Lohse, K. A. | bioRxiv Science

bioRxiv2023

Microbial Responses to Biochar Soil Amendment and Influential Factors: A Three-level Meta-analysis

Biochar is a multifunctional soil conditioner capable of enhancing soil health and crop production while reducing greenhouse gas emissions. Understanding how soil microbes respond to biochar amendment is a vital step towards precision biochar application. Here, we synthesized 3899 observations of 24 microbial responses from 61 primary studies, applied a three-level mixed-effects model to estimate biochar effects, and evaluated the importance of biochar characteristics (feedstock, pyrolysis temperature), soil properties (pH, C:N, cation exchange capacity, bulk or rhizosphere), and treatment protocols (application rate, fertilization, duration, field or laboratory). Biochar significantly boosts microbial abundance (microbial biomass carbon > CFU), nitrite reductase gene (nirS), the activity of C- and N-cycling enzymes (dehydrogenase > cellulase > urease > invertase), and potential nitrification rate. Biochar characteristics, soil properties, and treatment protocols strongly determine the direction and extent of microbial response changes. Feedstock, pyrolysis temperature, application rate, and soil pH are important predictors most frequently included in the final models. Our study highlights the promise of purpose-driven biochar production and application such that biochar production parameters can be tuned to elicit the desired microbial responses and application protocols could be optimized to invoke multiple benefits. It also underlines current knowledge gaps and future research needs. SynopsisMeta-analysis reveals overall effect sizes of soil microbial responses to biochar amendment and the most influential factors, highlighting the potential of purpose-driven precision biochar towards sustainable agriculture.

ecology↗

bioRxiv2019

Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the U.S. to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.\n\nImportanceSoil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the U.S., we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored distinct communities compared to the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising amount of novel microbes with unique adaptations to oligotrophic subsurface conditions.

microbiology↗