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Therefore, the phylotypes from the 16S rDNA amplicon libraries were sorted on genus level and a similarity comparison of the soil-compost mixture and fertilized soil samples based on genera relative abundance data were performed by cluster analyses.
Indicator genera analyses (999 permutations) based on sample groups predefined by treatment were carried out using the multipatt function of R to evaluate whether significant indicator genera were associated with pyrene treatment by calculating the group-equalized point-biserial correlation coefficient based on genera relative abundance data (Cáceres and Legendre 2009).
Non-parametric MANOVA (999 permutations, Bray Curtis matrix) using the adonis function of R was used to test whether the soil-compost mixture and fertilized soil differ in relative abundances of bacteria classes and whether grouping based on genera abundances is significant.
The results presented here might be driven by only some hosts, and detailed analyses based on genera could only be done for few genera.
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We used data from these deep-sea chemosynthetic studies (including their controls) in order to evaluate univariate diversity measurements such as nematode genera richness (S), Shannon diversity index (H'), and Pielou's evenness (J) (all based on standardized genera richness data).
Predefined sample groups (selected times of incubation as well as pyrene treatment versus controls) were statistically evaluated based on microbial genera relative abundance data and related to the degradation kinetics.
Multidimensional scaling of deep-sea seep, vent and control samples, based on nematode genera data, gives no evidence for distinction into large biogeographic provinces such as the Atlantic and the Pacific (Fig 4; data originally from [25] [27], [33], [35] [39,]. ANOSIM (with R = 0.52; p = 0.001) also shows that there is no major difference between samples from both oceans.
A close affinity between Arcovomer and Hamptophryne was previously suggested [ 51] based on both genera lacking neopalatines and having divided prevomers.
To see whether our results also hold for closely related hosts, we repeated the analysis based on bacterial genera with at least three CRISPR - and three CRISPR + phages.
Abundance data are also related to different taxonomic levels, allowing searches based on family, genera and species levels among and within data sets.
Our results suggest that delimitations based on membership to genera, position in the phylogeny, growth form and native range size need to be considered to produce objective and defendable approaches for formal risk assessments.
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