Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil

Abstract

Recent studies have highlighted the surprising richness of soil bacterial communities; however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the diversities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an individual soil sample. We used metagenomic and small-subunit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an operational taxonomic unit [OTU]), we found that the archaeal and fungal communities were consistently less even than the bacterial communities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral communities using a metagenomic approach, we found that soil viruses are taxonomically diverse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse.

Identifying airborne fungi in Seoul, Korea using metagenomics

“…For example, temperature (Fernández et al, 1998) and humidity (Levetin, 1989(Levetin, , 1990Wu et al, 2004), which change at both seasonal and short-term scales, are positively correlated with fungal spore density. On a smaller scale, sporadic phenomena such as soil disturbances or sporulation events also have an influence on fungal diversity in the air (Lighthart and Stetzenbach, 1994;Madelin, 1994;Fierer et al, 2007). Interestingly, in our study, there is more similarity in fungal diversity in the beginning (A21) and end (M30) of spring compared to our sample in the middle (A28) (Fig.…”

“…Rarefaction curves describe the growth of a number of species discovered as a function of the number of samples. For all of our samples, curves have begun to flatten, which is typical in metagenomic studies (Tringe et al, 2005;Fierer et al, 2007), indicating that representative, unbiased sampling of fungal diversity has been recovered (Fig. 2).…”

Examining the global distribution of dominant archaeal populations in soil

“…The phylogenetic placement of the archaeal phylotypes represented by these sequences is shown in Figure 1. As only the most abundant archaea were recovered by our method, it should be stressed that the phylogenetic tree represents relationships among the most dominant archaea and does not depict the full extent of archaeal diversity in these soils, which is potentially much greater (Fierer et al, 2007). The majority of the archaeal phylotypes (90.9% of all archaeal sequences) were contained within the group 1.1b crenarchaeotal clade (Jurgens et al, 2000), which has been shown previously to be dominant in soils (Auguet et al, 2009).…”

Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally

“…only bacteria), with far less attention paid to unicellular and multicellular eukaryotes despite increasing evidence that the diversity of soil fungi, protists and metazoa is likely far higher than often considered [14][15][16]. Indeed, there are few cross-domain assessments of below-ground diversity (but see [17,18]). Additionally, the vast majority of soil diversity studies have been conducted in natural settings, yet anthropogenic pressures now structure many ecosystems and it remains unclear whether there are consistent processes structuring soil biodiversity and biogeography in natural and urban ecosystems.…”