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1. Seasonal effects of long-term warming on ecosystem function and bacterial diversity

   https://doi.org/10.1371/journal.pone.0311364  

   Shinfuku, Melissa S; Domeignoz-Horta, Luiz A; Choudoir, Mallory J; Frey, Serita D; Mitchell, Megan F; Ranjan, Ravi; DeAngelis, Kristen M (October 2024, PLOS ONE)

   Vestergård, Mette (Ed.)

   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. 

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2. Heavy Metal Pollution Impacts Soil Bacterial Community Structure and Antimicrobial Resistance at the Birmingham 35th Avenue Superfund Site

   https://doi.org/10.1128/spectrum.02426-22  

   Goswami, Anuradha; Adkins-Jablonsky, Sarah J.; Barreto Filho, Marcelo Malisano; Shilling, Michelle D.; Dawson, Alex; Heiser, Sabrina; O’Connor, Aisha; Walker, Melissa; Roberts, Qutia; Morris, J. Jeffrey (April 2023, Microbiology Spectrum)

   Veach, Allison (Ed.)

   ABSTRACT Heavy metals (HMs) are known to modify bacterial communities both in the laboratory and in situ . Consequently, soils in HM-contaminated sites such as the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that heavy metal-resistant (HMR) bacteria often also display antimicrobial resistance (AMR), and therefore HM-contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility, topsoil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in six public areas in the neighboring zip code, 35214. 35027 soils had significantly elevated levels of the HMs As, Mn, Pb, and Zn, and sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated HM concentrations correlated with reduced microbial diversity and altered community structure. While there was no difference between zip codes in the proportion of total culturable HMR bacteria, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUSt2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters the soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human disease. IMPORTANCE Heavy metals cross-select for antimicrobial resistance in laboratory experiments, but few studies have documented this effect in polluted soils. Moreover, despite decades of awareness of heavy metal contamination at the EPA Superfund site in North Birmingham, Alabama, this is the first analysis of the impact of this pollution on the soil microbiome. Specifically, this work advances the understanding of the relationship between heavy metals, microbial diversity, and patterns of antibiotic resistance in North Birmingham soils. Our results suggest that polluted soils carry a risk of increased exposure to antibiotic-resistant infections in addition to the direct health consequences of heavy metals. Our work provides important information relevant to both political and scientific efforts to advance environmental justice for the communities that call Superfund neighborhoods home. 

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3. Ecological relevance of flagellar motility in soil bacterial communities

   https://doi.org/10.1093/ismejo/wrae067  

   Ramoneda, Josep; Fan, Kunkun; Lucas, Jane M.; Chu, Haiyan; Bissett, Andrew; Strickland, Michael S.; Fierer, Noah (April 2024, The ISME Journal)

   Abstract Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26 192 unique genomes). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in environments with higher carbon availability. To test this hypothesis, we applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data and quantified the prevalence of flagellar motility across four independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). We observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations. 

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4. Site-specific responses of fungal and bacterial abundances to experimental warming in litter and soil across Arctic and alpine tundra

   https://doi.org/10.1139/as-2020-0053  

   Jeanbille, Mathilde; Clemmensen, Karina; Juhanson, Jaanis; Michelsen, Anders; Cooper, Elisabeth J.; Henry, Greg H.R.; Hofgaard, Annika; Hollister, Robert D.; Jónsdóttir, Ingibjörg S.; Klanderud, Kari; et al (September 2022, Arctic Science)

   Vegetation change of the Arctic tundra due to global warming is a well-known process, but the implication for the belowground microbial communities, key in nutrient cycling and decomposition, is poorly understood. We characterized the fungal and bacterial abundances in litter and soil layers across 16 warming experimental sites at 12 circumpolar locations. We investigated the relationship between microbial abundances and nitrogen (N) and carbon (C) isotopic signatures, indicating shifts in microbial processes with warming. Microbial abundances were 2–3 orders of magnitude larger in litter than in soil. Local, site-dependent responses of microbial abundances were variable, and no general effect of warming was detected. The only generalizable trend across sites was a dependence between the warming response ratios and C:N ratio in controls, highlighting a legacy of the vegetation on the microbial response to warming. We detected a positive effect of warming on the litter mass and δ 15 N, which was linked to bacterial abundance under warmed conditions. This effect was stronger in experimental sites dominated by deciduous shrubs, suggesting an altered bacterial N-cycling with increased temperatures, mediated by the vegetation, and with possible consequences on ecosystem feedbacks to climate change. 

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5. Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria

   https://doi.org/10.1128/mBio.02293-19  

   Pold, Grace; Domeignoz-Horta, Luiz A.; Morrison, Eric W.; Frey, Serita D.; Sistla, Seeta A.; DeAngelis, Kristen M. (February 2020, mBio)

   Giovannoni, Stephen J. (Ed.)

   ABSTRACT The strategy that microbial decomposers take with respect to using substrate for growth versus maintenance is one essential biological determinant of the propensity of carbon to remain in soil. To quantify the environmental sensitivity of this key physiological trade-off, we characterized the carbon use efficiency (CUE) of 23 soil bacterial isolates across seven phyla at three temperatures and with up to four substrates. Temperature altered CUE in both an isolate-specific manner and a substrate-specific manner. We searched for genes correlated with the temperature sensitivity of CUE on glucose and deemed those functional genes which were similarly correlated with CUE on other substrates to be validated as markers of CUE. Ultimately, we did not identify any such robust functional gene markers of CUE or its temperature sensitivity. However, we found a positive correlation between rRNA operon copy number and CUE, opposite what was expected. We also found that inefficient taxa increased their CUE with temperature, while those with high CUE showed a decrease in CUE with temperature. Together, our results indicate that CUE is a flexible parameter within bacterial taxa and that the temperature sensitivity of CUE is better explained by observed physiology than by genomic composition across diverse taxa. We conclude that the bacterial CUE response to temperature and substrate is more variable than previously thought. IMPORTANCE Soil microbes respond to environmental change by altering how they allocate carbon to growth versus respiration—or carbon use efficiency (CUE). Ecosystem and Earth System models, used to project how global soil C stocks will continue to respond to the climate crisis, often assume that microbes respond homogeneously to changes in the environment. In this study, we quantified how CUE varies with changes in temperature and substrate quality in soil bacteria and evaluated why CUE characteristics may differ between bacterial isolates and in response to altered growth conditions. We found that bacterial taxa capable of rapid growth were more efficient than those limited to slow growth and that taxa with high CUE were more likely to become less efficient at higher temperatures than those that were less efficient to begin with. Together, our results support the idea that the CUE temperature response is constrained by both growth rate and CUE and that this partly explains how bacteria acclimate to a warming world. 

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