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Abstract Soil microbial traits drive ecosystem functions, which can explain the positive correlation between microbial functional diversity and ecosystem function. However, microbial adaptation to climate change related warming stress can shift microbial traits with direct implications for soil carbon cycling. Here, we investigated how long-term warming affects the relationship between microbial trait diversity and ecosystem function. Soils were sampled after 24 years of +5°C warming alongside unheated control soils from the Harvard Forest Long-Term Ecological Research site. Ecosystem function was estimated from six different enzyme activities and microbial biomass. Functional diversity was calculated from metatranscriptomics sequencing, where reads were assigned to yield, acquisition, or stress trait categories. We found that in organic horizon soils, warming decreased the richness of acquisition-related traits. In the mineral soils, we observed that heated soils exhibited a negative relationship with the richness of acquisition-related traits. These results suggest that microbial communities exposed to long-term warming are shifting away from a resource acquisition life history strategy. 

ABSTRACT 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 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. 

ABSTRACT 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. IMPORTANCESoils 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. 

Across biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained within ecosystems under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5°C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having a higher intercept than summer samples in our model, suggesting a higher overall baseline of ecosystem function in the fall. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial evenness in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community evenness. 

Paenibacillussp. RC80 was isolated from temperate deciduous forest soil in New England. The assembled genome is a single contig with 5,977,337 bp and 97.15% estimated completion. RC80 contains features for 2,3-butanediol dehydrogenase production and pathways involved in ethanol production. 

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. 

Microbes are responsible for cycling carbon (C) through soils, and predicted changes in soil C stocks under climate change are highly sensitive to shifts in the mechanisms assumed to control the microbial physiological response to warming. Two mechanisms have been suggested to explain the long-­ term warming impact on microbial physiology: microbial thermal acclimation and changes in the quantity and quality of substrates available for microbial metabolism. Yet studies disentangling these two mechanisms are lacking. To resolve the drivers of changes in microbial physiology in response to long-­ term warming, we sampled soils from 13-­ and 28-­ year-­ old soil warming experiments in different seasons. We performed short-­ term laboratory incubations across a range of temperatures to measure the relationships between temperature sensitivity of physiology (growth, respiration, carbon use efficiency, and extracellular enzyme activity) and the chemical composition of soil organic matter. We observed apparent thermal acclimation of microbial respiration, but only in summer, when warming had exacerbated the seasonally-­ induced, already small dissolved organic matter pools. Irrespective of warming, greater quantity and quality of soil carbon increased the extracellular enzymatic pool and its temperature sensitivity. We propose that fresh litter input into the system seasonally cancels apparent thermal acclimation of C-­ cycling processes to decadal warming. Our findings reveal that long-term warming has indirectly affected microbial physiology via reduced C availability in this system, implying that earth system models including these negative feedbacks may be best suited to describe long-­ term warming effects on these soils. 

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.