scholarly journals Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome Functionality

2021 ◽  
Vol 9 (2) ◽  
pp. 381
Author(s):  
Robert Starke ◽  
Maysa Lima Parente Fernandes ◽  
Daniel Kumazawa Morais ◽  
Iñaki Odriozola ◽  
Petr Baldrian ◽  
...  
Keyword(s):  
Species Richness ◽  
Functional Diversity ◽  
Meta Analysis ◽  
Parametric Bootstrap ◽  
Saturated Model ◽  
Logarithmic Model ◽  
Bootstrap Estimate ◽  
Level 3 ◽  
Bacteria And Fungi ◽  
The Relationship

Revealing the relationship between taxonomy and function in microbiomes is critical to discover their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi is known, this is not the case for archaea. Here, we used a meta-analysis of 417 completely annotated extant and taxonomically unique archaeal genomes to predict the extent of microbiome functionality on Earth contained within archaeal genomes using accumulation curves of all known level 3 functions of KEGG Orthology. We found that intergenome redundancy as functions present in multiple genomes was inversely related to intragenome redundancy as multiple copies of a gene in one genome, implying the tradeoff between additional copies of functionally important genes or a higher number of different genes. A logarithmic model described the relationship between functional diversity and species richness better than both the unsaturated and the saturated model, which suggests a limited total number of archaeal functions in contrast to the sheer unlimited potential of bacteria and fungi. Using the global archaeal species richness estimate of 13,159, the logarithmic model predicted 4164.1 ± 2.9 KEGG level 3 functions. The non-parametric bootstrap estimate yielded a lower bound of 2994 ± 57 KEGG level 3 functions. Our approach not only highlighted similarities in functional redundancy but also the difference in functional potential of archaea compared to other domains of life.

scholarly journals Explorative meta-analysis of 417 extant archaeal genomes to predict their contribution to the total microbiome functionality

2020 ◽  
Author(s):  
Robert Starke ◽  
Maysa Lima Parente Fernandes ◽  
Daniel Kumazawa Morais ◽  
Iñaki Odriozola ◽  
Nico Jehmlich ◽  
...  
Keyword(s):  
Species Richness ◽  
Functional Diversity ◽  
Meta Analysis ◽  
Saturated Model ◽  
Logarithmic Model ◽  
Archaeal Species ◽  
Bootstrap Estimate ◽  
Level 3 ◽  
Bacteria And Fungi ◽  
The Relationship

AbstractUnveiling the relationship between taxonomy and function in microbiomes is crucial to determine their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi was reported, this is not the case for archaea. Here, we used a meta-analysis of completely annotated extant genomes of 417 taxonomically unique archaeal species to describe intergenome and intragenome redundancy of functions and to predict the extent of microbiome functionality on Earth contained within archaeal genomes using accumulation curves of all known functions from the level 3 of KEGG Orthology. We found that intergenome redundancy as functions present in multiple genomes was inversely related to intragenome redundancy as multiple copies of a gene in one genome, implying the trade of between additional copies of functionally important genes or a higher number of different genes. A logarithmic model described the relationship between functional diversity and species richness better than both the unsaturated and the saturated model, which suggests a limited total number of archaeal functions in contrast to the potential of bacteria and fungi. Using a global archaeal species richness estimate of 13,159, the logarithmic model predicts a total of 4,164.1 ±2.9 KEGG level 3 functions while the non-parametric bootstrap estimate yields a lower bound of 2,994 ±57 KEGG level 3 functions. Our approach not only highlights similarities in functional redundancy but also the difference in functional potential of archaea compared to other domains of life.

scholarly journals Assessing above-ground biomass-functional diversity relationships in temperate forests in northern Mexico

2020 ◽  
Author(s):  
Benedicto Vargas-Larreta ◽  
Jorge Omar Lopez Martinez ◽  
Edgar J. González ◽  
Jose Javier Corral-Rivas ◽  
Francisco Javier Hernández
Keyword(s):  
Species Richness ◽  
Functional Diversity ◽  
Taxonomic Diversity ◽  
Maximum Height ◽  
Above Ground Biomass ◽  
Northern Mexico ◽  
Ground Biomass ◽  
Sierra Madre ◽  
Community Weighted Mean ◽  
The Relationship

Abstract Background: Studies on the relationship between biodiversity and ecosystem productivity have suggested that species richness and functional diversity are the main drivers of ecosystem processes. Several patterns on this relationship have been found, including positive, unimodal, negative, and neutral trends, keeping the issue controversial. In this study, taxonomic diversity and functional diversity as drivers of above-ground biomass (AGB) were comparated, and the mechanisms that influence biomass production were investigated by testing the complementarity and the mass-ratio hypotheses.Methods: Using data from 414 permanent sample plots, covering 23% of temperate forest in the Sierra Madre Oriental (México). We estimated the above-gound biomass (AGB), taxonomic and functional diversity indices, as well as community weighted mean values (CWM) for three functional trais (maximum height, leaf size and wood density) for trees ≥7.5 cm d.b.h., in managed and unmanaged stands. To compare taxonomic diversity differences between managed and unmanaged stands we carried out a rarefaction analysis. Furthermore, we evaluated the relationship between AGB and taxonomic and functional diversity metrics, as well as CWM traits throught spatial autoregressive models.Results: We found a hump-shaped relationship between AGB and species richness in managed and unmanaged forests. CMW of maximum height was the most important predictor of AGB in both stands, which suggested that the mechanism underlaying the AGB-diversity relationship is the dominance of some highly productive species, supporting the mass-ratio hypothesis. Above-ground biomass was significantly correlated with three of the five functional diversity metrics, CWM maximum height and species richness. Our results show the importance of take into account spatial autocorrelation in the construction of predictive models to avoid spurious patterns in the AGB-diversity relationship.Conclusion: Species richness, maximum height, functional richness, functional dispersion and RaoQ indices relate with above-ground biomass production in temperate mixed-species and uneven-aged forests of northern Mexico. These forests show a hump-shaped AGB-species richness relationship. Functional diversity explains better AGB production than classical taxonomic diversity. Community weighted mean traits provide key information to explain stand biomass in these forests, where maximum tree height seems to be a more suitable trait for understanding the biomass accumulation process in these ecosystems. Although the impact of forest management on biodiversity is still debated, it has not changed the AGB-diversity relationships in the forests of the Sierra Madre Occidental, Mexico.

scholarly journals Assessing above-ground biomass-functional diversity relationships in temperate forests in northern Mexico

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Benedicto Vargas-Larreta ◽  
Jorge Omar López-Martínez ◽  
Edgar J. González ◽  
José Javier Corral-Rivas ◽  
Francisco Javier Hernández
Keyword(s):  
Species Richness ◽  
Functional Diversity ◽  
Taxonomic Diversity ◽  
Maximum Height ◽  
Above Ground Biomass ◽  
Northern Mexico ◽  
Ground Biomass ◽  
Sierra Madre ◽  
Community Weighted Mean ◽  
The Relationship

Abstract Background Studies on the relationship between biodiversity and ecosystem productivity have suggested that species richness and functional diversity are the main drivers of ecosystem processes. Several patterns on this relationship have been found, including positive, unimodal, negative, and neutral trends, keeping the issue controversial. In this study, taxonomic diversity and functional diversity as drivers of above-ground biomass (AGB) were compared, and the mechanisms that influence biomass production were investigated by testing the complementarity and the mass-ratio hypotheses. Methods Using data from 414 permanent sample plots, covering 23% of temperate forest in the Sierra Madre Oriental (México), we estimated the above-gound biomass (AGB), taxonomic and functional diversity indices, as well as community weighted mean values (CWM) for three functional traits (maximum height, leaf size and wood density) for trees ≥7.5 cm DBH, in managed and unmanaged stands. To compare taxonomic diversity differences between managed and unmanaged stands we carried out a rarefaction analysis. Furthermore, we evaluated the relationship between AGB and taxonomic and functional diversity metrics, as well as CWM traits throught spatial autoregressive models. Results We found a hump-shaped relationship between AGB and species richness in managed and unmanaged forests. CMW of maximum height was the most important predictor of AGB in both stands, which suggested that the mechanism underlaying the AGB-diversity relationship is the dominance of some highly productive species, supporting the mass-ratio hypothesis. Above-ground biomass was significantly correlated with three of the five functional diversity metrics, CWM maximum height and species richness. Our results show the importance of taking into account spatial autocorrelation in the construction of predictive models to avoid spurious patterns in the AGB-diversity relationship. Conclusion Species richness, maximum height, functional richness, functional dispersion and RaoQ indices relate with above-ground biomass production in temperate mixed-species and uneven-aged forests of northern Mexico. These forests show a hump-shaped AGB-species richness relationship. Functional diversity explains better AGB production than classical taxonomic diversity. Community weighted mean traits provide key information to explain stand biomass in these forests, where maximum tree height seems to be a more suitable trait for understanding the biomass accumulation process in these ecosystems. Although the impact of forest management on biodiversity is still debated, it has not changed the AGB-diversity relationships in the forests of the Sierra Madre Occidental, Mexico.

scholarly journals Meta-analysis of 139 extant Tara ocean metagenomes to unveil the relationship between taxonomy and functionality in prokaryotes inhabiting aquatic ecosystems

2020 ◽  
Author(s):  
Robert Starke
Keyword(s):  
Functional Diversity ◽  
Aquatic Ecosystems ◽  
Local Community ◽  
North Atlantic Ocean ◽  
Meta Analysis ◽  
Terrestrial Ecosystems ◽  
Global Distribution ◽  
Small Subset ◽  
Functional Richness ◽  
The Relationship

The total microbiome functionality of bacteria was recently predicted to be 35.5 ±0.2 million of KEGG functions. Logically, due to the limitation in space and resource availability of the local community, local functionality will only comprise a small subset of the total functionality but the relationship between taxonomy and functionality is still uncertain. Here, I used a meta-analysis of 139 extant Tara ocean seawater samples from 68 locations across to globe with information on prokaryotic taxonomy on species level from 16S metabarcoding and functionality of prokaryotes on eggNOG gene family level from metagenomes to unveil the relationship between taxonomy and functionality, and to predict the global distribution of functionality. Functional richness showed a statistically significant increase with increasing species richness (P <0.0001, R2 =0.64) and increasing species diversity (P <0.0001, R2 =0.26) while functional diversity was similar across the different waters, ranging from 2.96 to 3.22. Globally, the highest functional richness was found in the Northern Pacific Ocean and in the North Atlantic Ocean, and decreased at extreme latitudes. Taken together, I unveil the relationship between taxonomy and functionality, and predict the global distribution of functional richness in prokaryotes inhabiting aquatic ecosystems, implying more pronounced effects in terrestrial ecosystems due to larger differences in environmental parameters especially for functional diversity.

scholarly journals Assessing above-ground biomass-functional diversity relationships in temperate forests in northern Mexico

2020 ◽  
Author(s):  
Benedicto Vargas-Larreta ◽  
Jorge Omar Lopez Martinez ◽  
Edgar J. González ◽  
Jose Javier Corral-Rivas ◽  
Francisco Javier Hernández
Keyword(s):  
Species Richness ◽  
Functional Diversity ◽  
Taxonomic Diversity ◽  
Maximum Height ◽  
Above Ground Biomass ◽  
Northern Mexico ◽  
Ground Biomass ◽  
Sierra Madre ◽  
Community Weighted Mean ◽  
The Relationship

Abstract Background: Studies on the relationship between biodiversity and ecosystem productivity have suggested that species richness and functional diversity are the main drivers of ecosystem processes. Several patterns on this relationship have been found, including positive, unimodal, negative, and neutral trends, keeping the issue controversial. In this study, taxonomic diversity and functional diversity as drivers of above-ground biomass (AGB) were comparated, and the mechanisms that influence biomass production were investigated by testing the complementarity and the mass-ratio hypotheses. Methods: Using data from 414 permanent sample plots, covering 23% of temperate forest in the Sierra Madre Oriental (México). We estimated the above-gound biomass (AGB), taxonomic and functional diversity indices, as well as community weighted mean values (CWM) for three functional trais (maximum height, leaf size and wood density) for trees ≥7.5 cm d.b.h., in managed and unmanaged stands. To compare taxonomic diversity differences between managed and unmanaged stands we carried out a rarefaction analysis. Furthermore, we evaluated the relationship between AGB and taxonomic and functional diversity metrics, as well as CWM traits throught spatial autoregressive models. Results: We found a hump-shaped relationship between AGB and species richness in managed and unmanaged forests. CMW of maximum height was the most important predictor of AGB in both stands, which suggested that the mechanism underlaying the AGB-diversity relationship is the dominance of some highly productive species, supporting the mass-ratio hypothesis. Above-ground biomass was significantly correlated with three of the five functional diversity metrics, CWM maximum height and species richness. Our results show the importance of take into account spatial autocorrelation in the construction of predictive models to avoid spurious patterns in the AGB-diversity relationship. Conclusion: Species richness, maximum height, functional richness, functional dispersion and RaoQ indices relate with above-ground biomass production in temperate mixed-species and uneven-aged forests of northern Mexico. These forests show a hump-shaped AGB-species richness relationship. Functional diversity explains better AGB production than classical taxonomic diversity. Community weighted mean traits provide key information to explain stand biomass in these forests, where maximum tree height seems to be a more suitable trait for understanding the biomass accumulation process in these ecosystems. Although the impact of forest management on biodiversity is still debated, it has not changed the AGB-diversity relationships in the forests of the Sierra Madre Occidental, Mexico.

The relationship between species richness and evenness: a meta-analysis of studies across aquatic ecosystems

Oecologia ◽  
2011 ◽  
Vol 169 (3) ◽  
pp. 803-809 ◽  
Author(s):  
Janne Soininen ◽  
Sophia Passy ◽  
Helmut Hillebrand
Keyword(s):  
Species Richness ◽  
Aquatic Ecosystems ◽  
Meta Analysis ◽  
The Relationship

scholarly journals Mechanisms of species coexistence and functional diversity of ant assemblages in forest and pasture habitats in southwestern Brazilian Amazon

Sociobiology ◽  
2020 ◽  
Vol 67 (1) ◽  
pp. 33
Author(s):  
Andressa Silvana Oliveira de Menezes ◽  
Fernando Augusto Schmidt
Keyword(s):  
Species Richness ◽  
Functional Diversity ◽  
Species Coexistence ◽  
Asymptotic Relation ◽  
Niche Partitioning ◽  
Brazilian Amazon ◽  
Functional Redundancy ◽  
Forest Habitat ◽  
Ant Assemblages ◽  
The Relationship

In this study, we investigated the mechanisms behind species coexistence and the relationships between functional diversity and species richness in ant assemblages in both forest and pasture habitats in the southwestern Brazilian Amazon. We addressed the specific question: What is the primary mechanism for species coexistence in forest and pasture habitats? According to the identified mechanism in each habitat, we had the following alternative expectations: (i) niche partitioning – we expected to observe a linear positive relationship between functional diversity and species richness, indicating a complementary relationship; or (ii) niche filtering – a positive constant asymptotic relation between functional diversity and species richness, indicating a functional redundancy relationship. In total, we sampled 91 ant species, 82 species in a forest habitat and 16, in a pasture habitat. In the forest habitat we identified niche filtering as the structuring mechanism of the ant assemblage, but we were unable to identify a clear mechanism in the pasture habitat. Although the relationship between functional diversity and species richness was positive in both habitats, the relationship was weaker in the forest habitat, indicating a greater functional redundancy among the ant species in this habitat. Our results reinforce the divergence of species coexistence mechanisms and ant assemblage structures in both natural and human-modified habitats in the Southwestern Brazilian Amazon.

scholarly journals The total fungal microbiome functionality

2019 ◽  
Author(s):  
Robert Starke ◽  
Petr Capek ◽  
Daniel Morais ◽  
Nico Jehmlich ◽  
Petr Baldrian
Keyword(s):  
Species Richness ◽  
Ecosystem Functioning ◽  
Meta Analysis ◽  
Taxonomic Diversity ◽  
Fungal Species ◽  
Saturated Model ◽  
P Value ◽  
Functional Richness ◽  
Fungal Microbiome ◽  
Non Parametric

Unveiling the relationship between taxonomy and function of the microbiome is crucial to determine its contribution to ecosystem functioning. However, while there is a considerable amount of information on microbial taxonomic diversity, our understanding of its relationship to functional diversity is still scarce. Here we used a meta-analysis of 377 completely annotated and taxonomically different fungal genomes to predict the total fungal microbiome functionality on Earth with all known functions from level 3 of KEGG Orthology using both parametric and non-parametric estimations. The unsaturated model described the accumulation of functions with increasing species richness significantly better (P-value < 2.2e−16) than the saturated model suggesting the presence of widespread and rare functions. Consistent with the parametric approach, the non-parametric Chao-1 estimator that assumes a maximum functional richness did not reach a plateau. Based on previous estimates of fungal species richness on Earth, we propagated the unsaturated model to predict a total fungal microbiome functionality of 42.4 million. Of those, only 0.06% are known today since the vast majority belongs to yet unknown rare functions. Logically, our approach not only highlighted the presence of two types of functions but pointed towards the necessity of novel and more sophisticated methods to unveil the entirety of functions to fully understand the involvement of the fungal microbiome in ecosystem functioning.

Relationship between total plasma homocysteine and the risk of aneurysms – a meta-analysis

VASA ◽  
2020 ◽  
pp. 1-6
Author(s):  
Hanji Zhang ◽  
Dexin Yin ◽  
Yue Zhao ◽  
Yezhou Li ◽  
Dejiang Yao ◽  
...  
Keyword(s):  
Large Scale ◽  
Meta Analysis ◽  
Single Species ◽  
Total Plasma ◽  
Control Groups ◽  
Randomized Controlled ◽  
Randomized Controlled Studies ◽  
The Difference ◽  
The Relationship ◽  
Healthy Participants

Summary: Our meta-analysis focused on the relationship between homocysteine (Hcy) level and the incidence of aneurysms and looked at the relationship between smoking, hypertension and aneurysms. A systematic literature search of Pubmed, Web of Science, and Embase databases (up to March 31, 2020) resulted in the identification of 19 studies, including 2,629 aneurysm patients and 6,497 healthy participants. Combined analysis of the included studies showed that number of smoking, hypertension and hyperhomocysteinemia (HHcy) in aneurysm patients was higher than that in the control groups, and the total plasma Hcy level in aneurysm patients was also higher. These findings suggest that smoking, hypertension and HHcy may be risk factors for the development and progression of aneurysms. Although the heterogeneity of meta-analysis was significant, it was found that the heterogeneity might come from the difference between race and disease species through subgroup analysis. Large-scale randomized controlled studies of single species and single disease species are needed in the future to supplement the accuracy of the results.

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