Site and land-use associations of soil bacteria and fungi define core and indicative taxa

Abstract

Soil microbial diversity has major influences on ecosystem functions and services. However, due to its complexity and uneven distribution of abundant and rare taxa, quantification of soil microbial diversity remains challenging and thereby impeding its integration into long-term monitoring programs. Using metabarcoding, we analyzed soil bacterial and fungal communities at thirty long-term soil monitoring sites from the three land-use types arable land, permanent grassland, and forest with a yearly sampling between snowmelt and first fertilization over five years. Unlike soil microbial biomass and alpha-diversity, microbial community compositions and structures were site- and land-use-specific with CAP reclassification success rates of 100%. The temporally stable site core communities included 38.5% of bacterial and 33.1% of fungal OTUs covering 95.9% and 93.2% of relative abundances. We characterized bacterial and fungal core communities and their land-use associations at the family-level. In general, fungal families revealed stronger land-use associations as compared to bacteria. This is likely due to a stronger vegetation effect on fungal core taxa, while bacterial core taxa were stronger related to soil properties. The assessment of core communities can be used to form cultivation-independent reference lists of microbial taxa, which may facilitate the development of microbial indicators for soil quality and the use of soil microbiota for long-term soil biomonitoring.

Plant G x Microbial E: Plant genotype interaction with soil bacterial community shapes rhizosphere composition during invasion

“…This was the only family to be overrepresented on a genotype across both soil environments. The Micropepsaceae has been found to be an indicator taxon associated with specific plant species or site conditions in other studies (D. Wu et al 2023;Gschwend et al 2022). For studies that compared different environmental manipulations, the family was associated with early phases of restoration (grasslands; (Barber et al 2023)), early responses to agricultural planting (tobacco; (Cao et al 2022)), and response to cold treatments of plants (lettuce; (Persyn et al 2022)), all conditions in which a system had been perturbed recently.…”

Humate application alters microbiota–mineral interactions and assists in pasture dieback recovery

“…Significantly reduced over time in control but not in Hum-treated soils was the genus Marmoricola, also found to be a biomarker of Pb and Zn pollution [ 63 ]. Actinoplanes genus is known for phosphate solubilisation [ 64 ], Asanoa hydrolysing cellulose bacteria [ 65 ], BIrii 41 genus of denitrifying bacteria with a preference for arable and grassland [ 66 , 67 ]. Dactylosporangium genus has antimicrobial properties against Gram-Positive bacteria [ 68 ].…”

Core taxa underpin soil microbial community turnover during secondary succession

“…Interestingly, the composition of core taxa in managed grasslands differed from those found in abandoned grasslands (Figure 4C) and managed grasslands had more OTUs classified as indicator species, and a higher proportion of stage‐specific indicator taxa than the two abandoned grassland successional stages (Figure 4D; Table S4). Overall, bacteria are emerging as indicators of perturbations and land‐use change (Gschwend et al, 2021; Hermans et al, 2016), especially when perturbations cause substantial variation in physicochemical properties. With the improved capacity to describe and characterise unculturable microbes and their life history strategies in detail, the current rather blunt classifications surrounding bacterial habitat preferences could also give way to more nuanced views at higher taxonomic resolution (Stone et al, 2023).…”