been recognized, notably by James J. McCarthy in studies as early as the 1970s. Utilization of urea involves a two-step enzymatic process in phytoplankton, with urea first entering the cell via transport (i.e., urea uptake), followed by the conversion of urea into ammonium by the enzyme urease. This article describes a series of field observations and experiments conducted in the Chesapeake Bay, USA, from 2001 through 2018, aimed at understanding the relationship between urea uptake and urease activity and the role of environmental factors on that relationship. Principal component analysis revealed a few patterns. Urea uptake, for example, was consistently positively related to combined variables that included urea concentrations. Similarly, urease activity was consistently positively related to combined variables that included temperature. Contrary to findings in culture studies, however, relationships with environmental factors within different phytoplankton taxa in the field were not clear. This suggests that factors other than those examined may be involved in the regulation of urea uptake and urease activity. New insights into the role of the urea cycle in phytoplankton nitrogen dynamics suggest that the regulation of urease may not be directly impacted by environmental factors, but indirectly regulated by different metabolic pathways responding to nutrient availability, light, and temperature conditions.

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