Biology subjects

Kearns, P. J.

Publications and source records attributed to Kearns, P. J..

4 recordsLinked to original sources

bioRxiv2020

Abiotic treatment contributes to an alteration of the seed microbiome of common bean

There has been a growing interest in the seed microbiome due to its important role as an end and starting point of plant microbiome assembly that can have consequences for plant health. However, the effect of abiotic conditions on the seed microbial community remains unknown. We performed a pilot study in a controlled growth chamber to investigate how the endophytic seed microbiome of the common bean (Phaseolus vulgaris L. (var. Red Hawk)) was altered under abiotic treatments relevant for crop management with changing climate. Bean plants were subjected to one of three treatments: 66% water withholding to simulate mild drought, 50% Hoagland nutrient solution to simulate fertilization, or control with sufficient water and baseline nutrition. We performed 16S rRNA gene amplicon sequencing and ITS1 amplicon sequencing of the endophytic DNA to assess seed bacterial/archaeal and fungal community structure, respectively. We found that variability in the seed microbiome structure was high while alpha diversity was low, with tens of taxa present. Water withholding and nutrient addition altered the seed microbiome structure for bacterial/archaeal communities as compared to the control, and each treatment resulted in a distinct microbiome structure. There were no statistically supported differences in the fungal microbiome across treatments. While we discuss several limitations of this study, the promising results suggest that further investigation is needed to better understand abiotic or stress-induced changes in the seed microbiome, the mechanisms that drive those changes, and their implications for the health and stress responses of the next plant generation. ImportanceSeed microbiome members initiate the assembly of plant-associated microbial communities, but the environmental drivers of endophytic seed microbiome composition are unclear. Here, we exposed plants to short-term drought and fertilizer treatments during early vegetative growth and quantified the microbiome composition of the seeds that were ultimately produced. We found that seeds produced by plants stressed by water limitation or receiving nutrient addition had statistically different endophytic bacterial/archaeal microbiome compositions from each other and from seeds produced by control plants. This work suggests that the abiotic experience of a parental plant can influence the composition of its seed microbiome, with unknown consequences for the next plant generation.

microbiology↗

bioRxiv2019

Locally-adapted Mimulus ecotypes differentially impact rhizosphere bacterial and archaeal communities in an environment-dependent manner

Plant root-microbe interactions influence plant productivity, health, and resistance to stress. Although there is evidence that plant species and even genotypes can alter soil microbial community structure, environmental conditions can potentially outweigh plant genetic effects. Here, we used a reciprocal transplant experiment to understand the contributions of the environment and the host plant to rhizosphere microbiome composition in locally-adapted ecotypes of Mimulus guttatus (syn. Erythranthe guttata (Fisch. ex DC.) G.L. Nesom). Two genotypes of a coastal ecotype and two genotypes of an inland ecotype were planted at coastal and inland sites. After three months, we collected rhizosphere and bulk soil and assessed microbial communities by 16S rRNA gene sequencing. We found that local environment (coastal versus inland site) strongly influenced rhizosphere communities, at least in part due to distinct local microbial species pools. Host identity played a smaller role: at each site, the ecotypes exhibited remarkably similar composition of microbial communities at the class level, indicating that divergent M. guttatus ecotypes recruit phylogenetically similar rhizosphere communities, even in environments to which they are maladapted. Nevertheless, the two ecotypes significantly differed in community composition at the inland site due to an exclusive set of rare taxa associated with each ecotype. Although our results indicate that locally-adapted M. guttatus ecotypes are genetically diverged in factors shaping rhizosphere communities, environmental factors can trump genetic factors in shaping the M. guttatus microbiome. Overall, our findings demonstrate that wild plants strongly impact root-associated microbial communities, but hierarchical drivers interact to shape microbial community assembly outcomes.

plant biology↗

bioRxiv2018

16S rRNA:rDNA ratios and cell activity staining reveal consistent patterns of soil microbial activity

Microbial activity plays a major role in the processes that support life on Earth. Nevertheless, across diverse ecosystems many microbes are in a state of dormancy, characterized by strongly reduced metabolic rates. Of the methods used to assess microbial activity-dormancy dynamics, 16S rRNA: rDNA amplicons (\"16S ratios\") and active cell staining with 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) are two of the most common, yet each method has its own limitations. To better understand the applicability and potential complementarity of these two methods, we conducted two experiments investigating microbial activity in the rhizosphere. In the first experiment, we treated corn rhizosphere soil with common phytohormones to simulate plant-soil signaling during plant stress, and in the second experiment, we used bean exposed to drought or nutrient enrichment to more directly assess the impacts of plant stress on soil microbial activity. Overall, 16S ratios revealed numerous taxa with detectable RNA but no detectable DNA. However, overarching patterns in percent activity across treatments were unaffected by the method used to account for active taxa, or by the threshold 16S ratio used for taxa to be classified as active. 16S ratio distributions were highly similar across microbial phyla and were only weakly correlated with ribosomal operon number. Lastly, over relatively short time courses, 16S ratios are responsive earlier than CTC staining, a finding potentially related to the temporal sensitivity of activity changes detectable by the two methods. Our results suggest that 16S ratios and CTC staining provide robust and complementary estimates of bulk community activity.\n\nImportanceAlthough the majority of microorganisms in natural ecosystems are dormant, relatively little is known about the dynamics of the active and dormant microbial pools through both space and time. The limited knowledge of microbial activity-dormancy dynamics is in part due to uncertainty in the methods currently used to quantify active taxa. Here, we directly compared two of the most common methods (16S ratios and active cell staining) for estimating microbial activity in rhizosphere soil, and found that they were largely in agreement in the overarching patterns, suggesting that either method is robust for assessing comparative activity dynamics. Thus, our results suggest that 16S ratios and active cell staining provide robust and complementary information for measuring and interpreting microbial activity-dormancy dynamics in soils. They also support that 16S rRNA:rDNA ratios have comparative value and offer a high-throughput, sequencing-based option for understanding relative changes in microbiome activity.

microbiology↗

bioRxiv2017

Human activities influence the direction and magnitude of local biodiversity change over time

In recent decades, environmental drivers of community change have been associated with changes in biodiversity from local to global scales. Here we evaluate the role of anthropogenic drivers in marine ecosystems as drivers of change in local species richness with a meta-analysis of a novel dataset of temporal change in species richness. We paired biodiversity data from 144 sites with large-scale drivers derived from geospatial databases: human cumulative impact scores, sea surface temperature change, nutrient loading, and invasion potential. Three specific drivers (nutrient inputs, rate of linear temperature change, and non-native species invasion potential) explained patterns in local marine species richness change. We show that these drivers have opposing effects on biodiversity trends. In some cases, variability in drivers can create contrasting directions of change yielding observations of no net change when localities are pooled in an attempt to find a global average. Further, long-term studies reveal different effects of drivers that are not observed in short-term studies. These findings begin to explain high variability observed in species diversity trends at local scales. Formally attributing local species diversity change to human drivers is essential to understanding global patterns of local species diversity change and their consequences.

ecology↗