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Abstract Not all bacteria are fast growers. In soil as in other environments, bacteria exist along a continuum—from copiotrophs that can grow rapidly under resource-rich conditions to oligotrophs that are adapted to life in the “slow lane.” However, the field of microbiology is built almost exclusively on the study of copiotrophs due, in part, to the ease of studying them in vitro. To begin understanding the attributes of soil oligotrophs, we analyzed three independent datasets that represent contrasts in organic carbon availability. These datasets included 185 samples collected from soil profiles across the USA, 950 paired bulk soil and rhizosphere samples collected across Europe, and soils from a microcosm experiment where carbon availability was manipulated directly. Using a combination of marker gene sequencing and targeted genomic analyses, we identified specific oligotrophic taxa that were consistently more abundant in carbon-limited environments (subsurface, bulk, unamended soils) compared to the corresponding carbon-rich environment (surface, rhizosphere, glucose-amended soils), including members of the Dormibacterota and Chloroflexi phyla. In general, putative soil oligotrophs had smaller genomes, slower maximum potential growth rates, and were under-represented in culture collections. The genomes of oligotrophs were more likely to be enriched in pathways that allow oligotrophs to metabolize a range of energy sources and store carbon, while genes associated with energy-intensive functions like chemotaxis and motility were under-represented. However, few genomic attributes were shared, highlighting that oligotrophs likely use a range of different metabolic strategies and regulatory pathways to thrive in resource-limited soils. 

Abstract Forest disturbance has well-characterized effects on soil microbial communities in tropical and northern hemisphere ecosystems, but little is known regarding effects of disturbance in temperate forests of the southern hemisphere. To address this question, we collected soils from intact and degraded Eucalyptus forests along an east–west transect across Tasmania, Australia, and characterized prokaryotic and fungal communities using amplicon sequencing. Forest degradation altered soil microbial community composition and function, with consistent patterns across soil horizons and regions of Tasmania. Responses of prokaryotic communities included decreased relative abundance of Acidobacteriota, nitrifying archaea, and methane-oxidizing prokaryotes in the degraded forest sites, while fungal responses included decreased relative abundance of some saprotrophic taxa (e.g. litter saprotrophs). Forest degradation also reduced network connectivity in prokaryotic communities and increased the importance of dispersal limitation in assembling both prokaryotic and fungal communities, suggesting recolonization dynamics drive microbial composition following disturbance. Further, changes in microbial functional groups reflected changes in soil chemical properties—reductions in nitrifying microorganisms corresponded with reduced NO3-N pools in the degraded soils. Overall, our results show that soil microbiota are highly responsive to forest degradation in eucalypt forests and demonstrate that microbial responses to degradation will drive changes in key forest ecosystem functions. 

ABSTRACT Anthropogenic nitrogen (N) deposition is unequally distributed across space and time, with inputs to terrestrial ecosystems impacted by industry regulations and variations in human activity. Soil carbon (C) content normally controls the fraction of mineralized N that is nitrified (ƒ_nitrified), affecting N bioavailability for plants and microbes. However, it is unknown whether N deposition has modified the relationships among soil C, net N mineralization, and net nitrification. To test whether N deposition alters the relationship between soil C and net N transformations, we collected soils from coniferous and deciduous forests, grasslands, and residential yards in 14 regions across the contiguous United States that vary in N deposition rates. We quantified rates of net nitrification and N mineralization, soil chemistry (soil C, N, and pH), and microbial biomass and function (as beta‐glucosidase (BG) andN‐acetylglucosaminidase (NAG) activity) across these regions. Following expectations, soil C was a driver ofƒ_nitrifiedacross regions, whereby increasing soil C resulted in a decline in net nitrification andƒ_nitrified. Theƒ_nitrifiedvalue increased with lower microbial enzymatic investment in N acquisition (increasing BG:NAG ratio) and lower active microbial biomass, providing some evidence that heterotrophic microbial N demand controls the ammonium pool for nitrifiers. However, higher total N deposition increasedƒ_nitrified, including for high soil C sites predicted to have lowƒ_nitrified, which decreased the role of soil C as a predictor ofƒ_nitrified. Notably, the drop in contemporary atmospheric N deposition rates during the 2020 COVID‐19 pandemic did not weaken the effect of N deposition on relationships between soil C andƒ_nitrified. Our results suggest that N deposition can disrupt the relationship between soil C and net N transformations, with this change potentially explained by weaker microbial competition for N. Therefore, past N inputs and soil C should be used together to predict N dynamics across terrestrial ecosystems. 

Abstract Soil biota are increasingly recognized as a primary control on litter decomposition at both local and regional scales, but the precise mechanisms by which biota influence litter decomposition have yet to be identified.There are multiple hypothesized mechanisms by which biotic communities may influence litter decomposition—for example, decomposer communities may be specially adapted to local litter inputs and therefore decompose litter from their home ecosystem at elevated rates. This mechanism is known as the home‐field advantage (HFA) hypothesis. Alternatively, litter decomposition rates may simply depend upon the range of metabolic functions present within a decomposer community. This mechanism is known as the functional breadth (FB) hypothesis. However, the relative importance of HFA and FB in litter decomposition is unknown, as are the microbial community drivers of HFA and FB. Potential relationships/trade‐offs between microbial HFA and FB are also unknown.To investigate the roles of HFA and FB in litter decomposition, we collected litter and soil from six different ecosystems across the continental US and conducted a full factorial litter × soil inoculum experiment. We measured litter decomposition (i.e. cumulative CO₂‐C respired) over 150 days and used an analytical model to calculate the HFA and FB of each microbial decomposer community.Our results indicated clear functional differences among decomposer communities, that is, litter sources were decomposed differently by different decomposer communities. These differences were primarily due to differences in FB between different communities, while HFA effects were less evident.We observed a positive relationship between HFA and the disturbance‐sensitive bacterial phylum Verruomicrobia, suggesting that HFA may be an important mechanism in undisturbed environments. We also observed a negative relationship between bacterial r versus K strategists and FB, suggesting an important link between microbial life‐history strategies and litter decomposition functions.Microbial FB and HFA exhibited a strong unimodal relationship, where high HFA was observed at intermediate FB values, while low HFA was associated with both low and high FB. This suggests that adaptation of decomposers to local plant inputs (i.e. high HFA) constrains FB, which requires broad rather than specialized functionality. Furthermore, this relationship suggests that HFA effects will not be apparent when communities exhibit high FB and therefore decompose all litters well and also when FB is low and communities decompose all litters poorly. Overall, our study provides new insights into the mechanisms by which microbial communities influence the decomposition of leaf litter. Read the freePlain Language Summaryfor this article on the Journal blog.