Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

Abstract

Along a long-term ecosystem development gradient, soil nutrient contents and mineralogical properties change, therefore probably altering soil microbial communities. However, knowledge about the dynamics of soil microbial communities during long-term ecosystem development including progressive and retrogressive stages is limited, especially in mineral soils. Therefore, microbial abundances (quantitative PCR) and community composition (pyrosequencing) as well as their controlling soil properties were investigated in soil depth profiles along the 120,000 years old Franz Josef chronosequence (New Zealand). Additionally, in a microcosm incubation experiment the effects of particular soil properties, i.e., soil age, soil organic matter fraction (mineral-associated vs. particulate), O2 status, and carbon and phosphorus additions, on microbial abundances (quantitative PCR) and community patterns (T-RFLP) were analyzed. The archaeal to bacterial abundance ratio not only increased with soil depth but also with soil age along the chronosequence, coinciding with mineralogical changes and increasing phosphorus limitation. Results of the incubation experiment indicated that archaeal abundances were less impacted by the tested soil parameters compared to Bacteria suggesting that Archaea may better cope with mineral-induced substrate restrictions in subsoils and older soils. Instead, archaeal communities showed a soil age-related compositional shift with the Bathyarchaeota, that were frequently detected in nutrient-poor, low-energy environments, being dominant at the oldest site. However, bacterial communities remained stable with ongoing soil development. In contrast to the abundances, the archaeal compositional shift was associated with the mineralogical gradient. Our study revealed, that archaeal and bacterial communities in whole soil profiles are differently affected by long-term soil development with archaeal communities probably being better adapted to subsoil conditions, especially in nutrient-depleted old soils.

Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons

“…Most of these eukaryotic rRNA gene reads were classified as Fungi (58%), followed by Charophyta (16%), Metazoa (9.3%), and Cercozoa (7.0%). These results are in line with previous work showing that the contributions of eukaryotes, most notably fungi, to microbial biomass pools typically decrease with soil depth (25).…”

The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA

“…In alignment with that, no significant difference was found in root mass below 90 cm soil profile when comparing both crops at each site ( P > 0.22). Intensifying substrate and oxygen limitations in deeper soil layers also impose a selective pressure on the bacterial communities, reducing their diversity and richness compared to the top soil layers [57].…”

Assessing Microbial Community Patterns During Incipient Soil Formation From Basalt

“…An exciting addition to this concept would be understanding lineage‐specific age‐related shifts in microbial communities. A recent study (Turner et al, ) revealed that long‐term soil development differentially affected bacterial and archaeal communities, the latter better adapted to subsoil environment. Therefore, conceptually, one can hypothesize that bacterial, archaeal, and fungal communities assemble in a differential manner and ask whether their assembly processes, community dynamics, and adaptability change over time as incipient soil develops into topsoil and subsoil.…”