scholarly journals A Family of Interaction-Adjusted Indices of Community Similarity

2016 ◽  
Author(s):  
Thomas Sebastian Benedikt Schmidt ◽  
Joao Frederico Matias Rodrigues ◽  
Christian von Mering
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Biological Significance ◽  
Interaction Networks ◽  
Ecological Community ◽  
Community Similarity ◽  
Structure And Dynamics ◽  
Ecological Association ◽  
Plankton Diversity ◽  
Traditional Approaches

Interactions between taxa are essential drivers of ecological community structure and dynamics, but they are not taken into account by traditional indices of diversity. In this study, we propose a novel family of indices that quantify community similarity in the context of taxa interaction networks. Using publicly available datasets, we assess the performance of two specific indices which are Taxa INteraction-Adjusted (TINA, based on taxa co-occurrence networks), and Phylogenetic INteraction-Adjusted (PINA, based on phylogenetic similarities). TINA and PINA outperformed traditional indices when partitioning human-associated microbial communities according to habitat, even for extremely downsampled datasets, and when organising ocean micro-eukaryotic plankton diversity according to geographical and physicochemical gradients. We argue that interaction-adjusted indices capture novel aspects of diversity outside the scope of traditional approaches, highlighting the biological significance of ecological association networks in the interpretation of community similarity.

Microbial community structure and dynamics in restored subtropical seagrass sediments

2015 ◽  
Vol 74 (1) ◽  
pp. 43-57 ◽  
Author(s):  
AS Bourque ◽  
R Vega-Thurber ◽  
JW Fourqurean
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Structure And Dynamics

Levels of Spatial Variability: The “Community” Problem

1990 ◽  
Vol 5 ◽  
pp. 13-30 ◽  
Author(s):  
D. A. Springer ◽  
A. I. Miller
Keyword(s):  
Community Structure ◽  
Spatial Variability ◽  
Species Distribution ◽  
Distribution Patterns ◽  
The Past ◽  
Structure And Dynamics ◽  
Evolutionary Units ◽  
The Way

The way we view species distribution patterns, particularly at the level commonly referred to as the “community”, has changed over the past 70 years in biology and, subsequently, in paleontology. Because the degree to which species associations can be interpreted as ecological and evolutionary units depends ultimately on recognition and interpretation of faunal spatial variability, we need to understand the nature of this variability at all levels of resolution before we can adequately address questions of “community” structure and dynamics. While it is possible to recognize spatial variability at several levels, from the distributions of individuals within a species to the overall pattern created by the global biota, we must ask whether these patterns really comprise a hierarchy with natural discontinuities (Fig. 1), or whether it is more realistic to view them as a continuous variability spectrum.

A null model to study community structure of microcrustacean assemblages in north Patagonian urban wetlands (39-41°S, Chile)

Crustaceana ◽  
2014 ◽  
Vol 87 (11-12) ◽  
pp. 1377-1385
Author(s):  
Patricio De los Ríos-Escalante ◽  
Andrés Muñoz-Pedreros ◽  
Patricia Möller
Keyword(s):  
Community Structure ◽  
Trophic Status ◽  
Null Model ◽  
Model Analysis ◽  
Jaccard Index ◽  
Field Observations ◽  
Urban Wetlands ◽  
Community Similarity ◽  
Chilean Patagonia ◽  
Inland Water Bodies

The inland water bodies of northern Chilean Patagonia (38-41°S) have many lakes, wetlands and ponds with different littoral and zooplanktonic crustacean assemblages. This study presents field observations of species associations sampled from shallow wetlands located in the urban zones of Valdivia (39°S) and Puerto Montt (41°S). A species presence-absence matrix was created for calculating the Jaccard Index of community similarity and for testing null models of species associations, with the aim of determining whether species associations are random or not. The results of the Jaccard Index calculations indicated the existence of non-defined groups. The results of the null model analysis denoted the presence of regulating factors for Valdivia wetlands, whereas for Puerto Montt wetlands no such factors could be demonstrated. The outcomes of both the Jaccard Index and the significant null model analysis agree with previous ecological descriptions of changes in trophic status as a consequence of changes in the surrounding basin as a determinant of species associations. The ecology of these communities is also discussed.

scholarly journals Microbiome Interaction Networks and Community Structure From Laboratory-Reared and Field-Collected Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus Mosquito Vectors

2018 ◽  
Vol 9 ◽  
Author(s):  
Shivanand Hegde ◽  
Kamil Khanipov ◽  
Levent Albayrak ◽  
George Golovko ◽  
Maria Pimenova ◽  
...  
Keyword(s):  
Community Structure ◽  
Aedes Aegypti ◽  
Aedes Albopictus ◽  
Culex Quinquefasciatus ◽  
Interaction Networks ◽  
Mosquito Vectors

Phylum-Specific Primer Design and Implication in Quantification of the Microbial Community Structure in GuJingGong Pit Mud

2014 ◽  
Vol 1051 ◽  
pp. 311-316 ◽  
Author(s):  
Xi Mei Luo ◽  
Zhi Lei Gao ◽  
Hui Min Zhang ◽  
An Jun Li ◽  
Hong Kui He ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Real Time Quantitative Pcr ◽  
Sequencing Technologies ◽  
Specific Pcr ◽  
Pit Mud ◽  
Almost All ◽  
Polymerase Chain Reaction Primers

In recent years, despite the significant improvement of sequencing technologies such as the pyrosequencing, rapid evaluation of microbial community structures remains very difficult because of the abundance and complexity of organisms in almost all natural microbial communities. In this paper, a group of phylum-specific primers were elaborately designed based on a single nucleotide discrimination technology to quantify the main microbial community structure from GuJingGong pit mud samples using the real-time quantitative PCR (qPCR). Specific PCR (polymerase chain reaction) primers targeting a particular group would provide promising sensitivity and more in-depth assessment of microbial communities.

scholarly journals An equation-free method reveals the ecological interaction networks within complex microbial ecosystems

2016 ◽  
Author(s):  
Kenta Suzuki ◽  
Katsuhiko Yoshida ◽  
Yumiko Nakanishi ◽  
Shinji Fukuda
Keyword(s):  
Time Series ◽  
Microbial Communities ◽  
Microbial Processes ◽  
Interaction Networks ◽  
List Type ◽  
Metagenomic Sequencing ◽  
Ecological Interactions ◽  
Microbial Interaction ◽  
Ecological Interaction ◽  
Dataset Size

AbstractMapping the network of ecological interactions is key to understanding the composition, stability, function and dynamics of microbial communities. In recent years various approaches have been used to reveal microbial interaction networks from metagenomic sequencing data, such as time-series analysis, machine learning and statistical techniques. Despite these efforts it is still not possible to capture details of the ecological interactions behind complex microbial dynamics.We developed the sparse S-map method (SSM), which generates a sparse interaction network from a multivariate ecological time-series without presuming any mathematical formulation for the underlying microbial processes. The advantage of the SSM over alternative methodologies is that it fully utilizes the observed data using a framework of empirical dynamic modelling. This makes the SSM robust to non-equilibrium dynamics and underlying complexity (nonlinearity) in microbial processes.We showed that an increase in dataset size or a decrease in observational error improved the accuracy of SSM whereas, the accuracy of a comparative equation-based method was almost unchanged for both cases and equivalent to the SSM at best. Hence, the SSM outperformed a comparative equation-based method when datasets were large and the magnitude of observational errors were small. The results were robust to the magnitude of process noise and the functional forms of inter-specific interactions that we tested. We applied the method to a microbiome data of six mice and found that there were different microbial interaction regimes between young to middle age (4-40 week-old) and middle to old age (36-72 week-old) mice.The complexity of microbial relationships impedes detailed equation-based modeling. Our method provides a powerful alternative framework to infer ecological interaction networks of microbial communities in various environments and will be improved by further developments in metagenomics sequencing technologies leading to increased dataset size and improved accuracy and precision.

scholarly journals High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

2020 ◽  
Author(s):  
Wu Qu ◽  
Boliang Gao ◽  
Jie Wu ◽  
Min Jin ◽  
Jianxin Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Fungal Community ◽  
Amplicon Sequencing ◽  
Biotic Factors ◽  
Community Structures ◽  
Mangrove Sediments ◽  
Element Cycling ◽  
Microbial Community Structures

Abstract Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

scholarly journals Assessment of Effect of Hydropower Plant Projects on Socio-Environmental Sustenance and Development in Rwanda: A Review Done At Rubagabaga Hydropower Ltd.

2022 ◽  
Vol 10 (01) ◽  
pp. 2888-2904
Author(s):  
Dr. MUTESI Jean Claude
Keyword(s):  
Community Structure ◽  
Null Hypothesis ◽  
Quantitative Research ◽  
Target Population ◽  
Positive Influence ◽  
Hydropower Plant ◽  
P Value ◽  
Structure And Dynamics ◽  
Hydropower Plants ◽  
The Impact

The study investigated the socio-economic and environmental impact of hydropower projects in Rwanda with a case study of Rubagabaga hydropower Ltd operating from Nyabihu District. It examines the impact of a socio-economic and environmental hydropower plant in Rwanda, identifies the challenge hydropower plants face in Rwanda, and finally investigates the relationship between hydro powers and their socio-economic impact in Rwanda? In this research, the quantitative research design is based on statistical data of the research that was used with quantitative and qualitative methods. Questionnaires were used to collect data. The target population of this study was made up of 252 participants including 154 respondents all from ten different villages surrounding the Rubagabaga plant in Nyabihu District. Data were analyzed using descriptive and correlation analysis and tables that were interpreted to confirm or deny the relevance of the main and specific objectives. Based on results from table no.16 demonstrates that the beta= 0.397 with the t value of 2.333 and the p-value of 0. 021. Since the p-value is less than 0.05, the researcher rejected the null hypothesis and considered it an alternate. There is a strong positive relationship between environmental assessment of hydropower plant projects and socio-environmental sustenance and development. In a nutshell, the researcher has rejected the null hypothesis and considered its alternate. Community structure and dynamics have a positive influence on socio-environmental sustenance and development. Table no.16 shows that beta= 0.341 with the t value of 2.668 as the p-value was 0.009. Since the p-value is less than 0.05. Therefore, the researcher rejected the null hypothesis and considered it an alternate. According to table no.21, the changes in community structure and dynamics of the hydropower plant project cause the increase of 0.341 (34.1%) of the socio-environment sustenance and development. The ratio of beta modal results for the t value expressed t=2.66 hence the probability value is significant on socio-environment sustenance and development noting that sig. =0.009. Carefully, the researcher has rejected the null hypothesis and considered its alternate. With this in mind, community structure and dynamics has a positive influence on socio-environmental sustenance and development. Table no.16 has shown beta= 0.478 with the t value of 4.543 as the p-value was 0.000 which is less than 0.05. According to the findings, the changes in government policies, stability, and support of hydropower plant project causes the increase of 0.478 (47.80%) of the socio-environment sustenance and development. The ratio of beta modal results for the t value expressed t= 4.54 hence the probability value is significant on socio-environment sustenance and development noting that sig. =0.000.

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