The collection reviews the distribution of biodiversity in space, explaining the definitions of alpha, beta and gamma diversity for measuring diversity within and between ecosystems. To assess gamma-diversity by habitat, we plotted an OTU accumulation curve for each habitat with specaccum() from package ‘vegan’ in R [39] using the 150 OTU-by-geocluster tables. Yes Climate, geological history and ecological randomness are considered to be the main factors affecting species diversity pattern at large scales [31], [32], whereas the local ecological processes and regional species pool are considered to be important at a small scale [33], [34]. (A) Heatmap shows degree of correlation (r from a Spearman’s mantel test with all EMP samples used in analysis). Conceptualization, It is closely related to resource heterogeneity or the niche processes [27]. The epsilon or regional diversity is defined as the total diversity of … Each point represents an individual EMP soil sample (not a geocluster) and is colored by biome. Biodiversity can be termed as and measured like an attribute consisting of two components such as richness and evenness. Raup-Crick is not an appropriate metric when communities do not share the same species pool [40]. At the same time, biofilms and mats, despite being spatially structured, also displayed low alpha-diversity [50]. In that situation, the use of the ‘several small’ strategy will be superior to the “single large” strategy in reserve design for species diversity conservation [11]. Competing interests: The authors have declared that no competing interests exist. Data Availability: No new data were used in this research. https://doi.org/10.1371/journal.pone.0233872.s001. Within soils, we found that agricultural soils had among the highest richness and exhibited just as much compositional variation (beta-diversity) as other biomes. In the high precipitation grassland region, more species appeared in the community, and inter-specific competition was relatively strong. The α diversity increased with γ diversity, and the increase was gradually saturates and could be described by a logarithmic curve (P<0.001) (Fig. On average, for any given sample, ESV richness is equal to 95.26% of OTU richness. Non-saline inland water samples have a regression line with a slope of 1.152 (P < 0.0001, r2 = 0.902), shown as light pink on the graph. Richness refers to the number of groups of genetically are functionally related individuals in the species. Large-Scale Patterns of Biological Diversity Discussion. The β diversity reflects different degrees of species composition. Validation, Beta-diversity patterns are not dependent on the beta-diversity metric used. Excluding air samples, OTU richness (ANCOVA: F = 54.68, P < 0.0001, r2 = 0.229), but not habitat (F = 2.14, P = 0.0775) was a predictor of evenness. The environmental factors that affect these patterns of spatial diversity are briefly discussed. PLOS ONE promises fair, rigorous peer review, The averaged alpha-diversities were then cube root transformed to achieve normality and homoscedasticity. In contrast, marine water, inland water, air, and biofilms/mats contain the lowest alpha-diversity (Fig 2A). Roles Geocluster accumulation curves (gamma-diversity) for mean OTU richness from a random sampling of geoclusters (permutations = 999) with 95% confidence intervals drawn for each habitat. https://doi.org/10.1371/journal.pone.0093518.g003. Overall, bacterial community composition differed significantly by habitat (PERMANOVA: P = 0.001, Pseudo-F = 9.8601, r2 = 0.210; Fig 2E) and by biome for soils (P = 0.001, Pseudo-F = 4.221, r2 = 0.227; Fig 2F). The α diversity is more important in communities with an homogeneous environment and strong-diffusion species, whereas β diversity is, on the contrary, more important in communities with an heterogeneous environment and weak-diffusion species. However, the correlations between β diversity and latitude were inconsistent; they could be positively [13], [14], negatively [15], [16], or not correlated [9], [17]. Overall, the results support the idea that spatial environmental heterogeneity is an important driver of bacterial diversity. All data used can be found on the Earth Microbiome Project (https://doi.org/10.1038/nature24621) or WorldClim (https://doi.org/10.1002/joc.5086) websites. Top Educators. Of course, other unmeasured environmental factors and/or ecological interactions are likely influencing soil diversity. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Yes Bacterial 16S rDNA (V4 region) sequence data and associated metadata (e.g., sample location, sample type, date of sampling) were downloaded from the Earth Microbiome Project (EMP) on September 1, 2016. It has more than 2,300 vascular plant species [38], and is recognised as the second most species-rich grassland biome in the world in terms of indigenous plant biodiversity after the African savanna [39]. While extracellular DNA (eDNA) may be particularly prevalent in ocean sediments [58], evidence thus far suggests that eDNA has minimal effect on sediment diversity estimates from sequencing surveys [59]. 2A); the contribution of α diversity was higher in desert steppe than in meadow steppe, and conversely the contribution of β diversity was lower in desert steppe than in meadow steppe. The term was introduced by R. H. Whittaker together with the terms alpha diversity (α-diversity) and gamma diversity (γ-diversity). Gamma diversity equals alpha diversity x beta diversity. This rarefaction depth provided a high sequence count per sample while minimizing sample loss to 4.74% of samples. Yes In ecology, beta diversity (β-diversity or true beta diversity) is the ratio between regional and local species diversity. Alpha diversity (2). Thus, for the analysis with just soil samples, we used temperature data from WorldClim. Because we averaged OTU abundances for all samples of the same habitat type located within the same geographic area (geocluster), beta-diversity provides an approximation of the amount of community variation from location to location within one habitat (as opposed to variation from sample to sample within one location). Various levels/parameters of measuring the biodiversity are: (1). We used the mean and SE to compare the trends in dissimilarity to those generated with the Bray-Curtis metric. Our results suggest that for local species diversity patterns, the site species pool is more important in lower precipitation areas, while local ecological processes are more important in high precipitation areas. Zhang Q, Hou X, Li FY, Niu J, Zhou Y, Ding Y, al... Yet, we analyzed alpha-, beta-, and gamma-diversity of bacterial assemblages using alpha, beta gamma diversity biology discussion samples compiled the! 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