However, when phylogenetic similarity was included, the fungi growing on straw substrates at T = 1 were more diverse than the fungi growing on wood substrates at T = 1, within the range of 1 ≤ q ≤ 5 (Figure 4B). This indicates that the fungal communities growing on straw substrates in the grassland at T = 1 contained taxa that were less Selleck GSK458 closely related to each other (more phylogenetically diverse) than the taxa growing on wood substrates at LY411575 solubility dmso T = 1, because when phylogenetic similarity was considered, the diversity of straw substrate fungal communities increased. There was also considerable overlap and crossing in the phylogenetic

diversity profile between 1 ≤ q ≤ 3, which was not apparent in the taxonomic profile. Figure 4 Substrate-associated soil fungi grassland diversity profiles. (A) Naïve and (B) similarity-based (phylogenetic relatedness) diversity profiles calculated from the substrate-associated JIB04 soil fungi grassland data. This demonstrated capacity of diversity profiles to incorporate effective phylogenetic diversity, as well as other measures of similarity between taxa, is particularly meaningful for analyzing microbial diversity data. Macro-organismal ecologists have long been concerned with the interactions between an organism’s traits and aspects of its ecology, such as its niche axes or its role in ecosystem processes [54–57].

Many macro-eukaryote traits, when mapped to phylogenies, show evidence for phylogenetic conservatism [58, 59]. That is, certain traits are shared more often by closely

related taxa than would be expected by chance. Even bacteria and archaea show evidence for trait conservatism, despite the role of non-homologous recombination in their evolutionary history [60, 61]. This implies that the phylogenetic distribution of a microbial assemblage can, thus, influence ecosystem processes via differences in the suite of traits present. Phylogenetic trait conservatism in microbes also has practical implications, such as potentially guiding current research in drug discovery or biodegradation Erastin purchase [62–64]. Diversity analyses of environmental microbial samples can span all domains of life. It is thus highly desirable to evaluate and critically assess a method that can address the diversity of a microbial assemblages effectively across domains, as well as across samples with substantial differences in rare membership, while using a full complement of the information contained in DNA and RNA sequence analysis. As there is no universal marker gene for viruses, there are no robust means of determining viral phylogeny from community sequencing data. Apart from a few groups of well-characterized viruses, it is difficult to characterize viral phylogenetic relationships at all.