Bacterial and fungal community composition across the soil depth profiles in a fallow field

Abstract

Background: Soil microorganisms play key roles in nutrient cycling and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depths, we analyzed microbial activities and bacterial and fungal community composition in soils up to a 120 cm depth at a fallow field located in central Korea. To examine the vertical difference of microbial activities and community composition, β-1,4-glucosidase, cellobiohydrolase, β-1,4-xylosidase, β-1,4-N-acetylglucosaminidase, and acid phosphatase activities were analyzed and barcoded pyrosequencing of 16S rRNA genes (bacteria) and internal transcribed spacer region (fungi) was conducted. Results: The activity of all the soil enzymes analyzed, along with soil C concentration, declined with soil depth. For example, acid phosphatase activity was 125.9 (± 5.7 (± 1 SE)), 30.9 (± 0.9), 15.7 (± 0.6), 6.7 (± 0.9), and 3.3 (± 0.3) nmol g −1 h −1 at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1,[15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30], and 90-120 cm soil depths, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3,[15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30], and 90-120 cm soil depths, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51. 2, 48.6, 65.7, 46.1, and 45.7% at 15, 30, 60, 90, and 120 cm depths, respectively), a dominant fungal group at this site, showed no clear trend along the soil profile. Conclusions: Our results show that soil C availability can determine soil enzyme activity at different soil depths and that bacterial communities have a clear trend along the soil depth at this study site. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of soil microbial communities and their relationship with biogeochemical factors.

Cover cropping and no-till increase diversity and symbiotroph:saprotroph ratios of soil fungal communities

“…We did not observe differences in diversity indices or species richness with depth. Similar lack of change in fungal diversity and community composition with depth has been described in fallow fields dominated by Ascomycetes (Ko et al, 2017), although several other studies have observed decreasing richness and diversity with increasing soil depth (Rahman et al, 2008;Degrune et al, 2016;Schlatter et al, 2018). The observed increase in relative abundance of AMF and undefined saprotrophs below 5 cm in the no-till treatments may have been due to specific taxa within these groups showing greater sensitivity to daily temperature swings, wet-dry cycles or other environmental effects that are more pronounced near soil surface.…”

Root-associated endophytic fungal community composition and structure of three medicinal licorices in Xinjiang

“…Moreover, our results showed that the relative abundance of Ascomycota gradually decreased with the downward movement of root depths (Fig. 2b), which was consistent with the results of Ko, Daegeun et al [54]. On this basis, we found that the relative abundance of Ascomycota in Glycyrrhiza in ata had a signi cant difference at different root depth, but Glycyrrhiza uralensis and Glycyrrhiza glabra were not signi cant difference, indicating that some endophytes may preferentially proliferate in a certain ecological region and play different ecological roles from other endophytes.…”

One-time nitrogen fertilization shifts switchgrass soil microbiomes within a context of larger spatial and temporal variation

“…Though the overall Proteobacteria were more abundant in 5–15 cm soils, the class Betaproteobacteria was most abundant in 0–5 cm, which was also found in other study [70]. Similar to our results, others have also reported that Chloroflexi [67, 68] and Nitrospirae [71] increase in abundance with soil depth.…”