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Phylogenetic conservation of soil bacterial responses to simulated global changes.

ABSTRACT: Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, elevated CO2 concentration and phosphorus (P) addition. Bacterial responses were phylogenetically conserved to all perturbations. The phylogenetic depth of these responses varied minimally among the types of perturbations and was similar when merging data across locations, implying that the context of particular locations did not affect the phylogenetic pattern of response. We further identified taxonomic groups that responded consistently to each type of perturbation. These patterns revealed that, at the level of family and above, most groups responded consistently to only one or two types of perturbations, suggesting that traits with different patterns of phylogenetic conservation underlie the responses to different perturbations. We conclude that a phylogenetic approach may be useful in predicting how soil bacterial communities respond to a variety of global changes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

SUBMITTER: Isobe K

PROVIDER: S-EPMC7133522 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Phylogenetic conservation of soil bacterial responses to simulated global changes.

Isobe Kazuo K Bouskill Nicholas J NJ Brodie Eoin L EL Sudderth Erika A EA Martiny Jennifer B H JBH

Philosophical transactions of the Royal Society of London. Series B, Biological sciences 20200323 1798

Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, ...[more]

PMID: 32200749

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Project description:Plant primary productivity and crop yields have been reduced due to the doubled level of global tropospheric ozone. Little is known about how elevated ozone affects soil microbial communities in the cropland ecosystem and whether such effects are sensitive to the nitrogen (N) supply. Here, we examined the responses of bacterial and fungal communities in maize soils to elevated ozone (+60 ppb ozone) across different levels of N fertilization (+60, +120, and +240 kg N ha-1yr-1). The fungal alpha diversity was decreased (P < 0.05), whereas the bacterial alpha diversity displayed no significant change under elevated ozone. Significant (P < 0.05) effects of N fertilization and elevated ozone on both the bacterial and fungal communities were observed. However, no interactive effects between N fertilization and elevated ozone were observed for bacterial and fungal communities (P > 0.1). The bacterial responses to N fertilization as well as the bacterial and fungal responses to elevated ozone were all phylogenetically conserved, showing universal homogeneous selection (homogeneous environmental conditions leading to more similar community structures). In detail, bacterial Alphaproteobacteria, Actinobacteria, and Chloroflexi, as well as fungal Ascomycota, were increased by elevated ozone, whereas bacterial Gammaproteobacteria, Bacteroidetes, and Elusimicrobia, as well as fungal Glomeromycota, were decreased by elevated ozone (P < 0.05). These ozone-responsive phyla were generally correlated (P < 0.05) with plant biomass, plant carbon (C) uptake, and soil dissolved organic C, demonstrating that elevated ozone affects plant-microbe interactions. Our study highlighted that microbial responses to elevated ozone display a phylogenetic clustering pattern, suggesting that response strategies to elevated ozone stress may be phylogenetically conserved ecological traits. IMPORTANCE The interactions of plant and soil microbial communities support plant growth and health. The increasing tropospheric ozone decreases crop biomass and also alters soil microbial communities, but the ways in which crops and their associated soil microbial communities respond to elevated tropospheric ozone are not clear, and it is also obscure whether the interactions between ozone and the commonly applied N fertilization exist. We showed that the microbial responses to both elevated ozone and N fertilization were phylogenetically conserved. However, the microbial communities that responded to N fertilization and elevated ozone were different, and this was further verified by the lack of an interactive effect between N fertilization and elevated ozone. Given that the global tropospheric ozone concentration will continue to increase in the coming decades, the decrease of specific microbial populations caused by elevated ozone would result in the extinction of certain microbial taxa. This ozone-induced effect will further harm crop production, and awareness is urgently needed.

Project description:Global change experiments often observe shifts in bacterial community composition based on 16S rRNA gene sequences. However, this genetic region can mask a large amount of genetic and phenotypic variation among bacterial strains sharing even identical 16S regions. As such, it remains largely unknown whether variation at the sub-16S level, sometimes termed microdiversity, responds to environmental perturbations and whether such changes are relevant to ecosystem processes. Here, we investigated microdiversity within Curtobacterium, the dominant bacterium found in the leaf litter layer of soil, to simulated drought and nitrogen addition in a field experiment. We first developed and validated Curtobacterium-specific primers of the groEL gene to assess microdiversity within this lineage. We then tracked the response of this microdiversity to simulated global change in two adjacent plant communities, grassland and coastal sage scrub (CSS). Curtobacterium microdiversity responded to drought but not nitrogen addition, indicating variation within the genus of drought tolerance but not nitrogen response. Further, the response of microdiversity to drought depended on the ecosystem, suggesting that litter substrate selects for a distinct composition of microdiversity that is constrained in its response, perhaps related to tradeoffs in resource acquisition traits. Supporting this interpretation, a metagenomic analysis revealed that the composition of Curtobacterium-encoded carbohydrate-active enzymes (CAZymes) varied distinctly across the two ecosystems. Identifying the degree to which relevant traits are phylogenetically conserved may help to predict when the aggregated response of a 16S-defined taxon masks differential responses of finer-scale bacterial diversity to global change. IMPORTANCE Microbial communities play an integral role in global biogeochemical cycling, but our understanding of how global change will affect microbial community structure and functioning remains limited. Microbiome analyses typically aggregate large amounts of genetic diversity which may obscure finer variation in traits. This study found that fine-scale diversity (or microdiversity) within the bacterial genus Curtobacterium was affected by simulated global changes. However, the degree to which this was true depended on the type of global change, as the composition of Curtobacterium microdiversity was affected by drought, but not by nitrogen addition. Further, these changes were associated with variation in carbon degradation traits. Future work might improve predictions of microbial community responses to global change by considering microdiversity.

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Phylogenetic conservation of soil bacterial responses to simulated global changes.

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Phylogenetic conservation of soil bacterial responses to simulated global changes.

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