Limited effects of depth (0–80 cm) on communities of archaea, bacteria and fungi in paddy soil profiles

Abstract

Most current microbial studies in paddy soils have focused on the top (0–20 cm) layer where rice roots are concentrated. To better understand the vertical distribution of microorganisms in paddy soils, we investigated the abundances, diversities and community compositions of archaea, bacteria and fungi in six geographically and climatically distinct paddy soil profiles from 0–80‐cm depth. Although microbial abundances and operational taxonomic unit (OTU) diversities largely decreased with soil depth, only the community composition of archaea (not bacteria or fungi) was associated with soil depth, echoing that only one archaeal OTU, but no bacterial or fungal OTUs, differed significantly in relative abundance between depth intervals. Mean annual temperature, precipitation and soil iron and manganese concentrations were significantly correlated with the ordinations of microbial communities for all three domains. Besides these common environmental factors, bacterial and archaeal community structures were also influenced by soil chloride and sulphate concentrations, whereas the concentrations of organic matter and total nitrogen were important explanatory factors for the variation in fungal community composition. Further analyses on putative bacterial functions showed significant differences between sampling sites rather than depth intervals, and suggested that bacterial OTUs that significantly varied in relative abundance across sampling sites might be functionally related to organic matter decomposition, sulphur oxidation and reduction, as well as nitrate reduction. Altogether, in the studied paddy soil profiles, the community composition and putative functions of bacteria were largely the same between different vertical layers, each with a thickness of 20 cm. This study suggests that the community compositions of archaea, bacteria and fungi are mainly driven by different soil chemical properties rather than soil depth, which could be linked to the ecological traits of the three microbial domains. Highlights Communities of archaea, bacteria and fungi were investigated in six paddy soil profiles. Soil depth was only correlated with archaeal community structure Environmental factors influenced community composition differently for different domains. Bacterial OTUs contributing to variation in community composition among sites were functionally linked to C, N and S cycling.

Reshaping of soil carbon and nitrogen contents in quincentenary ancient rice terraces: The role of both short-term abandonment and prokaryotic functional groups

“…Soil organic carbon and TN contents decreased with the soil horizon, which was consistent with the findings of Yuan et al ( 2020 ) and Li W. et al ( 2022 ). In this study, SOC and TN contents were higher in the 0–20-cm soil horizon than in the 20–120- and 70–120-cm soil horizons.…”

“…Studies on the variability of prokaryotic community composition and functional groups have been more biased toward surface soils, but little is known about its response in the deep layer (Eilers et al, 2012 ; Yuan et al, 2020 ). Ancient rice terraces have experienced hundreds of years of management measures (repeated tillage and fertilization), as well as long-term leaching and enrichment effects, resulting in significant soil horizons in the profile (Gong, 1995 ).…”

Spatial Distribution of Toxic Metal(loid)s and Microbial Community Analysis in Soil Vertical Profile at an Abandoned Nonferrous Metal Smelting Site

“…As reflected by Figure 4 b, however, Pielou’s evenness index was slightly higher in top soil (1–3 m) than in subsoil (4–10 m). As shown in Table S2 , the diversity indexes were impacted by soil properties and the contents of metal(loid)s, indicating environmental conditions, such as pH, TK, CEC, ORP, and Bio-Cu ( p < 0.05), impacted the soil microbial evenness through limiting the survival of certain microorganisms [ 27 , 28 ]; while, soil microbes adapt to higher metal(loid)s pollution in top soil by changing microbial communities, rather than changing their evenness [ 29 ]. Moreover, Shannon’s diversity index and Simpson’s index of diversity exhibited a decreasing trend from 1 m to 10 m of soil depth, which might be ascribed to the decrease in evenness with increase in depth, as shown in Figure 4 c,d.…”

Vertical and temporal variations of soil bacterial and archaeal communities in wheat-soybean rotation agroecosystem

“…Bacterial diversity generally decreased towards deeper soil, while archaeal diversity increased along with soil depth in the desert ( Wang et al, 2021 ) and alpine ecosystems ( Xu et al, 2021 ). However, others reported that bacterial and archaeal richness negatively correlated with soil depth in paddy soils ( Yuan et al, 2020 ). The varying conclusions of these studies emphasize the need for further comparisons between the vertical distribution patterns of archaeal and bacterial communities.…”