Dataset Information

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities.

ABSTRACT: Microbial traits related to ecological responses and functions could provide a common currency facilitating synthesis and prediction; however, such traits are difficult to measure directly for all taxa in environmental samples. Past efforts to estimate trait values based on phylogenetic relationships have not always distinguished between traits with high and low phylogenetic conservatism, limiting reliability, especially in poorly known environments, such as soil. Using updated reference trees and phylogenetic relationships, we estimated two phylogenetically conserved traits hypothesized to be ecologically important from DNA sequences of the 16S rRNA gene from soil bacterial and archaeal communities. We sampled these communities from an environmental change experiment in California grassland applying factorial addition of late-season precipitation and soil nutrients to multiple soil types for 3 years prior to sampling. Estimated traits were rRNA gene copy number, which contributes to how rapidly a microbe can respond to an increase in resources and may be related to its maximum growth rate, and genome size, which suggests the breadth of environmental and substrate conditions in which a microbe can thrive. Nutrient addition increased community-weighted mean estimated rRNA gene copy number and marginally increased estimated genome size, whereas precipitation addition decreased these community means for both estimated traits. The effects of both treatments on both traits were associated with soil properties, such as ammonium, available phosphorus, and pH. Estimated trait responses within several phyla were opposite to the community mean response, indicating that microbial responses, although largely consistent among soil types, were not uniform across the tree of life. Our results show that phylogenetic estimation of microbial traits can provide insight into how microbial ecological strategies interact with environmental changes. The method could easily be applied to any of the thousands of existing 16S rRNA sequence data sets and offers potential to improve our understanding of how microbial communities mediate ecosystem function responses to global changes.

SUBMITTER: Gravuer K

PROVIDER: S-EPMC5504382 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities.

Gravuer Kelly K Eskelinen Anu A

Frontiers in microbiology 20170711

Microbial traits related to ecological responses and functions could provide a common currency facilitating synthesis and prediction; however, such traits are difficult to measure directly for all taxa in environmental samples. Past efforts to estimate trait values based on phylogenetic relationships have not always distinguished between traits with high and low phylogenetic conservatism, limiting reliability, especially in poorly known environments, such as soil. Using updated reference trees a ...[more]

PMID: 28744266

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Project description:In order to increase O2 concentration in the rhizosphere and reduce the continuous cropping obstacles under high-density cultivation, ventilation is often used to increase soil aeration. Yet, the effect of ventilation on soil microbial communities and nutrient cycling and, further, the extent to which they influence strawberry growth under greenhouse conditions are still poorly understood. Thus, four treatments-no ventilation + low planting density (LD), ventilation + LD, no ventilation + high planting density (HD), and ventilation + HD-of strawberry "Red cheeks" (Fragaria × ananassa Duch. cv. "Benihopp") were studied in a greenhouse for 3 years. The ventilation pipe (diameter = 10 cm) was buried in the soil at a depth of 15 cm from the surface and fresh air was sent to the root zone through the pipe by a blower. Ten pipes (one pipeline in a row) were attached to a blower. Soil samples were collected using a stainless-steel corer (five-point intra-row sampling) for the nutrient and microbial analyses. The composition and structure of the soil bacterial and fungal communities were analyzed by high-throughput sequencing of the 16S and 18S rRNA genes, and functional profiles were predicted using PICRUSt and FUNGuild, respectively. The results showed that soil ventilation increased the net photosynthetic rate (Pn), transpiration rate (Tr), and water use efficiency (WUE) of strawberry plants across two growth stages [vegetative growth stage (VGS) and fruit development stage (FDS)]. Soil ventilation increased its available nutrient contents, but the available nutrient contents were reduced under the high planting density compared with low planting density. Both the O2 concentration and O2:CO2 ratio were increased by ventilation; these were positively correlated with the relative abundance of Bacilli, Gamma-proteobacteria, Blastocatella, as well as Chytridiomycota and Pezizomycetes. Conversely, ventilation decreased soil CO2 concentration and the abundance of Beta-proteobacteria and Gemmatimonadetes. The greater planting density increased the relative abundance of Acidobacteria (oligotrophic group). Ventilation altered soil temperature and pH along with carbon and nitrogen functional profiles in the VGS (more nitrogen components) and FDS (more carbon components), which benefited strawberry plant growth under high planting density. The practice of soil ventilation provides a strategy to alleviate hypoxia stress and continuous cropping obstacles for improving crop production in greenhouse settings.

Dataset Information

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities.

Publications

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities.

Similar Datasets

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