AOB in the ALK were dominated by cluster 3a (87 %), while the percentage of cluster 3a decreased and clusters 9 and 10 accounted for almost 77 % of the AOB community in the ACI soil. Moreover, the ALK and ACI soils harbored contrasting community compositions of AO. No significant difference in the abundance of cbbL was found between the two soils, but the ratio of AOB and AOA amoA to cbbL genes in the ACI soil samples was higher than that in the ALK sample. The results revealed that abundances of AOB and AOA were significantly lower in the ACI purple soil sample than in the ALK sample, but a higher ratio of AOA to AOB was found in the ACI purple soil sample. The abundance of amoA (gene encoding ammonia monooxygenase) of ammonia-oxidizing bacteria (AOB) and archaea (AOA) and that of the cbbL gene (encoding ribulose-1,5-biphosphate carboxylase/oxygenase) were determined by real-time PCR, and the community structures of AOB and AOA were investigated by cloning and sequencing. In this study, two typical purple soils with different pH values (acidic: ACI alkaline: ALK) were collected and studied. However, the dynamics of the AO community in acidic purple soils, which are widely distributed in Southwest China, remain largely unknown. , k-th nearest neighbor are determined and a directional beta diversity curve is constructed using the resulting sequence of plots.Soil pH has been suggested as one of the most important factors affecting the ecological characteristics of soil ammonia-oxidizers (AO), which mediate the conversion of ammonia to nitrate via nitrite and contribute significantly to the leaching of nitrate to groundwater and the production of atmospheric nitrous oxide (N 2O). In the simplest case, given a set of N plots, for each plot, the first, second. The methodology to construct the directional curve relies on the standard procedure in which adjacent plots are combined step by step using the specified distance among plots as a constraining factor. Spatially-explicit or gradient-oriented (directional) turnover curves as a function of sampling effort have been firstly defined by Ricotta et al. \[HCDT=\frac\) is the functional dissimilarity between species \(k\) and \(l\). In the table below, for functions implemented in Rarefy, the set of indices available are detailed. Rarefy offers the possibility to calculate a large set of diversity indices and new metrics will be implemented in future packages updates. Diversity indices and dataset available in Rarefy Phylogenetic spatially-explicit rarefaction ġ.Rarefaction of alpha diversity indices.Diversity indices and dataset available in Rarefy.The vignette is organized in the following sections, exploring different package features and applications: This vignette aims at describing some applications of the Rarefy package helping the user to calculate different types of spatially and non-spatially explicit rarefaction curves. Rarefy and the functions therein represent an ultimate solution for ecologists to rarefy any diversity metric by taking into account the contribution of any distance-based ordination of sampling units, providing more ecological meaningful (unbiased) estimates of the expected diversities. Rarefy is an R package including a set of new functions able to cope with any diversity metric and to calculate expected values of a given taxonomic, functional or phylogenetic index for a reduced sampling size under a spatially-constrained and distance-based ordering of the sampling units.
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