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Soil carbon loss is likely to increase due to climate warming, but microbiomes and microenvironments may dampen this effect. In a 30-year warming experiment, physical protection within soil aggregates affected the thermal responses of soil microbiomes and carbon dynamics. In this study, we combined metagenomic analysis with physical characterization of soil aggregates to explore mechanisms by which microbial communities respond to climate warming across different soil microenvironments. Long-term warming decreased the relative abundances of genes involved in degrading labile compounds (e.g., cellulose), but increased those genes involved in degrading recalcitrant compounds (e.g., lignin) across aggregate sizes. These changes were observed in most phyla of bacteria, especially for Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes. Microbial community composition was considerably altered by warming, leading to declined diversity for bacteria and fungi but not for archaea. Microbial functional genes, diversity, and community composition differed between macroaggregates and microaggregates, indicating the essential role of physical protection in controlling microbial community dynamics. Our findings suggest that microbes have the capacity to employ various strategies to acclimate or adapt to climate change (e.g., warming, heat stress) by shifting functional gene abundances and community structures in varying microenvironments, as regulated by soil physical protection. 

Adaptation of soil microbes due to warming from climate change has been observed, but it remains unknown what microbial growth traits are adaptive to warming. We studied bacterial isolates from the Harvard Forest Long-Term Ecological Research site, where field soils have been experimentally heated to 5°C above ambient temperature with unheated controls for 30 years. We hypothesized that Alphaproteobacteria from warmed plots have (i) less temperature-sensitive growth rates; (ii) higher optimum growth temperatures; and (iii) higher maximum growth temperatures compared to isolates from control plots. We made high-throughput measurements of bacterial growth in liquid cultures over time and across temperatures from 22°C to 37°C in 2–3°C increments. We estimated growth rates by fitting Gompertz models to the growth data. Temperature sensitivity of growth rate, optimum growth temperature, and maximum growth temperature were estimated by the Ratkowsky 1983 model and a modified Macromolecular Rate Theory (MMRT) model. To determine evidence of adaptation, we ran phylogenetic generalized least squares tests on isolates from warmed and control soils. Our results showed evidence of adaptation of higher optimum growth temperature of bacterial isolates from heated soils. However, we observed no evidence of adaptation of temperature sensitivity of growth and maximum growth temperature. Our project begins to capture the shape of the temperature response curves, but illustrates that the relationship between growth and temperature is complex and cannot be limited to a single point in the biokinetic range.

Soils are the largest terrestrial carbon sink and the foundation of our food, fiber, and fuel systems. Healthy soils are carbon sinks, storing more carbon than they release. This reduces the amount of carbon dioxide released into the atmosphere and buffers against climate change. Soil microbes drive biogeochemical cycling and contribute to soil health through organic matter breakdown, plant growth promotion, and nutrient distribution. In this study, we determined how soil microbial growth traits respond to long-term soil warming. We found that bacterial isolates from warmed plots showed evidence of adaptation of optimum growth temperature. This suggests that increased microbial biomass and growth in a warming world could result in greater carbon storage. As temperatures increase, greater microbial activity may help reduce the soil carbon feedback loop. Our results provide insight on how atmospheric carbon cycling and soil health may respond in a warming world.

 

The complete genome sequence ofBacillus thuringiensisstrain RC340, isolated from an environmental microbiology experiment soil sample is presented here.B. thuringiensisstrain RC340 sequenced by GridION consists of a single genome consisting of 5.86 million bases, 8,152 predicted genes, and 0.23% contamination.

 

Paenibacillussp. strain RC67 was isolated from the Harvard Forest long-term soil warming experiment. The assembled genome is a single contig with 7,963,753 bp and 99.4% completion. Genome annotation suggests that the isolate is of a novel bacterial species.

 

ABSTRACT Paenibacillus spp. RC334 and RC343 were isolated from heated soil in a long-term soil warming experiment. Both genomes were 5.98 Mb and assembled as a single contig. We describe the assembly and annotation of the two high-quality draft genomes for these isolates here. 

Microbial-derived soil organic matter (SOM), or necromass, is an important source of SOM and is sensitive to climate warming. Soil classification systems consider soil physicochemical properties that influence SOM, hinting at the potential utility of incorporating classification systems in soil carbon (C) projections. Currently, there is no consensus on climate warming effects on necromass and if these responses vary across reference soil groups. To estimate the vulnerability of necromass to climate warming, we performed a meta-analysis of publications examining in situ experimental soil warming effects on microbial necromass via amino sugar analysis. We built generalized linear models (GLM) to explore if soil groups and warming methodologies can be used to predict necromass stocks. Our results showed that warming effect sizes on necromass were not uniform across reference soil groups. Specifically, warming effect sizes were generally positive in permafrost soils but negative in calcic soils. However, warming did not significantly change average necromass. Our GLMs detected significant differences in necromass across soil groups with similar texture and clay percentage. Thus, we advocate for further research to define what predictors of necromass are captured in soil group but not in soil texture. We also show warming methodology is a significant predictor of necromass, depending on the necromass biomarker. Future research efforts should uncover the mechanistic reason behind how passive versus active warming methodology influences necromass responses. Our study highlights the need for more in situ soil warming experiments measuring microbial necromass as this will improve predictions of SOM feedback under future climate scenarios. 

ABSTRACT We report the draft genome sequence of Leifsonia poae strain BS71. This bacterium was isolated from a low soil moisture content model soil microcosm inoculated with forest soil that had been subject to chronic warming.