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.

scholarly journals Impact of urbanization on functional diversity in macromycete communities along an urban ecosystem in Southwest Mexico

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12191
Author(s):  
Marko Gómez-Hernández ◽  
Emily Avendaño-Villegas ◽  
María Toledo-Garibaldi ◽  
Etelvina Gándara
Keyword(s):  
Species Richness ◽  
Functional Diversity ◽  
Ecosystem Functioning ◽  
Urban Ecosystem ◽  
Niche Space ◽  
Urbanization Gradient ◽  
Urbanization Level ◽  
Functional Value ◽  
Functional Richness ◽  
Available Resources

Macromycetes are a group of fungi characterized by the production of fruit bodies and are highly relevant in most terrestrial ecosystems as pathogens, mutualists, and organic matter decomposers. Habitat transformation can drastically alter macromycete communities and diminish the contribution of these organisms to ecosystem functioning; however, knowledge on the effect of urbanization on macrofungal communities is scarce. Diversity metrics based on functional traits of macromycete species have shown to be valuable tools to predict how species contribute to ecosystem functionality since traits determine the performance of species in ecosystems. The aim of this study was to assess patterns of species richness, functional diversity, and composition of macrofungi in an urban ecosystem in Southwest Mexico, and to identify microclimatic, environmental, and urban factors related to these patterns in order to infer the effect of urbanization on macromycete communities. We selected four oak forests along an urbanization gradient and established a permanent sampling area of 0.1 ha at each site. Macromycete sampling was carried out every week from June to October 2017. The indices used to measure functional diversity were functional richness (FRic), functional divergence (FDig), and functional evenness (FEve). The metric used to assess variation of macrofungal ecological function along the study area was the functional value. We recorded a total of 134 macromycete species and 223 individuals. Our results indicated a decline of species richness with increased urbanization level related mainly to microclimatic variables, and a high turnover of species composition among study sites, which appears to be related to microclimatic and urbanization variables. FRic decreased with urbanization level, indicating that some of the available resources in the niche space within the most urbanized sites are not being utilized. FDig increased with urbanization, which suggests a high degree of niche differentiation among macromycete species within communities in urbanized areas. FEve did not show notable differences along the urbanization gradient, indicating few variations in the distribution of abundances within the occupied sections of the niche space. Similarly, the functional value was markedly higher in the less urbanized site, suggesting greater performance of functional guilds in that area. Our findings suggest that urbanization has led to a loss of macromycete species and a decrease in functional diversity, causing some sections of the niche space to be hardly occupied and available resources to be under-utilized, which could, to a certain extent, affect ecosystem functioning and stability.

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 Functional diversity of Himalayan bat communities declines at high elevation without the loss of phylogenetic diversity

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rohit Chakravarty ◽  
Ram Mohan ◽  
Christian C. Voigt ◽  
Anand Krishnan ◽  
Viktoriia Radchuk
Keyword(s):  
Species Richness ◽  
Functional Diversity ◽  
Phylogenetic Diversity ◽  
Environmental Filtering ◽  
Taxonomic Diversity ◽  
High Elevation ◽  
Elevational Gradients ◽  
Functional Richness ◽  
Functional Dispersion ◽  
Functional And Phylogenetic Diversity

AbstractSpecies richness exhibits well-known patterns across elevational gradients in various taxa, but represents only one aspect of quantifying biodiversity patterns. Functional and phylogenetic diversity have received much less attention, particularly for vertebrate taxa. There is still a limited understanding of how functional, phylogenetic and taxonomic diversity change in concert across large gradients of elevation. Here, we focused on the Himalaya—representing the largest elevational gradients in the world—to investigate the patterns of taxonomic, functional and phylogenetic diversity in a bat assemblage. Combining field data on species occurrence, relative abundance, and functional traits with measures of phylogenetic diversity, we found that bat species richness and functional diversity declined at high elevation but phylogenetic diversity remained unchanged. At the lowest elevation, we observed low functional dispersion despite high species and functional richness, suggesting a niche packing mechanism. The decline in functional richness, dispersion, and divergence at the highest elevation is consistent with patterns observed due to environmental filtering. These patterns are driven by the absence of rhinolophid bats, four congeners with extreme trait values. Our data, some of the first on mammals from the Himalayan region, suggest that in bat assemblages with relatively high species diversity, phylogenetic diversity may not be a substitute to measure functional diversity.

scholarly journals Do carabids (Coleoptera: Carabidae) and chironomids (Diptera: Chironomidae) exhibit similar diversity and distributional patterns along a spatio-temporal gradient on a glacier foreland?

2018 ◽  
Author(s):  
Mauro Gobbi ◽  
Valeria Lencioni
Keyword(s):  
Species Richness ◽  
Species Turnover ◽  
Aquatic Insect ◽  
Taxonomic Diversity ◽  
Carabid Beetles ◽  
Species Assemblages ◽  
Glacier Foreland ◽  
Distributional Patterns ◽  
Glacier Front ◽  
Spatio Temporal

Carabid beetles and chironomid midges are two dominant cold-adapted taxa, respectively on glacier forefiel terrains and in glacial-stream rivers. Although their sensitivity to high altitude climate warming is well known, no studies compare the species assemblages exhibited in glacial systems. Our study compares diversity and distributional patterns of carabids and chironomids in the foreland of the receding Amola glacier in central-eastern Italian Alps. Carabids were sampled by pitfall traps; chironomids by kick sampling in sites located at the same distance from the glacier as the terrestrial ones. The distance from the glacier front was considered as a proxy for time since deglaciation since these variables are positively correlated. We tested if the distance from the glacier front affects: i) the species richness; ii) taxonomic diversity; and iii) species turnover. Carabid species richness and taxonomic diversity increased positively from recently deglaciated sites (those c. 160 m from the glacier front) to sites deglaciated more than 160yrs ago (those located >1300 m from glacier front). Species distributions along the glacier foreland were characterized by mutually exclusive species. Conversely, no pattern in chironomid species richness and turnover was observed. Interestingly, taxonomic diversity increased significantly: closely related species were found near the glacier front, while the most taxonomically diverse species assemblages were found distant from the glacier front. Increasing glacial retreat differently affect epigeic and aquatic insect taxa: carabids respond faster to glacier retreat than do chironomids, at least in species richness and species turnover patterns.

scholarly journals The Effect of Climate and Human Pressures on Functional Diversity and Species Richness Patterns of Amphibians, Reptiles and Mammals in Europe

Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 275
Author(s):  
Mariana A. Tsianou ◽  
Maria Lazarina ◽  
Danai-Eleni Michailidou ◽  
Aristi Andrikou-Charitidou ◽  
Stefanos P. Sgardelis ◽  
...  
Keyword(s):  
Species Richness ◽  
Functional Diversity ◽  
Agricultural Land ◽  
Influential Factor ◽  
Climatic Variables ◽  
Quadratic Entropy ◽  
Functional Richness ◽  
Precipitation Seasonality ◽  
Rao’S Quadratic Entropy ◽  
Richness Patterns

The ongoing biodiversity crisis reinforces the urgent need to unravel diversity patterns and the underlying processes shaping them. Although taxonomic diversity has been extensively studied and is considered the common currency, simultaneously conserving other facets of diversity (e.g., functional diversity) is critical to ensure ecosystem functioning and the provision of ecosystem services. Here, we explored the effect of key climatic factors (temperature, precipitation, temperature seasonality, and precipitation seasonality) and factors reflecting human pressures (agricultural land, urban land, land-cover diversity, and human population density) on the functional diversity (functional richness and Rao’s quadratic entropy) and species richness of amphibians (68 species), reptiles (107 species), and mammals (176 species) in Europe. We explored the relationship between different predictors and diversity metrics using generalized additive mixed model analysis, to capture non-linear relationships and to account for spatial autocorrelation. We found that at this broad continental spatial scale, climatic variables exerted a significant effect on the functional diversity and species richness of all taxa. On the other hand, variables reflecting human pressures contributed significantly in the models even though their explanatory power was lower compared to climatic variables. In most cases, functional richness and Rao’s quadratic entropy responded similarly to climate and human pressures. In conclusion, climate is the most influential factor in shaping both the functional diversity and species richness patterns of amphibians, reptiles, and mammals in Europe. However, incorporating factors reflecting human pressures complementary to climate could be conducive to us understanding the drivers of functional diversity and richness patterns.

scholarly journals Zumba®, Fat Mass and Maximum Oxygen Consumption: A Systematic Review and Meta-Analysis

2020 ◽  
Vol 18 (1) ◽  
pp. 105
Author(s):  
Manuel Chavarrias ◽  
Santos Villafaina ◽  
Ana Myriam Lavín-Pérez ◽  
Jorge Carlos-Vivas ◽  
Eugenio Merellano-Navarro ◽  
...  
Keyword(s):  
Systematic Review ◽  
Oxygen Consumption ◽  
Body Mass ◽  
Fat Mass ◽  
Evidence Synthesis ◽  
Meta Analysis ◽  
P Value ◽  
Maximum Oxygen Consumption ◽  
Mass Percentage ◽  
Large Heterogeneity

Background and objectives: Obesity or overweight is associated with many health risk factors and preventable mortality. Even people with normal weight and without history of obesity or overweight should avoid weight gain to reduce health risks factors. In this regard Latin aerobic dances involved in Zumba® practice make this modality motivating for people. Apart from weight loss and VO2peak benefits, Zumba practice is also interesting by the increase in adherence which can also avoid weight regain. The aim was to systematically review the scientific literature about the effects of any randomized intervention of Zumba® practice on total fat mass (%) and maximum oxygen consumption (VO2peak), besides establishing directions for the clinical practice. Evidence acquisition: Two systematic searches were conducted in two electronic databases following the PRISMA guidelines. The eligibility criteria were (a) outcomes: body mass or VO2peak data including mean and standard deviation (SD) before and after Zumba® intervention, (b) study design: randomized controlled trial (RCT) and (c) language: English. GRADE guidelines were used to assess the quality of evidence. A meta-analysis was performed to determine mean differences. Nine and four studies were selected for fat mass percentage and VO2peak in the systematic review, respectively. However, only eight studies for fat mass percentage and three for VO2peak could be included in the meta-analysis. Evidence synthesis: The overall standardized mean difference for fat mass was −0.25 with a 95% CI from −0.67 to 0.16 with a p-value of 0.69, with large heterogeneity. On the other hand, the overall effect size for VO2peak was 0.53 (95% CI from 0.04 to 1.02 with a p-value of 0.03) with large heterogeneity. Conclusions: Based on the evidence, we cannot conclude that Zumba® is effective at reducing body mass but it may improve VO2peak. However, the limited number of studies that met the inclusion criteria makes it too early to reach a definite conclusion, so more research is needed.

scholarly journals The Effects of Sterilization Procedures on the Cutting Efficiency of Endodontic Instruments: A Systematic Review and Network Meta-Analysis

Materials ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 1559
Author(s):  
Mario Dioguardi ◽  
Enrica Laneve ◽  
Michele Di Cosola ◽  
Angela Pia Cazzolla ◽  
Diego Sovereto ◽  
...  
Keyword(s):  
Systematic Review ◽  
Selection Process ◽  
Meta Analysis ◽  
Indirect Comparison ◽  
Physical And Mechanical Properties ◽  
Surface Characteristics ◽  
Cyclic Fatigue ◽  
P Value ◽  
Cutting Efficiency ◽  
Dental Instruments

Sterilization processes guarantee the sterility of dental instruments but can negatively affect instrument features by altering their physical and mechanical properties. The endodontic instrumentation can undergo a series of alterations, ranging from corrosion to variation in the cutting angle and then changes in the torsional properties and torsional fatigue resistance. This systematic literature review and meta-analysis aims to investigate alterations to the cutting efficiency of endodontic instruments that are induced by procedures for their disinfection and sterilization. Methodologies adopted for this investigation follow the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guidelines. The following were used as search terms on PubMed and Scopus: “endodontic sterilization”, “endodontic autoclave”, “cyclic fatigue”, “torsional”, “cutting efficiency”, “sterilization”, “surface characteristics”, and “corrosion”. At the end of the selection process, 36 articles were identified, and seven of them are included in this systematic review. The results of a meta-analysis conducted for the use of 10 autoclaving cycles shows a standardized mean difference (SMD) of 0.80 with a p-value equal to 0.04 with respect to effect on cutting efficiency. The network meta-analysis, through direct and indirect comparison between the different autoclave cycles (0, 1, 5, 10, and 15 cycles), revealed that treatment involving 15 autoclave cycles produced the most robust results in terms of having the greatest effects in terms of altered cutting efficiency with a probability of 57.7% and a SUCRA (surface under the cumulative ranking) of 80%. The alterations in the effects on cutting efficiency appear to be triggered after five cycles of sterilization by heat (autoclave). In conclusion, the meta-analysis of the data indicates that the autoclave sterilization protocol must not be repeated more than five times to preserve cutting efficiency. Within the limitations of this review, we can therefore establish that sterilization by autoclaving alone results in steel and NiTi instruments becoming less efficient in cutting after five cycles, as measured by a reduction in cutting efficiency.

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